ARTICLE | doi:10.20944/preprints202305.0587.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: air travel; infectious disease; sentinel surveillance; wastewater surveillance; aircraft
Online: 9 May 2023 (07:49:15 CEST)
Modern commercial air travel connects disparate human populations with the global airline industry transporting up to 4.5 billion passengers annually in the years leading up to the COVID-19 pandemic. While such connections are convenient for commerce and tourism, air travel networks can also be efficient distributors of infectious diseases such as influenza, SARS-CoV-1, hemorrhagic fevers, and more recently SARS-CoV-2 and monkeypox. During the COVID-19 pandemic, public health agencies used multi-layered control strategies including pre-departure testing and vaccination requirements, masking, post-arrival testing, and quarantine to manage the risk of COVID-19 transmission associated with air travel. Simultaneously, the surveillance of aircraft wastewater emerged as a promising new data source to screen for SARS-CoV-2 infections, including newly emergent lineages, among international air travelers. Herein, we review the potential of aircraft wastewater for public health surveillance. The known contributing population and flight itinerary combined with the highly concentrated waste stream and convenient sampling during routine lavatory servicing make aircraft wastewater a strategic opportunity for unintrusive surveillance of the global fluxes of human pathogens. We estimate for the cases of fecal- or urine-shed pathogens, sampling from 3,500 and 1,250 flights per week, respectively, would be required to survey 10% of all global long-haul flight passengers. In the case of the United States, achieving 10% coverage of all international arrivals would require sampling from 925 and 322 flights per week, respectively. Aircraft wastewater surveillance could also be integrated with network and infectious disease models to better inform traditional public health control measures during emerging epidemics. Given the tremendous potential for public good and the massive economic costs of epidemics, governments should consider international collaboration to create a global aircraft wastewater surveillance system.
ARTICLE | doi:10.20944/preprints202305.1285.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: postmarketing surveillance; pharmacovigilance; registry data
Online: 18 May 2023 (07:18:52 CEST)
Abstract: Our research analyzed the characteristics of phase IV clinical trials in oncology using data from the ClinicalTrials.gov registry. The included trials were conducted between January 2013 and December 2022 and were examined for key characteristics, including outcome measures, interventions, sample sizes, and study design, different cancer types, and geographic regions. Our analysis included 368 phase IV oncology studies. We found that 50% of these studies aimed to examine both safety and efficacy, while 43.5% only reported efficacy outcome measures, and 6.5% only described safety outcome measures. Only 16.9% of studies were powered to detect adverse events with a frequency of 1 in 100. Targeted therapies accounted for the majority of included studies (53.5%), with breast (32.91%) and hematological cancers (25.82%) being the most frequently investigated malignancies. Most phase IV oncology studies lacked sufficient power to detect rare adverse events due to their small sample sizes and instead focused on effectiveness. To ensure that there is no gap in drug safety data collection and detection of rare adverse events due to limited phase IV clinical trials, there is a significant need for additional education and participations by both health care providers and patients in spontaneous reporting processes.
REVIEW | doi:10.20944/preprints202010.0267.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: AMR; sewage; epidemiology; wastewater; surveillance
Online: 21 June 2021 (11:25:51 CEST)
We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) the strength of the evidence for a wastewater-human AMR association, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin’s concordance correlation coefficient (CCC) to quantify agreement between AMR prevalence in wastewater and human compartments, and logistic regression to identify study features (e.g. sampling methods) associated with high-agreement (defined as wastewater-human AMR prevalences within ±10%). Of 8,867 records and 232 full-text methods reviewed, 29 studies were included. AMR prevalence data was extractable from 20 studies conducting phenotypic-only (n=11), genotypic-only (n=1) or combined (n=8) AMR detection. Overall wastewater-human AMR concordance was reasonably high for both phenotypic (CCC=0.81 [95% CI 0.74-0.87]) and genotypic comparisons (CCC=0.88 (95% CI 0.85-0.91)) despite diverse species-phenotypes/genotypes and study design. Logistic regression was limited by inconsistent reporting of study features, and limited sample size; no significant relationships between study features and high wastewater-human AMR agreement were identified. Based on descriptive synthesis, composite/flow-proportional sampling of wastewater influent, longitudinal sampling >12 months, and time/location-matched comparisons generally had higher-agreement. Further research and clear and consistent reporting of study methods is required to confirm optimal practice.
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: SARS-CoV-2; wastewater surveillance
Online: 7 June 2021 (13:01:18 CEST)
Wastewater surveillance for SARS-CoV-2 has garnered extensive public attention during the COVID-19 pandemic as a proposed complement to existing disease surveillance systems. Over the past year, methods for detection and quantification of SARS-CoV-2 viral RNA in untreated sewage have advanced, and concentrations in wastewater have been shown to correlate with trends in reported cases. Despite the promise of wastewater surveillance, for these measurements to translate into useful public health tools, it is necessary to bridge the communication and knowledge gaps between researchers and public health responders. Here we describe the key uses, barriers, and applicability of SARS-CoV-2 wastewater surveillance for supporting public health decisions and actions, including establishing ethical consideration for monitoring. Overall, while wastewater surveillance to assess community infections is not a new idea, by addressing these barriers, the COVID-19 pandemic may be the initiating event that turns this emerging public health tool into a sustainable nationwide surveillance system.
ARTICLE | doi:10.20944/preprints202305.1703.v1
Subject: Biology And Life Sciences, Virology Keywords: herpesvirus; bat; surveillance; complete genome; Zambia
Online: 24 May 2023 (05:30:03 CEST)
Bats are of significant interest as reservoirs for various zoonotic viruses with high diversity. During the past two decades, many herpesviruses have been identified in various bats worldwide by genetic approaches, whereas there have been few reports on the isolation of infectious herpesviruses. Herein, we report the prevalence of herpesvirus infection of bats captured in Zambia and genetic characterization of novel gammaherpesviruses isolated from Macronycteris vittatus bats. By our PCR screening, herpesvirus genomes were detected in 29.2% (7/24) of Rousettus aegyptiacus, 78.1% (82/105) of Macronycteris vittatus, and 100% (1/1) of Hipposideros caffer bats in Zambia. Phylogenetic analyses of the detected herpesvirus genomes revealed that the Zambian bat herpesviruses were divided into seven betaherpesvirus groups and five gammaherpesvirus groups. Two infectious strains of a novel gammaherpesvirus, tentatively named Macronycteris gammaherpesvirus 1 (MaGHV1), were successfully isolated from Macronycteris vittatus bats, and their complete genomes were sequenced. The genome of MaGHV1 encoded 79 open reading frames, and phylogenic analyses of the DNA polymerase and glycoprotein B demonstrated that MaGHV1 formed an independent lineage sharing a common origin with other bat-derived gammaherpesviruses. Our findings provide new information regarding the genetic diversity of herpesviruses maintained in African bats.
ARTICLE | doi:10.20944/preprints201901.0309.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: legionella; legionellosis; environmental surveillance; water system
Online: 30 January 2019 (10:12:29 CET)
Legionnaires’ disease is normally acquired by inhalation of legionellae from a contaminated environmental source. Water systems of large buildings, such as hospitals, are often contaminated with legionellae and therefore represent a potential risk for the hospital population. In this study, we demonstrated the constant presence of Legionella in water samples from the water system of a large university hospital in Messina (Sicily, Italy) consisting of 11 separate pavilions during a period of 15 years (2004-2018). In total, 1346 hot water samples were collected between January 2004 and December 2018. During this period, to recover Legionella spp. from water samples the standard procedures reported by the Italian Guidelines emanated in 2000 were adopted; from May 2015 to 2018 Italian Guidelines revised in 2015 (ISS, 2015), were used. The most water samples (72%) were positive to L. pneumophila serogroups 2-14 whereas L. pneumophila serogroup 1 accounted for the 18% and Legionella spp. for the 15%. Most of the positive samples were found in the buildings where are situated critical wards as ICU, Neurosurgery, Surgeries, Pneumology and Neonatal Intensive Unit Care. We highlighted the importance of a continuous monitoring of hospital water samples to prevent the potential risk of nosocomial legionellosis.
ARTICLE | doi:10.20944/preprints202105.0691.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Alerts; Village Health Teams; Community Based Surveillance; Integrated Disease Surveillance and Reporting; Elgon; Climate Change; One Health
Online: 28 May 2021 (10:20:13 CEST)
In mountain communities like Sebei, Uganda, that are highly vulnerable to emerging and reemerging infectious diseases, community-based surveillance plays an important role in the monitoring of public health hazards. In this survey, we explored capacities of Village Health Teams (VHTs) in Sebei communities of Mount Elgon in undertaking surveillance tasks for emerging and reemerging infectious diseases in the context of a changing climate. We used participatory epidemiology techniques to elucidate VHTs’ perceptions on climate change and public health and assess their capacities in conducting surveillance for emerging and reemerging infectious diseases. Overall, VHTs perceived climate change to be occurring with wider impacts on public health. However, they have inadequate capacities in collecting sur-veillance data. The VHTs lack transport to navigate through their communities and have in-sufficient capacities in using mobile phones for sending alerts. They do not engage in reporting other hazards related with the environment, wildlife and domestic livestock that would ac-celerate infectious disease outbreaks. Records are not maintained for disease surveillance ac-tivities and the abilities of VHTs to analyze data are also limited. However, VHTs have access to platforms that can enable them to disseminate public health information. The VHTs thus need to be retooled to conduct their work effectively and efficiently through equipping them with adequate logistics and knowledge on collecting, storing, analyzing, and relaying data, which will improve infectious disease response and mitigation efforts.
ARTICLE | doi:10.20944/preprints202310.1952.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Aedes aegypti; sticky trap; lure; entomological surveillance.
Online: 30 October 2023 (15:12:43 CET)
Surveillance is the systematic data collection, analysis, and interpretation essential to planning and implementing control activities. The lack of success in control and surveillance elsewhere for the Ae. aegypti mosquito demands developing new accessible and effective strategies. This work aimed to develop and evaluate an adhesive and lure trap for household indoor and outdoor surveillance of Ae. aegypti. Based on a bibliographic review, four compounds with significant attraction percentages for Ae. aegypti were considered. Our more effective blend was determined by preliminary bioassays using the high-throughput screening system (HITSS) and 90 × 90 cm mosquito cages. We designed a low-cost, pyramid-shaped, sticky cardboard trap to incorporate the selected blend. Semi-field 2 x 2 m cages and field tests were conducted to evaluate its effectiveness through mosquito capture percentages. In laboratory tests, blend number 2 presented an attraction percentage of 47.5 ± 4.8%; while in semi-field cages, a 4-inch, 110-v powered fan was used to disperse the attractants, then a similar capture percentage of 43.2 ± 4.0 % was recorded. Field evaluation of the at-house indoor environment and comparing it with the golden standard BG-Sentinel trap recorded interesting results, i.e., an average of our prototype 6.0 ± 1.5 trapped mosquitoes versus 10.0 ± 2.6. In most Latin American countries, there is a lack of formal and accessible strategies for monitoring adult populations of Ae. aegypti, therefore, must develop tools that reinforce entomological surveillance methods.
ARTICLE | doi:10.20944/preprints202307.1265.v1
Subject: Biology And Life Sciences, Virology Keywords: hepatitis virus; HBV; HCV; surveillance; Gabon; Africa
Online: 19 July 2023 (08:09:22 CEST)
Viral hepatitis remains one of the largest public health concerns worldwide. Especially in Central Africa, information on hepatitis virus infections has been limited, although the prevalence in this region has been reported to be higher than the global average. To reveal the current status of hepatitis B and C viruses (HBV and HCV) infections and the genetic diversity of the viruses, we conducted longitudinal surveillance in Gabon. We detected 22 HBV and 9 HCV infections in 2,047 patients with febrile illness. Genetic analyses of HBV identified subgenotype A1 for the first time in Gabon and an insertion generating a frameshift to create an X-preC/C fusion protein. We also revealed that most of the detected HCVs belonged to the “Gabon-specific” HCV subtype 4e (HCV-4e), and the entire nucleotide sequence of the HCV-4e polyprotein was determined to establish the first reference sequence. HCV-4e strains possessed resistance-associated substitutions similar to those of other HCV-4 strains, indicating that the use of direct-acting antiviral therapy may be complex. These results provide a better understanding of the current situation of hepatitis B and C virus infections in Central Africa, and will help public health organizations develop effective countermeasures to eliminate chronic viral hepatitis in this region.
ARTICLE | doi:10.20944/preprints202306.0746.v1
Subject: Biology And Life Sciences, Virology Keywords: HIV-1 subtype D; Phylodynamics; Genomic surveillance
Online: 12 June 2023 (03:33:40 CEST)
(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: to achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3,704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains.
ARTICLE | doi:10.20944/preprints202305.1380.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Antimicrobial resistance (AMR), Antibiotics; Surveillance; India; Taiwan
Online: 19 May 2023 (05:01:35 CEST)
Human exposure to antimicrobial resistance (AMR) through food is now very imperfectly understood, creating a significant gap in the design of interventions. The interchange of AMR genes and the transfer of AMR bacteria from animals to humans through the food chain necessitate comprehensive methods to risk reduction. With a focus on AMR in bacterial species isolated from food products, foods (of both animal and non-animal origin), and ambient samples, the current meta-analysis gathered up-to-date information on the epidemiology of AMR in animal-source food chain. As a result, the combined prevalence of AMR across the various food sources was calculated. From the 18,784 food samples obtained as a result of selected publications, 7,676 (40.9%) samples were contaminated, including 4343 (56.6%) and 3363 (43.4%) samples from Taiwan and India, respectively. Meat (chicken, pork, and beef), fish and milk all have moderate to medium potential for AMR exposure to both Gram-positive and Gram-negative foodborne pathogens such S. aureus, Clostridium, E. coli, Salmonella, etc. Antibiotic resistance to β-lactam, fluoroquinolone, carbapenem etc, is present in the majority of food samples. The results of this study emphasize the persistent danger of antimicrobial residue in animal-derived foods in Taiwan, India, and other nations with comparable customs.
ARTICLE | doi:10.20944/preprints202209.0343.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Lymphatic Filariasis; Indonesia; National Surveillance; Registry; BELKAGA
Online: 22 September 2022 (10:41:18 CEST)
Lymphatic filariasis (LF) is a vector-borne disease caused by parasitic helminths and constitutes a serious public health issue in tropical regions. According to the World Health Organization (WHO), infected cases in Southeast Asia constitute 50% of the estimated 120 million infections globally. In Indonesia, LF is caused by all filarial species, and in 2018, 236 districts from a total of 514 districts in the entire country were declared as endemic areas. The global program to eliminate filariasis has been running for the last 19 years and has been conducted as a full national initiative for the last 8 years in Indonesia. The study describes the surveillance of LF cases and prevalence in Indonesia for the past 17 years (2001-2017) – during the global and national LF elimination programs-, using national registry-based data. The data demonstrates that the national program has been largely effective in the areas it has been active the longest, while there are provinces lagging behind in the successful suppression of LF. The high geographical fragmentation of the country with the associated ecological parameters relating to LF incidence, likely play an important role in maintaining the highly varied incidence rate across Indonesia.
ARTICLE | doi:10.20944/preprints202103.0188.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: disability; quality of life; cerebral palsy; surveillance
Online: 5 March 2021 (11:51:51 CET)
Secondary and tertiary prevention strategies targeting people with disabilities to improve their health and wellbeing is important. In Sweden, >95% of all children with cerebral palsy (CP) participate in a follow-up program, where one of the goals is the prevention of hip dislocations. We reviewed the incidence of hip dislocations from 2010 to 2019 and the number of children who underwent different types of hip surgeries. The number of hip dislocations was reduced from 8.8% before introduction of the program to 0.3-0.4% up to 2015, followed by a gradual increase to 0.8% in 2019. The proportion of children who underwent adductor-psoas lengthening as their primary preventive surgery decreased from 50% in 2017 to 37% in 2019 with a corresponding increase of children undergoing femoral osteotomy, indicating more children underwent surgery at a later stage. Reasons for the increased number of children with hip dislocation may be that more children have moved to Sweden in recent years without corresponding compensation in health care resources and increased waiting times for surgery due to, among other things, a shortage of nurses. The results highlight the importance of constantly monitoring follow-up programs.
ARTICLE | doi:10.20944/preprints202102.0597.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: Surveillance; COVID; Football; Infection; Professional; PCR; Elite
Online: 26 February 2021 (08:59:29 CET)
Medical surveillance and risk mitigation protocols to reduce viral transmission have underpinned the return of elite football during the COVID-19 pandemic. This article describes the evidence-informed approach and surveillance findings from the English Football League across a 9-week period at the end of the 2019-20 season. Protocols were devised by the lead EFL Medical Advisor with specialist occupational medicine input. Isolation requirements for cases and contacts were in-line with UK Government regulations, with external contact tracing conducted by local public health authorities. Quantitative PCR testing was conducted twice weekly and within 72 hours of fixtures. 43 individuals, including 18 players returned positive tests. No positive results were returned after week 5 (round 10). Our findings support those from other leagues that with appropriate compliance, elite football can continue safely during this pandemic. We recommend that protocols and compliance should be revised as necessary according to community prevalence and changes in viral transmission dynamics.
ARTICLE | doi:10.20944/preprints201712.0151.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: foodborne diseases; outbreaks; surveillance; epidemiology; public health
Online: 21 December 2017 (05:00:55 CET)
Background: Foodborne disease is a major public health concern in both developed and developing countries. China has established a nationwide Foodborne Disease Outbreak Surveillance System (FDOSS) for collection and periodic reporting of data on the occurrence and causes of foodborne disease outbreaks in China. Each provincial Centers for Disease Control and Prevention (CDC) conducts the system working. Methods We reviewed foodborne disease outbreaks that occurred during 2011-2016 in Shandong Province from the FDOSS. The Wilcoxon test was used to compare the median number of ill persons in outbreaks. All data analysis was performed using Epi Info 7. Results: During 2011-2016, Shandong CDC received reports of 1043 foodborne disease outbreaks, resulting in 8078 illnesses, 2442 hospitalizations, and 17 deaths. Hotels were the most common setting. Among the 744 (71.3%) outbreaks with an implicated food or contaminated ingredient reported, 704 (94.6%) could be assigned to one of 17 predefined commodity categories. Of the 280 outbreaks with a known aetiology, 117(41.8%) were caused by poisonous plants and animals and their toxins, 39(13.9) were caused by nitrite, and 27(9.6%) were caused by vibrio parahaemolyticus. Conclusion: Timely investigation, disposal and reporting of foodborne disease outbreaks provides information that might help FDOSS to make full use of efficiency and FDOSS should be continued and strengthened even more in Shandong Province, such as an increase in diagnostic laboratory capacities.
ARTICLE | doi:10.20944/preprints202310.0814.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Agent-based modelling; antimicrobial-resistant gonorrhea; surveillance systems
Online: 12 October 2023 (11:24:24 CEST)
We aim to evaluate efficiency of two American surveillance systems for monitoring the spread of antimicrobial-resistant (AMR) gonorrhea among men who have sex with men (MSM) using the novel continuous-time agent-based model of gonorrhea transmission. The model was developed using the simulation modelling tool AnyLogic and accounts for susceptible and resistant strains of N. gonorrhoeae, symptomatic and asymptomatic infection and various routes of transmission between different anatomical sites. The model was calibrated using a Bayesian calibration approach. The surveillance systems are the Gonococcal Isolate Surveillance Project (GISP) and the enhanced Gonococcal Isolate Surveillance Project (eGISP). We calculated accuracy, sensitivity, specificity and estimation error for each surveillance system based on the number of isolates submitted in 2018. We also varied that number to see its effect on the outcomes. Our results show that the accuracy of eGISP was between 66% and 92%, while GISP demonstrates low accuracy between 44% and 48%. We also determined that increasing the number of isolates results in improved performance for eGISP, while GISP is not particularly sensitive to it.
ARTICLE | doi:10.20944/preprints202309.1757.v1
Subject: Biology And Life Sciences, Virology Keywords: Herpes B virus; zoonosis; LAMP; surveillance; cynomolgus macaque
Online: 26 September 2023 (13:39:13 CEST)
Herpes B virus (BV) is a zoonotic virus which can be transmitted from macaques to humans, which is often associated with high mortality rates. Because macaques often exhibit asymptomatic infections, individuals who come into contact with these animals face unexpected risks of BV infections. Serological test is widely performed to investigate BV infections. However, the assay’s sensitivity and specificity appeared to be inadequate, and it does not necessarily indicate ongoing viral shedding. Here, we developed LAMP and qPCR assays aiming to detect BVs with high sensitivity and specificity in various macaque species and validated them using oral swab samples collected from 97 wild cynomolgus macaques living in Thailand. Our LAMP and qPCR assays detected more than 50 and 10 copies of the target sequences per reaction, respectively. The LAMP assay could detect BV within 25 min, indicating its advantages for the rapid detection of BV. Collectively, our findings indicated that both assays developed in this study exhibit advantages and usefulness for BV surveillance and diagnosis of BV infections in macaques. Furthermore, for the first time, we determined the partial genome sequences of BVs detected in cynomolgus macaques in Thailand. Phylogenetic analysis revealed the species-specific evolution of BV within macaques.
ARTICLE | doi:10.20944/preprints202309.1376.v1
Subject: Biology And Life Sciences, Virology Keywords: DENV; Genomic surveillance; Epidemiology; molecular clock; SNPs; arboviruses
Online: 20 September 2023 (10:42:22 CEST)
The dengue virus (DENV) is an arbovirus belonging to the Flaviviridae family; the species comprises four antigenically distinct serotypes (DENV–1, DENV–2, DENV–3, and DENV–4), which are further subdivided into genotypes. The virus is transmitted to humans through mosquito bites, primarily from the Aedes spp. genus. Dengue is endemic in various parts of the world, including tropical and subtropical regions of Asia, Latin America, Africa, and Oceania. In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of arboviral disease cases, particularly dengue. This study aimed to monitor DENV circulation within the state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. During this period, both DENV-1 and DENV-2 serotypes were identified. Our findings confirm the circulation of DENV serotypes 1 and 2 in Tocantins, affecting males and females equally, with younger age groups (4 to 43 years old) being the most susceptible. Phylogenetic analysis revealed that the circulating viruses belong to DENV–1 genotype V American and DENV–2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 Genotype V sequenced here is closely related to genomes previously sequenced in the state of São Paulo. Regarding DENV-2 genotype III genomes, these are clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. In both cases, our results suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the significant impact of major population centers in Brazil on virus dispersion, including other Latin-American countries and the USA. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here reveal the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of the DENV and the ongoing significance of surveillance efforts in supporting public health policies.
ARTICLE | doi:10.20944/preprints202308.1533.v2
Subject: Computer Science And Mathematics, Computer Vision And Graphics Keywords: wildlife; Surveillance; quad-rotor; target identification; Blob Detection
Online: 5 September 2023 (05:17:43 CEST)
Owing to the upsurge in the number of endangered species and understanding animal patterns in general as well as population demographics; the monitoring of wildlife species is an essential for the conservation and safety of animals. In order to organize and manage the reserves, the nature bequeaths to us, we need to have hands-on information of their population and food trends, conditions where they survive and other species in the ecosystem. The paper presents a vision-based approach to monitor wildlife using an aerial platform. A quad-rotor based aerial platform is used for the very first time for this purpose. Field imaging is done using a digital cellphone camera mounted on the platform to acquire video of horses in the field. Two techniques, Lucas-Kanade and Horn-Schunck methods are applied on the acquired set of images and the results are compared. Noise due to fluctuations and light conditions are minimized using Gaussian and HSV filters. Experiments show results with an absolute mean difference of 2.84 pixels and 8.50 pixels for changes in X and Y directions respectively for the two approaches.
ARTICLE | doi:10.20944/preprints202308.0649.v1
Subject: Biology And Life Sciences, Virology Keywords: zoonosis; emerging diseases; influenza; epidemiology; NGS sequencing; surveillance
Online: 8 August 2023 (09:29:08 CEST)
Influenza A viruses (IAV) are still a cause of concern for public health and veterinary services worldwide. With (-) RNA-segmented genome architecture, influenza viruses are prone to reassortment and can generate a great variety of strains, some capable of crossing interspecies barriers. The latest 2009 pandemic and numerous reports of zoonotic infections worldwide show that these capabilities cannot be underestimated. Seasonal IAV strains continuously spread from humans to pigs, leading to multiple reassortation events with strains endemic to swine. Due to high adaptability to human, reassortant strain based on “human-like” genes could potentially be a carrier of avian origin segments responsible for high virulence, hence become next pandemic strain with unseen pathogenicity. We must foresee this kind of event, paying close attention to the surveillance of common human-animal interfaces. The rapid evolution of sequencing methods has provided a fast and cost-efficient way to assess the genetic diversity of IAV. In this study, we investigated the genetic diversity of swine influenza viruses (swIAVs) collected from Polish farms. A total of 376 samples were collected from 11 farms. The infection was confirmed in 112 cases. The isolates were subjected to next-generation sequencing (NGS), resulting in 93 full genome sequences. Phylogenetic analysis classified 59 isolates as genotype T (H1avN2g) and 34 isolates as genotype P (H1pdmN1pdm), all of which had an internal gene cassette (IGC) derived from the H1N1pdm09-like strain. These data are consistent with evolutionary trends in European swIAVs. The applied methodology proved to be useful in monitoring the genetic diversity of IAV at the human-animal interface.
ARTICLE | doi:10.20944/preprints202306.0801.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; diagnostic workflow; surveillance
Online: 12 June 2023 (08:44:37 CEST)
The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection, and successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled testing of over 8,000 pooled samples per day and provided results for over 2 million samples. Automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turn-around time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response.
COMMUNICATION | doi:10.20944/preprints202304.0343.v1
Subject: Biology And Life Sciences, Virology Keywords: Zika; arboviruses; vector-borne infections; genomic surveillance; phylogenetics
Online: 14 April 2023 (03:51:13 CEST)
The Americas, particularly Brazil, were greatly impacted by the widespread outbreak of Zika virus (ZIKV) in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We perform a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA and Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.
REVIEW | doi:10.20944/preprints202210.0291.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: eDNA; eRNA; fish disease; surveillance; hydrolysis; degradation; qPCR
Online: 19 October 2022 (14:45:21 CEST)
Organisms release their nucleic acid in the environment including the DNA and RNA which can be used to detect their presence. eDNA/eRNA techniques are being used in different sectors to identify organisms from soil, water, air, and ice since long. The advancement in technology led to easier detection of different organisms without impacting the environment and the organism itself. These methods are being employed in different areas including surveillance, history, and conservation. eDNA and eRNA methods are being extensively used in aquaculture and fisheries setting to understand the presence of different fish species and pathogens in water. However, there are some challenges associated with the reliability of the results because of the degradation of nucleic acid by several factors. In aquaculture there are several diseases and parasites detected with these methods. In this review we discuss different aquaculture diseases and parasites detected with eDNA/eRNA approach and the fate of these nucleic acids when subjected to different water quality and environmental parameters. This review intends to help the researcher about the potential of eDNA/eRNA based detection of pathogens in aquaculture; this will be useful to predict the potential outbreak before it occurs. Along with that this paper intends to make people understand several factors that degrade and can hamper the detection of these nucleic acids.
CONCEPT PAPER | doi:10.20944/preprints202208.0072.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Image Processing System; Drones; Surveillance system; FANET operations
Online: 3 August 2022 (03:54:45 CEST)
The major goal of this paper is to use image enhancement techniques for enhancing and extracting data in FANET applications to improve the efficiency of surveillance. The proposed conceptual system design can improve the likelihood of FANET operations in oil pipeline surveillance, and sports and media coverage with the ultimate goal of providing efficient services to those who are interested. The system architecture model is based on current scientific principles and developing technologies. A FANET, which is capable of gathering image data from video-enabled drones, and an image processing system that permits data collection and analysis are the two primary components of the system. Based on the image processing technique, a proof of concept for efficient data extraction and enhancement in FANET situations and possible services is illustrated
ARTICLE | doi:10.20944/preprints202206.0335.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: metadata; contextual data; harmonization; genomic surveillance; data management
Online: 24 June 2022 (08:46:04 CEST)
COMMUNICATION | doi:10.20944/preprints202203.0336.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Covid-19; SARS-CoV-2; Wastewater; research; surveillance
Online: 25 March 2022 (03:30:23 CET)
Background: In the span of just two years, tracking the COVID-19 pandemic through wastewater surveillance has advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. Objectives: We examine the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition of early monitoring efforts to more formalized programs within the public health system. Discussion: Wastewater surveillance has rapidly developed as a public health tool Clinical testing programs are ramping down and home testing is on the rise, making wastewater monitoring important for future surveillance of COVID-19. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and organizational challenges and draw useful lessons. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should continue and should promote knowledge co-development. While wastewater surveillance has demonstrated utility for tracking COVID-19, there remain technical challenges and open scientific questions that researchers are equipped to address, which will contribute to building robust surveillance programs that provide public health practitioners with new insights into population health.
ARTICLE | doi:10.20944/preprints202202.0233.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: AI; disease surveillance; pandemics; global public health; ethics
Online: 18 February 2022 (10:36:04 CET)
Infectious diseases, as COVID-19 is proving, pose a global health threat in an interconnected world. In the last 20 years, resistant infectious diseases such as SARS, MERS, H1N1, Ebola, Zika and now COVID-19 have been impacting global health defences, and aggressively flourishing within the rise of global travel, urbanization, climate change and ecological degradation. In parallel, this extraordinary episode in global human health highlights the potential for artificial intelligence (AI)-enabled disease surveillance to collect and analyse vast amounts of unstructured and real-time data to inform epidemiological and public health emergency responses. The uses of AI in these dynamic environments are increasingly complex, challenging the potential for human autonomous decisions. In this context, our study of qualitative perspectives will consider a responsible AI framework to explore its potential application to disease surveillance in a global health context. Thus far, there is a gap in the literature in considering these multiple and interconnected levels of disease surveillance and emergency health management through the lens of a responsible AI framework.
ARTICLE | doi:10.20944/preprints202303.0523.v1
Subject: Medicine And Pharmacology, Other Keywords: Zimbabwe Stimulated Telephone Assisted Rapid Safety Surveillance (Zm-STARSS); mHealth active participant-centred (MAPC) Adverse Events Following Immunisation(AEFI) surveillance
Online: 30 March 2023 (03:51:08 CEST)
Abstract Introduction: The mHealth active participant centred (MAPC) adverse events following immunisation (AEFI) surveillance is a promising area for early AEFI detection resulting in risk minimisation. Passive (spontaneous) AEFI surveillance is the backbone for vaccine pharmacovigilance, but has inherent drawbacks of under reporting, and requires strengthening with active surveillance methods. The Zimbabwe stimulated telephone assisted rapid safety surveillance (Zm-STARSS) randomized controlled trial (RCT) sought to evaluate the efficacy and feasibility of AEFI detection using a short message service (SMS) and computer assisted telephone interview (CATI) approach. Method: A multicentre Zm-STARSS RCT enrolled consented adult vaccinees or parents or guardians of children receiving vaccines, including COVID-19 vaccines, at study vaccination clinics. At enrolment study participants were randomised to either SMS-CATI group or control group. SMS prompts were sent on days 0-2 and 14 post-vaccination to SMS-CATI group to ascertain if a medical event following immunisation (MEFI) had occurred. However, no SMSs were sent to the control group. SMS-CATI group who responded “Yes” to SMS prompts were interviewed by research healthcare workers (RHCWs) who completed a CATI to determine if an MEFI/AEFI had occurred whilst an AEFI in control group was determined from passive AEFI reporting channels. The primary study outcome was the AEFI detection rate in the SMS-CATI group compared to the control group. Results: A total of 704 (31%) participants responded to the SMS prompts, with 75% (528/704) indicating “No” and 25% (176/704) "Yes” to experiencing a MEFI. However, 31% (55/176) who responded “Yes” did not complete a CATI survey, but 69% (121/176) did; and 64% (77/121) of these indicated negative to AEFI experience whilst 36% (44/121) were affirmative. There were no AEFI reported in control group participants. Zm-STARSS showed promising results in that the AEFI detection rate using SMS-CATI was 2% (44/2280) on an intention to treat cohort. Conclusion: Despite the low SMS response and CATI completion rate, we demonstrated that Zm-STARSS SMS system improves AEFI detection compared to passive AEFI surveillance. We recommend cost-effective multi-channel digital approaches for holistic pharmacovigilance to improve AEFI detection in LMICs for all vaccines.
ARTICLE | doi:10.20944/preprints202311.0412.v1
Subject: Engineering, Marine Engineering Keywords: big data; artificial intelligence; maritime surveillance; maritime security; sustainability
Online: 7 November 2023 (06:46:46 CET)
In today's world, wherein more than 80% of world trade is carried out by maritime routes, the safety and security of the seas where this trade takes place is of vast importance for nations and the in-ternational community. For this reason, ensuring the sustainable safety and security of the seas has become an integral part of the mission of all maritime-related entities. The utilization of big data extracted from the seas and maritime activities into meaningful information with artificial intelli-gence applications and developing applications that can be used in maritime surveillance will be of great importance for augmenting maritime safety and security. In this article, data sources which can be used by a maritime surveillance system based on big data and artificial intelligence tech-nologies and which can be established around sensitive sea areas and critical coastal facilities, are identified and a model proposal using this maritime big data is put forward.
REVIEW | doi:10.20944/preprints202310.0582.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: Ministry of Health; Public Health Surveillance; COVID-19; Brazil
Online: 10 October 2023 (12:15:40 CEST)
To describe the main health surveillance strategies for the control of COVID-19 in Brazil, with emphasis on decisions and actions taken at the federal level to prevent the infection caused by the new SARS-CoV-2. This is a scoping review study carried out from November 2019 to January 2021 using the DECS and MeSH health descriptors in Portuguese and English in four databases, in addition to the legislation found on the Brazilian Government's legislation portal. Based on the analysis of the documents, the actions describe non-pharmacological and pharmacological measures, measures related to decisions on closing and opening international borders, the acquisition of supplies and essential services. Although some strategies for containing the pandemic were identified, discrete and unnoticed surveillance measures are observed in view of the number of cases and number of deaths during the period of research analysis. The results show the absence of the federal level as support for the states and municipalities and imply decision-making and planning of actions by the Unified Health System to control the pandemic.
COMMUNICATION | doi:10.20944/preprints202309.1616.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: wastewater surveillance; livestock; zoonotic pathogens; one health; animal epidemiology
Online: 25 September 2023 (04:58:41 CEST)
Wastewater surveillance, initially conceived in the early 20th century during typhoid fever outbreaks, has evolved into a powerful tool for monitoring public health-relevant analytes. Recent applications in tracking SARS-CoV-2 infection highlight its potential. Beyond humans, it can be extended to livestock populations due to the increasing demand for livestock products. Livestock intensification poses risks of zoonotic disease emergence. Wastewater surveillance offers non-invasive, cost-effective means to detect potential outbreaks. This approach aligns with the "One Health" paradigm, emphasizing the interconnectedness of human, animal, and ecosystem health. By monitoring viruses in livestock wastewater, early detection, prevention, and control strategies can be employed, safeguarding both animal and human health, economic stability, and international trade. This integrated One Health approach enhances collaboration and a comprehensive understanding of disease dynamics, supporting proactive measures in the Anthropocene era where animal and human diseases are on the rise.
ARTICLE | doi:10.20944/preprints202308.0448.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; genomic surveillance; NGS; deletion; variants.; clusters
Online: 4 August 2023 (13:34:25 CEST)
Next generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion between ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last 3 aminoacids of ORF8. Interestingly, the deleted region was flanked by 2 small repeats, likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, 7 out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nuclotides deletion. It is noteworthy that 3 out of 6 cases were detected in patients with immunodeficiency and is conceivable that this clinical condition could promote the replication and selection of these mutations.
ARTICLE | doi:10.20944/preprints202306.0147.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Metadata generation; abnormal recognition; metadata retrieval; intelligent surveillance system
Online: 2 June 2023 (07:27:50 CEST)
Huge-scale video surveillance systems have become essential in crime prevention and situation recording. Traditional surveillance systems relied on human monitoring of video streams, which often led to errors and difficulties in understanding events. Furthermore, locating specific scenes within recorded videos required extensive human investigation. To overcome these challenges of inefficiency, inconvenience, and potential risks, we propose an intelligent analysis scheme that utilizes abnormal behavior recognition and metadata retrieval algorithms to replace human monitoring. The proposed method consists of three stages: i) metadata generation through object detection and tracking, ii) abnormal behavior recognition, and iii) SQL-based metadata retrieval. By incorporating specific information such as object color and aspect ratio, our technique enhances the usability of retrieval. Moreover, our abnormal behavior recognition module demonstrates robust classification capabilities for activities such as pushing, violence, falling, and crossing barriers. The proposed method can be seamlessly deployed on both edge cameras and analysis servers, making it adaptable to various surveillance setups. This approach revolutionizes the traditional surveillance paradigm, enabling more efficient, reliable, and secure video monitoring and analysis.
ARTICLE | doi:10.20944/preprints202305.0521.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Aircraft; Wastewater; Surveillance; Indicator viruses; Enteric viruses; Respiratory viruses
Online: 8 May 2023 (10:39:58 CEST)
The effective detection of viruses in aircraft wastewater is crucial to establish surveillance programs for monitoring virus spread via aircraft passengers. This study aimed to compare the performance of two virus concentration workflows, adsorption-extraction (AE) and Nanotrap® Microbiome A Particles (NMAP), in detecting the prevalence and concentrations of 15 endogenous viruses in aircraft lavatory wastewater samples. The viruses tested include two indicator viruses, four enteric viruses, and nine respiratory viruses. The results showed that cross-assembly phage (crAssphage), human polyomavirus (HPyV), rhinovirus A (RhV A), and rhinovirus B (RhV B) were detected in all wastewater samples using both workflows. However, enterovirus (EV), human norovirus (HNoV GII), human adenovirus (HAdV), bocavirus (BoV), parechovirus (PeV), epstein-barr virus (EBV), influenza A virus (IAV), and respiratory syncytial virus B (RsV B) were infrequently detected by both workflows, and hepatitis A virus (HAV), influenza B virus (IBV), and respiratory syncytial virus B (RsV A) were not detected in any samples. The NMAP workflow had greater detection rates of EV, PeV, and RsV B than the AE workflow, while the AE workflow had greater detection rates of HAdV, BoV, and EBV than the NMAP workflow. The concentration of each virus was also analyzed, and the results showed that CrAssphage had the highest mean concentration (6.76 log10 GC/12.5 mL) followed by HPyV (5.46 log10 GC/12.5 mL using the AE workflow, while the mean concentrations of enteric and respiratory viruses ranged from 2.48 to 3.63 log10 GC/12.5 mL. Using the NMAP workflow, the mean concentration of crAssphage was 5.18 log10 GC/12.5 mL and the mean concentration of HPyV was 4.20 log10 GC/12.5 mL, while mean concentrations of enteric and respiratory viruses ranged from 2.55 to 3.74 log10 GC/12.5 mL. The mean concentrations of CrAssphage, HPyV, RhV A, and RhV B between the two workflows were statistically significant (p < 0.05). In summary, the present study provides valuable insights into the performance of virus concentration workflows in detecting and quantifying different viruses in aircraft lavatory wastewater samples. The findings can aid in the selection of an appropriate concentration workflow for virus surveillance studies and contribute to the development of efficient and reliable virus detection methods.
ARTICLE | doi:10.20944/preprints202109.0334.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: organic producer; organic practices; surveillance data; health and safety
Online: 20 September 2021 (13:40:18 CEST)
Research indicates that farmers’ demographic characteristics and production practices have safety and health implications. However, current systems do not identify organic farmers independently from conventional farmers, and literature on how organic and conventional farmers compare is very limited. We conducted a secondary analysis of 2012 Census of Agriculture data to compare organic and non-organic farms and principal operators (POs) in New Mexico (NM). Organic farms were smaller in size, and POs of farms with organic sales were significantly younger (55.8±9.5 vs. 60.5±5.5 years) and less experienced (19.5±6.8 vs. 25.2±6.8 years). Significant differences were also found in POs ethnicity, race, and primary occupation. More farms with organic sales had a female PO compared to farms with non-organic sales (27% vs. 19%). Other significant differences related to work arrangements, household income, living conditions, and access to Internet. National surveys and regional studies may not accurately typify and describe the local organic producer, which is essential in order to advance policy, develop health interventions, and properly address occupational safety and risk among organic farmers. This study makes a unique contribution to understanding the importance of surveillance and collecting place-based data that are specific to the organic producer.
Subject: Biology And Life Sciences, Virology Keywords: Phylogenetics; Subclinical infection; FMD outbreaks; Disease control; Surveillance; Sentinels
Online: 30 August 2021 (11:54:39 CEST)
The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate sampling of clinically healthy livestock at slaughterhouses as a strategy for genomic FMDV surveillance. Serum samples (n = 11875) and oropharyngeal fluid (OPF) samples (n = 5045) were collected from asymptomatic cattle and buffalo on farms in eight provinces in southern and northern Vietnam (2015 to 2019) to characterize viral diversity. Outbreak sequences were collected between 2009 and 2019. In two slaughterhouses in southern Vietnam, 1200 serum and OPF samples were collected from asymptomatic cattle and buffalo (2017 to 2019) as a pilot study on the use of slaughterhouses as sentinel points of surveil-lance. VP1 sequences were analyzed using discriminant principal component analysis and time-scaled phylodynamic trees. Six of seven serotype O and A clusters circulating in southern Vietnam from 2017-19 were detected at least once in slaughterhouses, sometimes pre-dating outbreak sequences associated with the same cluster by 4-6 months. Routine sampling at slaughterhouses may provide timely and cost-effective strategy for genomic surveillance to identify circulating and emerging FMDV strains.
ARTICLE | doi:10.20944/preprints202108.0223.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: nephroblastoma; clinical malformations; cancer predisposition syndromes; tumor surveillance; outcome
Online: 10 August 2021 (09:55:14 CEST)
Background: About 10% of Wilms Tumor (WT) patients have a malformation or cancer predisposition syndrome (CPS) with causative germline genetic or epigenetic variants. Knowledge on CPS is essential for genetic counselling. Methods: This retrospective analysis focused on 2927 consecutive patients with WTs registered between 1989 and 2017 in the SIOP/GPOH studies. Results: (GU, N=66, 2,3%), Beckwith-Wiedemann spectrum (BWS, N=32, 1,1%), isolated hemihypertrophy (IHH, N=29, 1,0%), Denys-Drash syndrome (DDS, N=24, 0,8%) and WAGR syndrome (N=20, 0,7%) were reported most frequently. Compared to others, these patients were younger at WT diagnosis (median age 24,5 months vs. 39,0 months), had smaller tumors (334,8mL vs. 496,9mL), less often metastasis (8,2% vs. 18%), but more often nephroblastomatosis (12,9% vs. 1,9%). WT with IHH was associated with blastemal WT and DDS with stromal subtype. Bilateral WTs were common in WAGR (30%), DDS (29%) and BWS (31%). Chemotherapy induced reduction in tumor volume was poor in DDS (7,7% increase) and favorable in BWS (84,6% reduction). The event-free survival (EFS) of patients with BWS was significantly (p=0,002) worse than in others. Conclusions: CPS should be considered in WTs with specific clinical features resulting in referral to a geneticist. Their outcome was not always favorable.
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Drug Safety Surveillance; Adverse Drug Reaction; Ophthalmic; Ciprofloxacin; Dexamethasone
Online: 5 January 2021 (11:51:06 CET)
Background: drugs provide a significant benefit; however, their use implies an intrinsic potential danger, with the possibility to cause unwanted effects. These effects are known as adverse drug reactions (ADRs). Post-marketing drug safety surveillance detects unknown risks that have not been identified in clinical trials and it is necessary to monitor marketed medications under real-life practice. Due to the scarce information about fixed combination of ciprofloxacin 0.3% / dexamethasone 0.1% (SDO), we performed a drug safety surveillance study. (2) Methods: A prospective non-controlled drug safety surveillance study was conducted in Peruvian population. A total of 236 patients prescribed SDO were included derivates from 12 sites. Patients' standardized information was collected through two phone calls, including demographics, medical history, prescribing patterns of SDO, concomitant medication, and ADRs in detail. The ADRs were classified by causality and severity, followed by outcome measures to identify new risk. (3) Results: 236 patients prescribed with SDO participated in the study and 220 were included. A total of 82 ADRs/220 patients were reported after the use of SDO, presenting a ratio 0.37 ADR/patient. The most frequent ADR with SDO administration was eye irritation (30%). The totality of the ADR was classified as non-serious, and the 97.5% (n=80) was classified as mild and 2.5% as moderate (n=2). No cases under the severe category were identified. (4) Conclusion: No new risks were found in the population where this study was conducted.
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: public health nursing; epidemiological surveillance; nursing diagnosis; arterial hypertension
Online: 7 December 2020 (08:22:22 CET)
Background: Epidemiological surveillance of nursing diagnosis is an approach anchored on a post-modern epidemiology focused on persons health-disease responses. Regarding to public health priorities, the population where our study occurred had as priority problem the arterial hypertension. Related to this chronical disease, nursing diagnoses about health-disease responses in primary healthcare has as major focus Therapeutic Regime Management. Our aim was to study the nursing diagnosis in this issue, from an epidemiological approach. Methods: A descriptive study from an epidemiological approach was developed, analyzing nursing diagnoses in hypertensive patients. Results: We found 17,7% of undiagnosed patients and better diagnoses in patients with complications than in those without complications. Conclusions: nursing records need to be improved in order to promote more robust studies in the post-modern epidemiology defended for the future.
ARTICLE | doi:10.20944/preprints202006.0194.v1
Subject: Computer Science And Mathematics, Mathematics Keywords: network flow; combinatorial optimization; tracking-by-detection; video surveillance
Online: 15 June 2020 (11:26:25 CEST)
In tracking-by-detection paradigm for multi-target tracking, target association is modeled as an optimization problem that is usually solved through network flow formulation. In this paper, we proposed combinatorial optimization formulation and used a bipartite graph matching for associating the targets in the consecutive frames. Usually, the target of interest is represented in a bounding box and track the whole box as a single entity. However, in the case of humans, the body goes through complex articulation and occlusion that severely deteriorate the tracking performance. To partially tackle the problem of occlusion, we argue that tracking the rigid body organ could lead to better tracking performance compared to the whole body tracking. Based on this assumption, we generated the target hypothesis of only the spatial locations of person’s heads in every frame. After the localization of head location, a constant velocity motion model is used for the temporal evolution of the targets in the visual scene. Qualitative results are evaluated on four challenging video surveillance dataset and promising results has been achieved.
ARTICLE | doi:10.20944/preprints202005.0071.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: COVID-19; coronavirus; SARS-CoV-2; Simultaneous surveillance; Jordan
Online: 5 May 2020 (10:57:53 CEST)
The outbreak of coronavirus 2 (SARS-CoV-2) has already taken on pandemic proportions and has affected more than 100 countries in recent weeks. It is imperative that global healthcare systems are prepared. Containment initiatives in Jordan, on the other hand, have decreased new cases by over 63%. The Jordanian national health system has been very pleased with its ability to adequately meet the needs of the patients diagnosed with SARS-CoV-2 pneumonia, and includes intensive care. From 2 March to 14 April 2020, between 4% and 8% of active infected patients in Jordan registered daily in intensive care. The percentage is very low.
ARTICLE | doi:10.20944/preprints201907.0210.v1
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: post-marketing surveillance; vaccine safety; pertussis; Tdap; pregnancy; infant
Online: 18 July 2019 (09:26:02 CEST)
We aimed to evaluate the safety of maternal Tdap we assessed health events by examining the difference in birth and hospital-related outcomes of infants with and without fetal exposure to Tdap. This was a retrospective cohort study using linked administrative datasets. The study population were all live-born infants in New Zealand (NZ) weighing at least 400 grams at delivery and born to women who were eligible for the government funded, national-level vaccination program in 2013. Infants were followed from birth up to one year of age. There were a total of 69,389 eligible infants in the cohort. Of these, 8,299 infants were born to 8,178 mothers exposed to Tdap (12%), primarily between 28-38 weeks gestation as per the national schedule. Among the outcomes, we found a reduced risk for moderate to late preterm birth, low birth weight, small for gestational age, large for gestational age, respiratory distress syndrome, transient tachypnea of newborn, tachycardia or bradycardia, haemolytic diseases, other neonatal jaundice, anaemia, syndrome of infant of mother with gestational diabetes, and hypoglycemia in infants born to vaccinated mothers. There was no association between maternal Tdap and stillbirth, infant Apgar score at 5 minutes after birth, microcephaly, asphyxia, sepsis or infection, or hypoxic ischemic encephalopathy. Infant exposure to Tdap during pregnancy was associated with a higher mean birthweight (not clinically significant) and higher odds for ankyloglossia and neonatal erythema toxicum diagnoses. There were insufficient observations to allow examination of the effect of Tdap on extreme preterm and very preterm birth, and infant death. Overall, we found no outcomes of concern associated with the administration of Tdap during pregnancy.
REVIEW | doi:10.20944/preprints201712.0014.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: pancreatic cancer; immune surveillance; galectins; immunotherapy; immune checkpoints; stroma
Online: 4 December 2017 (05:17:15 CET)
Pancreatic ductal adenocarcinoma (PDA), the most frequent type of pancreatic cancer, is one of the main unfinished businesses in the biomedical and clinical fields, with still discouraging 5 year survival rates and poor therapy efficiency. PDA abundant desmoplasia has for long played the lead in the mechanisms involved in poor drug performance, being the main source of cytokines and chemokines orchestrating rapid and silent tumor progression and guilty of isolating tumor cells into a extense fibrotic reaction resulting in inefficient drug delivery. However, since immunotherapy was proclaimed the breakthrough of the year back to 2013, the focus in the stroma of pancreatic cancer has interestingly moved from activated fibroblasts to the immune compartment, trying to understand the immunosuppressive factors that play part in the strong immune evasion that characterizes PDA. PDA microenvironment is highly immune-suppressive, being basically composed of T regulatory cells (Tregs), tumor-associated macrophages (TAMs) and myeloid-derived suppressive cells (MDSCs), which boycott CD8+ T-cell duties in tumor recognition and clearance. Interestingly, preclinical data have highlighted the importance of this immune evasion as the source of resistance to single checkpoint immunotherapies and cancer vaccines and point at pathways inhibiting the immune attack as the key to solve the therapy puzzle. Here, we will discuss the molecular mechanisms involved in PDA immune escape as well as the state of the art of the PDA immunotherapy.
ARTICLE | doi:10.20944/preprints201703.0159.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: object detection; background subtraction; video surveillance; Kinect sensor fusion
Online: 20 March 2017 (10:21:40 CET)
Depth-sensing technology has led to broad applications of inexpensive depth cameras that can capture human motion and scenes in 3D space. Background subtraction algorithms can be improved by fusing color and depth cues, thereby allowing many issues encountered in classical color segmentation to be solved. In this paper, we propose a new fusion method that combines depth and color information for foreground segmentation based on an advanced color-based algorithm. First, a background model and a depth model are developed. Then, based on these models, we propose a new updating strategy that can eliminate ghosting and black shadows almost completely. Extensive experiments have been performed to compare the proposed algorithm with other, conventional RGB-D algorithms. The experimental results suggest that our method extracts foregrounds with higher effectiveness and efficiency.
ARTICLE | doi:10.20944/preprints202305.0969.v1
Subject: Biology And Life Sciences, Virology Keywords: yellow fever virus; vectors; Aedes albopictus; outbreak; entomo-virological surveillance
Online: 15 May 2023 (03:25:34 CEST)
After eight decades, the largest outbreak of sylvatic yellow fever virus (YFV) was recorded in Brazil between 2016-2018. Besides human and NHP surveillance, the entomo-virological approach is considered as a complementary tool. For this study, a total of 2904 mosquitoes of Aedes, Haemagogus and Sabethes genera from six Brazilian states (Bahia, Goiás, Mato Grosso, Minas Gerais, Pará, and Tocantins), were collected and grouped in 246 pools, which were tested for YFV using RT-qPCR. We detected 20 positive pools from Minas Gerais, 5 from Goiás, and 1 from Bahia, including 12 of Hg. janthinomys and 5 of Ae. albopictus. This is the first description of natural YFV infection in this species and warns of the likelihood of urban YFV re-emergence with the Ae. albopictus as a potential bridge vector. Three YFV sequences from Hg. janthinomys from Goiás and one from Minas Gerais, as well as one from Ae. albopictus from Minas Gerais clustered within the 2016-2018 outbreak clade, indicating YFV spread from Midwest and its infection in a main and in a likely-novel bridging vector species. Entomo-virological surveillance is critical in the YFV monitoring in Brazil, which could highlight the need to strengthen YFV surveillance, vaccination coverage, and vector control measures.
REVIEW | doi:10.20944/preprints202209.0214.v1
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: Drinking water; potable water; public health surveillance; quality control; government.
Online: 15 September 2022 (02:17:24 CEST)
This study identified and mapped worldwide surveillance actions and initiatives of drinking water quality implemented by government agencies or public health services. The scoping review was conducted between July 2021 and August 2022 based on the Joanna Briggs Institute. The search was performed in relevant databases and grey literature; 49 studies were obtained. Quantitative variables were presented as absolute and relative frequencies, while qualitative variables were analyzed using the IRaMuTeQ software. The actions developed worldwide and their impacts and results provided four thematic classes: (1) assessment of coverage, accessibility, quantity, and drinking water quality in routine and emergency situations; (2) analysis of physical-chemical and microbiological parameters in public supply networks or alternative water supply solutions; (3) identification of household water contamination, communication, and education with the community; (4) and investigation of water-borne disease outbreaks. Preliminary results were shared with stakeholders to favor early knowledge dissemination.
ARTICLE | doi:10.20944/preprints202205.0131.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Variants of Concern; Delta Variant; genomic surveillance.
Online: 10 May 2022 (09:44:11 CEST)
In this study, we analyzed sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which completely replaced other previously circulating variants in the country due to its transmission advantage. Among Delta sublineages detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these sublineages only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described, and phylogenetic analyses and haplotype networks were used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the principal sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variants associated to the third wave of the COVID-19 pandemic in Mexico and reinforces the importance of SARS-CoV-2 genomic surveillance for timely identification of emerging variants that may impact public health.
ARTICLE | doi:10.20944/preprints202204.0266.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS CoV-2; Variant of Concern; Omicron; mutation; genomic surveillance
Online: 28 April 2022 (03:28:50 CEST)
Genomic surveillance represents an important strategy for understanding evolutionary mechanisms, transmission profile, and infectivity of different SARS-CoV-2 variants. We assessed the epidemiological profile of 366 individuals who tested positive for SARS-CoV-2 from 29 municipalities in Rondônia between December 2021 to March 2022. Samples were collected, RNA was ex-tracted and screened using RT-qPCR for Alpha, Beta, Gamma, Delta and Omicron VOCs and viral quantification was performed. Sequences were analyzed for phylogeny, mutations and lineages. Of the samples analyzed, 93.71% were positive for the Omicron variant and 6.28% were positive for the Delta variant. The symptoms observed were cough, sore throat, and fever, with a mean duration of 5 days; no hospitalizations or deaths were reported. We noted that among the positive individuals, 51% had been immunized with two doses, 22% received three doses, 13% received one dose, and 13% were not immunized. Just 242 samples were amenable to analysis for alignment and phylogenetic characterization; corresponding to variants BA.1 and BA.1.1; a total of 120 mutations were identified, 36% of which were found in the S gene. In conclusion, there was a high frequency of mutations in the SARS-CoV-2 genome, but no record of clinical severity, demonstrating the positive effect of vaccination.
REVIEW | doi:10.20944/preprints202105.0075.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Schistosomiasis; diagnosis; non-human hosts; surveillance; systematic review; meta-analysis
Online: 6 May 2021 (12:04:50 CEST)
Background Reliable and field-applicable diagnosis of schistosome infections in non-human animals is important for surveillance, control, and verification of interruption of human schistosomiasis transmission. This study aimed to summarize uses of available diagnostic techniques through a systematic review and meta-analysis. Methods and principal findings We systematically searched the literature and reports comparing two or more diagnostic tests in non-human animals for schistosome infection. Out of 4,909 articles and reports screened, 18 met our inclusion criteria, four of which were considered in the meta-analysis. A total of 14 techniques (parasitologic, immunologic, and molecular) and nine types of non-human animals were involved in the studies. Notably, four studies compared parasitologic tests (miracidium hatching test (MHT), Kato-Katz (KK), the Danish Bilharziasis Laboratory technique (DBL), and formalin-ethyl acetate sedimentation-digestion (FED-SD)) with quantitative polymerase chain reaction (qPCR), and sensitivity estimates (using qPCR as the reference) were extracted and included in the meta-analyses, showing significant heterogeneity across studies and animals hosts. The pooled estimate of sensitivity was 0.21 (95% confidence interval (CI): 0.03 – 0.48) with FED-SD showing highest sensitivity (0.89, 95% CI: 0.65 – 1.00). Conclusions and significance Our findings suggest that the parasitologic technique FEA-SD and the molecular technique, qPCR, are the most promising field-applicable techniques for schistosome diagnosis in non-human animal hosts. Future studies are needed for validation and standardization of the techniques for real-world field applications.
ARTICLE | doi:10.20944/preprints202103.0609.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; Aerosols; Environmental Surveillance; Air Sampling
Online: 24 March 2021 (17:29:23 CET)
The worldwide spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has ubiquitously impacted many aspects of life. As vaccines continue to be manufactured and administered, limiting the spread of SARS-CoV-2 will rely more heavily on the early identification of contagious individuals occupying reopened and increasingly populated indoor environments. In this study, we investigated the utility of an impaction-based aerosol sampling system with multiple nucleic acid collection media. Heat-inactivated SARS-CoV-2 was utilized to perform bench-scale, short-range aerosol, and room-scale aerosol experiments. Through bench-scale experiments, AerosolSense Capture Media (ACM) and nylon flocked swabs were identified as the highest utility media. In room-scale aerosol experiments, consistent detection of aerosol SARS-CoV-2 was achieved at a concentration equal to or greater than 0.089 genome copies per liter of room air (gc/L) when air was sampled for eight hours or more at less than one air change per hour (ACH). Shorter sampling periods (~75 minutes) yielded consistent detection at ~31.8 gc/L of room air and intermittent detection down to ~0.318 gc/L at (1 and 6+ ACH respectively). These results support further exploration in real-world testing scenarios and suggest the utility of indoor aerosol surveillance as an effective risk mitigation strategy in occupied buildings.
ARTICLE | doi:10.20944/preprints202012.0502.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: invasive species; ecological niche models; species distribution models; vector surveillance
Online: 21 December 2020 (10:50:19 CET)
Aedes scapularis is a neotropical mosquito known to transmit pathogens of medical and veterinary importance. Its recent establishment in southeastern Florida has potential public health implications. We used an ecological niche modeling approach to predict the abiotic environmental suitability for Ae. scapularis across much of the Americas and Caribbean Islands. Georeferenced occurrence data obtained from the Global Biodiversity Inventory Facility and recent collection records of Ae. scapularis from southern Florida served as input for model calibration. Environmental layers included bioclimatic variables provided in 2000 to 2010 average Modern Era Retrospective-analysis for Research and Applications climatic (MERRAclim) data. Models were run in the software program Maxent. Isothermality values found often in costal environments contributed strongest to model performance. Model projections suggested areas predicted suitable for Ae. scapularis across portions of the Amazon Basin, the Yucatán Peninsula, the Florida Peninsula, and multiple Caribbean Islands. Additionally, model predictions suggested connectivity of highly suitable or relatively suitable environments spanning the United States Gulf Coast, which may facilitate geographic expansion of this species. At least sixteen Florida counties were predicted highly suitable for Ae. scapularis, suggesting vigilance is needed by vector control and public health agencies to recognize further spread of this vector.
ARTICLE | doi:10.20944/preprints202008.0067.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: adverse drug reaction; healthcare professionals; pharmacovigilance; surveillance form; suspected ADR
Online: 3 August 2020 (08:49:10 CEST)
Objectives: The aim of this study was to assess the knowledge, attitude and practice of healthcare professionals regarding adverse drug reaction [ADR] monitoring and pharmacovigilance [PV] in India. Materials and Methods: It was a questionnaire based cross sectional observational study. Data was collected with the help of data collection Google form that included the demographics and twenty two survey based questions. Data were analysed by using Microsoft Excel sheet, further analysed for results, including frequency, percentage, mean and standard deviation. Result: The questionnaire was filled by two hundred ten healthcare professionals in which 52.9 % were male and 47.10% of female. Most of the respondents were pharm d students (50.47%). Out of the total 91.4% responded to the definition of pharmacovigilance correctly. 87.6% participants said all ADR should be reported. 86.20% participants think Pharmacovigilance should be taught in detail to healthcare professionals. Most of the respondents (43.8%) always informed the patients about ADR while prescribing the medicines. Conclusion: Study revealed most of the participants have good knowledge about ADR and pharmacovigilance. Difficult to decide whether ADR occur or not and extra work load being major factors responsible for under reporting.
ARTICLE | doi:10.20944/preprints202305.1955.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Egg shortage; Poultry supply chain; Influenza; Economic crisis; One Health surveillance
Online: 29 May 2023 (03:59:14 CEST)
Poultry eggs are a critical source of protein, vitamins, and minerals for people worldwide; facing the current global egg shortage is a significant concern. The shortage results from various factors, including avian flu outbreaks, changes in consumer demand, and supply chain disruptions caused by the COVID-19 pandemic. The economic crisis caused by the pandemic has also impacted the availability and affordability of eggs, particularly in low-income countries. The global egg shortage has implications for public health, particularly for vulnerable populations who rely on eggs for essential nutrients. One Health, an approach that recognizes the interconnectedness of human, animal, and environmental health, provides a useful framework for understanding and addressing the egg shortage. One Health approaches to the egg shortage involve collaboration between agriculture and environmental sectors to address the root causes of the lack and ensure the sustainable production and distribution of eggs. Addressing the global egg shortage requires a multifaceted approach considering the complex social, economic, and environmental factors. One Health perspectives offer a way to understand and address the interconnected factors contributing to the shortage to ensure access to affordable, nutritious eggs for all in a healthy way
ARTICLE | doi:10.20944/preprints202210.0241.v1
Subject: Medicine And Pharmacology, Other Keywords: evolution; mutation; genomic surveillance; SARS-CoV-2; COVID-19; ViralVar; webtool
Online: 17 October 2022 (12:59:07 CEST)
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. A majority of the currently available tools either require computational expertise to deploy or limit user input to pre-selected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: 1) visualization of spatiotemporal dynamics of SARS-CoV-2 lineages, and 2) structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in the pediatric, adult, and elderly population (n > 1.7 million genomes). While the spatiotemporal dynamics of variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate large-scale surveillance of circulating pathogens. The ViralVar webserver is freely available at http://viralvar.org/.
ARTICLE | doi:10.20944/preprints202201.0234.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: AMR, Surveillance; One Health Approach; Alternative Antibiotics; Comparative Medicine; Phage Therapy
Online: 17 January 2022 (14:46:22 CET)
Antibiotics are in excessive use that has extensively increased antimicrobial resistance worldwide which has become the major public concern among the countries. To control this threat proper monitoring of the antimicrobial usage along with the increasing rate of antimicrobial resistance (AMR) is required. Further, surveillance of both the parameters is highly recommended for comparing the differences in distinct countries. Moreover, alternatives for antibiotics are also surveyed and are being researched for quick use in the near future. AMR is an issue that needs immense attention from various sectors. Thus, intervention of multisector is highly encouraged for better outcomes. One Health is one of the approaches that play a vital role in resolving this issue. In this research paper, six different European countries are discussed in terms of antimicrobial usage and AMR in the human and livestock sectors with the help of literature study and various reports published by different organizations. Data study has been conducted to collect the data for comparison study. Data sources of AMR and antimicrobial usage are analyzed and a thorough comparison of both antimicrobial use and AMR are conducted. Also, the application of One Health is studied for a balanced system. This article provides about various surveillance systems that are formed only to keep a track on the upcoming situation of AMR and the consumption of antimicrobials by the humans as well as animals. The article does not provide about all the details required to monitor the AMR issue but firmly allow the readers to get acknowledged with the broad information about the antimicrobial resistance across the six countries of Europe. The regular data collected by the different organizations play a vital role in monitoring the status of AMR and antimicrobial usage by humans and in live stocks. These annual reports have highly helped the government to decide for alternatives and have focused in many training activities to combat the AMR situation globally. AMR prevention is linked to the One Health concept. As antibiotic resistance genes persist on an interface between environment and animal and animal health, an approach is required in all three areas that stress the concept of 'One Approach to Health.'
Subject: Engineering, Control And Systems Engineering Keywords: UAV; Object Detection; Object Tracking; Deep Learning; Kalman Filter; Autonomous Surveillance
Online: 28 September 2021 (11:27:07 CEST)
The ever-burgeoning growth of autonomous unmanned aerial vehicles (UAVs) has demonstrated a promising platform for utilization in real-world applications. In particular, UAV equipped with a vision system could be leveraged for surveillance applications. This paper proposes a learning-based UAV system for achieving autonomous surveillance, in which the UAV can be of assistance in autonomously detecting, tracking, and following a target object without human intervention. Specifically, we adopted the YOLOv4-Tiny algorithm for semantic object detection and then consolidated it with a 3D object pose estimation method and Kalman Filter to enhance the perception performance. In addition, a back-end UAV path planning for surveillance maneuver is integrated to complete the fully autonomous system. The perception module is assessed on a quadrotor UAV, while the whole system is validated through flight experiments. The experiment results verified the robustness, effectiveness, and reliability of the autonomous object tracking UAV system in performing surveillance tasks. The source code is released to the research community for future reference.
REVIEW | doi:10.20944/preprints202009.0654.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: breast cancer; BARD1; surveillance; management; genetic testing; predisposition; susceptibility; neoadjuvant; chemotherapy
Online: 26 September 2020 (17:32:52 CEST)
Current oncological developments are based on improved understanding of genetics, and especially the discovery of genes whose alterations affect cell functions with consequences for the whole body. Our work is focused on the one of these genes, the BARD1 and its oncogenic role in breast cancer. Most importantly, the study points to new avenues in the treatment and prevention of the most frequent female cancer based on BARD1 research. The BARD1 and BRCA1 proteins have similar structures and functions, and they combine to form the new molecule BARD1-BRCA1 heterodimer. The BARD1-BRCA1 complex is involved in genetic stabilization at the cellular level. It allows to mark abnormal DNA fragments by attaching ubiquitin to them. In addition, it blocks (by ubiquitination of RNA polymerase II) the transcription of damaged DNA. Ubiquitination, as well as stabilizing chromatin, or regulating the number of centrosomes, confirms the protective cooperation of BARD1 and BRCA1 in the stabilization of the genome. The overexpression of the oncogenic isoforms BARD1β and BARD1δ permit cancer development. The introduction of routine tests, for instance, to identify the presence of the BARD1β isoform, would make it possible to detect patients at high risk of developing cancer. On the other hand, introducing BARD1δ isoform blocking therapy, which would reduce estrogen sensitivity, may be a new line of cancer therapy with potential to modulate responses to existing treatments. It is possible that the BARD 1 gene offers new hope for improving breast cancer therapy.
REVIEW | doi:10.20944/preprints202008.0371.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: breast cancer; BARD1; surveillance; management; genetic testing; predisposition; susceptibility; neoadjuvant; chemotherapy
Online: 18 August 2020 (03:08:11 CEST)
Current oncological developments are based on improved understanding of genetics, and especially the discovery of genes whose alterations affect cell functions with consequences for the whole body. Our work is focused on the most important of these genes, the BARD1 and its oncogenic role in breast cancer. Most importantly, the study points to new avenues in the treatment and prevention of the most frequent female cancer based on BARD1 research. The BARD1 and BRCA1 proteins have similar structures and functions, and they combine to form the new molecule BARD1-BRCA1 heterodimer. Through ubiquitination, this heterodimer has significant effects on individual proteins, enabling, among others, the destruction of damaged DNA fragments. Ubiquitination, as well as stabilizing chromatin, or regulating the number of centrosomes, confirms the protective cooperation of BARD1 and BRCA1 in the stabilization of the genome. The overexpression of the oncogenic isoforms BARD1β and BARD1δ permit cancer development. The introduction of routine tests, for instance, to identify the presence of the BARD1β isoform, would make it possible to detect patients at high risk of developing cancer. On the other hand, introducing BARD1δ isoform blocking therapy, which would reduce estrogen sensitivity, may be a new line of cancer therapy with potential to modulate responses to existing treatments. It is possible that the BARD 1 gene offers new hope for improving breast cancer therapy.
Subject: Public Health And Healthcare, Health Policy And Services Keywords: SARS-CoV-2; COVID-19; Infection Control; Epidemic Surveillance; International Cooperation
Online: 3 March 2020 (11:30:01 CET)
The disease COVID-19 is highly infectious, and infectious in asymptomatic incubation period. The national epidemic development has been effectively controlled and continues improving, especially in areas outside Hubei province. Such periodical results were achieved by the joint efforts of the whole society, including not only the hard work and dedication of the front-line medical workers but also the active cooperation of the general public. The strict epidemic prevention and control measurements have brought remarkable control results. In the present study, the basic infection number of the coronavirus R0 (basic replication number of the infection) before and after prevention and control measurements was simulated to elaborate the measurements of the Chinese government on epidemic prevention and control, providing reference for the people around the world.
ARTICLE | doi:10.20944/preprints202311.1179.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: reporting; system; chemical; drug overdose; poisoning; surveillance; Makkah Almukarramah; Saudi Arabia
Online: 17 November 2023 (15:04:33 CET)
Background: Poisoning is a growing public problem that has shown increased prevalence in many countries worldwide, contributing to increased costs and mortalities. A lack of or insufficient information regarding the circumstances, chemicals, drugs and people at risk due to imperfect reporting system is regarded as a barrier to successful poisoning prevention and intervention efforts. In Saudi Arabia, poisoning cases are monitored at the central level in the Ministry of Health, with meticulous follow-up of cases across country areas through public health departments. The current study's objective was to describe the poisoning notification and reporting system in Makkah.Subjects and methods: All reports of chemical and drug overdose poisoning delivered to the environmental health and occupational safety department in Makkah Almukarramah over two years (2018-2019) were reviewed, together with verification of all systems, rules and guidelines organizing the performance of the department.Results: The total number of cases reported in 2018 was 209 cases, while it reached 42 cases in 2019. The overwhelming majority of the cases were Saudi (91.6%), with a slight predominance of males (57.4%) over females (42.6%). Generally, almost two-thirds of the cases occurred in children below 13 years (61.4%), most of the poisoning cases resulted from drug overdose (63.3%), while 34.7% were chemical poisoning. The most common drug poisoning was attributed to analgesics followed by antiepileptics, antihypertensive drugs, antipsychotics and antimicrobials, while cleaning and detergent agents were the most commonly poisoned chemicals. The majority of these agents were taken by the oral route. Children's chemical poisoning was significantly higher than that in older age groups (p<0.05). All intentional poisoning occurred in adults; the great majority of them (88.9%) used drug overdosing rather than chemical substances.Conclusion and recommendations: The current study results are consistent with most of the previous studies carried out in different regions in Saudi Arabia. Reviewing the performance and adherence of the “Environmental Health and Occupational Safety Department” to the guidelines and instruction regulating monitoring, notification and reporting of poison cases are satisfactory and the poisoning surveillance system is effective. Further in-depth studies are needed to elaborate other socioeconomic and demographic factors associated with chemical and drug overdose poisoning. Public health plans, policies and legislations should be implemented to reduce these factors, including prohibition over-the-counter pharmaceutical sales, selling the possibly harmful substances in kid-proof bottles and additional stringent rules governing chemical sale and storage. Intensive supervision of children is needed. Suicidal poisoning patients should seek psychiatric help to limit the possibility of attempting suicide again in the future. Furthermore, efforts are needed to plan and implement health education programs and campaigns about the factors proven in the current study to be significantly related to chemical and drug overdose poisoning to raise public knowledge about exposure to chemicals and its consequences. Popular communication media, commercial malls, road ads, learning institutions and workplaces can be used to deliver health education campaigns and programs. Advice on how to store chemicals safely and how to keep kids safe should be focused on during such programs.
REVIEW | doi:10.20944/preprints202304.0234.v1
Subject: Public Health And Healthcare, Physical Therapy, Sports Therapy And Rehabilitation Keywords: Irish dance; injuries; risk factors; injury prevention; epidemiology; prevalence; incidence; surveillance system
Online: 12 April 2023 (03:35:52 CEST)
Background: Irish dance is growing in popularity, evolving to a more athletic and demanding dance style. Aims: To conduct a systematic review, previously registered with PROSPERO, to identify prevalence, incidence, and injury pattern among Irish dancers and analyse associated risk factors. Methods: Six online databases, plus two dance-specific science publications were searched systematically. Studies were included if the pattern of injuries among Irish dancers were evaluated or the factors associated with injury were analysed, published in English or Portuguese, in peer-reviewed scientific journals. Four reviewers assessed the quality and level of evidence using the Downs and Black criteria and a modified Oxford Centre of Evidence-Based Medicine 2009 model, respectively. Results: Eleven articles were included, 8 level 3c (cross-sectional) and 3 level 3b (prospective). Mean DB percentage score was 63% ± 7,2%. Prevalence ranged from 72,2% to 92,6%, affecting mostly the foot/ankle complex. Only 2 articles reported incidence, which ranged from 3,4–10,6 injuries/1000 hours danced depending on injury definition. Psychological factors, elite level, and insufficient/poor sleep were associated with musculoskeletal injury. Conclusions: Injury prevalence and incidence is high in Irish dancers, with the foot and ankle more affected. Due to heterogeneity in injury definitions, methods, and populations, along with the need for improvement in studies quality, recommendations were made for future research.
ARTICLE | doi:10.20944/preprints202208.0207.v3
Subject: Medicine And Pharmacology, Ophthalmology Keywords: Adverse Drug Reaction; Spontaneous reporting; Active surveillance; Underreporting; Antiglau-coma; Artificial tear
Online: 11 October 2022 (03:18:55 CEST)
(1)Aims of the study: calculating the underreporting ratio for two different medications, a fixed combination of 0.5% timolol + 0.2% brimonidine + 2.0% dorzolamide (antiglaucoma) and a fixed combination of sodium hyaluronate 0.1% + chondroitin sulfate 0.18% (artificial tear) and characterizing the features influencing the reporting of adverse drug reactions (ADRs) in spontaneous reporting; (2) Methods: the underreporting ratio was calculated by comparing the adverse drug reactions reported in the spontaneous reporting database for every 10,000 defined daily doses marketed and the adverse drug reactions from an active surveillance study for every 10,000 defined daily doses used for different drugs (antiglaucoma and artificial tear). The factors related to the report in spontaneous reporting through statistical tests were also determined; (3) Results: The underreporting ratio of spontaneous reporting was 0.006029% for antiglaucoma and 0.003552% for artificial tear; additionally, statistically significant differences were found for severity, unexpected adverse drug reactions, and incidence of adverse drug reactions in females; (4) Conclusions: The underreporting ratio of ADRs related to ophthalmic medications indicates worry since the cornerstone of pharmacovigilance focuses on spontaneous reporting. Besides, since underreporting seems to be selective, the role of certain aspects like gender, seriousness, severity, and unexpected ADRs, must be considered in future research.
REVIEW | doi:10.20944/preprints202204.0015.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Wastewater; Surveillance; SARS-CoV-2; Wastewater based epidemiology; COVID-19; Detection; Sewage
Online: 4 April 2022 (11:04:30 CEST)
Coronavirus Disease-19 (COVID-19) is presently wreaking havoc on public health and socio-economic development. Besides the upper and lower respiratory tract involvement, gastrointestinal symptoms are also reported in COVID-19 patients through gut-lung axis. Finding its way through the feces of infected individuals and other sources, the genetic material of SARS-CoV-2 (ssRNA) is reported widely in wastewater and is being used as a fingerprint for its detection. With millions of cases arriving every day, there is a need to level up the testing speed efficiency. Due to the restricted sampling potential of testing laboratories, clinical testing is unable to track all the symptomatic and asymptomatic cases. Wastewater-based epidemiology (WBE) bestows an auxiliary monitoring tool that will contribute in community level screening. Sample collection, concentration, RNA extraction, quantification and data analysis are the main steps involved in implementation of WBE that can be relied upon as an alarm call for an upcoming wave, emergence of a new variant or any future pandemic. WBE can be a cheaper and more practical alternative to high end and sophisticated clinical testing for community transmission detection. Worldwide, there are more than 300 reports entailing the occurrence of SARS-CoV-2 in wastewater exhibiting unique temporal trends with five of them in India. This review aims to address the present knowledge on surveillance of SARS-CoV-2 in wastewater and its implications.
ARTICLE | doi:10.20944/preprints202202.0035.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Aedes albopictus; ovitrap; regularized logistic regression; ecological niche model; environmental factors; surveillance
Online: 2 February 2022 (13:18:11 CET)
Background: In Switzerland, Aedes albopictus is well established in Ticino, south of the Alps, where surveillance and control are implemented. The mosquito has also been observed in Swiss cities north of the Alps. Decision-making tools are urgently needed by the local authorities in order to optimize surveillance and control. Methods: A regularized logistic regression was used to link the long-term dataset of Ae. albopictus occurrence in Ticino with socio-environmental predictors. The probability of establishment of Ae. albopictus was extrapolated to Switzerland and more finely to the cities of Basel and Zurich. Results: The model performed well, with an AUC of 0.86. Ten so-cio-environmental predictors were selected as informative, including the road-based distance in minutes of travel by car from the nearest cell established in the previous year. The risk maps showed high suitability for Ae. albopictus establishment in the Central Plateau, the area of Basel and the lower Rhone Valley in the Canton of Valais. Conclusions: The areas identified as suitable for Ae. albopictus establishment are consistent with the actual current findings of tiger mosquito. Our approach provides a useful tool to prompt authorities’ intervention in the areas where there is higher risk of introduction and establishment of Ae. albopictus.
ARTICLE | doi:10.20944/preprints202111.0264.v1
Subject: Medicine And Pharmacology, Orthopedics And Sports Medicine Keywords: exercise; marriage; sedentary behavior; gender; age groups; behavioral risk factors surveillance system
Online: 15 November 2021 (13:44:23 CET)
Abstract: The aim of the present study was to identify the age and sex-related associations between marital status with PA and TV time. We used data from Vigitel, an annual telephone survey started in 2006 in Brazil. We applied a complex sample logistic regression model to estimate the odds for PA and TV time comparing marital statuses according to age and sex subgroups, independent of obesity, hypertension, diabetes, self-assessed poor health, and smoking. Our sample included 561,837 individuals with a TV time > 3 h/day (prevalence = 25.2%) and PA > 150 min/week (prevalence = 35%). Compared to single individuals, married men and women were less likely to watch TV more than 3 h/day in participants > 30 years old. When compared to single, married participants were less likely to do more than 150 min of PA/week at younger age groups. Married women older than 40 years were more likely to do more than 150 min of PA/week than the single ones, while there were no differences among married men by age group. In conclusion, married individuals are less likely to spend more than 3 hours a day watching TV than single individuals. Single men and women were more likely to do more than 150 min of PA/week at younger age groups and married women older than 40 years were more likely to do 150 min of PA/week than single women.
REVIEW | doi:10.20944/preprints202106.0320.v1
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: RT-qPCR; assay validity; standard curve; quality assurance; quality control; wastewater surveillance
Online: 11 June 2021 (14:10:51 CEST)
The coronavirus disease 2019 (COVID-19) pandemic has led to wastewater surveillance becoming an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. As a result, molecular methods, in particular reverse transcription-quantitative PCR (RT-qPCR), have been employed to generate large data sets aimed at the detection and quantification of SARS-CoV-2 in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method that fits all use cases, there are no certified quantification standards and experiments are carried out using numerous different assays, reagents, instruments, and data analysis protocols. These variations can lead to the reporting of erroneous quantitative data resulting in potentially misleading interpretations and conclusions. We have reviewed the SARS-CoV-2 wastewater surveillance literature focusing on the variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices as described in The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
ARTICLE | doi:10.20944/preprints202103.0671.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic health; surveillance program; aplasia genitalis; atresia ani et recti; hernia cerebralis
Online: 26 March 2021 (15:09:33 CET)
This study aims to analyze the pedigrees of calves affected by one of three congenital defects: aplasia genitalis, atresia ani et recti and hernia cerebralis. The defects were diagnosed by veterinary surgeons in the Czech surveillance program for bovine genetic disorders. The sires fathering affected calves were born in the Czech Republic or imported from 1986-2001. The cases occurred on farms across the Czech Republic. The pedigree of each case was examined for common maternal and paternal ancestors (inbreeding loops) and for ancestors shared by other cases of the defect. The 13 calves affected by aplasia genitalis had common ancestors in all cases. The results indicate hereditary causation with recessive inheritance. Additionally, in atresia ani et recti, some of the pedigrees of 25 affected calves support hereditary causation, and repeating ancestors were found for 11 calves. In contrast, our analysis of 11 hernia cerebralis cases did not confirm the genetic background. We demonstrated that the pedigree analysis of congenital defects could help in controlling genetic health, although the final goal in terms of inherited defects is the description of causal genes and mutations. Measures to control sires that father affected calves should be appropriate under the current knowledge, which include culling or prudent use of breeding with the monitoring of descendants.
REVIEW | doi:10.20944/preprints202012.0283.v3
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: SARS-CoV-2; Covid-19; wildlife; host-switching; reservoirs; risk assessment; surveillance
Online: 26 March 2021 (10:25:36 CET)
The novel coronavirus SARS-CoV-2 likely emerged from a wildlife source with transmission to humans followed by rapid geographic spread throughout the globe and severe impacts on both human health and the global economy. Since the onset of the pandemic, there have been many instances of human-to-animal transmission involving companion, farmed and zoo animals, and limited evidence for spread into free-living wildlife. The establishment of reservoirs of infection in wild animals would create significant challenges to infection control in humans and could pose a threat to the welfare and conservation status of wildlife. We discuss the potential for exposure, onward transmission and persistence of SARS-CoV-2 in an initial selection of wild mammals (bats, canids, felids, mustelids, great apes, rodents and cervids). Dynamic risk assessment and targeted surveillance are important tools for the early detection of infection in wildlife, and here we describe a framework for collating and synthesising emerging information to inform targeted surveillance for SARS-CoV-2 in wildlife. Surveillance efforts should be integrated with information from public and veterinary health initiatives to provide insights into the potential role of wild mammals in the epidemiology of SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202101.0173.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; genetic diversity; molecular surveillance; natural selection; non-synonymous substitution
Online: 11 January 2021 (09:50:55 CET)
In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.
ARTICLE | doi:10.20944/preprints202008.0204.v2
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-Cov-2; epidemic surveillance; emerging infectious disease; epidemic threshold
Online: 23 September 2020 (11:10:15 CEST)
Background: Understanding SARS-CoV-2 dynamics and transmission is a serious issue. Its propagation needs to be modeled and controlled. The Alsace region in the East of France has been among the first French COVID-19 clusters in 2020. Methods: We confront evidence from three independent and retrospective sources: a population-based survey through internet, an analysis of the medical records from hospital emergency care services, and a review of medical biology laboratory data. We also check the role played in virus propagation by a large religious meeting that gathered over 2,000 participants from all over France mid-February in Mulhouse. Results: Our results suggest that SARS-CoV-2 was circulating several weeks before the first officially recognized case in Alsace on February 26th 2020 and the sanitary alert on March 3rd. The religious gathering seems to have played a role for secondary dissemination of the epidemic in France, but not in creating the local outbreak. Conclusions: Our results illustrate how the integration of data coming from multiple sources could help trigger an early alarm in the context of an emerging disease. Good information data systems, able to produce earlier alerts, could have avoided a general lockdown in France.
ARTICLE | doi:10.20944/preprints201609.0014.v1
Subject: Biology And Life Sciences, Virology Keywords: HIV/AIDS; testing; trends; Behavioral Risk Factor Surveillance System; socio-demographic; Georgia
Online: 5 September 2016 (11:21:36 CEST)
Georgia is ranked fifth highest among states for rates of HIV diagnosis. About 4% of persons living with HIV infection in the United States reside in Georgia, and almost 19% of these people do not know their HIV status. The present study examined the trends and associated factors of HIV testing among adults in Georgia between 2010 and 2014 by analyzing data of the Behavioral Risk Factor Surveillance System (BRFSS). A total of 30,791 persons aged ≥18 years were identified who responded to the question “Have you ever been tested for HIV?” Overall, there were 11,543 respondents who had been tested for HIV, with a decrease in percentage from 49.4% in 2010 to 43.7% in 2014 (p<0.001). Factors associated with HIV testing were being black (p<0.001), being younger than 55 years (p<0.001), single (p=0.02), attaining education level above high school (P<0.001), engaging in HIV high-risk behaviors (p<0.001), and not having healthcare coverage (p=0.03). Overall in Georgia, there has been a decline in the temporal trend of HIV testing, and more than half of adults have never been tested for HIV. For reducing HIV transmission in Georgia, enhancing access and utilization of HIV testing should be a public health priority.
BRIEF REPORT | doi:10.20944/preprints202106.0341.v2
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Impact of COVID on TB; TB Notification in India; Integrated TB COVID Activity; Threats and Opportunity during COVID; Initiatives to improve TB Surveillance; TB Surveillance during COVID Pandemic
Online: 22 June 2021 (14:05:04 CEST)
Introduction: Due to COVID-19 pandemic, performance of many program has been declined and Tuberculosis (TB) program is not an exception. TB case detection and notification has been recognized as one of worst hit area. The objective of this study was to explore the TB notification status of India during this pandemic and explore options to mitigate the issue. Methods: A secondary data analysis was performed on open source TB notification database of India. Relevant literature review was done to find out remedies based on the different initiative taken by different states of India. Results: In 2020, total TB notification decreased in all the states in comparison to 2019. The percentage of loss in the country was 34%. Private TB notification also decreased in 2020 in all the states except in Jharkhand. The percentage of loss in private TB notification in the country was 35%. Notification started declining in the month of February 2020 and it was lowest in the month of April-2020. The trend of notification began to improve since May 2020 when the States started taking innovative initiatives like Integrated TB Covid Case Search. Conclusion: Due to the ongoing COVID-19 pandemic the notifications of TB cases declined noticeably which has a serious implication in terms of silent spread within household and community. But the picture can be improved with integrated approach for TB-COVID case finding and management.
ARTICLE | doi:10.20944/preprints202305.1181.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: influenza vaccination; health personnel; health care worker; surveillance system; epidemiology; prevention; public health
Online: 17 May 2023 (04:27:18 CEST)
(1) Influenza causes a significant health and socio-economic burden every year, and health personnel (HP) are at higher risk of exposure to respiratory pathogens than general population. (2) The study purpose was to describe and compare influenza vaccine uptake and its prognostic factors among Medical Doctors (MDs) and Non-Medical Health Personnel (NMHP) vs Non-HP (NHP). We analysed 2014-2018 data (N=105,608) from the Italian Behavioural Risk Factor Surveillance System PASSI that, since 2008, has been collecting health-related information continuously in sampled adults. (3) MDs and NMHP represented, respectively, 1.1% and 4.6% of the sample. Among HP, 22.8% (CI 19.8% - 26.1%) of MDs and 8.5% (CI 7.5% - 9.5%) of NMHP reported to have been vaccinated vs 6.3% (CI 6.1% - 6.5%) in NHP. This difference is confirmed in the three categories (MDs, NMHP, NHP), even more across age groups: in 18-34yy, respectively, 9.9%, 4.4%, 3.4% vs 28.4%, 13.9%, 10.6% in 50-64yy. PASSI surveillance shows an increasing influenza vaccination uptake over time, especially among MDs (22.2% in 2014 vs 30.5% in 2018). (4) Despite such increase, especially among younger HP, influenza vaccination uptake is low. Even more under pandemic scenarios, these figures represent key information to address effective strategies for disease prevention and health promotion.
ARTICLE | doi:10.20944/preprints202111.0301.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: ductal carcinoma in situ (DCIS); invasive breast carcinoma; breast; biopsy; overtreatment; active surveillance.
Online: 17 November 2021 (11:03:55 CET)
Background: We aimed to create a model of radiological and pathological criteria able to predict the upgrade rate of low-grade ductal carcinoma in situ (DCIS) to invasive carcinoma, in patients undergoing vacuum-assisted breast biopsy (VABB) and subsequent surgical excision. Methods: 3100 VABBs were retrospectively reviewed among which we reported 295 low-grade DCIS who subsequently underwent surgery. The association between patients’ features and the upgrade rate to invasive breast cancer (IBC) was evaluated by univariate analysis. Finally, we developed a predictive multivariable model based on the features which were significantly associated with the univariate analysis outcome. Results: the upgrade rate to invasive carcinoma was 10.8 %. At univariate analysis, the risk of upgrade was significantly lower in the absence of post- biopsy residual lesion (p<0.001), age > 50 (p=0.029), and in presence of low-grade DCIS only in specimens with microcalcifications (p=0.002). According to the final multivariable model, the predicted probability of diagnostic underestimation for a patient with all the three favourable features selected at univariate analysis was 1% (95% CI: 0.3%-4%). Conclusions: An easy to use predictive model of radiological and pathological criteria is able to identify patients with low-grade carcinoma in situ with low risk of upstaging to infiltrating carcinomas.
ARTICLE | doi:10.20944/preprints202105.0557.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: SARS-CoV-2; Wastewater; treatment; plant; Environmental Virology Monitoring and Surveillance; E gene
Online: 24 May 2021 (10:35:04 CEST)
The experience gained over the last hundred years clearly indicates that two groups of viruses represent the main risk for the development of highly transmissible epidemics and pandemics in the human species: influenza viruses and coronaviruses (CoV). Although the search for viruses with pandemic potential in the environment may have an important predictive and monitoring role, it is still based on empirical methodologies, mostly translated from the clinic and not fully validated for environmental matrices.As far as the SARS-CoV-2 pandemic, currently underway, is concerned, environmental monitoring activities aiming at checking the presence of SARS-CoV-2 in wastewater can be extremely useful to predict and control the diffusion of the disease. For this reason, the present study aims to evaluate the SARS-CoV-2 diffusion by means of a wastewater-based environmental monitoring developed in Piedmont, N-W Italy, during the pandemic second and third waves. Sampling strategies, sampling points, sample pre-treatments and analytical methods have been developed and validated to give representative and reliable results. The outcomes highlighted by the present paper demonstrate a strong correlation between SARS-CoV-2 concentration in untreated wastewater and epidemic evolution in the considered areas as well as a predictive potential that could provide decision-makers with indications for establishing effective policies to mitigate the effects of the ongoing pandemic and to prepare response plans for future pandemics that could certainly arise in the decades to come.Moreover, the study highlights the potential of wastewater treatment plants to degrade the genetic material referable to SARS-CoV-2 as well.In conclusion, the preliminary data reported in the present paper, although they need to be complemented by further studies considering other geographical regions as well, are very promising.
REVIEW | doi:10.20944/preprints202104.0481.v1
Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: COVID-19; SARS-CoV-2; Wastewater; Surveillance; False-positive; False-negative; RT-PCR
Online: 19 April 2021 (13:08:13 CEST)
Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.
ARTICLE | doi:10.20944/preprints202011.0512.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: antimicrobials; meropenem; generic drug; real-life studies; product surveillance, postmarketing; treatment outcome; pharmacovigilance
Online: 19 November 2020 (13:34:26 CET)
Background. To determine the effectiveness and safety of meropenem in routine clinical practice, in terms of clinical and microbiological response. Methods. A real-world, observational, descriptive, longitudinal study with daily monitoring of clinical history records was conducted on all patients who were medically prescribed meropenem during a period between October 2015 and March 2016 at a university hospital in Bucaramanga (Colombia). Results. The study evaluated 84 patients with an average age of 63.2 years, mostly older adults with multiple comorbidities, of whom 54.8% were men. A positive clinical or microbiological response was obtained in 98.8% of the patients. At the end of the treatments, significant improvements in dysthermia (0% vs 29% at the beginning, p = 0.000), tachycardia (13% vs 47%, p = 0.049) and leukocytosis (39% vs 15% at the beginning, p = 0.008) were evidenced. The improvement in the indicator that combines all the SIRS criteria was also significant (p = 0.000). The treatment was well tolerated, although we identified some non-serious and expected adverse reactions. Conclusions. Generic meropenem proved to be effective and well tolerated for different types of infection in routine clinical practice. The results are consistent with the findings of the clinical studies with the innovator drug.
REVIEW | doi:10.20944/preprints202309.1224.v1
Subject: Biology And Life Sciences, Virology Keywords: Influenza A virus; avian influenza virus; genomic surveillance; poultry farms; wild birds; HPAI H5N1.
Online: 19 September 2023 (03:54:36 CEST)
The Influenza A virus (IAV) is a highly infectious virus that poses a significant threat to global public health and food supplies. The current subtype of avian influenza virus (AIV), H5N1, is being closely monitored worldwide due to its unprecedented spread from Europe to North America and now to Central and South America. This review summarizes recent updates on the evolution of the different IAV subtypes in birds and mammals including humans, in Chile. The distribution and spread of AIV H5N1 in Chile indicated a complex interplay between ecological and human factors in that it was negatively correlated with distance to the closest urban center and precipitation and temperature seasonality. It is evident that highly pathogenic avian influenza (HPAI) H5N1 in Chile was introduced from North America via the Atlantic migratory flyways as opposed to local transmission from other countries in South America. The presence of these viruses in Chile underscores the need for increased biosecurity on poultry farms and continuous genomic surveillance approaches to understand and control AIVs in both wild and domestic bird populations in Chile.
Subject: Public Health And Healthcare, Primary Health Care Keywords: Nutritional Surveillance; Public Health; Community Health Nursing; Public Health Nursing; Children’s health; Community Participation
Online: 17 August 2020 (10:08:36 CEST)
Effectively responding to children’s nutritional status and eating behaviors in Mozambique requires a community-based care approach grounded in sound nursing research that is evidence-based. The Community Assessment, Intervention, and Empowerment Model (MAIEC) is a nursing theoretical model that bases clinical decision-making for community health nurses using communities as a unit of care. We used the MAIEC to identify a community-based nursing diagnosis to address children’s nutritional status and eating behaviors in Mozambique. Objectives: (1) To conduct a descriptive study of children’s nutritional status and eating behaviors in a school community in Mavalane, Mozambique, and (2) to identify a community-based nursing diagnosis using the MAIEC clinical decision-making matrix in the same school community. Method: A cross-sectional, quantitative study was conducted to assess the nutritional status of children using anthropometric data, including brachial perimeter and the tricipital skinfold, and standard deviation for the relation of weight-height, in a sample of 227 children. To assess community management of the problem and identify a community-based nursing diagnosis, we surveyed 176 parents/guardians and 49 education professionals, using a questionnaire based on the MAIEC clinical decision matrix as a reference. Results: Malnutrition was identified in more than half of the children (51.3%). We also identified a community-based nursing diagnosis of impaired community management related to the promotion of child health and healthy eating as evident by lack of community leadership, participation, and processing among more than 70% of the community members (parents/guardians and education professionals). Conclusion: A nursing diagnosis and diagnostic criteria for nutritional status and community management were identified. The need to intervene using a multidisciplinary public health approach is imperative, with the school community as the unit of care. In addition, reliable anthropometric data were used to complement the nursing diagnosis and guide future public health interventions.
ARTICLE | doi:10.20944/preprints201703.0211.v2
Subject: Biology And Life Sciences, Virology Keywords: Zika virus; Flavivirus; RNA Viruses; Viruses; surveillance; occurrence; epidemiology; West Nile virus; Aedes; Culicidae
Online: 30 March 2017 (04:53:34 CEST)
In 2015 in Brazil, Zika virus showed features of geographic expansion and potentially increased virulence. In 2016, New York State issued emergency regulations after the World Health Organization declared Zika virus a Public Health Emergency of International Concern. In this study, mosquito surveillance was conducted in Westchester County, New York, to identify Zika virus and other arboviruses. Twenty trap sites were used for surveillance of Aedes albopictus mosquitoes, the Zika virus vector. The Westchester County Department of Health performed testing for Zika, West Nile, Eastern equine encephalitis, and other flaviviruses on 369 batches comprising 8,891 mosquitoes. Aedes albopictus mosquitoes were identified in Nassau, Rockland, Suffolk, Westchester, and New York City. Despite the increased capacity for specimen analysis, Zika virus was not detected. This study provides the first evidence of appropriate Zika virus surveillance. However, the results do not allow determination of the potential mechanism of local vector-to-human transmission of Zika virus among Aedes albopictus mosquitoes. This study adds to the evidence regarding the distribution, emergence, and trapping capabilities of potential Zika virus vectors.
ARTICLE | doi:10.20944/preprints202307.1532.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; pandemic; variants; RT-PCR; sequencing; surveillance; vaccination; vaccine breakthrough; comorbidity.
Online: 21 July 2023 (13:55:29 CEST)
New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOC) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5,007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOC, including Alpha (n =714), Delta (n =1,877), and Omicron (n =1,802). Omicron isolates were further sub-typed as BA.1 (n =899), BA.2 (n =853), and BA.4/BA.5 (n =50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1,577/5,007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p <0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p <0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p <0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.
ARTICLE | doi:10.20944/preprints202209.0242.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: pancreatic cancer (PC); abdominal ultrasonography (US); surveillance; prognosis; medical checkup; 5-year survival; cancer screening
Online: 16 September 2022 (08:08:33 CEST)
Recent advancements in surgical and anti-cancer therapies have provided significant hope of long survival in patients with pancreatic cancer (PC). To realize this hope, routine medical checkups of asymptomatic people should be performed to identify operable PCs. In this study, we evaluated the efficacy of medical checkups using abdominal ultrasonography (US). We retrospectively analyzed 374 patients with PC at our institute between 2010 and 2021. We divided these patients into several groups according to the diagnostic approach and compared their background and prognosis. These groups comprised PCs diagnosed through (a) symptoms, 242 cases; (b) US during medical checkup for asymptomatic individuals, 17; and other means. Of the 375 patients, 192 were men (51.3%), and the median age was 74 years (34–105). Tumors were located in the pancreatic tail in 67 patients (17.9%). Excision ratio and 5-year survival rate were significantly better in group (b) than in (a) (58.8% vs. 23.1%, P<0.01 and 42.2% vs. 9.4%, P<0.001, respectively). The prognosis of patients diagnosed using US during medical checkup was better than that of patients identified through symptomatic presentation of PC. US for asymptomatic individuals with PC might be useful for promoting better prognosis of PCs.
ARTICLE | doi:10.20944/preprints202105.0381.v1
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: SARS-CoV-2; wastewater monitoring; environmental surveillance; RT-LAMP; building-level; near-source; passive sampling
Online: 17 May 2021 (10:07:04 CEST)
Community-level wastewater monitoring for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has demonstrated useful correlation with both coronavirus disease 2019 (COVID-19) case numbers and clinical testing positivity. Wastewater monitoring on college campuses has demonstrated promising predictive capacity for the presence and absence of COVID-19 cases. However, to date, such monitoring has largely relied upon composite or grab samples and reverse transcription quantitative PCR (RT-qPCR) techniques, which limits the accessibility and scalability of wastewater monitoring. In this study, we piloted a workflow that uses tampons as passive swabs for collection and reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect SARS-CoV-2 RNA in wastewater. Results for the developed workflow were available same day, with a time to result following tampon swab collection of approximately three hours. The RT-LAMP 95% limit of detection (76 gene copies reaction-1) was greater than RT-droplet digital PCR (ddPCR; 3.3 gene copies reaction-1). Nonetheless, during a building-level wastewater monitoring campaign conducted in the midst of weekly clinical testing of all students, the workflow demonstrated a same-day positive predictive value (PPV) of 33% and negative predictive value (NPV) of 80% for incident COVID-19 cases. The NPV is comparable to that reported by wastewater monitoring using RT-qPCR. These observations suggest that even with lower analytical sensitivity the tampon swab and RT-LAMP workflow offers a cost-effective and rapid approach that could be leveraged for scalable same-day building-level wastewater monitoring for COVID-19.
COMMUNICATION | doi:10.20944/preprints202004.0253.v1
Subject: Biology And Life Sciences, Virology Keywords: Genomic Epidemiology; GenomeTrakr; microbial pathogen surveillance, NCBI submission; whole genome sequencing; QA/QC; One Health
Online: 16 April 2020 (05:26:42 CEST)
The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings.Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.
Subject: Computer Science And Mathematics, Information Systems Keywords: video surveillance; visual layer attack; electrical network frequency (ENF) signal; false frame injection (FFI) attack
Online: 1 April 2019 (09:50:05 CEST)
Over the past few years, the importance of video surveillance in securing the national critical infrastructure has significantly increased, whose applications include detecting failures and anomalies. Accompanied by video proliferation is the increasing number of attacks against surveillance systems. Among the attacks, false frame injection (FFI) attacks that replay video frames from a previous recording to mask the live feed has the highest impact. While many attempts have been made to detect FFI frames using features from the video feeds, video analysis is computationally too intensive to be deployed on-site for real-time false frame detection. In this paper, we investigate the feasibility of FFI attacks on compromised surveillance systems at the edge and propose an effective technique to detect the injected false video and audio frames by monitoring the surveillance feed using the embedded Electrical Network Frequency (ENF) signals. An ENF operates at a nominal frequency of 60 Hz/50 Hz based on its geographical location and maintains a stable value across the entire power grid interconnection with minor fluctuations. For surveillance system video/audio recordings connected to the power grid, the ENF signals are embedded. The time-varying nature of the ENF component is used as a forensic application for authenticating the surveillance feed. The paper highlights the ENF signal collection from a power grid creating a reference database and ENF extraction from the recordings using conventional short-time Fourier Transform and spectrum detection for robust ENF signal analysis in the presence of noise and interference caused in different harmonics. The experimental results demonstrate the effectiveness of ENF signal detection and/or abnormalities for FFI attacks.
ARTICLE | doi:10.20944/preprints202109.0427.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Hand sanitizer; COVID-19; alcohol; methanol substitution; gas chromatography; substandard products; falsified products; post-market surveillance
Online: 24 September 2021 (12:25:25 CEST)
The emergence of the COVID-19 pandemic has propelled the use of alcohol-based hand sanitizers to the fore as a SARS-CoV-2 control measure. To be effective these products must comply with relevant quality parameters such as alcohol concentration, methanol limits and purity. The current study was designed to determine the quality of alcohol-based hand sanitizer products in the Nairobi metropolitan area. For this purpose, 74 commercially marketed samples were collected and subjected to analysis by gas chromatography. Only three samples (4.1%) complied with the regulatory specifications for alcohol content, methanol limits and pH. Five samples (6.8%) complied with the specification for alcohol content but did not meet methanol or pH limits. A total of 44 (59.5%) samples had methanol levels that exceeded threshold limits. Eleven samples (14.9%) were found with methanol substitution (i.e., methanol, instead of ethanol or isopropanol, was the main alcohol component). The results show that users of alcohol-based hand sanitizers are being exposed to substandard and falsified products which in addition to being non-efficacious pose harm due to unacceptable levels of toxic impurities. Regular, routine post-market surveillance is needed to prevent such products from reaching the market.
ARTICLE | doi:10.20944/preprints202103.0330.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Barrett’s esophagus; biomarker; surveillance; screening; surface-enhanced Raman spectroscopy; SERS; complement component; liquid biopsy; lectin; glycoprotein.
Online: 12 March 2021 (08:03:55 CET)
Esophageal adenocarcinoma (EAC) detection relies on endoscopy-biopsy diagnosis, with routine endoscopic surveillance recommended for Barrett’s esophagus (BE) patients. Here, we examine the utility of blood biomarkers in patient risk stratification by translating the EAC blood biomarker Jacalin lectin binding complement C9 (JAC-C9) into a novel microfluidic immunoassay, the EndoScreen Chip. Cohort evaluation (n=46) showed elevated serum total C9 and JAC-C9 in EAC. Logistic regression modeling demonstrated that addition of C9 and JAC-C9 to patient risk factors (age, body mass index and heartburn/reflux history) improved EAC prediction from AUROC of 0.838 to 0.931. Serum JAC-C9 strongly predicted EAC (vs BE OR= 4.6, 95% CI: 1.6-15.6, p = 0.014; vs Healthy OR=4.1, 95% CI:1.2-13.7, p = 0.024) while total C9 was moderately predictive for BE (vs EAC OR=1.4; 95% CI: 1.0-1.8, p = 0.032; vs Healthy OR=0.8; 95% CI: 0.6-1.0, p = 0.039). This translational study demonstrates the potential utility of blood biomarkers in improving triaging for diagnostic endoscopy.
ARTICLE | doi:10.20944/preprints202004.0328.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; coronavirus; enhanced surveillance; real-time forecasts; phenomenological models; sub-exponential growth; Kadiogo; Burkina Faso
Online: 19 April 2020 (05:23:40 CEST)
On 9 March 2020, two cases of COVID-19 were reported in Burkina Faso. As of 10 April 2020, a total number of 484 cases (404 cases in the Kadiogo province) were reported nationwide. Real-time forecasts of COVID-19 are important to inform decision-making in the country. Here, we propose an approach that tests the performance of four models (Exponential Growth model, the Generalized Growth model (GGM), the Generalized Logistic Growth, and Richards Growth model) to select the model that best fit data and to generate short-term forecasting (5-, 10-, and 15-day forecasts from 11 to 25 April 2020) in Kadiogo, the epicenter of the outbreak. Using daily number of confirmed COVID-19 cases, the results suggests that GGM performed the best out of the 4 models. Overall, our GGM predictions suggested an average total number of cumulative cases of 514 (95% CI, 464–559), 629 (95% CI, 559–691), and 750 (95% CI, 661–840) between 11 to 15 April, 16 to 20 April, and 20 to 25 April 2020, respectively. COVID-19 in this province was best approximated by sub exponential growth rather than exponential or logistic growth. Current data suggest that COVID-19 cases would continue to increase over the next 15-days.
ARTICLE | doi:10.20944/preprints202305.0997.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: SARS-CoV-2; COVID-19; temporary disability; cumulative incidence; healthcare workers; National Network of Epidemiological Surveillance; Spain
Online: 15 May 2023 (07:49:18 CEST)
Healthcare workers (HCW) have been the professional category most exposed to SARS-CoV-2. The pandemic’s impact on HCW was analyzed in terms of COVID-19-related temporary disability (TD) between February 15 2020 and May 1 2021. TDs in HCW for COVID-19 infection or quarantine were described. TD quarantine/infection ratios and TDs per 100,000 affiliated HCW were compared with the cumulative incidence (CI) of COVID-19 cases notified to the National Network of Epidemiological Surveillance. TDs rates by economic activity and occupation were computed. A total of 429,127 TDs were recorded, 36,6% for infection. Three-quarters (76%) were women. The median TD quarantine/infection ratio was 2.5 (Interquartile range [IQR] 1.5-3.9). TDs rates in HCW were always above the CI except for the last two months of the fourth wave. Hospital activities accounted for 84% of TDs and showed the highest TD rate for infection (8,279/100,000). The highest TDs rates were registered among Nursing assistants, Nursing professionals and Physicians: 7,426, 6,925 and 5,508/100,000, respectively. The results demonstrate the high impact of COVID-19 on HCW in Spain and it’s inequalities. They also confirm that TDs represent a complementary source of information for epidemiological and public health surveillance and could provide an early warning of new emerging infections.
ARTICLE | doi:10.20944/preprints202301.0035.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: BRFSS; Bereavement; Grief; Mental Health; Physical Health; Population Surveillance; Social de-terminants of health; Multiple Imputation; Screening
Online: 4 January 2023 (01:54:29 CET)
The BRFSS is an annual survey conducted by each state and designed to identify trends in a representative sample of the resident population. In its 2019 field survey, the U.S. state of Georgia tested a new 3 – item module to measure the numbers of bereaved, resident adults. Bereavement means that participants answered, ‘Yes’ to the item ‘Have you experi-enced the death of a family member or close friend in the years 2018 or 2019?’. This analysis addresses two questions. Can estimates for bereavement prevalence be derived without large sampling errors, low precision, and small subsamples? Can multiple imputation techniques be applied to overcome non-response and missing data to support multivari-ate modeling? Analyses in this study were conducted under two scenarios. Scenario 1 ap-plies the complex sample weights created by the Centers for Disease Control and imputes values for missing responses. Scenario 2 treats the data as a panel – no weighting com-bined with removal of persons with missing data. Scenario 1 reflects the use of BRFSS data for public health and policy, while Scenario 2 reflects data as it is commonly used in so-cial science research. The bereavement item has a response rate (RR) of 70.8% (5206 of 7534 persons). Subgroups have RR of 55% or more. Under Scenario 1, the prevalence of bereavement is 45.38%, meaning that 3,739,120 adults reported bereaved in 2018 or 2019. The prevalence is 46.02% with Scenario 2 which removes persons with any missing data (4,289 persons). Scenario 2 overestimates the bereavement prevalence by 1.39%. An il-lustrative logistic model is included to show the performance of exposure to bereavement under each scenario. Recent bereavement can be ascertained in a surveillance survey without biases in response. This survey is limited to one US state in a single year and ex-cludes persons aged 17 years and younger.
ARTICLE | doi:10.20944/preprints202206.0322.v1
Subject: Biology And Life Sciences, Virology Keywords: Viral Ecology; APMV; wild birds; Surveillance of Avian Paramyxoviruses; phylogenetics; MinION; Azov-Black Sea region in Ukraine
Online: 23 June 2022 (09:33:18 CEST)
Emerging RNA virus infections are a growing concern among domestic bird and poultry industries due to the severe impact it can have on the flock health and economic livelihoods. Avian paramyxoviruses (APMV) are pathogenic, negative sense RNA viruses that cause serious infections in the respiratory and central nervous system. APMV was detected in multiple avian species during the 2017 migration season in Ukraine, and studied using PCR, virus isolation, and sequencing. Of the 4090 wild bird samples, eleven swabs were isolated in chicken embryos and identified for APMV serotype by hemagglutinin inhibition test: APMV-1, APMV-4, APMV-6, APMV-7. At a variety of sites in Ukraine we characterized the virulence of the virus and further analyzed and predicted the potential risks of spillover to immunologically naïve populations. RNA was extracted and amplified using a multiplex-tiling primer approach to encompass full cDNA genomes. Full-length APMV-1 (n=5) and APMV-6 (n=2) genomes were sequenced on an Oxford Nanopore MinION device in Ukraine. All APMV-1 and APMV-6 fusion (F) proteins possessed a monobasic cleavage site, suggesting these APMV were likely low virulence, annually circulating strains. Utilization of this low-cost method will identify gaps in viral evolution and circulation in this understudied but important critical region for Eurasia.
REVIEW | doi:10.20944/preprints202101.0055.v1
Subject: Physical Sciences, Acoustics Keywords: magnetic microwires; magnetic bistability; magnetic tag; electronic surveillance; domain wall propagation; post-processing; magnetic anisotropy; magnetostatic interaction.
Online: 4 January 2021 (16:18:01 CET)
Applications in security and electronic surveillance require combination of excellent magnetic softness with good mechanical and anti-corrosive properties and low dimensionality. We overviewed the properties of soft magnetic glass-coated microwires and different post-processing making them quite attractive for electronic article surveillance and security applications. We studied the magnetostatic interaction between the microwires and routes to tune the non-linear hysteresis loops by using the arrays of different types of amorphous microwires. The presence of neighbouring microwire (either Fe or Co-based) significantly affects the hysteresis loop of the whole microwires array. In a microwires array containing magnetically bistable microwires we observed splitting of the initially rectangular hysteresis loop with a number of Barkhausen jumps correlated with the number of magnetically bistable microwires. Essentially, non-linear and irregular hysteresis loops have been observed in mixed arrays containing Fe and Co-rich microwires. The observed non-linearity in hysteresis loops allowed to increase the harmonics and tune their magnetic field dependencies. Non-linear hysteresis loops have been also observed upon devitrification of amorphous microwires. On the other hand, several routes allowing to tune the switching field by either post-processing or modifying the magnetoelastic anisotropy have been reviewed. Observed unique combination of magnetic properties together with thin dimensions and excellent mechanical and anti-corrosive properties provide excellent perspectives for the use of glass-coated microwires for security and electronic surveillance applications.
ARTICLE | doi:10.20944/preprints202011.0453.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: coastal patrol and surveillance network; UDTN-Prob; UDTN-RS; DTN networks; DTN routing protocols; DESERT underwater simulator
Online: 17 November 2020 (14:06:30 CET)
The Coastal Patrol and Surveillance Application (CPSA) is developed and deployed to detect, track and monitor water vessel traffic using automated devices. Latest advancements of marine technologies, including the Automatic Underwater Vehicles, have allowed the development of this type of applications. To facilitate their operations, installation of a Coastal Patrol and Surveillance Network (CPSN) is mandatory. One of the primary design objectives of this network is to deliver adequate amount of data within an effective time period. This is particularly essential for reporting a detection and notifying the current status of an intruder’s vessel through the adverse underwater communication channels. Additionally, intermittent connectivity of the nodes remain another important obstacle to overcome to allow smooth functioning of CPSA. Taking these objectives and obstacles into account, this work proposes a new protocol, named UDTN-RS, which is developed by ensembling forward error correction technique (namely Reed-Solomon codes or RS) in Underwater Delay Tolerant Network (UDTN) routing protocol with probabilistic spraying technique. In addition, the existing binary packet spraying technique is enhanced for supporting encoded packet exchange between the contacting nodes. A comprehensive simulation campaign is performed in identifying the effectiveness of the proposed protocol. The obtained results suggest that the proposed UDTN-RS protocol can be considered a suitable alternative of the existing protocols for sparse networks like CPSN.
Subject: Medicine And Pharmacology, Dietetics And Nutrition Keywords: obesity; eating context; nutrient-poor foods; nutritional surveillance; adolescents; survey data analysis; data-mining; correspondence analysis; biplots
Online: 9 June 2020 (13:52:45 CEST)
Obesity is a global public health problem and the environment as its major determinant. To identify interventions an evidence base is warranted. To this aim we investigate the relationship between the consumption of foods and eating locations (like home, school/work and others) in British adolescents, using data from the UK National Diet and Nutrition Survey Rolling Program (2008–2012 and 2013-2016). Cross-sectional analysis of 62,523 food diary entries from this nationally representative sample then focused on foods contributing up to 80% total energy to the daily adolescent´s diet. Correspondence Analysis (CA) was first used to generate food-location relationship hypotheses and Logistic Regression (LR) to quantify the evidence in terms of odds ratios and formally test those hypotheses. The less-healthy foods that emerged from CA were chips, soft drinks, chocolate and meat pies. Adjusted Odds Ratios (99% CI) for consuming specific foods at a location “Other” than home (H) or school/work (S) in the 2008-12 survey sample were: for soft drinks 2.8 (2.1 to 3.8) vs. H and 2.0 (1.4 to 2.8) vs. S; for chips 2.8 (2.2 to 3.7) vs. H and 3.4 (2.1 to 5.5) vs. S; for chocolates 2.6 (1.9 to 3.5) vs. H and 1.9 (1.2 to 2.9) vs. S; and for meat pies 2.7 (1.5 to 5.1) vs. H and 1.3 (0.5 to 3.1) vs. S. These trends were confirmed in the 2013-16 survey sample. Interactions between location and BMI were not significant in either sample. In conclusion, our study showed that adolescents are more likely to consume specific less-healthy foods at locations away from home and school/work, irrespective of BMI. Such locations include leisure places, food outlets and “on the go”, hence public health policies to discourage less-healthy food choices in these locations is warranted for all adolescents.
REVIEW | doi:10.20944/preprints202008.0495.v1
Subject: Computer Science And Mathematics, Analysis Keywords: coronavirus pandemic (COVID-19); analysis; modeling; recommendations; surveillance; social media analytics; meteorological effects; image processing; business and economy
Online: 24 August 2020 (02:54:47 CEST)
COVID-19 has created anxiety not only in individuals but also in health organizations, and countries worldwide. Not a single industry is left un-influenced and loss is being estimated in billions of dollars. The widespread of this pandemic disease has challenged researchers all over the world. Some of the researchers are working to invent its cure while, others are applying computing technologies to stop its spread, by analyzing and identifying patterns for prediction and forecasting. This is by no doubt the hottest area of research for the last 100 years. This survey has targeted the research published in computing sub-domains to combat the pandemic. The survey has clustered the scientific efforts into logical groups: surveillance, metrological effects, social media analytics, image processing and business and economy, analysis and modeling. It will serve as a leading source for the followings: researchers who want to identify what has been achieved in different computing sub-domains, those who need fresh authenticated datasets openly accessible for different research contexts and what are future directions in this area of research. The findings of analysis and modeling can be also useful for government agencies who want to set priorities and formulate policies.
ARTICLE | doi:10.20944/preprints201809.0513.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Malawi, HIV, tuberculosis, anti-retroviral therapy, surveillance, patient monitoring, epidemic trends, drug supply, unique patient identifiers, data analysis
Online: 27 September 2018 (15:29:43 CEST)
Malawi has developed an excellent, nation-wide system for monitoring people infected with HIV and keeping track of key epidemic markers. Their success lies in two things: the focus on simplicity and the use of data collection not only to track the epidemic and identify problems but also to give regular feedback and support to every clinic in the country. This achievement is the more remarkable given that Malawi is one of the poorest countries in the world, ranking 190 out of 194 countries by GDP, but has one of the most severe epidemics of HIV in the world, ranking 9th out of 168 countries by HIV prevalence. We first discuss the current state and likely future epidemic trends in Malawi: unless we know where we are and where we are going we cannot decide what to do or how to do it to in order to achieve a better outcome. We then discuss the history and development of Malawi’s patient monitoring system, as reported in their Integrated HIV Program Reports,ix which have been published quarterly since the beginning of 2004. We consider the current state of patient monitoring and support as reflected in the most recent report for the third quarter (Q3) of 2016 and comment on some of the questions that this raises. Finally, we consider ways in which the current system could be improved by strengthening Malawi’s analytical capacity and making better use of this unique data set. The focus here is on HIV in adultsv because if ART is initiated early in all adults living with HIV this should include testing all pregnant women for HIV and starting them on treatment immediately. However, PMTCT is especially important and care must be given to reducing MTCT and identifying the long-term child survivors of mother-to-child transmission and this demands a complementary assessment. There is an ongoing debate about the relative merits of treatment and prevention in reducing transmission and it should be made clear that the primary reason for starting people on treatment early is that it is in the best interest of the individual patient to start treatment as soon as possible after becoming infected. Allowing a person’s immune system to deteriorate to any degree is not consistent with the clinician’s commitment to ‘first do no harm’ and even those with the highest CD4+ cell count are at a substantially increased risk of death. What matters, therefore, is to get as many people as possible onto ART, ensure that they remain virally suppressed, and consider prevention in this context.
ARTICLE | doi:10.20944/preprints202311.0110.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Human violence recognition; video surveillance; real-time; spatial attention; spatial motion extractor; short temporal extractor; global temporal extractor; VioPeru
Online: 2 November 2023 (04:06:10 CET)
Human violence recognition is an area of great interest in the scientific community, given its broad spectrum of applications, especially in video surveillance systems, since detecting violence in real-time could prevent criminal acts and save lives. Despite the number of existing proposals and research, most focus on the precision of results, leaving aside efficiency and its practical implementation. Thus, this work proposes a model that is effective and efficient in recognizing human violence in real-time. The proposed model consists of three modules: a first module called Spatial Motion Extractor (SME), in charge of extracting regions of interest from a frame; a second module called Short Temporal Extractor (STC), whose function is to extract temporal characteristics of rapid movements, finally the Global Temporal Extractor (GET) module, responsible for identifying long-lasting temporal features and fine-tuning the model. The proposal was evaluated regarding efficiency, effectiveness, and ability to operate in real-time. The results obtained on Hockey, Movies, and RWF-2000 datasets demonstrated that this approach is highly efficient compared to other alternatives. A VioPeru dataset was created to validate real-time applicability with violent and non-violent videos captured by real video surveillance cameras in Peru. The effectiveness results in this dataset outperformed the best existing proposal. Therefore, our proposal has contributions in efficiency, effectiveness, and real-time.
ARTICLE | doi:10.20944/preprints202012.0806.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Ductal carcinoma in situ (DCIS); Invasive Breast Carcinoma; Underestimation; Upgrade Rate; Vacuum assisted breast biopsy (VABB); Breast Microcalcifications; Active Surveillance.
Online: 31 December 2020 (12:52:08 CET)
(1) Background: Considering highly selected patients with ductal carcinoma in situ (DCIS), active surveillance is a valid alternative to surgery. Our study is aimed at showing the reliability of post-biopsy complete lesion removal, documented by mammogram, as additional criterion to select these patients. (2) Methods: 2173 Vacuum Assisted Breast Biopsies (VABB) documented as DCIS have been reviewed. Surgery has been performed in all cases. We retrospectively collected the reports of post-VABB complete lesion removal and the histological results of the biopsy and surgery. We calculated the rate of upgrade of DCIS identified on VABB upon excision for patients with post-biopsy complete lesion removal and for those showing residual lesion. (3) Results: We observed 2173 cases of DCIS: 408 classified as low grade; 1262 as intermediate grade; 503 as high grade. The overall upgrading rate to invasive carcinoma was 15.2% (330/2173). The upgrade rate was significantly lower (8.2%) when considering patients showing mammographically documented complete removal of the lesion. (4) Conclusion: The absence of mammographically documented residual lesion following VABB is associated to a lower upgrading rate of DCIS to invasive carcinoma on surgical excision and should be considered when deciding the proper management DCIS diagnosis.
ARTICLE | doi:10.20944/preprints201909.0123.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Active case findings; Tuberculosis; TOUCH Agent; High TB burden area; TB Surveillance; 4S Screening; THALI Project; SORT IT; Operational Research
Online: 11 September 2019 (13:30:30 CEST)
Background: Active case finding for TB was implemented in selected sixty high TB burden wards of Kolkata, India. Community volunteers called TOUCH agents (TAs) identified and referred presumptive TB patients (PTBPs) to health facilities for TB diagnosis and treatment. We aimed to describe the ‘care cascade’ of PTBPs identified during July to December, 2018 and to explore the reasons for attrition as perceived by TAs and PTBPs. Methods: An explanatory mixed methods study with quantitative phase of cohort study using routinely collected data followed by descriptive qualitative study with in-depth interviews was conducted. Results: Of the 3, 86,242 individuals enumerated, 1132 (0.3%) PTBPs were identified. Only 713 (63.0%) PTBPs visited referred facility for TB diagnosis. TB was diagnosed in 177 (24.8%) and the number needed to screen for one TB was 2,183 individuals. The potential reasons for low yield were stigma and apprehension about TB, distrust about TA, wage loss for attending health facilities and substance abuse among PTBPs. Conclusion: The yield of ACF was suboptimal with low PTBP identification rate and high attrition rate. Interviewing each individual for symptoms of TB and supporting PTBPs for diagnosis through sputum collection and transport can be adopted to improve the yield.
ARTICLE | doi:10.20944/preprints202304.0571.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: pedestrian detection; tracking; re-identification; Virtual Outlier Synthetic: In distribution; Out Of Distribution; Unmanned Aerial Vehicles; Drones; surveillance; von-Mises Fisher Distributions
Online: 19 April 2023 (08:30:35 CEST)
In recent years, pedestrian re-identification has gained a lot of interest due to its importance for many purposes such as security and safety. Many types of solutions have been proposed to solve this problem, where the majority are based on a features extraction such Convolution Neural Networks (CNNs). These approaches assume that only the identities that are in the training data can be recognized. The pedestrians in the training data are called In distribution (ID). However, in real world scenarios, new pedestrians and objects can appear in the scene and the model should detect them as Out Of Distribution (OOD). In our previous study , we proposed a pedestrian re-identification based on von-Mises Fisher (vMF) distribution. Each identity is embedded in the unit sphere as a compact vMF distribution far from other identities distributions. The embedding is done through a base CNN. Recently, proposed a framework called Virtual Outlier Synthetic (VOS), that detects OOD based on synthesising virtual outlier in the embedding space in an online manner. Their approach assumes that the samples from the same object maps to a compact space. This assumption aligns with the vMF based approach. Therefore, in this paper, we revisited the vMF approach and merged with VOS in order to detect OOD data points. We present our approach to merge both frameworks. We conducted several experiments to evaluate our proposed framework. Results showed that our framework was able to detect new pedestrian that do not exist in the training data in the inference phase. It also slightly helped to improve the re-identification performance.