Nigeria is the most populous country in the African continent. The aim of this study was to analyze risk factors for COVID-19 prevalence and deaths in all 6 geopolitical regions and 37 states in Nigeria. We analyzed the data retrieved from various sources, including Nigeria CDC, Nigeria National Bureau of Statistics, Unicef-Nigeria multiple indicator cluster survey and the Institute of Health Metrics and Evaluation, University of Washington. We examined 4 clinical risk factors (prevalence of TB, HIV, smoking and BCG vaccination coverage) and 5 sociodemographic factors (age ≥65, population density, literacy rate, unemployment and GDP per capita). Multivariate modeling was conducted using generalized linear model. Our analysis showed that the incidence of confirmed COVID-19 cases differed widely across the 37 states, from 0.09 per 100,000 in Kogi to 83.7 in Lagos. However, more than 70% of confirmed cases were concentrated in just 7 states: Lagos, Abuja, Oyo, Kano, Edo, Rivers and Delta. Case mortality rate (CMR) per million population also varied considerably, with Lagos, Abuja and Edo having CMR above 9. On bivariate analysis, higher CMR correlated positively with GDP and to a lesser extent with TB and population density. On multivariate analysis, which is more definitive, states with higher HIV prevalence and BCG coverage had lower CMR, while high GDP states had a greater CMR. This study indicates that COVID-19 has disproportionately affected certain states in Nigeria. Population susceptibility factors include higher economic development but not literacy or unemployment. Death rates were mildly lower in states with higher HIV prevalence and BCG vaccination coverage.

Real-time estimation of the parameters characterising infectious disease transmission is important for optimization quarantine interventions during outbreaks. One of the most significant parameters is the effective reproduction number - number of secondary cases produced by a single infection. The current study presents an approach for estimating the effective reproduction number and its application to COVID-19 outbreak. The method is based on fitting SIR epidemic model to observation data in a sliding time window and allows to show real-time dynamics of reproduction number at any phase of epidemic for countries globally. Online data on COVID-19 daily cases of infections, recoveries, deaths are used.Finally, time-dependent reproduction number is explored in connection with dynamics of peoples mobility. The method allows to assess the disease transmission potential and understand the effect of interventions on epidemics spread. It also can be easily adapted to future outbreaks of different pathogens. The tool is available online as Python code from the Github repository.

COVID-19 pandemic that started in China has spread within 3 months to the entire globe. We tested the hypothesis that the vaccination against tuberculosis by BCG correlates with a better outcome for COVID-19 patients. Our analysis covers 55 countries complying with predetermined thresholds on the population size and number of deaths per million (DPM). We found a strong negative correlation between the years of BCG administration and the DPM along with the progress of the pandemic, corroborated by permutation tests. The results from multivariable regression tests with 23 economic, demographic, health-related, and pandemic restriction quantitative properties, substantiate the dominant contribution of BCG years to the COVID-19 outcomes. The analysis of countries according to an age-group partition reveals that the strongest correlation is attributed to the coverage in BCG vaccination of the young population (0-24 years). Furthermore, a strong correlation and statistical significance are associated with the degree of BCG coverage for the most recent 15 years, but no association was observed in these years for other broadly used vaccination protocols for measles and rubella. We propose that BCG immunization coverage, especially among the most recently vaccinated contributes to attenuation of the spread and severity of the COVID-19 pandemic.

Chronic noncommunicable diseases (CNCDs) have been a major public health concern worldwide, especially diabetes, cardiovascular disease, chronic obstructive pulmonary disease, hypertension, in addition to obesity, which is even more worrying when the subject involves the covid-19 pandemic, because such incidences correlate with the need for intensive care units, including the possibility of death of the patient. Therefore, for countries with the highest numbers of critical cases, it is important to assess the incidence of these diseases to guide the public that most needs guidance on public policies for social isolation.

World Health Organization recommends adjusting the salt intake as a part of the nine global targets to reduce premature mortality from non-communicable chronic diseases as priority and most cost-effective intervention. In 2006. the main aim of the Croatian Action on Salt and Health was to decrease salt intake for 16% because of its critical intake and consequences on human health. We have organized educative activities for increasing awareness on salt harmfulness, defined food categories of prime interest, collaborate with industries and determine salt intake (24h urine-sodium excretion). It was determined that the proportion of salt in ready-to-eat baked bread should not exceed 1.4%. In the period 2014 –2022, salt in the semi-white bread was reduced 14%, in bakery 22% and in largest meat industry in Croatia 25%. Awareness of the harmfulness of salt on health increased from 65.3% in 2008 to 96.9% in 2023 and salt intake was reduced 15.9%-1.8 grams/day (22.8% men, 11.7% women). In last 18 years a significant decrease in salt intake was achieved in Croatia, awareness of its harmfulness increased, collaboration with food industry established and regulatory documents launched. However, salt intake is still very high underlying the need for continuation of efforts and even stronger activities.

Asthma is the most prevalent cause of chronic respiratory diseases. Herein, we evaluate asthma burden in Mexico based on results from the Global Burden of Disease (GBD 2019) study 2019. Using data from the GBD 2019, we estimated asthma prevalence, incidence, mortality, and disability-adjusted lived years (DALYs) counts and crude and age-standardized rates per 100,000 people with a 95% uncertainty interval (UI) by sex and age at the national and subnational levels in Mexico from 1990 to 2019. At the national level, asthma affected 3.35 million (95% UI, 2.59-4.37) people, with 606.0 thousand (433.0-811.1) new incident cases and 1,655 (3-1,931) deaths during 2019. Asthma caused a slightly higher burden in females and affected mainly age groups between 1 and 14 years of age. The burden of asthma gradually decreased from 1990 to 2010. However, during the last decade (2010-2019), prevalence increased by 8.2%, as did incidence by 11.3%, whereas mortality and DALYs decreased by 23.3 and 1.6%, respectively. Finally, the burden of asthma displayed a heterogeneous pattern of disease at the subnational level. In conclusion, asthma causes a significant health loss in Mexico that differentially affects the population distributed among the states of the country, thus causing health disparities that should be addressed to provide sustainable asthma diagnosis and control to reduce its burden, especially at early stages of life.

The study aimed to identify clinical pharmacology patterns of prescribed and taken medications in older cardiovascular patients using electronic health records (EHRs) (n = 704) (2019–2022). Medscape Drug Interaction Checker was used to identify pairwise drug-drug interactions (DDIs). Prevalence rates of DDIs were 73.5% and 68.5% among taken and prescribed drugs, respectively. However, total number of DDIs was significantly higher among prescribed medications compared with the list of taken drugs (p < 0.05). Serious DDIs comprised 16% and 7% of all DDIs among prescribed and taken medications, correspondingly (p < 0.05). Median DDI numbers between prescribed versus taken medications were Me = 2, IQR 0-7 and Me = 3, IQR 0-7 per record, respectively. Prevalence of polypharmacy was significantly higher among prescribed medications compared with taken medications (p < 0.05). Women were taking significantly more drugs and had higher rates of polypharmacy and DDIs (p < 0.05). No sex-related differences were observed in the list of prescribed medications. ICD code U07.1 (COVID-19, virus identified) was associated with the highest median DDI number per record. Further research is warranted to improve EHR structure, patient engagement in reporting adverse drug reactions, and genetic profiling of patients to avoid potentially serious DDIs.

In 2020, following the World Health Organization's declaration of COVID-19 as a pandemic, dental practices faced unprecedented disruptions globally. This retrospective cross-sectional study, conducted at a leading university dental hospital in the Lisbon Metropolitan Area, investigated the impact of these disruptions on dental caries. The study, spanning June 2019 to June 2021, included a full-mouth X-ray examination, along with sociodemographic, behavioral, and medical data. Our sample comprised 3,380 participants (2,007 females and 1,373 males), aged 18 to 99 years, divided into pre-lockdown and post-lockdown groups. We employed the Decayed, Missing, and Filled Teeth (DMFT) index to measure dental caries. Our findings revealed that nearly 90% of participants in both groups experienced dental caries, indicating a statistically significant difference between the pre-lockdown and post-lockdown periods. However, the impact of COVID-19 confinement varied among different demographic sectors, with age, educational background, and professional status emerging as the key determinants. This study highlights the need for a more nuanced understanding of the impact of the pandemic on oral health, emphasizing the role of sociodemographic factors in shaping dental health outcomes during such global health crises.

A large body of evidence has linked unhealthy eating patterns with an alarming increase in obesity and chronic disease worldwide. However, existing methods of assessing dietary intake in nutritional epidemiology rely on food frequency questionnaires or dietary records that are prone to bias and selective reporting. Herein, metabolic phenotyping was performed on 42 healthy participants from the Diet and Gene Intervention (DIGEST) pilot study, a parallel two-arm randomized clinical trial that provided complete diets to all participants. Matching urine and plasma specimens were collected at baseline and following 2 weeks of provision of either a Prudent or Western diet with a weight-maintaining menu plan designed by a dietician. Targeted and nontargeted metabolite profiling was conducted using three complementary analytical platforms, where 80 plasma metabolites and 84 creatinine-normalized urinary metabolites were reliably measured (CV < 30%) in the majority of participants (> 75%) after implementing a rigorous data workflow for metabolite authentication with stringent quality control. We classified a panel of metabolites with distinctive trajectories following 2 weeks of food provisions when using complementary univariate and multivariate statistical models. Unknown metabolites associated with contrasting dietary patterns were identified with high resolution MS/MS and/or co-elution after spiking with authentic standards. Overall, 3-methylhistidine and proline betaine concentrations increased consistently after participants were assigned a Prudent diet (q< 0.05) in both plasma and urine samples with a corresponding decrease in the Western diet group. Similarly, creatinine-normalized urinary imidazole propionate, hydroxypipecolic acid, dihydroxybenzoic acid, and enterolactone glucuronide, as well as plasma ketoleucine and ketovaline increased with a Prudent diet (p< 0.05) after adjustments for age, sex and BMI. In contrast, plasma myristic acid, linoelaidic acid, linoleic acid, a-linoleic acid, pentadecanoic acid, alanine, proline, carnitine and deoxycarnitine, as well as urinary acesulfame K increased among participants following a Western diet. Most metabolites were also correlated (r > ±0.30, p< 0.05) to changes in average intake of specific nutrients from self-reported diet records reflecting good adherence to assigned food provisions. Our study revealed robust biomarkers sensitive to short-term changes in habitual diet for accurate monitoring of healthy eating patterns in free-living populations, which is required for validating evidence-based public health policies for chronic disease prevention.

Background: Zika virus (ZIKV) infection has significantly affected Latin America in 2015–2017. Most studies have been reported from Brazil and Colombia, and only a few from Central America. For these reasons we analyzed the incidence, incidence rates and evolution of cases in Honduras from 2016–2017. Methods: Using epidemiological weeks (EW) surveillance data on the ZIKV epidemics in Honduras, we estimated incidence rates (cases/100,000 population), and developed maps at national, departmental and municipal levels. Results: From 1 January 2016 to 31 December 2017, a total of 32,607 cases of ZIKV were reported (98.5% in 2016 for an incidence rate of 36.85 cases/100,000 pop; 1% confirmed by RT-PCR). The highest peak was reached on the EW 6°, 2016 (2,559 cases; 29.34 cases/100,000 pop). The department with the highest number of cases and incidence rate was Cortés (13,128 cases, 791.08 cases/100,000 pop in 2016). Discussion: The pattern and evolution of ZIKV infection in Honduras has been similar to that which occurred for chikungunya in 2015. As previously reported, infection with chikungunya involved predominantly the central and capital area of the country, reaching incidences there >750 cases/100,000 pop. Studies using geographical information systems linked with clinical disease characteristics are necessary to attain accurate epidemiological data for public health systems. Such information is also useful for assessment of risk for travelers who visit specific areas in a destination country.

Background: After serious epidemics of chikungunya (CHIKV) and Zika (ZIKV) in the Americas, dengue (DENV) have reemerged in most countries. We analyzed the incidence, incidence rates, and evolution of DENV cases in Honduras from 2015-2018 and the ongoing 2019 epidemic. Methods: Using epidemiological weeks (EW) surveillance data on the DENV in Honduras, we estimated incidence rates (cases/100,000 population), and developed maps at national, departmental, and municipal levels. Results: From 1 January 2016 to 21 July 2019, a total of 109,557 cases of DENV were reported, 28,603 in 2019, for an incidence rate of 312.32 cases/100,000 pop this year; 0.13% laboratory-confirmed. The highest peak was reached on the EW 28°, 2019 (5,299 cases; 57.89 cases/100,000 pop). The department with the highest number of cases and incidence rate was Cortes (8,404 cases, 479.68 cases/100,000 pop in 2019). Discussion: The pattern and evolution of DENV epidemic in 2019 in Honduras has been similar to that which occurred for in 2015. As previously reported, this epidemic involved the north and central areas of the country predominantly, reaching municipality incidences there >1,000 cases/100,000 pop (1%). Studies using geographical information systems linked with clinical disease characteristics are necessary to attain accurate epidemiological data for public health systems. Such information is also useful for assessment of risk for travelers who visit specific areas in a destination country.

The COVID-19 infections in Pakistan are spreading at an exponential rate and a point may soon be reached where rigorous prevention measures would need to be adopted. Mathematical models can help define the scale of an epidemic and the rate at which an infection can spread in a community. I used ARIMA Model, Diffusion Model, SIRD Model and Prophet Model to forecast the magnitude of the COVID-19 pandemic in Pakistan and compared the numbers with the reported cases on the national database. Results depicts that Pakistan could hit peak number of infectious cases between June 2020 and July, 2020.

A recent manuscript (Zhou, P. et al. “A pneumonia outbreak associated with a new coronavirus of probable bat origin”, Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7) from Wuhan Institute of Virology claimed the identification of a bat coronavirus, RaTG13, which showed 96.2% genome homology with SARS-CoV-2. In this paper, we raise the puzzling observations surrounding the identification, characterization, unique genome features of this RaTG13 strain, as well as its 100% nucleotide identity in partial RdRp gene with another bat coronavirus strain BtCoV/4991. And the paper presented premature hypothesis of potential bat origin of SARS-CoV-2 while RaTG13 strain was not successfully isolated. We also present the concerns on the methodology, data quality and experiment procedures described in this paper. We call for the authors to provide additional data, to share related samples to be verified and further characterized by other scientists.

This study aimed to describe the injury profiles of young Korean baseball players according to position and age as the proportion and distribution of injuries based on playing position and age remains unclear. A total of 271 elite youth baseball players aged 8 to 16 years were divided into two groups: elementary school (ES) (n=135) and middle school (MS) (n=136). The participants' basic, baseball practice, and injury information were collected. Injuries in the MS group were not limited to the elbow and shoulder, and the injury prevalence varied by age group and baseball position. The most injured body region in the ES group was the elbow joint, regardless of the position. In contrast, the most injured body region in the MS group was the lower back, except for infielders whose elbows were the most injured. Additionally, the MS group was more likely to experience injuries of the lower back (OR=4.27, 95% CI=2.47–7.40), shoulder (OR=1.93, 95% CI=1.08–3.43; P=0.024), and knee (OR=2.15, 95% CI=1.17–3.94; P=0.012). Our findings indicate that excessive practice and lack of rest during MS (growth spurt period) can significantly increase the risk of lower back problems in young baseball players.

Leisure-time physical activity (LTPA) is associated with access and use of public open spaces. The “President João Goulart Elevated Avenue” and current denominated “Minhocão” is a facility for leisure activities that are open for people during the night/weekends. The aim of this study was to examine if the prevalence of LTPA among individuals living in the surroundings of Minhocão is different according to proximity to, and use of, the facility. We conducted a cross-sectional study with cluster sampling with people aged ≥18 years who lived in households until 500m and between 501m to 1500m of Minhocão. The survey was conducted between December/2017 until March/2019 with an electronic questionnaire self-responded. We conducted bivariate analysis and Poisson regression to examine possible differences in LTPA according to the proximity of residences and use of Minhocão. The analysis used post-stratification weights. A total of 12,030 telephone numbers of people were drawn (≤500m = 6,942; and &gt;500m to ≤1500m = 5,088). The final sample analyzed were of 235 residents who returned the questionnaires. There was a higher prevalence of individuals engaging in at least 150 minutes per week of LTPA among users than non-users (Prevalence Ratio=2.23, IC95%1.72-2.90). People who used the park had higher prevalence of all types of LTPA than non-users. The results can serve to inform government decision-making on the future of Minhocão.

Gene expression data is key for the functional annotation of single nucleotide polymorphisms (SNPs) identified in genome-wide association studies (GWAS). Expression and splicing quantitative trait loci (e/sQTLs) in normal colon tissue, such as those from the University of Barcelona and University of Virginia RNA sequencing project (BarcUVa-Seq) and the Genotype-Tissue Expression project (GTEx), are required to gain biological insight of colon-related diseases risk loci. Moreover, transcriptome-wide association studies (TWAS) rely on reference gene expression imputation panels in the tissue of interest to nominate susceptibility genes. Also, it is of high interest to study the relationships between genes in a network framework. For facilitating these analyses, we have updated and expanded the scope of the Colon Transcriptome Explorer (CoTrEx) to the version 2.0. This web-based resource provides exhaustive visualization and analysis of transcriptome-wide gene expression profiles of normal colon tissue from BarcUVa-Seq and GTEx. In addition to the integration of new datasets, CoTrEx 2.0 provides additional e/sQTLs sets, as well as gene expression prediction models and regulatory and co-expression networks. It is freely available at https://barcuvaseq.org/cotrex/. Overall, it is of high interest for researchers aiming to investigate the genetic susceptibility to colon-related complex traits and diseases.

Four new zoonotic coronaviruses outbreak occurred in the past two decades. The first coronavirus outbreak happened in 2003 and was named Severe Acute Respiratory Syndrome Coronavirus-1 (SARS-CoV-1), followed by Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2013, and by Swine Acute Diarrhoea Syndrome (SADS) in 2017. In late December 2019, a patient from Wuhan Seafood Wholesale Market, China, was admitted to Huang's hospital with respiratory distress syndrome (RDS) of apparently unknown etiology, which later was diagnosed with SARS-CoV-2-induced coronavirus disease-19 (COVID-19). SARS-CoV-2 was identified from another clade within the subgenus Sarbecovirus of the genus Betacoronavirus. This new CoV variant showed 96.2% similarity at whole-genome level to bat coronavirus. Based on genetic studies, pangolin, bats, and snakes are suspected to be a possible intermediate host of this virus, but further research is in progress to determine how this virus appeared and what is the exact source of infection. The SARS-CoV-2 outbreak has higher transmissibility, contagiosity and pathogenicity compared to that of SARS-CoV-1 and MERS-CoV. SARS-CoV-2 swiftly spread from continent to continent and is persistently causing a shocking global public health concern albeit the rate of infected cases and mortality is relatively decreasing over time. In this review, we provide an update on the origin, transmissibility, etiology, epidemiology, and evolution of COVID-19. We also highlight the current diagnostics, therapies, and prognostics for SARS-CoV-2. Eventually, we report and provide our humble opinion about the preventive strategies to control the ongoing related pandemic situation at global and individual levels, considering the international public health emergency and possible future epidemics and pandemics.

It is unclear why European countries have been more severely affected by COVID-19 than East Asian countries. In this ecological study we compared the COVID-19 epidemics (cumulative incidence and mortality rates), host genetic susceptibility and national responses (testing intensity) in all European versus all Western Pacific/East Asian countries reporting cases in the first month of the epidemic. The host-genetic-susceptibility assessment was limited to the frequency of the D-allele of the angiotensin converting enzyme-1 (ACE-1) which has been found to be positively associated with COVID-19 incidence within European countries. Despite earlier epidemics, countries from the Western Pacific reported lower cumulative numbers of COVID-19 cases/100 000 inhabitants than European countries (P=0.0002). The Western Pacific countries also reported fewer cumulative COVID-19 deaths/100 000 (P=0.0024). Whilst there was little difference in the cumulative number of tests conducted/100 000, the percent of COVID-19 tests reported positive was higher in Europe than the Western Pacific (P=0.0076). The frequency of the ACE-1 D-allele was lower in the Western Pacific than European countries (P=0.0007). Our results suggest that a combination of different testing strategies and host genetic susceptibility contribute to difference in severity of the COVID-19 epidemics in the Western Pacific/East Asia and Europe.

Background. Cardiorespiratory fitness (CRF) is a predictor of chronic disease that is impractical to routinely measure in primary care settings. We used a new estimated cardiorespiratory fitness (eCRF) algorithm that uses information routinely documented in electronic health care records to predict abnormal blood glucose incidence. Methods: Participants were adults (17.8% female) 20-81 years old at baseline from the Aerobics Center Longitudinal Study between 1979 and 2006. eCRF was based on sex, age, body mass index, resting heart rate, resting blood pressure, and smoking status. CRF was measured by maximal treadmill testing. Cox proportional hazards regression models were established using eCRF and CRF as independent variables predicting the abnormal blood glucose incidence while adjusting for covariates. Results: Of 8,602 participants at risk at baseline, 3,580 (41.6%) developed abnormal blood glucose during an average of 4.9 years follow-up. The average eCRF of 12.03 ± 1.75 METs was equivalent to the CRF of 12.15 ± 2.40 METs within the 10% equivalence limit. In fully adjusted models, the estimated risks were the same (HRs = 0.96), eCRF (95% CIs = 0.93−0.99), and CRF (95% CI of 0.94−0.98). Each 1-MET increase was associated with a 4% reduced risk. Conclusion: Higher eCRF is associated with a lower risk of abnormal glucose. eCRF can be a vital sign used for research and prevention.

The technology-driven world of the 21^st century is currently confronted with a major threat to humankind in the form of the coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). As of April 22, 2020, COVID-19 has claimed 169, 006 human lives and had spread to over 200 countries with more than 2,471,136 confirmed cases. The perpetually increasing figures associated with COVID-19 are disrupting the social and economic systems globally. The losses are unmatched and significantly higher compared to those from previously encountered pathogenic infections. Previously, two CoVs (SARS-CoV and Middle East respiratory syndrome-CoV) affected the human population in 2002 and 2012 in China and Saudi Arabia, respectively. Based on genomic similarities, animal-origin CoVs, primarily those infecting bats, civet cats, and pangolins, were presumed to be the source of emerging human CoVs, including the SARS-CoV-2. The cohesive approach amongst virologists, bioinformaticians, big data analysts, epidemiologists, and public health researchers across the globe has delivered high-end viral diagnostics. Similarly, vaccines and therapeutics against COVID-19 are currently in the pipeline for clinical trials. The rapidly evolving and popular technology of artificial intelligence played a major role in confirming and countering the COVID-19 pandemic using digital technologies and mathematical algorithms. In this review, we discuss the noteworthy advancements in the mitigation of the COVID-19 pandemic, focusing on the etiological viral agent, comparative genomic analysis, population susceptibility, disease epidemiology, animal reservoirs, laboratory animal models, disease transmission, diagnosis using artificial intelligence interventions, therapeutics and vaccines, and disease mitigation measures to combat disease dissemination.

Avian Influenza viruses (AIVs) has posed a significant pandemic threat since their discovery. This review mainly focuses on the epidemiology, virology, and pathogenesis, and treatments of avian influenza viruses. We delve into the global spread, past pandemics, clinical symptoms, severity, and immune response related to AIVs. The review also discusses various control measures, including antiviral drugs, vaccines, and potential future directions in influenza treatment and prevention. Lastly, by summarizing the insights from the previous pandemic control, this review aims to direct effective strategies for managing future influenza pandemics.

During autumn/winter in 2016 – 2017 and 2020 – 2021, highly pathogenic avian influenza viruses (HPAIV) caused severe outbreaks in Germany and Europe. Multiple clade 2.3.4.4b H5 HPAI subtypes were responsible for increased mortality in wild birds and high mortality and massive losses in the poultry sector. To clarify putative entry sources and delineate interconnections between outbreaks in poultry holdings and wild birds, we applied whole-genome sequencing and phylodynamic analyses combined with the results of epidemiological outbreak investigations. Varying outbreak dynamics of the distinct reassortants allowed for the identification of individual, putatively wild bird-mediated entries into backyard holdings, several clusters comprising poultry holdings, local virus circulation for several weeks, direct farm-to-farm transmission and potential reassortment within a turkey holding with subsequent spill-over of the novel reassorted virus into the wild bird population. Whole-genome sequencing allowed for allowed for a unique high-resolution molecular epidemiology analysis of HPAIV H5Nx outbreaks, recommended to be used as a standard tool. The presented detailed account of the genetic, temporal and geographical characteristics of the recent German HPAI H5Nx situation emphasizes the role of poultry holdings as an important source of novel genetic variants and reassortants.

Human leptospirosis cannot be investigated without studying zoonotic and environmental as-pects of the disease. The objectives of this study are to explore the abundance of Leptospira in dif-ferent climate zones of Sri Lanka and to describe the presence of Leptospira in same water source at different time points. First, water and soil samples were collected from whole-island, secondly, water sampling continued only in dry-zone, finally serial sampling of water from ten open wells was performed at five different time points. Quantitative PCR for water and metagenomic se-quencing for soil were used to detect Leptospira. In first component, 2 out of 12 water sites were positive and both are situated in wet-zone. Very small quantities of Genus Leptospira was detect-ed by metagenomic analysis of soil. Only 5 out of 26 samples were positive in the second compo-nent. Six, five, four, five, six wells were positive respectively in serial measurements of third component. All wells were positive at least one measurement while only one well was positive in all measurements. Closer to tank and higher distance from main road were significant risk fac-tors associated with well positivity. Presence of Leptospira seems not consistent indicating ran-dom abundance of Leptospira in natural environment.

Abstract: Cardiovascular Disease (CVD) is the most prevalent disease worldwide, which has been linked to work stress because of poor job design as explained by the Job Demand-Control (JDC) and the Effort-Reward Imbalance (ERI) models. In this paper we explore for the first time relative impact of a specific aspect of organisational climate, Psychosocial Safety Climate (PSC), on any CVD including angina, myocardial infarction, hypertension, and stroke. We used two waves of interview data from Australia, with an average lag of 5 years (excluding baseline CVD, final n = 1223). Logistic regression was conducted to estimate the prospective associations between PSC at baseline on incident CVD at follow-up. It was found that participants in low PSC environments were 59% more likely to develop new CVD than those in high PSC environments. Logistic regression showed that PSC at baseline predicts lower CVD risk at follow-up (OR = 0.98, 95% CI 0.96-1.00), and this risk remained unchanged even after joint adjustment for measures of ERI and JDC. These results suggest that PSC is an independent risk factor for CVD in Australia. Beyond job design this study implicates organisational climate and prevailing management values regarding worker psychological health as the genesis of CVD.

During a sanitary crisis, excess mortality measures the number of all-cause deaths, beyond what we would have expected if that crisis had not occurred. The high number of COVID-19 deaths started a debate in Italy with two opposite positions: those convinced that COVID-19 deaths were not, by default, excess deaths, because many COVID-19 deaths were not correctly registered, with the most part attributable to other causes and to the overall crisis conditions, and those who presented the opposite hypothesis. We analyzed the curve of the all-cause excess mortality, during the period January 5, 2020 – August 28, 2022, compared to the curve of the daily confirmed COVID-19 deaths, investigating the association between excess mortality and the recurrence of COVID-19 waves in Italy. We compared the two curves looking for the corresponding highest peaks and we found that 5 out of the 6 highest peaks (83.3%) of the excess mortality curve have occurred, on average, just a week before the concomitant COVID-19 waves hit their highest peaks of daily deaths (Mean 6.4 days; SD 2.4 days). This temporal correspondence between the moments when the excess mortality peaked and the highest peaks of the COVID-19 deaths provides further evidence that the all-cause excess mortality wave has been mostly driven by COVID-19 deaths

Mpox, formerly known as Monkeypox, is a rare viral disease initially discovered in Africa in 1958. Since its first identification, several outbreaks have occurred in various African nations. Recently, the global community has witnessed a resurgence in the number of Mpox cases reported worldwide, prompting the World Health Organization (WHO) to declare the ongoing multi-country outbreak a public health emergency in July 2022. This study reports on the first cases of Mpox detected in Khartoum State, Sudan, outlining the epidemiology, preparedness, and public health response to this new challenge. A total of 55 suspected cases were identified, with two confirmed cases. The clinical manifestations observed in these cases align with the classic skin rash typical of Mpox, presenting alongside symptoms like fever, headache, and joint pain. The findings underscore the need for heightened surveillance, early detection, and timely intervention to prevent the domestic spread of Mpox and its potential impact on public health. Continued global efforts are needed to support effective screening, diagnostic, and control measures, ultimately enhancing preparedness and response in the face of this emerging disease.

Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score <35) collected between May 5, 2020, and January 31, 2022 were analysed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. Results: The analyzed SARS-CoV-2 genomes could be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. Conclusion: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.

Since identified as the pathogen responsible for an outbreak of severe respiratory distress in Wuhan, China, the 2019-nCoV coronavirus has caused over 30M cases and 1M deaths globally. Sporadic cases were identified in several states in the US from early January, and large-scale community transmission is believed to have started in late February, leading to a first spike in COVID-19 deaths and overall mortality in late April, and a second spike later in the summer. I show here that the dynamics of the pandemic were different in different regions of the US, showing a north-south pattern, with a first pandemic wave mainly in northern regions, followed by a second wave mainly in southern regions. Analysis of overall mortality data shows that the increase in mortality correlates well with COVID-19 incidence in most regions, and that from April through August COVID-19 deaths accounted for a substantial proportion of all deaths in all parts of the US.

Bovine tuberculosis (bTB) outbreaks, caused by Mycobacterium bovis infection, are a costly animal health challenge. Understanding factors associated with the duration of outbreaks, known as breakdowns, could lead to better disease management policy development. We undertook a retrospective observational study (2012-2018) and employed Finite Mixture Models (FMM) to model the outcome parameter, and to investigate how factors were associated with duration for differing subpopulations identified. In addition to traditional risk factors (e.g. herd size, bTB history), we also explored farm geographic area, parcels/farm fragmentation, metrics of intensity via nitrogen loading, and whether herds were designated controlled beef finishing units (CBFU) as potential risk factors for increased duration. The final model fitted log-normal distributions, with two latent classes (k) which partitioned the population into a subpopulation around the central tendency of the distribution, and a second around the tails of the distribution. The latter subpopulation included longer breakdowns of policy interest. Increasing duration was positively associated with recent (<3 yrs) TB history and the number of reactors disclosed, (log) herd size, beef herd-type relative to other herd types, number of land parcels, area, and being designated a controlled finishing unit (“feedlot”), and having high annual inward cattle movements within the “tails” subpopulation. Breakdown length was negatively associated with year of commencement of breakdown (i.e. a decreasing trend) and non-significantly with the organic nitrogen produced on the farm (N kg/hectare), a measure of stocking density. The latter finding may be due to confounding effects with herd size and area. Most variables contributed only moderately to explaining variation in breakdown duration, that is, they had moderate size effects on duration. Herd-size and CBFU had greater effect sizes on the outcome. The findings contribute to evidence-based policy formation in Ireland.

Background: It is unclear why certain countries have been more severely affected by COVID-19 than other countries. Methods: In this ecological study we compared COVID-19 mortality and incidence/100,000 as well as 4 putative explanatory factors by WHO world region. Linear regression was then used to assess the country-level predictors of COVID-19 mortality/100,000 and incidence/100,000 in 204 countries with available data. Results: COVID-19 incidence and mortality/capita were greater in Europe than other regions. This was despite a higher testing rate in Europe than other regions. Europe had an older population than all other regions and a higher prevalence of obesity than Africa, South East Asia and the Eastern Mediterranean. Country level multiple linear regression revealed positive associations between mortality/capita and testing rate, percent of the population 65 years or older, and Europe compared to Western Pacific and South East Asia (all P<0.005). Results for the analyses with cases/100,000 as outcome variable were similar. Conclusion: Our results suggest that older populations as well as other undefined regional and national factors, possibly related to efficacy of control efforts, are responsible for differences in national severity COVID-19 epidemics.

A compartmental epidemiological model with seven groups is introduced herein, to account for the dissemination of diseases similar to the Coronavirus disease 2019 (COVID-19). In its simplified version, the model contains ten parameters, four of which relate to characteristics of the virus, whereas another four are transition probabilities between the groups; the last two parameters enable the empirical modelling of the effective transmissibility, associated in this study with the cumulative number of fatalities due to the disease within each country. The application of the model to the fatality data (the main input herein) of five countries (to be specific, of those which had suffered most fatalities by April 30, 2020) enabled the extraction of an estimate for the basic reproduction number $R_0$ for the COVID-19 disease: $R_0=4.91(33)$.

Corona viruses cause extensive SARS epidemics via super spread events (SSE). Due to variation in infection risk and heterogeneity of reproduction numbers specific distinction between SSE’s and typical case events is essential. SARS transmissions unveil a complex scenario in which SSE’s are shaped by multiple factors. Specific screening strategies for infection emergence within potential super spreading groups will help to efficiently control the SARS-2 pandemic and alleviate the partially effective general restriction measures.

1) Background: The use of linked data in Semantic Web are promising approaches to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiologic research; 2) Methods: First, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Second, existing data standards and manuscript reporting guidelines for nutritional epidemiology were converted into ontology, and the terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Third, the ontologies of the nutritional epidemiologic standards, reporting guidelines and the core concepts were gathered in ONE. Three case studies were illustrated for its potential applications. (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts; 3) Results: Ontologies for “food and nutrition” (n=33), “disease and special population” (n=86), “data description” (n=21), “research description” (n=32) and “supplementary (meta) data description” (n=44) were reviewed and listed. ONE consists of 339 classes (79 new classes to describe nutrition data and 24 new classes to describe the content of nutrition manuscripts). The case studies demonstrated the application of ONE. 4) Conclusion: ONE is a resource to automate data integration, searching and browsing, and can be used to assess reporting completeness in nutritional epidemiology.

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.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. Aim of the study was to identify the antimicrobial resistance and accessory genes, the clonal relatedness and the evolution dynamics of selected CRKP isolates recovered in an adult and a pediatric intensive care unit of a tertiary hospital in Greece. Methods: Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed applying various bioinformatics software. Results: The isolates belonged to eight sequence types 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16 and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323 and ST39 were classified in distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs. Conclusion: The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.

Several infectious agents are ascertained causes of cancer, but the burden of cancer mortality attributable to carcinogenic infections in Italy was still unknown. To tackle this issue, we calculated the rate and regional distribution of cancer deaths due to infections sustained by seven pathogens ranked as group-1 carcinogenic agents in humans by IARC. Population attributable fractions related to these agents were applied to annual statistics of cancer deaths coded according to 10th International Classification of Diseases. The estimated burden of cancer mortality attributable to carcinogenic infections in Italy during the period 2011-2015 was on average 8.7% of all cancer deaths registered yearly. Approximately 60% of deaths occurred in men and almost the whole burden was due to four infectious agents (Helicobacter pylori, HCV, HPV, and HBV). The analysis of regional distribution showed a higher number of infection-related cancer deaths in the northern regions, where the estimates reached 30 (Liguria) and 28 (Friuli Venezia Giulia) deaths per 100,000 inhabitants in 2015. Since one-twelfth of cancer deaths were attributable to these modifiable risk factors, the implementation of appropriate prevention and treatment interventions may help to reduce the impact of these infections on cancer mortality.

Quebec is the third-largest wine grape producing province in Canada, and the industry is constantly expanding. Traditionally, 90% of the grapevine cultivars grown in Quebec were rustic or semi-rustic and largely dominated by winter hardy interspecific hybrid Vitis sp. cultivars. Over the years, the winter protection techniques adopted by growers and climate changes have offered an opportunity to establish V. vinifera L. cultivars (e.g. Pinot Noir). We characterized the virome of leafroll-infected interspecific hybrid cultivar and compared it to the virome of V. vinifera cultivar to support and facilitate the transition of the industry. A dsRNA sequencing method was used to sequence symptomatic and asymptomatic grapevine leaves of different cultivars. The results suggested a complex virome in terms of composition, abundance, richness, and phylogenetic diversity. Three viruses, grapevine Rupestris stem pitting-associated virus, grapevine leafroll-associated virus (GLR) 3 and 2 and hop stunt viroid (HSVd) largely dominated the virome. However, their presence and abundance varied among grapevine cultivars. The symptomless grapevine cultivar Vidal was frequently infected by multiple virus and viroid species and different strains of the same virus, including GLR virus 3 and 2. Our data shows that viruses and viroids associated with the highest number of grapevines expressing symptoms included HSVd, GLR3 and GLR2, in gradient order. However, co-occurrence analysis revealed that the presence of GLR species was randomly associated with the development of virus-like symptoms. These findings and their implication for grapevine leafroll disease management were discussed.

In recent years, Lassa fever has been announced as an infectious disease in the world, a few imported cases have been accounted for in various pieces of the world and there are developing worries of the possibilities of Lassa fever Virus as an organic weapon. Regardless of its assaulting impact, no substantial arrangement has been created to reduce the hazard of the ailment, about a large portion of 10 years after identifying it. A Review based on the documents from the literature search on PubMed, Scopus, Goggle Scholar and Science direct. Out of these, the final 16 articles that met the criteria were selected. Relevant information on epidemiology, the burden of management and control were obtained. Timely and effective containment of the Lassa fever disease in Lassa village four decades ago could have minimized the devastating effect and threats posed by this illness in the West African sub-region and indeed the entire globe. That was a hard lesson calling for much more proactive measures towards the eradication of the illness at primary, secondary, and tertiary levels of health care. Hence, the paper is aimed at appraising the threats associated with Lassa fever disease; its demands on curtailing the menace of the epidemic, and recommendations on important focal points.

The emergence of novel SARS-CoV-2 virus in China in December 2019 has turned into a global pandemic through continued spread beyond borders. This review was aimed to extract up-to-date information on the evolution, transmission, clinical manifestations, diagnosis, treatment and prevention of COVID-19 to fight against this common enemy. PubMed, Scopus and Google Scholar were the sources of literature; whereas CDC, WHO and Worldometer provided updated information. Bats served as the reservoirs of this virus while pangolin is believed as an intermediate host to transmit the virus to humans. Direct human-to-human and indirect transmissions were involved. Major clinical manifestations included fever, cough, fatigue, sputum production and shortness of breath. Chest radiographs mostly showed bilateral ground-glass opacities. Aged patients and patients with comorbidities had higher case fatality ratios. Critical cases were vulnerable to develop pneumonia, multi-organ failure and deaths. Overall situation in China has improved substantially. The European region and region of the Americas were the worst hit out of six WHO global regions. PCR based methods are used for the diagnosis of COVID-19. Severe/critical cases essentially require supportive or intensive cares. Avoiding exposure to COVID-19 is the best way to prevent the disease. Thus, this review provides a snapshot on COVID-19.

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.

Analysis of the demographic, temporal and seasonal distribution of hantavirus infections in Barbados was conducted using national surveillance data for 861 laboratory confirmed cases during 2008-2016. The crude incidence rate of hantavirus infections varied from 5.05 to 100.16 per 100,000 persons per year. One major hantavirus epidemic occurred in Barbados during 2010. Hantavirus cases occurred throughout the year with low level transmission during the dry season (December to June) with increased transmission during rainy season (July to November) and a seasonal peak in August. Hantavirus incidence rates were significantly higher in females than males every year during the study period. More than 50% of hantavirus cases were 30 years of age or less. The highest incidence rate (63.36 cases per 100,000 population) was observed among patients 0–4 years of age. This represents the first epidemiological data for hantavirus disease among an entire population in the English-speaking Caribbean.

Burden of diseases measured as disability-adjusted life years per 100,000 people can be mined from public domain data, when they are made available by population health surveillance systems. This can be analysed to allow insightful comparisons with the national average, and to understand differences in trends between the sexes, age groups, time periods, geographic regions and sub-regions. In this illustrative case study, we have analysed the Scottish burden of disease database to understand what ailed the population of the Grampian region before the COVID-19 pandemic. We have identified selected cancers, ischaemic heart disease, Alzheimer’s disease and other dementias amongst the highest contributors to the burden; that drug use disorders and colorectal cancer are showing worsening trends and require health promotion and disease prevention measures from ages 15 and 25 respectively, especially in Aberdeen City; and that males are more vulnerable to atrial fibrillation and flutter, diabetes mellitus and oesophageal cancer, while females are to cerebrovascular disease. We demonstrate the usefulness of our analysis and methodology for the wider health system, allowing targeted medical research investments and coordinated response from public health and health service delivery. We also show the need for up-to-date surveillance data, forecasts and evidence on the impact of interventions to be made available widely.

Demographic change is leading to the aging of German society. As long as the baby boom co-horts are still of working age, the working population will also age - and decline as soon as this baby boom generation gradually reaches retirement age. At the same time, there has been a trend towards increasing absenteeism (times of inability to work) in companies since the zero years, with the number of days of absence increasing with age. We present a novel stochastic forecast approach that combines population forecasting with forecasts of labor force participation trends, considering epidemiological aspects. For this, we combine a stochastic Monte Carlo-based cohort-component forecast of the population with projections of labor force participation rates and morbidity rates. This article examines the purely demographic effect on the economic costs associated with such absenteeism due to the inability to work. Under expected future employment patterns and constant morbidity patterns, absenteeism is expected by close to 5 percent by 2050 relative to 2020, associated with increasing economic costs of almost 3 percent. Our results illustrate how strongly the pronounced baby boom/ baby bust phenomenon determines demographic development in Germany in the midterm.

Long COVID (LC) encompasses a constellation of long-term symptoms experienced by at least 10% of people after the initial SARS-CoV-2 infection, and so far has affected about 65 million people. The etiology of LC remains unclear; however, many pathophysiological pathways may be involved, including viral persistence; chronic, low grade inflammatory response; immune dysregulation and defective immune response; reactivation of latent viruses; autoimmunity; persistent endothelial dysfunction and coagulopathy; gut dysbiosis; hormonal dysregulation, mitochondrial dysfunction; and autonomic nervous system dysfunction. There are no specific tests for the diagnosis of LC, and clinical features including laboratory findings and biomarkers may not specifically relate to LC. Therefore, it is of paramount importance to develop and validate biomarkers that can be employed for the prediction, diagnosis and prognosis of LC and its therapeutic response. Promising candidate biomarkers that are found in some patients are markers of systemic inflammation including acute phase proteins, cytokines and chemokines; biomarkers reflecting SARS-CoV-2 persistence, reactivation of herpesviruses and immune dysregulation; biomarkers of endotheliopathy, coagulation and fibrinolysis; microbiota alterations; diverse proteins and metabolites; hormonal and metabolic biomarkers; as well as cerebrospinal fluid biomarkers. At present, there are only two reviews summarizing relevant biomarkers; however, they do not cover the entire umbrella of current biomarkers or their link to etiopathogenetic mechanisms, and the diagnostic work-up in a comprehensive manner. Herein, we aim to appraise and synopsize the available evidence on the typical laboratory manifestations and candidate biomarkers of LC, their classification based on main LC symptomatology in the frame of the epidemiological and pathogenetic aspects of the syndrome, and furthermore assess limitations and challenges as well as potential implications in candidate therapeutic interventions.

The epidemic of Coronavirus Disease 2019 (COVID-19) have affected all the regions of the world, nevertheless, in some countries there is a lack of studies on its main clinical and epidemiological features. We analyzed the incidence, incidence rates, and evolution of COVID-19 cases in Honduras from February 18-April 24, 2020.Methods: Using daily epidemiological data from surveillance about COVID-19 in Honduras, we calculated the rates of incidence (cases/100,000 population), and developed at national, departmental, and municipal levels GIS-based maps.Results: February 18 - April 24, 2020, a sum of 3,169 suspected COVID-19 cases have been assessed by RT-PCR, 533 (16.8%) of them were positive, for an incidence rate of 5.73 cases/100,000 pop. The highest peak was reached on March 31 (48 cases). The department with the highest number of cases and incidence rate was Cortes (383 cases, 71.9% of the total, 21.45 cases/100,000 pop). Discussion: The pattern and evolution of COVID-19 epidemic in Honduras has been particularly focused in the major urban areas, San Pedro Sula and Tegucigalpa, the capital city. Studies using geographical information systems linked with clinical disease characteristics are necessary to attain accurate epidemiological data for public health systems. Such information is also useful for assessment of the evolution of the pandemic and monitoring interventions.

This study investigates the emergence of ertapenem-resistant, meropenem-susceptible (ErMs) among non-carbapenemase producing (NCP) and carbapenemase producing (CP) Escherichia coli and Klebsiella pneumoniae. As mutations for ertapenem resistance establish the genetic background for non-carbapenemase meropenem resistance, there is a great need for antibiotic stewards and researchers to understand the determinants of a strain’s propensity to become resistant. Whole genome sequencing was conducted on clinical carbapenem-resistant E. coli (CREC) and K. pneumoniae (CRKP) across 5 hospitals in San Antonio, U.S. from 2012-2018. The majority of carbapenem resistant Enterobacterales (CRE) were NCP (54%; 41/76). The blaCTX-M was found to be most prevalent among NCP isolates (p = 0.02). LC-MS/MS analysis of carbapenem hydrolysis revealed that blaCTX-M-mediated carbapenem hydrolysis, indicating the need to reappraise the term, “non-carbapenemase (NCP)” for quantitatively uncharacterized CRE strains harboring blaCTX-M. Antimicrobial susceptibility results showed that 56% of all NCPE isolates had an ErMs phenotype (NCPE vs. CPE, p &lt; 0.001), with E. coli driving the phenotype (E. coli vs. K. pneumoniae, p &lt; 0.001). ErMs strains carrying blaCTX-M, had approximately 4-fold more copies of blaCTX-M than ceftriaxone-resistant but ertapenem and meropenem susceptible (EsMs) isolates (3.7 v. 0.9, p &lt; 0.001). ErMs also carried more mobile genetic elements (MGEs), particularly IS26 composite transposons, than EsMs (37 vs. 0.2, p &lt; 0.0001). Immunoblot analysis demonstrated the absence of OmpC expression in NCP-ErMs E. coli, with 92% of strains lacking full contig coverage of ompC. Overall, this work provides evidence of a collaborative effort between blaCTX-M and OmpC in NCP strains that confer resistance to ertapenem but not meropenem. To thwart potential mismanagement of CRE infected patients, future efforts should focus on understanding the mechanism(s) underlying OmpC loss, developing rapid methods to detect blaCTX-M copy number variants, and targeted antimicrobials for NCPE and ErMs strains.

The World Health Organization (WHO) added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 to August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. These regions were chosen for data mining as these regions recorded significant search interests related to Disease X during this timeframe. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, a brief analysis of specific features of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis.

Atopic dermatitis (AD) is a common chronic inflammatory skin disease with high prevalence worldwide, including countries from Asia, Africa and Latin America, and in different ethnic groups. In recent years, more attention on AD heterogeneity associated on multiple factors, including patient’s ethnic background, has been posed, resulting in an increasing body of clinical, genetic, epidemiologic, and immune-phenotypic evidence that delineate differences among racial groups with AD. Filaggrin (FLG) mutations, the strongest genetic risk factor for the development of AD, are detected in up to 50% of European and 27% of Asian AD patients, while very rarely in Africans. The Th2 activation is a common attribute of all ethnic groups, though the Asian endotype of AD is also characterized by an increased Th17-mediated signal whereas African Americans own a strong Th2/Th22 signature and the absence of Th1/Th17 skewing. In addition, the ethnic heterogeneity may own important therapeutic implications as the genetic predisposition may affect treatment response and, thereby, a tailored strategy that better targets the dominant immunologic pathways in each ethnic subgroup may be envisaged. Nevertheless, white patients with AD represent the largest ethnicity enrolled and tested in clinical trials and the most treated in a real-world setting, limiting the investigation about safety and efficacy across different ethnicities. The purpose of this review is to describe the heterogeneity of pathophysiology across ethnicities and its potential therapeutic implications.

Background: Real-world data on the molecular epidemiology of EGFR resistance mutations at or after progression with first- or second-generation EGFR-TKIs in patients with advanced NSCLC are lacking. Methods: This ongoing observational study was carried out by 23 hospital-based physicians in Greece. The decision to perform Cobas® EGFR Mutation Test v2 in tissue and/or plasma at disease progression was made before enrollment. For patients with negative/inconclusive T790M plasma-based results, tissue re-biopsy could be performed. Results: Ninety-six (96) eligible patients were consecutively enrolled (median age: 67.8 years) between July-2017 and September-2019. Of the patients, 98% were tested upon progression using plasma and 2% using tissue/cytology biopsy. The T790M mutation was detected in 16.0% of liquid biopsies. Tissue re-biopsy was performed in 22.8% of patients with a T790M-negative plasma result. In total, the T790M positivity rate was 21.9%, not differing between patients on first- or second-generation EGFR-TKI. Higher (≥2) ECOG performance status and longer (≥10 months) time to disease progression following EGFR-TKI treatment initiation were associated with T790M positivity. Conclusions: Results from plasma/tissue-cytology samples in a real-world setting, yielded a T790M positivity rate lower than previous reports. Fewer than one in four patients with negative plasma-based testing underwent tissue re-biopsy, indicating the challenges in routine care settings.

Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas9, Cas12, Cas13, Cas14) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, or lateral flow assay detection. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing coronoviral nCov-2019 infection) urgently need the developing of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.

A brief overview of the past and present trajectories made by the A(H5N1) avian influenza virus among domestic birds, avian and mammalian wildlife species and humans is presented here, thereby taking into special account the 2.3.4.4b clade of the virus recently emerged in several geographic areas of the globe.

The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called ‘the clones of high risk’ often drive the spread of resistance within particular species. Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. In this dataset, we present the results of a comprehensive genomic epidemiology analysis of 17,546 genomes of a dangerous bacterial pathogen Acinetobacter baumannii. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic blaOXA-51-like gene variants, capsular (KL) and oligosaccharide (OCL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to nine known international clones of high risk. The presence of antimicrobial resistance genes within the genomes is also reported. These data will be useful for researchers in the field of A. baumannii genomic epidemiology, resistance analysis and prevention measure development.

After the appearance of first cases of ‘pneumonia of unknown origin’ in the Wuhan city, China, during late 2019, the disease progressed fast. Its cause was identified as a novel coronavirus, named provisionally 2019-nCoV. Subsequently, an official name was given as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) by the International Committee on Taxonomy of Viruses (ICTV) study group. The World Health Organization (WHO) named the Coronavirus disease-2019 as COVID-19. The epidemics of COVID-2019 have been recorded over 113 countries/territories/areas apart from China and filched more than 4292 humans, affecting severely around 1,18,326 cases in a short span. The status of COVID-2019 emergency revised by the WHO within 42 days from Public Health International Emergency (January 30, 2020) to a pandemic (March 11, 2020). Nonetheless, the case fatality rate (CFR) of the current epidemic is on the rise (between 2-4%), relatively is lower than the previous SARS-CoV (2002/2003) and MERS-CoV (2012) outbreaks. Even though investigations are on its way, the researchers across the globe have assumptions of animal-origin of current SARS-CoV-2. A recent case report provides evidence of mild COVID-2019 infection in a pet dog that acquired COVID-2019 infection from his owner in Hong Kong. The news on travellers associated spread across the globe have also put many countries on alert with the cancellation of tourist visa to all affected countries and postponement of events where international visits were required. A few diagnostic approaches, including quantitative and differential real-time polymerase chain reaction assays, have been recommended for the screening of the individuals at risk. In the absence of any selective vaccine against SARS-CoV-2, re-purposed drugs are advocated in many studies. This article discourse the current worldwide situation of COVID-2019 with information on virus, epidemiology, host, the role of animals, effective diagnosis, therapeutics, preventive and control approaches making people aware on the disease outcomes.

Background: Online survey-based observational cross-sectional study aimed at elucidating experience and attitudes of unstructured population regarding diagnostic imaging. Methods: Invitations to participate were distributed using mixed-mode design to deidentified residents aged 18 years and older. Main outcome measures included morbidity structure and incidence of diagnostic imaging administrations. Results: Respondents (n = 1069) aged 44.3 ± 14.4 years; 32.8% suffered from cardiovascular diseases (CVD); 9.5% had chronic respiratory pathology; 28.9% considered themselves healthy. Respondents with COVID-19 history (49.7%) reported higher rates of computed tomography (CT) (p &lt; .0001), magnetic resonance imaging (MRI) (p &lt; .001), and ultrasound (p &lt; .05). COVID-19 history in CVD respondents shifted imaging administrations towards CT and MRI (p &lt; .05). Every tenth respondent received MRI, CT, and ultrasound on paid basis; 29.0% could not pay for diagnostic procedures; 13.1% reported unavailable MRI. Professional status significantly affected the pattern of diagnostic modalities (p &lt; .05). MRI and CT availability differed between respondents in urban and rural areas (p &lt; .0001). History of technogenic events predisposed responders to overestimate diagnostic value of fluorography (p &lt; .05). Conclusions: Preparedness to future pandemics requires development of community-based outreach programs focusing on people's awareness regarding medical imaging safety and diagnostic value.

Although the existing paradigm states that CMV reactivation is under control of cellular immune response, the role of humoral counterpart is underestimated. Anti-CMV positive woman after conditioning with Bu-Flu-ATG underwent stem cell transplantation from fully matched, seronegative sibling donor. In immunodeficient recipient fast and significant decrease of specific immune response was observed but reconstitution of marrow-derived B and NK cells was prior thymic origin T cells. The lowest CMV-IgG(89 U/ml) was observed just before CMV viremia. Noteworthy, the sole and exclusive factor of CMV-specific immune response is a residual recipient antibody class IgG. The CMV-quantiferon increase was observed later, but in the first phase immune reconstitution of the PHA-induced IFNγ release was significantly lower than that CMV-induced. It corresponds with NK cells increase at the top of lymphocyte reconstitution and undetected CMV-specific CD8 cells by pentamer technique. Most of NK cells are CD16+, thus are stimulated by residual IgG. In immunocompetent donor the cellular and humoral immune response increases in parallel manner but symptoms of CMV mononucleosis were observed till the increase of specific IgG. Our observations shed light on a unique host-CMV interaction: indicate that significant decrease of CMV-IgG is a good predictor for CMV reactivation during secondary immunodeficiency.

Indoor air quality and public health have always been an area of prime interest across the globe. The significance of low-cost air quality sensing and indoor public health practices spikes during the time of pandemic and epidemics when indoor air pollution becomes a threat to living beings especially human beings. Indoor diseases are hard to diagnose if they are due to the indoor environmental conditions. A major challenge was observed in establishing a baseline between the indoor air quality sensors and associated diseases. In this work, 10,000+ articles from top literature databases were reviewed using bibliometric analysis to formulate indoor air quality sensors and diseases correlation rubrics to critically review 500+ articles. A set of 200+ articles were selected based on for detailed study based on seven bibliometric indices for publications that used WHO, NIH, US EPA, CDC, and FDA defined principles. This review has been conducted to assist end-users, public health facilities, state agencies, researchers, scientists and air quality protection agencies.

Abstract: This review addresses the complexities of type 1 diabetes (T1D)and its associated complications, with a par-ticular focus on diabetic retinopathy (DR). This review outlines the progression from non-proliferative to proliferative diabetic retinopathy and diabetic macular edema, highlighting the role of dysglycemia in the pathogenesis of these conditions. A significant portion of the review is devoted to technological advances in diabetes management, particu-larly the use of Hybrid Closed Loop systems (HCLS) and to the potential of open-source HCLS systems, which could be easily adapted to different patiens’needs using big data analytics and machine learning. Personalized HCLS algorithms that integrate factors such as patient lifestyle, dietary habits, and hormonal variations are highlighted as critical to reducing the incidence of diabetes-related complications and improving patient outcomes.