BRIEF REPORT | doi:10.20944/preprints202004.0009.v2
Subject: Keywords: SARS-CoV-2; COVID-19; coronavirus; coding sequences; collections
Online: 4 May 2020 (18:28:01 CEST)
The world is facing a major health crisis, the global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus, for which no approved antiviral agents or vaccines are currently available. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available via Addgene. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.
ARTICLE | doi:10.20944/preprints202302.0126.v1
Subject: Life Sciences, Molecular Biology Keywords: Omicron; SARS-CoV-2; piRNAs; coronavirus genome; translation; replication
Online: 7 February 2023 (08:54:49 CET)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic still able to infect the population in many countries. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and the ability to evade immunity require a priority study of its properties in order to quickly create effective means of preventing it. The present work is devoted to the study of in silico interaction of piRNAs with the genome of the SARS-CoV-2 (gRNA) in order to identify endogenous piRNAs and propose synthetic piRNAs with high antiviral activity for drug development. The studies were carried out using proven bioinformatic methods of interaction of the entire SARS-CoV-2 genome with more than eight million piRNAs. Binding sites (BSs) of piRNAs in the 5'UTR were located with overlapping nucleotide sequences called clusters of BSs. Several clusters of BSs were found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a and nucleocapsid. 16 synthetic piRNAs have been proposed that interact with gRNA with free binding energy from -170 kJ/mol to -175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.
REVIEW | doi:10.20944/preprints202005.0487.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: coronavirus; COVID-19; coronavirus etiology; coronavirus pathogenicity
Online: 31 May 2020 (18:16:48 CEST)
Coronavirus Disease 2019 (COVID-19) is a respiratory illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It is considered to be first reported from Wuhan, Hubei Province, China in December 2019. As of present, there are over 3.7 million identified cases worldwide and more than 259,000 deaths have been reported. This disease, its incubation period, course, complications, and the basis of spread remains a potential question due to variation in the pattern of spread around the globe and relatively fewer number of large-scale studies at present. This literature review aims to study the available data on its spread and incubation period. A literature search using PubMed with regular keywords ‘coronavirus’ and ‘COVID-19’, and Medical Subject Headings (MeSH) search for their etiology and pathogenicity was done with the search builder. The literature search revealed 26,689 studies among which 14 studies were selected for review. Studies were selected after the application of inclusion criteria and exclusion criteria with the removal of duplicates, and careful review for the outcome of interest ‘incubation period’. Among the 14 studies selected for review, there were eight review articles, five case reports, and one comparative study. The current literature review concludes that the mean incubation period for most of the literature falls between five days to 12 days with minimum reported time from known exposure to the onset of a symptom being one day and the maximum reported time from exposure to the onset of a symptom being 18 days.
ARTICLE | doi:10.20944/preprints202004.0462.v1
Subject: Life Sciences, Virology Keywords: coronavirus; virus sterilization
Online: 25 April 2020 (11:18:57 CEST)
The induction of acoustic-mechanical oscillations to virus particles by illuminating them with microwave signals is analyzed theoretically. Assuming the virus particle being of spherical shape, its capsid consisting primarily of glycoproteins, a viscous fluid model is adopted while the outside medium of the sphere is taken to be ideal fluid. The electrical charge distribution of virus particle is assumed to be spherically symmetric with a variation along the radius. The generated acoustic-mechanical oscillations are computed by solving a boundary value problem analytically, making use of the Green’s function approach. Resonance conditions to achieve maximum energy transfer from microwave radiation to acoustic oscillation to the particle is investigated. Estimation of the feasibility of the technique to compete virus epidemics either for sterilization of spaces and/or use for future therapeutic applications is examined briefly.
BRIEF REPORT | doi:10.3390/sci2030055
Subject: Keywords: coronavirus; COVID-19; 2019-nCoV; novel (new) coronavirus; pandemic control
Online: 14 July 2020 (00:00:00 CEST)
The world is currently facing a serious pandemic of coronavirus disease 2019 (COVID-19) which started in Wuhan, China, and was then transmitted rapidly to other countries. Countries applied different methods and procedures in an attempt to prevent or reduce and/or control the incidence of cases and manage existing ones. This paper discusses the methods and procedures applied by Kuwait to control this epidemic, and how effective they have been. The State of Kuwait followed WHO, European CDC, US CDC, and/or other countries’ institutional guidelines, and is still working on containing the disease, given the rising number of cases among Kuwaitis returning from affected areas such as the UK and USA, and migrant workers who bear the highest burden, given their cramped living conditions.
ARTICLE | doi:10.20944/preprints202003.0206.v2
Subject: Medicine & Pharmacology, Other Keywords: 2019 novel coronavirus infection; corons; SARS-CoV; interferon; systems biology
Online: 23 March 2020 (10:27:57 CET)
As the outbreak of COVID-19 has accelerated, an urgent need for finding strategies to combat the virus is growing. Thus, gaining more knowledge on the pathogenicity mechanisms of SARS-CoV-2, the causing agent of COVID-19, and its interaction with the immune system is of utmost importance. Although this novel virus is not well known yet, its structural and genetic similarity with SARS-CoV as well as the comparable pattern of age-mortality relations suggest that the previous findings on SARS can be applicable for COVID-19. Therefore, a systems biology study was conducted to investigate the most important signaling pathways activated by the virus. The results were then validated through a literature review on COVID-19 and the other closely related viruses, SARS and MERS. Interferons have shown to play a crucial role in the defense against coronavirus diseases. CoV can impede the interferon induction in humans. Moreover, STAT1, a key protein in the interferon-mediated immune response, is antagonized by the virus. This could explain the increased response threshold of immune cells to IFNs during CoV infections. A vivid correlation between the innate immune response threshold and the fatality rates in COVID-19 can be found. Differences in the dynamics of the interferon-related innate immune responses in children, adults, and elderly may explain the reported fatality rates. The increased mortality rates in the elderly can be explained by the higher threshold of interferon-mediated immune responses. Earlier induction of interferons in children and their less developed immune system could contribute to their near to zero fatality rate. Administration of interferon-inducing agents, such as poly (ICLC), could reduce the mortality of SARS at the very early stages of the disease. Interferon-γ combination with an interferon-I might induce synergistic effects and maximize the benefits. However, in-depth research is needed to validate it and determine the optimum dosage and timing to prevent unwanted results. Such interventions can act as a double-edged sword and aid the imbalance of the immune reactions, which may occur at the later stages of the disease. With the advancement of the disease and the virus overload, the responses would shift toward immnopathogenic over-reactions and probably cytokine storm. Moderating the activity of the immune system and supportive care in such conditions might be the optimum approach.
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; SARS-CoV-2; coronavirus; severe acute respiratory syndrome coronavirus
Online: 5 July 2020 (10:16:43 CEST)
Background: The information on the difference in clinical characteristics between severe and non-severe cases is limited in some countries including Iran. The objective of this case series is to compare the clinical characteristics, radiologic features, and laboratory findings between COVID-19 severe cases who received the intensive care unit (ICU) care with non-severe cases who did not receive ICU care. Methods: In this retrospective cohort study, 186 laboratory-confirmed patients with COVID-19 diagnosed from 1 March 2020 to 30 March 2020 were investigated. Results: This study population included 186 hospitalized patients with confirmed COVID-19. The median age was 47 years, and 88 (47.31%) were female. Of these patients, 48 were admitted and transferred to ICU. Of 186 patients, 44.62% had medical comorbidities including hypertension and diabetes. The most common clinical manifestation were shortness of breath 86.56%, myalgia 74.19%, and headache. Higher neutrophil counts, CRP, and LDH as well as the lower levels of lymphocytes were the most important laboratory finding among COVID-19 patients. As of April 15, 2020, 33 were still hospitalized. A total of 116 patients (62.70 %) had been discharged, and 36 patients (19.94 %) had died. Of the 48 patients admitted to the ICU, 33.33% have died. Conclusion: In the present study, shortness of breath was the most common clinical symptom, and the mortality rate in patients admitted to the ICU was about 33%, indicating that about one-third of patients with severe illness who admitted to the ICU section died.
ARTICLE | doi:10.20944/preprints202005.0031.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: COVID-19; Coronavirus disease; Coronavirus; SARS-CoV-2; model; prediction; machine learning
Online: 3 May 2020 (07:44:03 CEST)
Several epidemiological models are being used around the world to project the number of infected individuals and the mortality rates of the COVID-19 outbreak. Advancing accurate prediction models is of utmost importance to take proper actions. Due to a high level of uncertainty or even lack of essential data, the standard epidemiological models have been challenged regarding the delivery of higher accuracy for long-term prediction. As an alternative to the susceptible-infected-resistant (SIR)-based models, this study proposes a hybrid machine learning approach to predict the COVID-19 and we exemplify its potential using data from Hungary. The hybrid machine learning methods of adaptive network-based fuzzy inference system (ANFIS) and multi-layered perceptron-imperialist competitive algorithm (MLP-ICA) are used to predict time series of infected individuals and mortality rate. The models predict that by late May, the outbreak and the total morality will drop substantially. The validation is performed for nine days with promising results, which confirms the model accuracy. It is expected that the model maintains its accuracy as long as no significant interruption occurs. Based on the results reported here, and due to the complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research.
ARTICLE | doi:10.20944/preprints202004.0311.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: COVID-19; coronavirus disease; coronavirus; SARS-CoV-2; model; prediction; machine learning
Online: 19 April 2020 (01:47:10 CEST)
Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models need to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak.
COMMUNICATION | doi:10.20944/preprints202003.0350.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: COVID-19; SARS-CoV-2; coronavirus; novel coronavirus; department policy; radiation oncology
Online: 23 March 2020 (09:55:24 CET)
The COVID-19 pandemic is placing unprecedented stress on healthcare systems around the world. Although Radiation Oncology Departments are not at the frontline of fighting this infectious disease, it is important to implement COVID-19 policies to reduce risk of staff and patient exposure, and to limit the risk of department shutdown or downtime. This brief report describes the policy implemented at George Washington University Radiation Oncology to manage the risks of COVID-19. This includes a General Statement related to the priorities of the Radiation Oncology department, a screening procedure for new and follow-up patients, management policies for critical and non-critical patients with COVID-19 or under quarantine, a policy for the management of patients currently under treatment who are diagnosed or placed in quarantine, a clinical escalation action plan, guidelines for staff meetings and travel, and procedure management. This policy was implemented at George Washington University Radiation Oncology after the first case of COVID-19 was reported in Washington DC on March 7, 2020.
ARTICLE | doi:10.20944/preprints202003.0444.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: COVID-19; SARS-CoV-2; coronavirus; novel coronavirus; 3D printing; N95; respirator; mask
Online: 31 March 2020 (04:44:06 CEST)
The 2019 Novel Coronavirus (COVID-19) has caused an acute reduction in world supplies of personal protective equipment (PPE) due to increased demand. To combat the impending shortage of equipment including N95 masks, the George Washington University Hospital (GWUH) developed a 3D printed reusable N95 comparable respirator that can be used with multiple filtration units. We evaluated several candidate prototype respirator models, 3D printer filaments, and filtration units detailed here. Our most recent working model was based on a respirator found on an open source maker website and was developed with PLA (printer filament), a removable cap, a removable filtration unit consisting of two layers of MERV 16 sandwiched between MERV 13, and removable elastic bands to secure the mask. Our candidate mask passed our own suction test protocol to evaluate leakage and passed a qualitative Bitrix N95 fit test at employee health at GWUH. Further efforts are directed at improving the current model for seal against face, comfort, and sizing. The 3D model is available upon request and in the supplement of this paper. We welcome collaboration with other institutions and suggest other facilities consider mask fit for their own population when exploring this concept.
Subject: Keywords: COVID-19; SARS-CoV-2; coronavirus; severe acute respiratory syndrome coronavirus; meta-analysis
Online: 16 March 2020 (01:06:04 CET)
Introduction: The 2019 novel coronavirus (COVID-19) is very contagious, and can be transmitted to other people by droplet, aerosol, sneezing, infected surface, and cough. There is no vaccine or effective treatment at this time. Therefore, the prevention of COVID-19 and the rapid diagnosis of infected patients is crucial. Method: We searched all relevant literature published up to February 28, 2020, from Embase, Scopus, PubMed, Web of Science, and the Cochrane library to collect the studies that reported clinical and laboratory characteristics of COVID-19 infected patients. The study quality was assessed with the Critical Appraisal Checklist. Depending on the heterogeneity test, we used either random or fixed-effect models to analyze the appropriateness of the pooled results. Result: Twenty studies were included in the meta-analysis, including a total of 52,251 patients with confirmed COVID-19 infection. 69.5% (95% CI 54.5-81, p < 0.001) of patients had a history of recent travel to Wuhan, contact with people from Wuhan, or lived in Wuhan. The most common symptoms among COVID-19 infected patients were fever 85.6 % (95% CI 73 -93, p < 0.001), and cough 63 % (95% CI 55.5-70, p < 0.001), respectively. The laboratory analysis showed that thrombocytosis was present in 91% (95% CI 81-98, p < 0.001) CRP was elevated in 81% (95% CI 65-91, p < 0.001), and lymphopenia in 62.5% of cases (95% CI 42-79, p < 0.001). The most common radiographic signs were bilateral involvement in 76.8% (95% CI 62.5-87, p < 0.001) and consolidation in 75.5% (95% CI 50.5-91, p < 0.001) of patients. Most patients (85.4%) were hospitalized, 20.6% of patients were admitted to the ICU in critical condition, and the mortality rate was 5.6%. Conclusions: Fever and cough are the most common symptoms of COVID-19 infection in the literature published to date. Thombocytosis, lymphopenia, and increased CRP were common lab findings although most patients included in the overall analysis did not have laboratory values reported. The most common radiographic sign was bilateral involvement in and consolidation. Among Chinese patients with COVID-19, rates of hospitalization, critical condition, and hospitalization were high in this study, but these findings may be biased by reporting only confirmed cases.
ARTICLE | doi:10.20944/preprints202109.0515.v1
Subject: Arts & Humanities, Other Keywords: Benefits; barriers; distance education; coronavirus
Online: 30 September 2021 (13:57:47 CEST)
This study aims to identify benefits and barriers to distance education, particularly from the perspective of teachers in Saudi Arabia. As the applied data collection tool, a questionnaire was distributed to the general education teachers in three districts. The sample size of the study was 1076 teachers. The results revealed that despite several benefits gained from distance learning, there are also some barriers. Teachers found that the most important advantage in distance learning is the acquisition of technical skills during the online teaching processes, they learn more and use digital education platforms, they have sufficient time to prepare the scientific content, they were able to provide adequate technical solutions for their courses, and they have the opportunity to use multiple media to deliver their courses. With the introduction of distance learning, teachers have explored new ways to deliver course contents to students. It has fostered better ways to provide more interactive real-time and on-demand teaching and learning using modern technology, thus, helping teachers become familiar with the use of electronic resources. It seems that teachers invest in technical methods to enhance students’ performance. Also, teachers reported some obstacles that they face during remote teaching. Most of these problems are connection problems applied with devices and the internet, lack of students’ motivation to learn in distance, problems associated with urban learners.
ARTICLE | doi:10.20944/preprints202003.0366.v3
Subject: Earth Sciences, Environmental Sciences Keywords: COVID-19; coronavirus; temperature; solutions
Online: 21 June 2020 (16:19:26 CEST)
This article investigated whether the atmospheric temperature had any role in the spread and vulnerability to COVID-19 worldwide and how that knowledge can be utilized to contain the fast-spreading disease. It highlighted that temperature was an important factor in transmitting the virus, and a moderately cool environment was the most favourable state for its susceptibility. In fact, the risk from the virus is reduced significantly in high temperature environment. Warm countries and places were likely to be less vulnerable. We identified various degrees of vulnerability based on temperature and specified countries for March and April. The maximum reported case, as well as death, was noted when the temperature was in the range of around 275°K (2°C) to 290°K (17°C). Countries like the USA, UK, Italy and Spain belonged to this category. The vulnerability was moderate when the temperature was less than around 275°K (2°C) and countries in that category were Russia, parts of Canada and few Scandinavian countries. For temperature 300°K (27°C) and above, a significantly lesser degree of vulnerability was noted. Countries from SAARC, South East Asia, the African continent and Australia fell in that category. In fact, when the temperature was more than 305°K (32°C), there was a unusually low number of reported cases and deaths. For warm countries, further analyses on the degree of vulnerability were conducted for the group of countries from SAARC and South East Asia and individual countries were compared. We also showed countries can switch from one vulnerability state to another based on the variability of temperature. We provided maps of temperature to identify countries of different vulnerability states in different months of the year. That influence of temperature on the virus and previous results of clinical trials with similar viruses gave us a useful insight that regulating the level of temperature can provide remarkable results to arrest and stop the outbreak. Based on that knowledge, some urgent solutions are proposed, which are practically without side effects and very cost-effective too.
COMMUNICATION | doi:10.20944/preprints202005.0395.v1
Subject: Medicine & Pharmacology, Other Keywords: epidemic; coronavirus; COVID-19; logistic
Online: 24 May 2020 (18:19:02 CEST)
We present a modification of the logistic model of epidemics that takes into account the possibility that an epidemic can develop from multiple physically-distinct hot spots with a range of starting times. This produces an improved understanding of the time evolution of the COVID-19 epidemic taking place in the United States in the spring of 2020.
CONCEPT PAPER | doi:10.20944/preprints202005.0298.v1
Subject: Medicine & Pharmacology, Other Keywords: Covid 19; coronavirus; pre-hotspots
Online: 18 May 2020 (08:01:52 CEST)
COVID-19 Pandemic management has become the top priority of Government Institutions globally, which is justifiable seeing the high mortality of the disease. In India, Lockdowns by National, State and Local level administrations have greatly reduced the spread of the SARS COV-2 Virus. Some areas with a greater proportion of COVID-19 patients have been declared hotspots with increased restrictions on public activities through law enforcement. But quite often delay in identification of these hotspots leads to community transmission of the Virus thus aggravating the problem. A method to identify the areas which are at risk of becoming the next hotspot for the disease is the need of the hour. In this Research document we will find the probable risk factors and make an appropriate scale to measure the vulnerability of an area, identified by its Postal code. To help with this a Pan India survey by the title of “Survey on General Indian population on the level of preparedness for COVID-19 pandemic” was launched and received around 1250 submissions, with the acquired data we will evaluate the risk factors and make appropriate scale to identify ‘pre-hotspots’.
TECHNICAL NOTE | doi:10.20944/preprints202004.0523.v1
Subject: Earth Sciences, Atmospheric Science Keywords: airborne; coronavirus; aerosol; transmission; lifetime
Online: 30 April 2020 (09:01:26 CEST)
There is a lot of discussion underway with conflicting opinions examining the airborne nature of the SARS-CoV2 virus. Surprisingly, important phenomena prevalent with respect to aerosols (suspended droplets) have not been considered. In this Technical Note, we propose a methodology for the coupling of aerosol phenomena (such as evaporation, particle transport accounting for drag) to accurately establish the lifetimes of the droplets. A characteristic time analysis illustrates the time scales for evaporation and settling: for example, the characteristic time for evaporation of a 10 µm droplet is 0.036 s at a relative humidity of 25%; compared to a settling time of about 500 s. For any particle smaller than ~ 100 µm, the evaporation of the emitted or exhaled droplet has to be considered. Coupling evaporation of the droplet as it settles, we estimate the horizontal distance traversed. Trajectories of a 10 µm and 100 µm particle emitted with a typical initial velocity of release associated with coughing and sneezing indicates the greater spread in the horizontal direction when evaporation is accounted for. The life time of the 10 µm particle increases from 8.3 min to 12 hours (will be intercepted prior and the actual airborne time will then be shorter); and for a 100 µm particle from 4.9 s to 39.4 s.
Subject: Keywords: COVID-19; SARS 2; coronavirus
Online: 31 March 2020 (22:41:36 CEST)
There is an urgent need to advance safe and affordable COVID-19 vaccines for low- and middle-income countries of Asia, Africa and Latin America. Such vaccines rely on proven technologies such as recombinant protein-based vaccines to facilitate its transfer for emerging market vaccine manufacturers. Our group is developing a two-pronged approach to advance recombinant protein-based vaccines to prevent COVID-19 caused by SARS CoV2 and other coronavirus infections. One vaccine is based on a yeast-derived (Pichia pastoris) recombinant protein comprised of the receptor binding domain (RBD) of the SARS-CoV formulated on alum and referred to as the CoV RBD219-N1 Vaccine. Potentially this vaccine could be used as a heterologous vaccine against COVID-19. A second vaccine specific for COVID-19 is also being advanced using the corresponding RBD of SARS-CoV-2. The first antigen has already undergone cGMP manufacture and is therefore “shovel ready” for advancing into clinical trials, following vialing and required GLP toxicology testing. Evidence for its potential efficacy to cross-protect against SARS-CoV-2 includes cross-neutralization and binding studies using polyclonal and monoclonal antibodies. Evidence in support of its safety profile include our internal assessments in a mouse challenge model using a lethal mouse adapted SARS strain, which show that SARS-CoV RBD 291N1 (when adsorbed to Alhydrogel®) does not elicit eosinophilic lung pathology. Together these findings suggest that recombinant protein-based vaccines based on the RBD warrant further development to prevent SARS, COVID-19 or other coronaviruses of pandemic potential.
ARTICLE | doi:10.20944/preprints202202.0333.v1
Subject: Medicine & Pharmacology, Allergology Keywords: antibody; BNT162b2; coronavirus disease 2019; severe acute respiratory syndrome coronavirus 2; vaccine hesitancy; vaccine booster
Online: 25 February 2022 (10:01:23 CET)
This was a retrospective cohort study, which aimed to investigate the factors associated with hesitancy to receive the third dose of coronavirus disease 2019 (COVID-19) vaccine. A paper-based questionnaire survey was administered to all participants. Accordingly, the study included participants who provided answer in the questionnaire whether they have an intent to receive the third dose of vaccine. Data on sex, age, area of residence, adverse reactions after the second vaccination, whether the third vaccination was desired, and reasons to accept or hesitate booster vaccination were retrieved. Among the 2439 participants with mean (±SD) age of 52.6±18.9 years, and median IgG-S antibody titer of 324.9 (AU/mL), 97.9% of participants indicated their intent to accept a third vaccination dose. The logistic regression revealed that younger age (OR=0.98; 95% CI: 0.96-1.00) and higher antibody level (OR=2.52; 95% CI: 1.27-4.99) are positively associated with the third vaccine hesitancy. The efficacy of the COVID-19 vaccine and concerns about adverse reactions had significant impact on the third vaccination behavior. A rapid increase in the booster dose rate is needed to control the pandemic, and specific approaches should be taken in these groups that are likely to hesitate the third vaccine, subsequently increasing booster contact rate.
ARTICLE | doi:10.20944/preprints202207.0276.v1
Subject: Life Sciences, Virology Keywords: COVID-19; coronavirus; transmission; meteorological impact
Online: 19 July 2022 (04:05:25 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known globally as COVID-19, originated in December 2019 in Wuhan, Hubei province in China and has rapidly spread across the globe ever since. The first recorded case in sub-Saharan Africa was in Nigeria, on the 25th February, 2020. The virus continues to spread, and new variants of the disease have emerged, the number of deaths and new infections in the countries of sub-Saharan Africa has been relatively low compared to predictive models. This could be due to several factors, such as slower transmission dynamics of the virus, a lower-case fatality rate, or a lack of testing or reliable data. Whilst this may also, in part, be due to the robustness of the nations' public health responses, there is scarce reporting on the specifics of this. However, emerging research has demonstrated that various environmental factors could influence virus transmission. The study adopted collected meteorological data that was critically analysed and discussed. The impact of three factors in the context of sub-Saharan African nations: temperature, ultraviolet (UV) exposure and pre-existing infection with Plasmodium (malaria) were discussed. These factors were discussed critically in light of the reduced rates of transmission and mortality observed.
ARTICLE | doi:10.20944/preprints202204.0154.v1
Subject: Medicine & Pharmacology, Other Keywords: coronavirus; COVID; tocilizumab; interleukin 6; cytokine
Online: 18 April 2022 (04:12:24 CEST)
The interleukin 6 (IL-6) receptor blocking antibody tocilizumab was repurposed in the coronavirus pandemic with the intention of blocking the excess inflammatory activation associated with severe disease. We retrospectively evaluated the response to tocilizumab based on measured levels of IL-6 as well as other inflammatory markers. In the sample of 41 patients with measured levels, 16 received tocilizumab. In patients who received tocilizumab, there was a statistically significant relationship between both higher IL-6 levels and measured acute phase reactants with mortality, but not in those who did not. Additionally, an improved mortality after tocilizumab was suggested with those with higher IL-6 measurements, but not in those with lower levels, but this finding failed to achieve statistical significance (p=0.14). Though this study is limited by a small sample size and retrospective design, an association is suggested between higher IL-6 levels and improved mortality after tocilizumab.
ARTICLE | doi:10.20944/preprints202103.0565.v1
Subject: Social Sciences, Accounting Keywords: nCOVID-19; pandemic; impacts of Coronavirus
Online: 23 March 2021 (11:31:44 CET)
The Novel Coronavirus Disease (nCOVID) has grabed the whole world recently since its origin in Wuhan city of China. There is very dire consequences the whole world is going through because of nCOVID. The unprecedented nCOVID and associated consequences pushed the public health system in the crisis. Undoubtedly, it has affected almost all countries of the world. Nevertheless, hardly a few country it has spared from its dire consequences in terms social and economical losses. However, it is worth of observing that some of the positive consequences are also results of this pandemic. Consequently, this paper discusses the pros and cons of the pandemic from various perspective such as social and economical impacts on human lives and livelihoods.
CONCEPT PAPER | doi:10.20944/preprints202012.0337.v1
Subject: Keywords: Feline Infectious Peritonitis (FIP); coronavirus; dsRNA
Online: 14 December 2020 (13:27:55 CET)
Our perspective article covers major findings concerning Feline Infectious Peritonitis (FIP) - a fatal coronaviral disease of cats. In the context of FIP pathogenesis, we outline disease signalment and focus on the challenges and promises of FIP invoking coronavirus RNA detection. In particular, we outline critical aspects of coronavirus RNA replication and biogenesis. We infer the replicative intermediates of feline coronavirus may constitute an underappreciated factor triggering the progression of the maladaptive immune response underlying FIP pathogenesis.
REVIEW | doi:10.20944/preprints202009.0425.v1
Subject: Medicine & Pharmacology, Other Keywords: SARS-CoV-2; Coronavirus; podiatry; foot
Online: 18 September 2020 (09:58:49 CEST)
The Coronavirus disease 2019 (COVID-19) pandemic is clearly taking a firmer grip on South Africa and more podiatrists will face the potential transmission of SARS-CoV-2. Government response was swift with the implementation of a travel ban, strict national lockdown as well as social distancing and hygiene protocols in line with international health regulations. Co-morbidities such as tuberculosis and HIV/AIDS, endemic to South Africa, are considered a dangerous combination with COVID-19, making many South Africans vulnerable to contracting the COVID-19. Patients with diabetes as well as the aged are vulnerable, both in terms of potential combined complications and challenges in continuity in foot care. The demands of the pandemic may outstrip the ability of the health systems to cope. Should this time arrive, all healthcare practitioners, including podiatrists, would have to step in and take on a role beyond their scope of practice in order to ensure that the healthcare system does not get overwhelmed. It is important for podiatrists to keep abreast with the developments around the COVID-19, in order that they may institute appropriate clinical practice which will ensure maximum protection for themselves, staff and patients as well as providing quality foot health care.
COMMUNICATION | doi:10.20944/preprints202009.0031.v1
Subject: Life Sciences, Other Keywords: coronavirus; sports; management; football; rules; games
Online: 2 September 2020 (06:09:34 CEST)
Each sport has its specific rules, which determine what is allowed (or not) impacting directly on the sport demands. Studies involving physiological and time-motion measurements have shown that soccer is a highly demanding sport. The new coronavirus disease 2019 (COVID-19) has been a world health crisis. Soccer seasons were interrupted worldwide to avoid spreading the virus. Leagues resumed the season (no fans at the arenas) after several weeks of interruption, causing overlay of schedule. This overlay (e.g., games every Sunday and Wednesday) will cause accumulated fatigue on players, raising the risk of injuries. Considering this condensed calendar, the Fédération Internationale de Football Association (FIFA) has changed (temporarily) up to five substitutions during elite games (instead of three as the regular rule allows). Considering the already published scientific evidence, clearly, the change in the soccer substitution rule due to COVID-19 is insufficient. Implementing unlimited substitutions may benefit soccer players' health, coaches’ jobs, more entertainment for fans and sponsors (e.g., keeping intensity during all game, including on the second half) and eventually prolonging the useful life of the players. A real game-changer!
ARTICLE | doi:10.20944/preprints202009.0028.v1
Subject: Life Sciences, Other Keywords: coronavirus; football; rules; sports medicine; prophylaxis
Online: 2 September 2020 (05:27:55 CEST)
The soccer injury rate is distinctly higher during matches than the training sessions. Rules determine how to play, generating specific kinds of fatigue which is associated with the injury incidence. No research has evaluated the impact of potential rule-induced physical demands in soccer or comparing sports. Understanding the differences might be useful for enhancing rules (e.g., safer sport). Therefore, the aims of this study were: a) to described the differences in the rule-induced physical demands of soccer, futsal, basketball, and handball; and b) to evaluate whether soccer rule-induced physical demands are different than the other invasion intermittent team sports, focusing the impact of the substitutions rules. Data were collected from different sports rules (i.e., soccer, futsal, basketball, and handball), and performed hypothetical corrections to equate the other team sports to the soccer (i.e., court dimensions/number of players). The data showed that soccer has higher rule-induced physical demands: lower substitutions, higher dimensions in absolute (eight to 15 times), and relative (four to eight times) values. Hypothetical corrections showed that soccer has remarkably large differences. Therefore, we conclude that soccer has remarkably higher rule-induced physical demands than other team sports, and allowing unlimited substitutions in soccer is a must.
ARTICLE | doi:10.20944/preprints202007.0702.v1
Online: 29 July 2020 (17:35:57 CEST)
The world is suffering from the Coronavirus pandemic and is undergoing some drastic changes in day to day lives. The survey was conducted to analyze the situation of Pharmacy students in India. What are the types of challenges being faced by them during this lockdown due to the Pandemic COVID-19 and how are they getting adapted to the situations? A cross sectional survey was conducted via snowball sampling technique in which 226 participants submitted their response. The chief issue of concern to students was the change in the study pattern which has made the process much difficult for both the faculties and students. Online examination was also be reported as a point of concern. The normal life that we used to have is not acceptable in today’s scenario, hence, the institutions have to make the students more comfortable and adaptable towards the online studies and make the most out of it.
ARTICLE | doi:10.20944/preprints202006.0356.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: anxiety; depression; stress; coronavirus; Dilla; Ethiopia
Online: 30 June 2020 (08:00:58 CEST)
Background: The COVID-19 pandemic is the global public health emergency concern and had an impact on the day to day life of individuals. Its effect on an individual’s mental health is significant to the extent of suicide. Objective: This study aimed to assess the magnitude of psychological problems and their associated factor among communities living in Dilla town in response to the pandemic. Methods: From Apr 1- Apr 15, 2020, a community-based cross-sectional study was conducted using multi-stage sampling techniques. Self-administered the questioner, Depression, Anxiety and Stress Scale (DASS-21), and logistic regression analysis (95% CI, p-value <0.05) was used. Results: This study included 445 respondents with a 94% non- response rate who was living in Dilla town. In total, 34.4% of respondents had a psychological problem (11.4 % mild and 23% moderate level of the psychological problem). Female, Greater secondary level of education, monthly income below 500 ETB, more than three family size, and wearing face mask were variables associated with the outcome variable (p < 0.05). Conclusions: Nearly one-third of the respondents had mild to moderate psychological among communities living in Dilla town. There is a need for mental health support on those identified groups of peoples to enhance their resilience in response to the pandemic.
Subject: Keywords: coronavirus; epidemiology; 2019-nCoV; COVID-19
Online: 10 June 2020 (05:17:01 CEST)
There is a current pandemic of a new type of coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The number of confirmed infected cases has been rapidly increasing. This paper analyzes the characteristics of SARS-CoV-2 in comparison with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and influenza. COVID-19 is similar to the diseases caused by SARS-CoV and MERS-CoV virologically and etiologically, but closer to influenza in epidemiology and virulence. The comparison provides a new perspective for the future of the disease control, and offers some ideas in the prevention and control management strategy. The large number of infectious people from the origin, and the highly infectious and occult nature have been two major problems, making the virus difficult to eradicate. We thus need to contemplate the possibility of long-term co-existence with COVID-19.
REVIEW | doi:10.20944/preprints202005.0410.v1
Subject: Biology, Other Keywords: coronavirus; prevention; species; symptom; virus origin
Online: 25 May 2020 (11:09:25 CEST)
There are many types of coronavirus on the bases of important hosts including human, rat, turkey, rabbit, etc. The virus looks like a crown or corona of the sun with its round projection, spike. Now a day, newly emerged coronavirus disease (COVID 19) was first detected at Wuhan, China in December 2019 and it became a public health emergency international concern. Although a couple of researches has been conducting, much secretes of the virus and disease is still not understood and not reached a common understanding yet. However, sharing basic information is crucial based on the existing published research articles and updated information. Therefore, this review aimed to draw attention to the COVID 19 pandemic facts, opportunities, and challenges based on up to date information on cases in Ethiopia. Accordingly, the coronavirus is a single-stranded, non-segmented RNA genome virus. Two third of the genome (5'end) consists of two genes that code nonstructural proteins and the other 2-7 genes (3' end) code structural proteins including spike, envelope, membrane, and nucleocapsid. The virus transmits from animal to human and suggested as it might be originated from a bat and/or seafood. Coronavirus transmit human to human by direct contact and droplets during coughing and sneezing and common symptoms like fever, dry cough, and tiredness, short breathing, etc. can be seen from the patient. So that stay at home and social distancing are the most practicing pre-prevention methods. The disease causes high economic loss, face to face education closure, community cultural practice, and mass gathering activities are prohibited. However, various charity associations and creativities found increase than before. To this end, peoples should accept and follow governmental advice and instructions to escape from the pandemic.
REVIEW | doi:10.20944/preprints202004.0346.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: coronavirus; heart; prognosis; COVID-19; ICU
Online: 19 April 2020 (13:15:27 CEST)
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging infectious disease with currently a pandemic state. Cardiac function can be involved, affecting prognosis, in addition with lung feature severity, particularly in patients with comorbidities. Since the renin angiotensin aldosterone (RAA) system may interact with SARS-Cov-2, researches are still ongoing to assess the prognostic value of RAA blockers in cardiology.
REVIEW | doi:10.20944/preprints202004.0289.v1
Subject: Medicine & Pharmacology, Other Keywords: SARS Coronavirus; COVID-19; AKI; CKD
Online: 17 April 2020 (01:53:32 CEST)
In December 2019, an animal human coronavirus transmission occurred in Wuhan, China. A state of global pandemic was shortly declared, among a very rapid contagious spread of the virus. The causative virus was identified as SARS CoV 2 virus and is genetically related to the previous SARS outbreak in 2003. The virus causes wide clinical spectrum from mild flu like symptoms to adult respiratory distress syndrome. Kidney involvement has been reported in several reports in patients with various degrees of severity of SARS CoV2 infection. As knowledge is evolving, the accurate incidence of AKI is not known. Many questions are yet to be answered as regards the effect of epidemiological variables and comorbidities on the occurrence of AKI. Some reports have observed the occurrence of hematuria and proteinuria in a percentage of infected patients. Moreover, chronic kidney disease has not been found in some reports to add to the adverse outcomes, an aspect that merits further exploration. Patients on regular hemodialysis may be vulnerable to contagion due to lower status of immunity and need for frequent attendance to healthcare facilities. Due to the previous factors, prevention and mitigation of SARS CoV2 virus in this vulnerable population constitutes a major challenge.
REVIEW | doi:10.20944/preprints202004.0019.v2
Subject: Life Sciences, Other Keywords: COVID-19; SARS-CoV-2; Coronavirus; 2019-nCoV; SARS
Online: 3 April 2020 (15:23:50 CEST)
OBJECTIVE: Recent worldwide outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of respiratory coronavirus disease 2019 (COVID-19), is a current, ongoing life-threatening crisis and international public health emergency. The early diagnosis and management of the disease remains a major challenge. In this review, we aim to summarize the updated epidemiology, causes, clinical manifestation and diagnosis, as well as prevention and control of the novel coronavirus SARS-CoV-2.MATERIALS AND METHODS: A broad search of the literature was performed in “PubMed” “Medline” “Web of knowledge”, and “Google Scholar” World Health Organization-WHO” using the keywords “severe acute respiratory syndrome coronavirus”, “2019-nCoV”, “COVID-19, “SARS”, “SARS-CoV-2” “Epidemiology” “Transmission” “Pathogenesis” “Clinical Characteristics”. We reviewed and documented the information obtained from literature on epidemiology, pathogenesis and clinical appearances of SARS-CoV-2 infection.RESULTS: The global cases of COVID-19 as of April 2, 2020 have risen to more than 900,000 and morbidity has reached more than 47,000. The incidence rate for COVID-19 has been predicted to be higher than the previous outbreaks of other coronavirus family members, including those of SARS-CoV and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The main clinical presentation of SARS-CoV-2 infection ranges from asymptomatic stages to severe lower respiratory infection in the form of pneumonia. Most of the patients also presented with fever, cough, sore throat, headache, fatigue, myalgia and breathlessness.Individuals at higher risk for severe illness include elderly people and patients with a weakened immune system or that are suffering from a underlying chronic medical condition like hypertension, diabetes, cancer, respiratory illness or cardiovascular diseases.CONCLUSIONS: SARS-Cov-2 has emerged as a worldwide threat, currently affecting 170 countries and territories across the globe. There is still much to be understood regarding SARS-CoV-2 about its virology, epidemiology and clinical management strategies; this knowledge will be essential to both manage the current pandemic and to conceive comprehensive measures to prevent such outbreaks in the future.
ARTICLE | doi:10.20944/preprints202002.0359.v1
Subject: Life Sciences, Immunology Keywords: novel coronavirus; Wuhan; vaccine; epitopes; peptide
Online: 25 February 2020 (05:18:22 CET)
During December 2019, a novel coronavirus named as 2019-nCoV, has emerged in Wuhan, China. The human to human transmission of this virus has also been established. Untill now the virus has infected more than seven thousand people and has spread to fifteen countries. The World Health Organization (WHO) has declared 2019-nCoV as global health emergency due to its outburst well beyond China. There is need to develop some vaccines or therapeutics to control or prevent 2019-nCoV infections. The bottleneck with current conventional approaches is that these require longer time for vaccine development. However, computer assisted approaches help us to produce effective vaccine in short time compared with conventional methods. In this study, bioinformatics analysis was used to predict B cell and T cell epitopes of surface glycoprotein of 2019-nCoV that could be suitable to trigger significant immune response. The sequence of surface glycoprotein was collected from the database and analyzed to identify the immunogenic epitope. Both B cell and T cell epitopes were analyzed so the predicted epitopes can stimulate both cellular and humoral immune responses. We predicted 13 B cell and 05 T cell epitopes that later on were joined with GPGPG linker to make a single peptide. This computational approach to design a multi epitope peptide vaccine against emerging 2019-nCoV allows us to find novel immunogenic epitopes against the antigen targets of surface 2019-nCoV surface glycoprotein. This multi epitope peptide vaccine may prove effective to combat 2019-nCoV infections.
REVIEW | doi:10.20944/preprints202002.0358.v3
Subject: Life Sciences, Virology Keywords: Infectious diseases; Coronavirus; SARS-CoV-2; COVID-19; Pneumonia; China
Online: 28 February 2020 (13:21:43 CET)
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) linked with coronavirus disease 2019 (COVID-19) poses a serious threat to public health worldwide. Firstly, the SARS-CoV-2 was reported in Wuhan, Hubei Province, China in December 2019. Initially, the major proportion of virus-infected cases (i.e. about 99%) was reported in China and now it is being reported in other counties as well. Humans begin to be infected within their communities and transmittance of the viral epidemic increased rapidly due to lack of understanding of its transmission routes and precautionary measures. The existence of SARS-CoV-2 in China threatened the population greatly due to the high incidence of fatal respiratory infections. Current investigations speculated that this virus transferred into a human from viral-infected bats. However, the process of interspecies viral transmission is an important scientific question to be addressed. Due to the continuous increase in the patients infected with COVID-19 associated pneumonia, the World Health Organization (WHO) has included this viral epidemic to the priority list of diseases. Therefore, accelerated research developments are required to control the spread of this outbreak, as it is declared as a public health emergency by WHO especially in the absence of efficacious drugs and vaccines. Our review encompasses the recent status of disease severity in China, a particular replication mechanism of SARS-CoV-2 and potential risks and precautionary measures required to avoid contact with this fatal viral infection.
ARTICLE | doi:10.20944/preprints202002.0179.v1
Subject: Medicine & Pharmacology, Other Keywords: novel coronavirus; SEIR model; outside China
Online: 14 February 2020 (02:34:55 CET)
Ongoing outbreak of pneumonia caused by novel coronavirus (2019-nCoV) began in December 2019 in Wuhan, China, and the number of new patients continues to increase. On the contrary to ongoing outbreak in China, however, there are limited secondary outbreaks caused by exported case outside the country. We here conducted simulations to estimate the impact of potential secondary outbreaks at a community outside China. Simulations using stochastic SEIR model was conducted, assuming one patient was imported to a community. Among 45 possible scenarios we prepared, the worst scenario resulted in total number of persons recovered or removed to be 997 (95% CrI 990-1,000) at day 100 and maximum number of symptomatic infectious patients per day of 335 (95% CrI 232-478). Calculated mean basic reproductive number (R0) was 6.5 (Interquartile range, IQR 5.6-7.2). However, with good case scenarios with different parameter led to no secondary case. Altering parameters, especially time to hospital visit could change the impact of secondary outbreak. With this multiple scenarios with different parameters, healthcare professionals might be able to prepare for this viral infection better.
COMMUNICATION | doi:10.20944/preprints202006.0044.v1
Subject: Life Sciences, Microbiology Keywords: Epidemiology; COVID-19; coronavirus; bat; RaTG13; BtCoV/4991; SARS-CoV-2; Pangolin Coronavirus; next generation sequencing
Online: 5 June 2020 (06:17:26 CEST)
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.
HYPOTHESIS | doi:10.20944/preprints202004.0317.v2
Subject: Keywords: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); COVID19; Middle East Respiratory Syndrome Coronavirus; bioaerosol; aerosol
Online: 30 April 2020 (05:30:30 CEST)
A short review of the important studies was conducted to evaluate the potential of aerosol transmission of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The minimum size of droplets potentially carrying the SARS-CoV-2 was newly estimated and discussed in this review.
ARTICLE | doi:10.20944/preprints202209.0116.v1
Subject: Medicine & Pharmacology, Other Keywords: parents’ motive to vaccinate; coronavirus disease; children
Online: 8 September 2022 (03:11:45 CEST)
Background: Vaccinating children against COVID-19 is an essential public health strategy in order to reach herd immunity and prevent illness among children and adults. Parents are facing tremendous stress in relation to the COVID-19 pandemic and the effectiveness of the COVID-19 vaccination program for children. In this study, we aimed to investigate parents’ willingness to vaccinate their children against COVID-19 in North Kivu province (DRC). Methods: A cross-sectional survey between December 01, 2021 to January 20, 2022 in 6 health zones (Goma, Karisimbi, Butembo, Beni, Kamango and Katwa) was conducted in the province of North Kivu. In each health zone, we selected 5 clusters (Health area) using the method of probabilistic selection proportional to population size. In total, 522 parents participated in our study. Results: Overall, 32.8% of parents intended to vaccinate their children. In the multivariate analysis, younger age of parents (aOR : 2.40, CI : [1.50-3.83]), higher level of fear that “a member of my family” could contract COVID-19 (aOR : 2.35, CI : [1.38-4.02]), higher level of perceived vulnerability to COVID-19 within the family (aOR : 1.70, CI : [1.005-2.2881]), higher level of perceived susceptibility to COVID-19 within the family (aOR : 3.07, CI : [1.80-5.23]), and history of vaccination against COVID-19 among parents (aOR : 16.47, CI : [8.39-32.33]), were significantly associated with the intention to have their children or adolescents vaccinated. Conclusion: Willingness of parents to vaccinate their children against the COVID-19 vaccination was low in North Kivu. There is undeniably in this region a need to reinsure the populations about vaccine safety for both children and adults. Public health authorities should also address widespread misinformation about vaccines in a timely manner.
ARTICLE | doi:10.20944/preprints202207.0041.v1
Subject: Mathematics & Computer Science, Computational Mathematics Keywords: coronavirus; COVID-19; pandemic; compartmental model; Nigeria
Online: 4 July 2022 (08:42:03 CEST)
It is no news that the COVID–19 pandemic has affected many persons in different ways. As the number of reported cases rises across the globe, efforts are geared towards production and administration of effective vaccines for the disease. However, many developing countries are faced with the dilemma of how to slow the spread and flatten the curves of the disease as the available vaccines are not enough. Interestingly, the dynamics of the disease can be analysed to get useful insights to enhance the making of suitable preventive policies that will slow the spread, ultimately flatten the curves of the disease and also help in managing any future occurrence. In this work, the aim is to analyse the dynamics, and estimate the basic reproduction number of the second wave of the pandemic in Nigeria using a Susceptible-Infected-Recovered-Deceased (SIRD) compartmental–based model. The dynamics of the disease is described by a system of nonlinear ordinary differential equations. The model takes into consideration the current control policies in place - social distancing, mask usage, personal hygiene and quarantine. Available data provided by Nigeria Centre for Disease Control (NCDC), World Health Organization (WHO) and Wolfram Data Repository were used for the computations. The Quasi–Newton algorithm was implemented in fitting the proposed model to the available data and a sensitivity analysis was presented. Major parameters - effective contact rate, average recovery time, average mortality rate, and overall effectiveness of the control policies - influencing the dynamics of the disease, and the basic reproduction numbers were estimated. The turning points of the disease during the second wave were also obtained. The proposed model gave estimated values for the parameters influencing the spread of the disease. Also, the measure of the overall effectiveness of the current control policies gave insight into how effective the measures are.
ARTICLE | doi:10.20944/preprints202109.0510.v1
Subject: Social Sciences, Education Studies Keywords: coronavirus pandemic; Online Final Examination; mathematics course
Online: 30 September 2021 (11:21:08 CEST)
The National Examination in Indonesia has been abolished since 2020. Hence, the Indonesian junior high schools makes its final examination items for the 9th-grade, and from the results, the school determines students' graduation. The final examination has an important role and significant value in making decisions about students' graduation. Therefore, this study is aimed to analyze the Online Final Examination items in one of the public junior high schools in Bandung. The sample was 234 students in grade 9 using their mathematics examination tests, comprising 20 multiple-choice items with 4 options, while the data processing used Winsteps software with the Rasch modeling technique. Subsequently, the Rasch model results showed an acceptable person separation statistic of 1.54 and sufficient person reliability at 0.74. The item separation statistics was in a good category at 4.59, while the item reliability at 0.95 was excellent. Although four online final examination items were in the fit category, 16 were good and capable of dividing students according to their abilities. The result also provided very detailed data about the quality of the items and the ability of each grade 9 student. Since each test item is included in the fit category, this study contributes information on preparing and analyzing the Online Final Examination to teachers..
ARTICLE | doi:10.20944/preprints202105.0474.v1
Subject: Medicine & Pharmacology, Allergology Keywords: COVID-19; coronavirus infection; inequalities; socioeconomic factors.
Online: 20 May 2021 (10:21:34 CEST)
Background: The aim of our study was to analyze the effect of socioeconomic inequalities, both at the individual and area of residence levels, on the probability of COVID-19 confirmed infection, and its variations across three pandemic waves. Methods: Retrospective cohort study. We included data from all individuals tested by COVID-19 during the three waves of the pandemic, from March to December 2020 (357,989 individuals). We studied the effect of inequalities on the risk of having a COVID-19 confirmed diagnosis after being tested using multilevel analyses with two levels of aggregation: individuals and basic healthcare area (BHA) of residence (deprivation level and type of zone). Results: Patient profile changed through the pandemic, with a predominance of low-paid employees living in deprived BHA. Workers with low salaries, unemployed and people on minimum integration income or who no longer receive the unemployment allowance, had a higher probability of COVID-19 infection than workers with salaries ≥€18,000 per year. Inequalities were higher in women and in the second wave. The deprivation level of BHA of residence influenced the risk of COVID-19 infection, especially in the second wave. Conclusions: There are inequalities in the risk of COVID-19 confirmed infection, both at individual and area level. It is necessary to develop individual and area coordinated measures in the control, diagnosis and treatment of the epidemic, in order to avoid an increase in the already existing inequalities.
ARTICLE | doi:10.20944/preprints202102.0429.v1
Subject: Medicine & Pharmacology, Allergology Keywords: coronavirus; pandemic; population survey; suicidal behavior; suicide
Online: 19 February 2021 (09:56:01 CET)
The aim of the study was to examine the prevalence of suicide thoughts and -attempts during the early stage of the COVID-19 outbreak and examine factors associated with suicide thoughts in the general Norwegian population. A sample of 4527 adults living in Norway were recruited via social media. Data related to suicide thoughts and attempts, mental health variables, pandemic-related concerns and sociodemographic variables were collected. Associations with suicide thoughts were analyzed with logistic regression analysis. In the sample, 3.6 % reported suicide thoughts during the last month, while 0.2 % had attempted to commit suicide during the same period. Lower age (OR: 0.66, p < 0.001), daily alcohol use (OR: 3.29, p < 0.001), being in the risk group for COVID-19 complications (OR: 2.38, p < 0.01), and having economic concerns related to the pandemic (OR: 2.51, p < 0.001) were associated with having suicide thoughts. In addition to known risk factors, the study suggests that aspects specific to COVID-19 may be important for suicidal behaviors during the pandemic.
Subject: Keywords: coronavirus; statistical analysis; Covid-19; pandemic spreading
Online: 13 January 2021 (12:50:37 CET)
The earlier analytical analysis (part A) of the Susceptible-Infectious-Recovered (SIR) epidemics model for a constant ratio k of infection to recovery rates is extended here to the semi-time case which is particularly appropriate for modeling the temporal evolution of later (than the first) pandemic waves when a greater population fraction from the first wave has been infected. In the semi-time case the SIR model does not describe the quantities in the past; instead they only hold for times later than the initial time t=0 of the newly occurring wave. Simple exact and approximative expressions are derived for the final and maximum values of the infected, susceptible and revovered/removed population fractions as well the daily rate and cumulative number of new infections. It is demonstrated that two types of temporal evolution of the daily rate of new infections j(tau) occur depending on the values of k and the initial value of the infected fraction I(0)=eta: in the decay case for k > 1-2 eta the daily rate monotonically decreases at all positive times from its initial maximum value j(0)=eta (1-eta). Alternatively, in the peak case for k<1-2 eta the daily rate attains a maximum at a finite positive time. By comparing the approximated analytical solutions for j(tau) and J(tau) with the exact ones obtained by numerical integration, it is shown that the analytical approximations are accurate within at most only 2.5 percent. It is found that the initial fraction of infected persons sensitively influences the late time dependence of the epidemics, the maximum daily rate and its peak time. Such dependencies do not exist in the earlier investigated all-time case.
ARTICLE | doi:10.20944/preprints202011.0617.v1
Subject: Medicine & Pharmacology, Allergology Keywords: coronavirus; mental health; Norway; population study; PTSD
Online: 24 November 2020 (13:33:17 CET)
The COVID-19 outbreak and the sudden lockdown of society in March 2020 had a large impact on people’s daily life and gave rise to concerns for the mental health in the general population. The aim of the study was to examine post-traumatic stress reactions related to the COVID-19 pandemic, the prevalence of symptom-defined post-traumatic stress disorder (PTSD), and factors associated with post-traumatic stress in the Norwegian population during the early stages of the COVID-19 outbreak. A survey was administered via social media channels, to which a sample of 4527 adults (≥18 years) responded. Symptom-defined PTSD was measured with the PTSD Checklist for the DSM-5. The items were specifically linked to the COVID-19 pandemic. We used the DSM-5 diagnostic guidelines to categorize participants as fulfilling the PTSD symptom criteria or not. Associations with PTSD were examined with single and multiple logistic regression analyses. The prevalence of symptom-defined PTSD was 12.5% for men and 19.5% for women. PTSD was associated with lower age, female gender, lack of social support, and a range of pandemic-related variables such as economic concerns, expecting economic loss, having been in quarantine or isolation, being at high-risk for complications from COVID-19 infection, and having concern for family and close friends. In conclusion, posttraumatic stress reactions were common in the Norwegian population in the early stages of the COVID-19 outbreak. Concerns about finances, health, and family and friends seem to matter.
ARTICLE | doi:10.20944/preprints202009.0459.v1
Subject: Biology, Other Keywords: COVID-19; coronavirus; drug repositioning; pathway enrichment
Online: 19 September 2020 (11:34:12 CEST)
The COVID-19 global pandemic has created dire consequences with an alarming rate of morbidity and mortality. There are not yet vaccine or efficacious treatment options to combat the causative SARS-CoV-2 infection. This paper describes the identification of potentially repurposable drugs for COVID-19 treatment by conducting pathway enrichment analysis on publicly available Gene Expression Omnibus datasets. We first determined SARS-CoV-2 infection-induced alterations of host gene expressions and pathways. We then identified drugs or compounds that target and counter virus-triggered cellular perturbations, suggesting their potential repurposing for COVID-19 treatment. The key findings are that SARS-CoV-2 infection in host cells induces mitochondrial dysfunction, inhibits oxidative phosphorylation, and activates several immune response and pro-inflammatory pathways. Triptolide, the major bioactive component of a traditional Chinese medicine herb, may rescue mitochondrial dysfunction by activating oxidative phosphorylation. Further in vitro and in vivo studies are necessary to verify these results prior to clinical application.
Subject: Keywords: COVID-19, coronavirus, population, density, hospital, pandemic
Online: 20 August 2020 (13:18:03 CEST)
In this four-month-long study (from April 1, 2020 to August 1, 2020), we have collected, modeled, and analyzed COVID-19 data from the top five most infected counties per top six most infected states in the United States (30 counties total). More specifically, we collected data on each state’s total COVID-19 cases, deaths, tests conducted, and their counties’ population, density, percentage of seniors, number of hospitals, total COVID-19 cases, and total COVID-19 related deaths. In this study, we have models illustrating the growth of COVID-19 cases and deaths per county, growth of COVID-19 cases and deaths per state (which is really the sum of our chosen five counties), and growth of COVID-19 tests conducted per state. In addition, our study also contains models illustrating the statistics of several variables that might have affected a county’s COVID-19 data, which has been mentioned above: population, density, percentage of seniors, and number of hospitals. An interesting finding we have noticed upon modeling the 30 counties’ density and total COVID-19 cases as an xy scatter plot is that there is a considerably strong relationship between the two variables. Los Angeles County (which was an extreme outlier), in particular, supports the idea that a county’s most populous city can greatly affect its entire county’s COVID-19 cases; if the largest city is extremely dense, it appears that the entire county has a greater total COVID-19 case count.
HYPOTHESIS | doi:10.20944/preprints202008.0426.v1
Subject: Life Sciences, Virology Keywords: enveloped virus, coronavirus, inactivation, persistence, surface, mechanisms
Online: 20 August 2020 (05:38:38 CEST)
The Covid-19 coronavirus, SARS-CoV-2, is inactivated much faster on paper (3h) than on plastic (7d). By classifying materials according to virus stability on their surface, the following list is obtained (from long to short stability): polypropylene (mask), plastic, glass, stainless steel, pig skin, cardboard, banknote, cotton, wood, paper, tissue, copper. These observations and other studies suggest that SARS-CoV-2 may be inactivated by dryness on water absorbent porous materials but sheltered by long-persisting micro-droplets of water on waterproof surfaces. If such physical phenomenons were confirmed by direct evidence, the persistence of the virus on any surface could be predicted, and new porous objects could be designed to eliminate the virus faster.
ARTICLE | doi:10.20944/preprints202008.0410.v1
Subject: Biology, Other Keywords: coronavirus; film; detergent; antiviral; virucide; inactivation; sanitization
Online: 19 August 2020 (10:45:07 CEST)
COVID-19 infection, caused by SARS-CoV-2, is inequitably distributed and more lethal among populations with lower socioeconomic status. Direct contact with contaminated surfaces has been one of the virus sources, as it remains infective up to days. Several disinfectants have been shown to inactivate SARS-CoV-2 but they rapidly evaporate, are flammable or toxic and may be scarce or inexistent for the vulnerable populations. Therefore, we are proposing a simple, easy to prepare, low-cost and efficient antiviral films, made with wide available dishwasher detergent, which can be spread in hands and inanimate surfaces and maintains virucidal activity for longer periods than the current sanitizers. Avian coronavirus (ACoV) was used as model of challenge to test the antivirus efficacy of proposed films. Polystyrene microplates were covered with a thin layer of detergent formula. After drying, the films were exposed to different virus doses for 10 minutes and virus infectivity were determined using embryonated chicken eggs and RNA virus quantification in allantoic fluids by RT-qPCR. The films showed to inactive the ACoV (ranging from 103.66 to 106.66 EID50), which is chemically and morphologically similar to SARSCoV-2 and may constitute an excellent alternative to minimize the spread of Covid-19.
ARTICLE | doi:10.20944/preprints202005.0332.v2
Subject: Life Sciences, Genetics Keywords: coronavirus; substitution rate; positive selection; demographic dynamics
Online: 21 June 2020 (16:10:26 CEST)
A new form of coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) is currently causing a pandemic. A six-month evolutionary history of SARS-CoV-2 is witnessed by characterising the total genome of 821 samples using comparative phylogenomic approaches. Our analyses produced striking inclusive results that may guide scientists/professionals for the past/future of pandemic. Phylogenetic and time estimation analyses suggest the proximate origin of pandemic strain as Guangdong and the origin time as first half of September 2019, not Wuhan and December 2019, respectively. The viral genome experienced a substitution rate similar to other RNA viruses, but it is particularly high in some of the peptides encoding sequences such as leader protein, E gene, orf8, orf10, nsp10, N gene, S gene and M gene and nsp4, while low in nsp11, orf7a, 3C-like proteinase, nsp9, nsp8 and endoRNase. Most strikingly, the divergence rate of amino acid sequences is high proportional to nucleotide divergence. Additionally, specific non-synonymous mutations in nsp3 and nsp6 evolved under positive selection. The exponential growth rate (r), doubling time (Td) and R0 were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. Comparison of synapomorphies distinguishing the SARS-CoV-2 and the candidate ancestor bat coronavirus indicates that mutation pattern in nsp3 and S gene enabled the new strain to invade human and become a pandemic strain. We arrive at the following main conclusions: (i) six months evolution of viral genome is nearly neutral, (ii) origin of pandemic is not Wuhan and predates formal reports, (iii) although viral population is ongoing an exponential growth, the doubling time is evolving towards shortening, and (iv) divergence rate of total genome is similar to other RNA viruses, but it is prominently high in some genes while low in some others and evolution in these genes should be closely monitored as their protein products intervening to pathogenicity, virulence and immune response.
REVIEW | doi:10.20944/preprints202005.0470.v1
Subject: Medicine & Pharmacology, Other Keywords: coronavirus; COVID-19; facial protection; masks; PAPR
Online: 31 May 2020 (15:02:43 CEST)
We live in extraordinary times, where COVID-19 pandemic has brought the whole world to a screeching halt. Tensions and contradictions that surround the pandemic ridden world include the availability, and the lack thereof, various facial protection measures to mitigate the viral spread. Here, we comprehensively explore the different type of facial protection measures, including masks, needed both for the pubic and the health care workers (HCW). We discuss the anatomy, the critical issues of disinfection and reusability of masks, the alternative equipment available for the protection of the facial region from airborne diseases, such as face shields and powered air purifying respirators (PAPR), and the skin-health impact of prolonged wearing of facial protection by HCW. Clearly, facial protection, either in the form of masks or alternates, appears to have mitigated the pandemic as seen from the minimal COVID-19 spread in countries where public mask wearing is strictly enforced. On the contrary, the healthcare systems, that appear to have been unprepared for emergencies of this nature, should be appropriately geared to handle the imbalance of supply and demand of personal protective equipment including face masks. These are two crucial lessons we can learn from this tragic experience.
REVIEW | doi:10.20944/preprints202004.0532.v1
Subject: Biology, Physiology Keywords: cellular senescence; SARS-CoV-2; coronavirus; aging
Online: 30 April 2020 (13:58:41 CEST)
The disproportionate incidences of COVID-19-related hospitalization and mortality for different age groups and various underlying health conditions is a result of a complex social predisposition to the exposure, resistance, and tolerance for the infection. Based on the observed data as well as the molecular mechanisms for viral entry and replication, cellular senescence related to aging, obesity, hypertension, and diabetes appears to be strongly correlated with the SARS-CoV-2 infections resulting in higher COVID-19 related complications and mortality. Establishing such a correlation may allow us to better explain the pathobiology as well as the differential nature of the SARS-CoV-2 infections and consider targeted control and therapeutic strategies to combat the disease.
Subject: Engineering, Electrical & Electronic Engineering Keywords: coronavirus; COVID-19; diagnosis; deep features; SVM
Online: 22 April 2020 (05:58:22 CEST)
The detection of coronavirus (COVID-19) is now a critical task for the medical practitioner. The coronavirus spread so quickly between people and approaches 100,000 people worldwide. In this consequence, it is very much essential to identify the infected people so that prevention of spread can be taken. In this paper, the deep feature plus support vector machine (SVM) based methodology is suggested for detection of coronavirus infected patient using X-ray images. For classification, SVM is used instead of deep learning based classifier, as the later one need a large dataset for training and validation. The deep features from the fully connected layer of CNN model are extracted and fed to SVM for classification purpose. The SVM classifies the corona affected X-ray images from others. The methodology consists of three categories of Xray images, i.e., COVID-19, pneumonia and normal. The method is beneficial for the medical practitioner to classify among the COVID-19 patient, pneumonia patient and healthy people. SVM is evaluated for detection of COVID-19 using the deep features of different 13 number of CNN models. The SVM produced the best results using the deep feature of ResNet50. The classification model, i.e. ResNet50 plus SVM achieved accuracy, sensitivity, FPR and F1 score of 95.33%,95.33%,2.33% and 95.34% respectively for detection of COVID-19 (ignoring SARS, MERS and ARDS). Again, the highest accuracy achieved by ResNet50 plus SVM is 98.66%. The result is based on the Xray images available in the repository of GitHub and Kaggle. As the data set is in hundreds, the classification based on SVM is more robust compared to the transfer learning approach. Also, a comparison analysis of other traditional classification method is carried out. The traditional methods are local binary patterns (LBP) plus SVM, histogram of oriented gradients (HOG) plus SVM and Gray Level Co-occurrence Matrix (GLCM) plus SVM. In traditional image classification method, LBP plus SVM achieved 93.4% of accuracy.
COMMUNICATION | doi:10.20944/preprints202004.0304.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: COVID-19; SARS-CoV-2; Neurology; coronavirus
Online: 17 April 2020 (15:27:14 CEST)
The recently emerged coronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) is the newest threat to human health. It has already infected more than half a million people worldwide, leading to a lot of deaths. Although it causes mild flu-like disease in most patients, lethality may increase to more than 20% in elderly subjects, especially those with comorbidities, like hypertension, diabetes or lung and cardiac disease, and the mechanisms are still elusive. Common symptoms at the onset of illness are fever, cough, myalgia or fatigue, headache, and diarrhea or constipation. Interestingly, respiratory viruses have also placed themselves as relevant agents for CNS pathologies. Here we discuss several CNS related features, referred by several patients, especially at the beginning of the disease. Thus, we also discuss the possibility by which SARS-CoV-2 may affect the olfactive system of patients, either directly or indirectly.
REVIEW | doi:10.20944/preprints202004.0299.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: SARS-CoV-2; COVID-19; coronavirus; remdesivir
Online: 17 April 2020 (13:02:03 CEST)
The global pandemic of SARS-CoV-2, the causative viral pathogen of COVID-19, has driven the biomedical community to action – to uncover and develop anti-viral interventions. One potential therapeutic approach currently being evaluated in numerous clinical trials is the agent remdesivir, which has endured a long and winding developmental path. Remdesivir is a nucleotide analog prodrug that perturbs viral replication, originally evaluated in clinical trials to thwart the Ebola outbreak in 2014. Subsequent evaluation by numerous virology laboratories demonstrated the ability of remdesivir to inhibit coronavirus replication, including SARS-CoV-2. Here, we provide an overview of its mechanism of action, discovery, and the current studies exploring its clinical effectiveness.
ARTICLE | doi:10.20944/preprints202004.0267.v1
Subject: Medicine & Pharmacology, Other Keywords: novel coronavirus; COVID-19; epidemic model; epidemiology
Online: 16 April 2020 (08:24:07 CEST)
Italy was the first country in Europe which imposed control measures of travel restrictions, quarantine and contact precautions to tackle the epidemic spread of the novel coronavirus (SARS-CoV-2) in all its regions. While such efforts are still ongoing, uncertainties regarding SARS-CoV-2 transmissibility and ascertainment of cases make it difficult to evaluate the effectiveness of restrictions. Here, we employed a Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model to assess SARS-CoV-2 transmission dynamics, working on the number of reported patients in intensive care unit (ICU) and deaths in Sicily (Italy), from 24 February to 13 April. Overall, we obtained a good fit between estimated and reported data, with a small fraction of unreported SARS-CoV-2 cases (19.5%; 95%CI=0%-34.7%) before 10 March lockdown. Interestingly, we estimated that the first set of restrictions reduced transmission rate in the community by 42% (95%CI=38%-46%), and that more stringent measures adopted on 23 March succeeded to drastically curb the transmission rate by 84% (95%CI=80%-88%). Thus, our estimates delineated the characteristics of SARS-CoV2 epidemic before restrictions taking into account unreported data. Further modeling after the adoption of control measures, moreover, indicated that restrictions reduced SARS-CoV2 transmission considerably.
Subject: Medicine & Pharmacology, Other Keywords: COVID-19; face masks; epidemiology; coronavirus; pandemics
Online: 12 April 2020 (08:41:58 CEST)
The current Coronavirus Disease 19 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, is unprecedented in recent history and threatens the lives and livelihoods of billions worldwide. The rapid spread and lack of modern parallels have left governments, health agencies, and the public racing to understand how to best mitigate and ultimately suppress the pandemic, but we are still working to understand the strengths and weaknesses of various interventions at our disposal. Few issues have been as contentious as the public use of face masks to control the pandemic’s spread. There is ongoing debate about their effectiveness, but an increasing body of evidence suggests that masks could be a useful in preventing the spread of coronavirus, leading several governments and health agencies to review and revise their policies. Here, we review the theory and evidence behind use of masks. The theory behind masks is that they prevent the spread of viral particles by infected persons, and inhalation of viral particles by uninfected persons. Even assuming masks are not 100% effective in preventing infection, they may reduce severity of infection by reducing viral dosing. Laboratory studies suggest masks may be effective in stopping both exhalation and inhalation of viral particles. However, real-world studies provided limited evidence for the use of masks in controlling influenza transmission and highlight potential problems associated with their misuse, such as poor compliance or improper use. Evidence for efficacy of face masks against the first SARS virus, SARS-CoV-1, implies that they may be effective against the current outbreak of SARS-Cov-2 virus. This is important as mathematical modeling suggests that even small reductions of in transmission rates can make a large difference over time, potentially slowing the pace of viral pandemics and limiting their spread. Perhaps the strongest argument for the use of masks is that countries with early adoption of masks have tended to see flatter pandemic curves, even without strict nationwide lockdowns. There is little evidence that respirators are more effective than surgical masks, but this may be due to misuse or poor compliance. Studies suggest some non-medical masks perform on par with medical masks. Improvised masks are less effective than medical masks, but may provide better protection than nothing at all. While many governments now encourage the use of improvised face coverings, more will need to be known about material, design, and who needs to wear masks, and when, to ensure effectiveness. Proper use of masks will also be important; if masks are used improperly or infrequently they may provide limited protection. It is important that public health policy makers consider the debate and the potential of masks as part of multi-faceted coronavirus control strategies.
Subject: Life Sciences, Virology Keywords: COVID-19; coronavirus; fulminant myocarditis; infection; echocardiography.
Online: 7 April 2020 (01:03:22 CEST)
Background: Coronavirus Disease 2019 (COVID-19) has been demonstrated to be the cause of pneumonia. Nevertheless, it has not been reported as the cause of acute myocarditis or fulminant myocarditis. Case presentation: A 63-year-old male was admitted with pneumonia and cardiac symptoms. He was genetically confirmed as having COVID-19 according to sputum testing on the day of admission. He also had elevated troponin I (Trop I) level (up to 11.37 g/L) and diffuse myocardial dyskinesia along with a decreased left ventricular ejection fraction (LVEF) on echocardiography. The highest level of interleukin-6 was 272.40 pg/ml. Bedside chest radiographs showed typical ground-glass changes indicative of viral pneumonia. Laboratory test results for viruses that cause myocarditis were all negative. The patient conformed to the diagnostic criteria of the Chinese expert consensus statement for fulminant myocarditis. After receiving antiviral therapy and mechanical life support, Trop I was reduced to 0.10 g/L, and interleukin-6 was reduced to 7.63 pg/ml. Moreover, the LVEF of the patient gradually recovered to 68%. The patient died of aggravation of secondary infection on the 33rd day of hospitalization. Conclusion: COVID-19 patients may develop severe cardiac complications such as myocarditis and heart failure. This is the first report of COVID-19 complicated with fulminant myocarditis. The mechanism of cardiac pathology caused by COVID-19 needs further study.
ARTICLE | doi:10.20944/preprints202004.0052.v1
Subject: Medicine & Pharmacology, Other Keywords: novel coronavirus; epidemiology; COVID-19; epidemic model
Online: 6 April 2020 (12:30:42 CEST)
In the midst of the novel coronavirus (SARS-CoV-2) epidemic, examining reported case data could lead to biased speculations and conclusions. Indeed, estimation of unreported infections is crucial for a better understanding of the current emergency in China and in other countries. In this study, we aimed to estimate the unreported number of infections in China prior to 23 March 2020 restrictions. To do that, we developed a Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model which estimated unreported cases and infections from the reported number of deaths. Our approach relied on the fact that observed deaths were less likely to be affected by reporting biases than reported infections. Interestingly, we estimated that R0 was 2.43 (95%CI= 2.42 – 2.44) at the beginning of the epidemic, and that 92.9% (95%CI= 92.5% - 93.1%) of total cases were not reported. Similarly, the proportion of unreported new infections by day ranged from 52.1% to 100%, with a total of 91.8% (95%CI= 91.6% - 92.1%) unreported infections. Agreement between our estimates and those from previous studies proved that our approach was reliable to estimate prevalence and incidence of undocumented SARS-CoV2 infections. Once tested on Chinese data, our model could be applied on other countries with different surveillance and testing policies.
REVIEW | doi:10.20944/preprints202004.0007.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: nCov-19, COVID-19, coronavirus, SARS-CoV
Online: 1 April 2020 (09:30:00 CEST)
Coronaviruse disease (COVID-19) outbreak has created an emergency globally, and social distancing and isolation is the only solution to prevent its spread. Several countries have announced fully locked on to tackle this pandemic. The recent COVID-2019 has shaken the globe with incidence cases of more than half-million cases, and a mortality toll of more than twenty thousand to date. The coronavirus family is inclusive of pathogen of both – animal species and humans, encapsulating the isolated severe acute respiratory syndrome coronavirus (SARS-CoV). Researchers round the globe have been dexterously working to decode this lethal virus. Many mathematical frameworks have also been depicted which have helped to understand the dynamics of the COVID-19. Research on coronaviruses continues to explore various aspects of viral replication and pathogenesis to understanding the predilection of these viruses to switch between species, to develop an infection in a new host, and to identify significant reservoirs of coronaviruses will dramatically aid in our potential to prophesize when and where potential epidemics may occur. Many of the non-structural and accessory proteins encoded by the viruses remain unclear and unknown. This systematic review highlights the current situation of the pandemic, virus genomic composition, pathogenesis, symptomatology, diagnosis, and prognosis along with mathematical models of disease transmission and dynamics.
REVIEW | doi:10.20944/preprints202003.0410.v2
Subject: Biology, Animal Sciences & Zoology Keywords: Coronavirus; 2019-nCoV; COVID-19; bat, pangolin
Online: 30 March 2020 (08:16:22 CEST)
The world is puzzling over the origin of the current outbreak of the coronavirus disease (COVID-19) that is caused by a novel coronavirus-2019 (2019-nCoV). As of 26th March 2020, the World Health Organization has reported 46,2,684 confirmed cases and 20,834 confirmed deaths in total due to COVID-19. To this end, two unique mammals namely bats and pangolins are being investigated for their potential link to COVID-19. However, the evidence so far gathered in this context is far from clear. This paper aimed to: (i) enlighten the major aspects of life of bats and pangolins; (ii) briefly discusses their potential link to COVID-19; and also (iii) to highlight the way forward. The outcomes may contribute to future research on the subject.
REVIEW | doi:10.20944/preprints202003.0271.v2
Subject: Medicine & Pharmacology, Ophthalmology Keywords: Coronavirus; 2019-nCOV; SARS-CoV-2; transmission; infection; conjunctiva; eye
Online: 24 March 2020 (06:42:35 CET)
The outbreak of recently identified 2019 novel coronavirus (2019-nCOV) infection has become a world-wide health threat. Currently, more information is needed for further understanding the transmission, clinical characteristics, and infection control procedures of 2019-nCOV. Recently, the role of the eye in transmitting 2019-nCOV has been intensively discussed. Previous investigations about other high infectious human COVs, that is, severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV), may provide helpful information. In this review, we describe the genomics and morphology of human CoVs, the epidemiology, systemic and ophthalmic manifestations, mechanisms of human CoVs infection, and infection control procedures. The role of the eye in the transmission of SARS-CoV and 2019-nCOV is discussed. Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of ocular surface and upper respiratory tract is connected by nasolacrimal duct and share same entry receptors for some respiratory viruses. The eye is rarely involved in human CoVs infection, conjunctivitis is quite rare in patients with SARS-CoV and 2019-nCoV infection, and COV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with SARS-CoV and 2019-nCoV infection is also very low, which imply that the eye is neither a preferred organ of human COVs infection, nor is a preferred gateway of entry for human COVs to infect respiratory tract. However, pathogens exposed to the ocular surface might be transported to nasal and nasopharyngeal mucosa by constant tear rinsing through lacrimal duct, and then cause respiratory tract infection. Considering close doctor-patient contact is quite common in ophthalmic practice which are apt to transmit human COVs by droplets and fomites, hand hygiene and personal protection are still highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice.
REVIEW | doi:10.20944/preprints202009.0076.v1
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: severe acute respiratory syndrome coronavirus 2; SARS-CoV-2; coronavirus disease 2019; COVID-19; viral infection; virus-host interaction
Online: 4 September 2020 (03:19:43 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (SARS-CoV and MERS-CoV) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to the some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summaries the possible and logic answers to these questions.
ARTICLE | doi:10.20944/preprints202302.0171.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; Syrian hamster; animal model; coronavirus
Online: 10 February 2023 (01:22:19 CET)
The Golden Syrian hamster (Mesocricetus auratus) is now commonly used in preclinical research for the study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the assessment of vaccines, drugs and therapeutics. Here we show that hamsters inoculated via the intranasal route with the same infectious virus dose of prototypical SARS-CoV-2 administered in a different volume present with different clinical signs, weight loss and viral shedding, with a reduced volume resulting in reduced severity of disease similar to that obtained by a 500-fold reduction in challenge dose. The tissue burden of virus and the severity of pulmonary pathology were also significantly affected by different challenge inoculum volumes. These findings suggest that direct comparison between the severity of SARS-CoV-2 variants or studies assessing the efficacy of treatments determined by hamster studies cannot be made unless both the challenge dose and inoculation volume are matched when using the intranasal route. Additionally, analysis of sub-genomic and total genomic RNA PCR data demonstrated no link between sub-genomic and live viral titres and that sub-genomic analyses do not provide any information beyond that provided by more sensitive total genomic PCR.
ARTICLE | doi:10.20944/preprints202301.0188.v1
Subject: Life Sciences, Virology Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; pandemic spreading
Online: 11 January 2023 (02:14:27 CET)
Monitored differential infection rates of past Corona waves are used to infer, a posteriori, the real time variation of the ratio of recovery to infection rate as key parameter of the SIR-epidemic model. From monitored Corona waves in five different countries it is found that this ratio exhibits a linear increase at early times below the first maximum of the differential infection rate before the ratios approach a nearly constant value close to unity at the time of the first maximum with small amplitude oscillations at later times. The observed time dependencies at early times and at times near the first maximum agree favorably well with the behavior of the calculated ratio for the Gaussian temporal evolution of the rate of new infections, although the predicted linear increase of the Gauss ratio at late times is not observed.
ARTICLE | doi:10.20944/preprints202204.0272.v1
Subject: Life Sciences, Biotechnology Keywords: immunochromatography; test strips; RBD protein; COVID-19; coronavirus
Online: 28 April 2022 (05:09:49 CEST)
Nowadays, the presence of pathogen-specific antibodies in the blood is widely controlled by a serodiagnostic technique based on the lateral flow immunoassay (LFIA). However, its common one-stage format with an antigen immobilized in the binding zone of a test strip and a nanodis-persed label conjugated with immunoglobulin-binding proteins is associated with risks of very low analytical signals. It is caused by the presence of non-specific immunoglobulins in very large excess to the target antibodies in the tested samples thus decreasing their binding with the detected labels. In this study, the first stage of the immunochromatographic serodiagnosis was carried out in its traditional format using a conjugate of gold nanoparticles with staphylococcal immunoglobulin-binding protein A and an antigen immobilized on a working membrane. At the second stage, a labeled immunoglobulin-binding protein was added, which enhanced the coloration of the bound immune complexes. The use of two separated steps, binding of specific antibodies, and further coloration of the formed complexes allowed a significant reducing the influence of non-specific immunoglobulins on the assay results. The proposed approach was ap-plied for the serodiagnosis using a recombinant RBD protein of SARS-CoV-2. As a result, an in-crease in the intensity of test zone coloration by more than two orders of magnitude was demonstrated, which enabled to significantly reduce false-negative results. When testing a panel of 16 positive and 8 negative serum samples, the diagnostic sensitivity of the LFIA was 62.5% for the common format and 100% for the enhanced format; the diagnostic specificity of both variants was 100%.
REVIEW | doi:10.20944/preprints202108.0071.v1
Subject: Life Sciences, Biochemistry Keywords: coronavirus; SARS-CoV-2; receptors; COVID-19; pandemic
Online: 3 August 2021 (11:05:23 CEST)
Several recent surges in COVID-19 cases due to newly emerging variant strains of SARS-CoV-2 with greater transmissibility have highlighted the virus’s capability to directly modulate spike-ACE2 interactions and promote immune evasion by sterically masking the immunogenic epitopes. Recently, there have also been reports of the bidirectional transfer of coronavirus between different animal species and humans. The ability of coronavirus to infect and adapt to a wide range of hosts can be attributed to new variants that modify the molecular recognition profile of the spike protein (S protein). The receptor-binding domain of the spike protein specifically interacts with key host receptor molecules present on the host cell membranes to gain entry into the host and begin the infection cycle. In this review, we discuss the molecular, structural, and functional diversity associated with the coronavirus receptors across their different phylogenetic lineages and its relevance to various symptomatology in the rapid human-to-human infection in COVID-19 patients, tropism, and zoonosis. Despite this seeming diversity of host receptors, there may be some common underlying mechanisms that influence the host range, virus transmissibility, and pathogenicity. Understanding these mechanisms may be crucial in not only controlling the ongoing pandemic but also help in stopping the resurgence of such virus threats in the future.
Subject: Keywords: coronavirus; extrapolation; 7-day incidence value; Covid-19
Online: 28 July 2021 (10:30:09 CEST)
Based on hospital capacities, facts from past experience with the coronavirus disease 2019 (COVID-19) virus and the number of dark infections during the second wave (DII = 2D2), a reasonable limiting value of 140/D2 for the 7-day incidence per 100,000 persons (MSDIHT) and a second wave herd immunization threshold fraction value of 0.26 in Germany were calculated. If the MSDIHT is held below this limiting value, the German hospital system can cope with the number of new seriously infected persons without any triage decisions. On the basis of the SIRV epidemics model, the classical threshold values for herd immunization were calculated for 18 countries. For these countries, the dates regarding when herd immunization against the second COVID-19 wave will be reached were estimated
ARTICLE | doi:10.20944/preprints202107.0145.v1
Subject: Medicine & Pharmacology, Allergology Keywords: saliva; COVID-19 diagnosis; coronavirus; SARS-CoV-2
Online: 6 July 2021 (12:26:41 CEST)
Background. A previous study demonstrated the performance of the Salivette® (SARSTEDT, Numbrecht, Germany) as a homogeneous saliva collection system to diagnose COVID-19 by RT-qPCR, notably for symptomatic and asymptomatic patients. However, for convalescent patients, the corroboration of molecular detection of SARS-CoV-2 in paired nasopharyngeal swabs (NPS) and saliva samples was unsatisfactory. Objectives. The aim of the present work was to assess the concordance level of SARS-CoV-2 detection between paired sampling of NPSs and saliva collected with Salivette® at two time points, with ten days of interval. Results. A total of 319 paired samples from 145 outpatients (OP) and 51 healthcare workers (HW) were collected. Due to significant waiting rate at hospital, most of the patients ate and/or drank in waiting their turn. Consequently, a mouth washing was systematically proposed prior saliva collection. None of the HW were diagnosed SARS-CoV-2 positive using NPS or saliva specimens at both time points (n=95) by RT-qPCR. The virus was detected in 56.3% (n=126/224) of the NPS samples from OP, but solely 26.8% (n=60/224) of the paired saliva specimens. The detection of the internal cellular control, the human RNase P, in more than 98% of the saliva samples, underlined that the low sensitivity of saliva specimens (45.2%) for SARS-CoV-2 detection was not attributed to an improper saliva sample storing or RNA extraction. Conclusions. Then, the mouth washing decreased viral load of buccal cavity conducting to impairment of SARS-CoV-2 detection. Viral loads in saliva neo-produced appeared insufficient for molecular detection of SARS-CoV-2. At the time that saliva tests could be a rapid, simple and noninvasive strategy to assess on large scale schooled children in France, the determination of the performance of saliva collection become imperative to standardize procedures.
ARTICLE | doi:10.20944/preprints202106.0534.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: COVID-19; Coronavirus; pandemic; bibliometric analysis; MERS; SARS
Online: 22 June 2021 (08:33:26 CEST)
India is ranked 5th in world in terms of Covid-19 publications accounting for 6.7% of the total. About 60% of the Covid-19 publications in the year 2020 are from United States, China, UK, Italy, and India. We present a bibliometrics analysis of the publi-cation trends and citation structure along with identification of major research clusters. By performing network analysis of authors, citations, institutions, key-words, and countries, we explore semantic associations by applying visualization techniques. Our study shows lead taken by United States, China, UK, Italy, India in Covid-19 research may be attributed to the high prevalence of Covid-19 cases in those countries witnessing the first outbreak and also due to access to Covid-19 data, access to labs for experimental trials, immediate funding, and overall support from the govt. agencies. Large number of publications and citations from India are due to co-authored publications with countries like United States, UK, China, and Saudi Arabia. Findings show health sciences with highest the number of publications and citations, while physical sciences and social sciences and humanities counts were low. A large proportion of publications fall into the open access category. With India as focus, by comparing three major pandemics SARS, MERS, Covid-19 from biblio-metrics perspective, we observe much broader involvement of authors from multiple countries for Covid-19 studies as compared to SARS and MERS. Finally, by applying bibliometric indicators, we see an increasing number of sustainable develop-ment-related studies from the Covid-19 domain, particularly concerning the topic of good health and well-being. This study allows for a deeper understanding on how the scholarly community from a populous country like India pursued research in the midst of a major pandemic which resulted in closure of scientific institutions.
REVIEW | doi:10.20944/preprints202106.0007.v1
Subject: Medicine & Pharmacology, Allergology Keywords: computerized tomography; coronavirus disease 2019; echocardiography; lung ultrasound
Online: 1 June 2021 (09:31:10 CEST)
Coronavirus Disease 2019 (COVID-19) is the pandemic challenge of the last year. Cardiovascular involvement is one of the main characteristics of this disease. Due to endothelial damage, consequent phlogosis may increase a thrombosis risk. Cardiac injury may occur in different ways. However, an ischemic involvement of the cardiovascular system is rarely implied. In this regard, direct and indirect effects of COVID-19 are described. Nonetheless, the possible evaluation of the cardiovascular system may require different modalities. The cardiovascular evaluation may be different in emergency compared to critical care, requiring different tools for each setting. The aim of this review is to explore these modalities according to the different involvement of the cardiovascular system..
ARTICLE | doi:10.20944/preprints202104.0052.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Coronavirus; COVID-19; Diseases Modeling; Time-fractional; Quarantine
Online: 2 April 2021 (11:32:28 CEST)
The emergence of the COVID-19 outbreak has caused a pandemic situation in over 210 countries. Controlling the spread of this disease has proven difficult despite several resources employed. Millions of hospitalization and deaths have been observed, and thousands of cases daily with many measures in place. Due to the complex nature of COVID-19, we proposed a system of time-fractional equations to understand the transmission of the disease better. Nonlocality involved in the model has made fractional differential equations appropriate for modeling the behavior. However, solving these types of models is computationally demanding. Our proposed generalized compartmental COVID-19 model incorporates effective contact rate, transition rate (from exposed quarantine and recovered to susceptible and infected quarantined individuals), quarantine rate, disease-induced death rate, natural death rate, natural recovery rate, recovery rate of quarantine infected for a holistic study of the coronavirus disease. A detailed analysis of the proposed model is carried out, including the existence and uniqueness of solutions, local and global stability analysis of the disease-free equilibrium analysis, and sensitivity analysis. Furthermore, numerical solutions of the proposed model are obtained with the generalized Adam-Bashforth-Moulton method developed for the fractional order model. Our analysis and solutions profile show that each of these incorporated parameters is very important in controlling the spread of COVID-19, especially quarantining exposed and infected individuals and the effective contact rate. Based on the results with different fractional order, we observe that there seems to be a third or even fourth wave of the spike in cases of COVID-19, which is what is happening right now in many countries.
ARTICLE | doi:10.20944/preprints202103.0718.v1
Subject: Life Sciences, Biochemistry Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; pandemic spreading
Online: 30 March 2021 (09:40:33 CEST)
With the now available vaccination against Covid-19 it is quantitatively explored how vaccination campaigns influence the mathematical modeling of epidemics. The standard susceptible-infectious-recovered/removed (SIR) epidemic model is extended to the fourth compartment V of vaccinated persons and the vaccination rate v(t) that regulates the relation between susceptible and vaccinated persons. The vaccination rate v(t) competes with the infection (a(t)) and recovery (\mu(t)) rates in determining the time evolution of epidemics. In order for a pandemic outburst with rising rates of new infections it is required that k+b<1-2\eta, where k=\mu_0/a_0 and b=v_0/a_0 denote the initial ratios of the three rates, respectively, and \eta << 1 is the initial fraction of infected persons. Exact analytical inverse solutions t(Q) for all relevant quantities Q=[S,I,R,V] of the resulting SIRV-model in terms of Lambert functions are derived for the semi-time case with time-independent ratios k and b between the recovery and vaccination rates to the infection rate, respectively. These inverse solutions can be approximated with high accuracy yielding the explicit time-dependences Q(t) by inverting the Lambert functions. The values of the three parameters k, b and \eta completely determine the reduced time evolution the SIRV-quantities Q(\tau). The influence of vaccinations on the total cumulative number and the maximum rate of new infections in different countries is calculated by comparing with monitored real time Covid-19 data. The reduction in the final cumulative fraction of infected persons and in the maximum daily rate of new infections is quantitatively determined by using the actual pandemic parameters in different countries. Moreover, a new criterion is developed that decides on the occurrence of future Covid-19 waves in these countries. Apart from Israel this can happen in all countries considered.
ARTICLE | doi:10.20944/preprints202102.0554.v1
Subject: Engineering, Other Keywords: Social media; Classification; Coronavirus; Word embedding; Artificial Intelligence
Online: 24 February 2021 (16:35:09 CET)
The widespread deployment of social media has helped researchers access an enormous amount of data in various domains, including the pandemic caused by the COVID-19 spread. This study presents a heuristic approach to classify Commercial Instagram Posts (CIPs) and explores how the businesses around the Holy Shrine – a sacred complex in Mashhad, Iran, surrounded by numerous shopping centers – were impacted by the pandemic. Two datasets of Instagram posts (one gathered data from March 14th to April 10th, 2020, when Holy Shrine and nearby shops were closed, and one extracted data from the same period in 2019), two word embedding models – aimed at vectorizing associated caption of each post, and two neural networks – multi-layer perceptron and convolutional neural network – were employed to classify CIPs in 2019. Among the scenarios defined for the 2019 CIPs classification, the results revealed that the combination of MLP and CBoW achieved the best performance, which was then used for the 2020 CIPs classification. It is found out that the fraction of CIPs to total Instagram posts has increased from 5.58% in 2019 to 8.08% in 2020, meaning that business owners were using Instagram to increase their sales and continue their commercial activities to compensate for the closure of their stores during the pandemic. Moreover, the portion of non-commercial Instagram posts (NCIPs) in total posts has decreased from 94.42% in 2019 to 91.92% in 2020, implying the fact that since the Holy Shrine was closed, Mashhad citizens and tourists could not visit it and take photos to post on their Instagram accounts.
ARTICLE | doi:10.20944/preprints202101.0449.v1
Subject: Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; pandemic spreading
Online: 22 January 2021 (14:00:51 CET)
We start out by deriving simple analytic expressions for all measurable amounts of cases and fatalities during a pandemic evolution exhibiting multiple waves, described by the semi-time SIR model. The approximant shares all relevant features with the exact solution, including time and position of the peak of daily new infections, as well as the asymptotic behaviors at small and large times. We derive exact analytic expressions for the early doubling time, late half decay time, and a half-early peak law, characterizing the dynamical evolution. We show, in particular, how the asymmetry of the first epidemic wave and its exponential tails are affected by the initial conditions; a feature that has no analogue in the all-time SIR model. We apply the approach to available data from different continents. Our analysis reveals that the immunity is very strongly increasing during the 2nd wave, while it was still at a very moderate level of a few percent in several countries at the end of the first wave. The wave-specific SIR parameters describing the infection and recovery rates we find to behave in a similar fashion, while their ratio k was decreasing only by a about 5% for most countries. Still, an apparently moderate change of k can have significant consequences for the relevant numbers like the final amount of infected or deceased population. As we show, the probability for an additional wave is however low in several countries due to the fraction of immune inhabitants at the end of the 2nd wave, irrespective the currently ongoing vaccination efforts. We compare with alternate approaches.
REVIEW | doi:10.20944/preprints202009.0198.v2
Subject: Life Sciences, Virology Keywords: coronavirus; aquatic organisms; fish; marine mammals; frogs; birds
Online: 22 September 2020 (11:45:01 CEST)
Coronaviruses are pathogens recognized for having an animal origin, commonly associated with terrestrial environments. However, although in a few cases, there are reports of their presence in aquatic organisms like fish, frogs, waterfowls and marine mammals. None of these cases has led to human health effects when contact with these infected organisms has taken place, whether they are alive or dead. Aquatic birds seem to be the main group carrying and circulating these types of viruses among healthy bird populations. Although the route of infection for CoVID-19 by water or aquatic organisms has not yet been observed in the wild, the relevance of its study is highlighted because there are cases of other viral infections known to have been transferred to humans by aquatic biota. It is encouraging to know that aquatic species, such as fish, marine mammals, and amphibians, shows very few cases of coronaviruses and that some other aquatic animals may also be a possible source of cure or treatment against then, as some evidence with algae and marine sponges suggest.
ARTICLE | doi:10.20944/preprints202009.0446.v1
Subject: Medicine & Pharmacology, Other Keywords: Novel coronavirus diseases 2019; vaccination; target population; China
Online: 19 September 2020 (05:02:54 CEST)
All countries are facing decisions about which groups to prioritise for COVID-19 vaccination after the first vaccine product has been licensed, at which time supply shortages are inevitable. Here we define the key target populations and their size in China for a phased introduction of COVID-19 vaccination with evolving goals, accounting for the risk of illness and transmission. Essential workers (47.2 million) like healthcare workers could be prioritized for vaccination to maintain essential services. Subsequently, older adults, individuals with underlying health conditions and pregnant women (616.0 million) could be targeted to reduce severe COVID-19 outcomes. Then it could be further extended to target adults without underlying health conditions and children (738.7 million) to reduce symptomatic infections and/or to stop virus transmission. The proposed framework could assist Chinese policy-makers in the design of a vaccination program, and could be generalized to inform other national and regional COVID-19 vaccination strategies.
ARTICLE | doi:10.20944/preprints202007.0416.v1
Subject: Physical Sciences, Mathematical Physics Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; epidemic spreading
Online: 19 July 2020 (15:35:44 CEST)
We revisit the Susceptible-Infectious-Recovered/Removed (SIR) model which is one of the simplest compartmental models. Many epidemological models are derivatives of this basic form. While an analytic solution to the SIR model is known in parametric form for the case of a time-independent infection rate, we derive an analytic solution for the more general case of a time-dependent infection rate, that is not limited to a certain range of parameter values. Our approach allows us to derive several exact analytic results characterizing all quantities, and moreover explicit, non-parametric, and accurate analytic approximants for the solution of the SIR model for time-independent infection rates. We relate all parameters of the SIR model to a measurable, usually reported quantity, namely the cumulated number of infected population and its first and second derivatives at an initial time t=0, where data is assumed to be available. We address the question on how well the differential rate of infections is captured by the Gauss model (GM). To this end we calculate the peak height, width, and position of the bell-shaped rate analytically. We find that the SIR is captured by the GM within a range of times, which we discuss in detail. We prove that the SIR model exhibits an asymptotic behavior at large times that is different from the logistic model, while the difference between the two models still decreases with increasing reproduction factor. This part A of our work treats the original SIR model to hold at all times, while this assumption will be released in part B. Releasing this assumption allows to formulate initial conditions incompatible with the original SIR model.
ARTICLE | doi:10.20944/preprints202007.0082.v1
Subject: Keywords: COVID-19; Coronavirus; Temperature; Environment; Relative Humidity; India
Online: 5 July 2020 (15:20:54 CEST)
The coronavirus disease 2019 (COVID-19), the pandemic is an unprecedented health emergency never seen in the recorded history of humankind due to its sheer scale, rapid spread, and subsequent shock to the global economy. The past respiratory viral pandemics of the 21st century (SARS-CoV-2 in 2003, Influenza AH1N1 in 2009) have revealed seasonality in environmental factors to play a role in the dynamics of their spread. Here, we report the observed state-level relationship between environmental factors such as temperature (T), relative humidity (RH), specific humidity (SH), and solar radiation (SR) on the COVID-19 spread over the Indian region. The results show that T and RH have a significant impact on the disease growth rate and doubling time. Every degree rise in temperature corresponds to a 0.99 % decrease in the number of cases and an increase in doubling time by ~ 1.13 days implying a slowing down of spread. A similar analysis for RH reveals that more moisture leads to a higher growth rate and reduced doubling time. Lower SH and higher surface-reaching SR are found to reduce the spread and increase the doubling time similar to that of temperature. The range of average state-level T (RH) encountered during this period was between 24 and 35oC (30 and 87%) which implies that environmental impact is still effective at all these T (RH) and is not limited to specific T (RH) ranges. The progression of the season towards monsoon, post-monsoon, and thereafter winter with a continuous reduction in temperature will prove a major challenge for health workers and policymakers attempting to enforce mitigation and control measures.
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; genomics coronavirus; COVID-19 evolution
Online: 3 July 2020 (09:45:43 CEST)
The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 48,635 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyze and annotate all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, the clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may drive local modulation of antiviral strategies based on the molecular specificities of this novel virus.
REVIEW | doi:10.20944/preprints202006.0105.v1
Subject: Keywords: Recycled Wastewater; Irrigation; Sprinkler; Coronavirus; SARS-CoV-2
Online: 7 June 2020 (16:00:25 CEST)
Recycled wastewater is considered as a sustainable source of irrigation water. Despite commendable safety records, viral contamination of agricultural products has occurred the past causing disease outbreaks. This review examines the apprehension that the novel coronavirus (SARS-CoV-2) may also spread through recycled wastewater irrigation (RWI) industry. The novel SARS-CoV-2 is now perceived as an enteric pathogen, and has been found to remain stable in the wastewater for days. Mounting evidences also suggest that viral particles shed by infected individuals through sewage, and greywater is much higher (up to 10 Log10) than the amount typically removed (6-7 Log10) through the recycled water disinfection processes. Such gap indicated an increased risk of infection through fecal-oral transmission route. This study also identified greywater irrigation schemes posing a higher risk of transmission of SARS-CoV-2. It was recommended that countries putting greywater in the ‘low risk’ category may rewrite the safety guidelines in post COVID-19 times. This review also suggest that the choice of irrigation method could be critical in protecting the farmers, and the consumers from possible infections during the pandemic. In this regard, irrigation methods (i.e. sprinkler) that generate airborne droplet (leading to aerosols) may be operated with caution when public spaces are in the vicinity. The study also indicated that the developing countries should regulate surface irrigation practice that pump water from polluted rivers during the pandemic.
ARTICLE | doi:10.20944/preprints202005.0399.v2
Subject: Mathematics & Computer Science, Analysis Keywords: IR; ML; Data Analysis; COVID-19; Coronavirus; Pandemic
Online: 28 May 2020 (03:09:38 CEST)
The world is facing new challenges every day; however, with the spread of the pandemic around the world, this new challenge is different. The pandemic is increasing and concentrating various challenges simultaneously. Although different sectors are facing consequences, the most important sectors, that is, health and economy are the most affected. When the pandemic began, it was not known how long it would last, which complicated health and economic planning. Therefore, it is important for decision makers and the public to know the predictions and expectations of the future of these challenges. In this work, the current situation is analyzed. Then, an expectation model is developed based on the statistics of the pandemic using a growth rate model based on an exponential and logarithmic rate of increase. Based on the available open data about the pandemic spread, the model can successfully predict future expectations, including the duration and maximum number of cases of the pandemic. The model uses the equilibrium point as the day the cases decrease. The model can be used for planning and the development of strategies to overcome these challenges.
ARTICLE | doi:10.20944/preprints202005.0442.v1
Subject: Medicine & Pharmacology, Dentistry Keywords: COVID-19; knowledge; awareness; perceptions; Indian dentists; coronavirus
Online: 27 May 2020 (07:56:19 CEST)
Introduction: COVID-19 is an unprecedented global public health emergency currently impacting India in an unprecedented manner. Aim of this study was to assess knowledge, awareness, perceptions and related factors of Indian dentists on COVID-19. Methodology: A cross-sectional, on-line questionnaire-based study was conducted over one week between 3rd May, 2020 to 10th May, 2020. The sample comprised 403 Indian dentists in solo, group practices and in the academic arena. The self-administered questionnaire assessed 1) knowledge/awareness on factors related to COVID-19 patient identification and symptomatology, 2) knowledge/awareness of COVID-19 transmission and 3) perceptions of COVID-19 history taking procedure. Statistical analyses were conducted using Statistical Package for Social Sciences for Windows, version 21.0 (IBM Corp., Armonk, NY., USA). Frequency distributions and logistic regression analyses were used. Results: Indian dentists demonstrated an overall modest level of knowledge on identification of patients with COVID-19. Moreover, they had a high level of awareness of the COVID-19 transmission means, and the generally accepted procedural perceptions on patient history taking. However, there were some gaps in specific aspects of knowledge and perceptions. Those who were aged ≥ 30-years had a significantly higher level of knowledge of patient identification means than those who were < 30-years (OR=1.78:1.12-2.83); p=0.01. Moreover, specialized dentists were significantly knowledgeable of COVID-19 transmission means than the general dentists (OR=1.89:1.22-2.93; p=0.004). Conclusions: Our findings demonstrate identifiable gaps in knowledge/awareness and perceptions of COVID-19 in Indian dental professionals. These gaps should be fulfilled, at the earliest, due to the rising burden of COVID-19 in India, to ensure safe dental care delivery.
ARTICLE | doi:10.20944/preprints202005.0219.v1
Subject: Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; pandemic spreading
Online: 13 May 2020 (03:40:22 CEST)
The Gauss model for the time evolution of the first corona pandemic wave rendered useful in the estimation of peak times, amount of required equipment, and the forecasting of fade out times. At the same time it is probably the simplest analytically tractable model that allows to quantitatively forecast the time evolution of infections and fatalities during a pandemic wave. In light of the various descriptors such as doubling times and reproduction factors currently in use to judge about lock-downs and other measures that aim to prevent spreading of the virus, we hereby provide both exact, and simple approximate relationships between the two relevant parameters of the Gauss model (peak time and width), and the transient behavior of two versions of doubling times, and three variants of reproduction factors including basic reproduction numbers.
ARTICLE | doi:10.20944/preprints202005.0171.v2
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: COVID-19; coronavirus; case-based reasoning; ontology; natural language processing
Online: 15 June 2020 (11:16:23 CEST)
Coronavirus, also known as COVID-19, has been declared a pandemic by the World Health Organization (WHO). At the time of conducting this study, it had recorded over 1.6 million cases while more than 105,000 have died due to it, with these figures rising on a daily basis across the globe. The burden of this highly contagious respiratory disease is that it presents itself in both symptomatic and asymptomatic patterns in those already infected, thereby leading to an exponential rise in the number of contractions of the disease and fatalities. It is therefore crucial to expedite the process of early detection and diagnosis of the disease across the world. The case-based reasoning (CBR) model is an effective paradigm that allows for the utilization of cases’ specific knowledge previously experienced, concrete problem situations or specific patient cases for solving new cases. This study therefore aims to leverage the very rich database of cases of COVID-19 to solve new cases. The approach adopted in this study employs the use of an improved CBR model for state-of-the-art reasoning task in classification of suspected cases of Covid19. The CBR model leverages on a novel feature selection and semantic-based mathematical model proposed in this study for case similarity computation. An initial population of the archive was achieved with 68 cases obtained from the Italian Society of Medical and Interventional Radiology (SIRM) repository. Results obtained revealed that the proposed approach in this study successfully classified suspected cases into their categories at an accuracy of 97.10%. The study found that the proposed model can support physicians to easily diagnose suspected cases of Covid19 base on their medical records without subjecting the specimen to laboratory test. As a result, there will be a global minimization of contagion rate occasioned by slow testing and as well reduce false positive rates of diagnosed cases as observed in some parts of the globe.
COMMUNICATION | doi:10.20944/preprints202005.0138.v1
Subject: Life Sciences, Virology Keywords: covid-19; epidemiology; epidemiological week; Brazil; coronavirus; viruses
Online: 8 May 2020 (08:08:40 CEST)
Amid the covid-19 pandemic, other diseases, including viruses, are still acting to the detriment of their seasonality and risk factors for contagion. For this reason, it is interesting to know the degree of impact of other viruses, mainly respiratory, in which they have similar symptoms, in diagnoses for contamination by the new coronavirus based on epidemiological surveys, via epidemiological weeks, in Brazil. To what extent there may be a hypothesis of confusion of contaminated data, harming the health system, with regard to the need for intensive care units and control of viruses, and negatively or positively implying in the control or uncontrolling of viruses in general.
ARTICLE | doi:10.20944/preprints202004.0466.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; coronavirus; ACE2; bioinformatics analysis; drug prediction
Online: 26 April 2020 (03:14:50 CEST)
Recently, the outbreak of coronavirus disease 2019 (COVID-19) is threatening human health globally. There is a dire need to find potential therapeutic agents. Angiotensin converting enzyme 2 (ACE2), as an entry receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is considered as potential therapeutic target in COVID-19 pandemic. Here, our bioinformatics analysis revealed that the biological function of ACE2 was correlated with regulation of blood pressure and mediation of SARS-CoV-2 entry into host cells. Ten ACE2 cooperative proteins were identified by using STRING with a high score. ACE2 expressed highly in the small intestine, testis, and kidney. The level of ACE2 expression in tumor tissues varies in different types of cancers compared with that in normal tissues. It was worth noting that the expression level of ACE2 in the tumor has no effect on patient survival. MiRNA hsa-miR-942-5p, and three transcription factors (TFs) including Signal transducer and activator of transcription 4 (STAT4), Estrogen related receptor α (ESRRA), and Signal transducer and activator of transcription 3 (STAT3) were selected as novel ACE2 regulators. Moreover, nine potential therapeutic drugs were predicted by two online databases. Thus, our research may expand the overall view of ACE2 in COVID-19 treatment.
REVIEW | doi:10.20944/preprints202004.0453.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: neurology; clinical features; coronavirus; stroke; encephalitis; headache; delirium
Online: 25 April 2020 (02:36:21 CEST)
The Coronavirus disease due to SARS-CoV-2 emerged in Wuhan city, China in December 2019 and rapidly spread more than 200 countries as a global health pandemic. There are more 3 million confirmed cases and around 207,000 fatalities. The primary manifestation is respiratory and cardiac but neurological manifestations are being reported in the literature as case reports and case series. The most common reported symptoms to include headache and dizziness followed by encephalopathy and delirium. Among the complications noted are Cerebrovascular accident, Guillian barre syndrome, acute transverse myelitis, and acute encephalitis. The most common peripheral manifestation was hyposmia. It is further noted that sometimes the neurological manifestations can precede the typical features like fever and cough and later on typical manifestations develop in these patients. Hence a high index of suspicion is required for timely diagnosis and isolation of cases to prevent the spread in neurology wards. We present a narrative review of the neurological manifestations and complications of COVID-19. Our aim is to update the neurologists and physicians working with suspected cases of COVID-19 about the possible neurological presentations and the probable neurological complications resulting from this novel virus infection.
CONCEPT PAPER | doi:10.20944/preprints202004.0412.v1
Subject: Life Sciences, Microbiology Keywords: coronavirus; COVID-19; antisense oligonucleotide; ASO; LNA GapmeR
Online: 23 April 2020 (11:30:39 CEST)
The severity of the global COVID-19 pandemic, with a high transmission rate, 2.6-4.7% lethality and a huge economic impact, poses an urgent need for efficient medical treatments and vaccines. Currently, there are only non-specific treatments to assist the patients in acute respiratory distress during the inflammatory step following the preliminary infection by SARS-CoV-2. Clinical trials of drug repurposing were quickly launched at the international level. Specific treatments such as the transfusion of plasma from patients who have recovered into infected patients or the use of specific inhibitors of the viral RNA-polymerase complex are promising strategies to block infection. To complete the therapeutic arsenal, we believe that the opportunity of targeting the SARS-CoV-2 genome by RNA therapy should be deeply investigated. In the present paper, we propose to design specific antisense oligonucleotides targeting transcripts encoding viral proteins associated to replication and transcription of SARS-CoV-2, aiming to block infection. We designed antisense oligonucleotides targeting the genomic 5’ untranslated region (5’-UTR), open reading frames 1a and 1b (ORF1a and ORF1b) governing expression of the replicase/transcriptase complex, and the gene N encoding the nucleoprotein that is genome-associated. To maximize the probability of efficiency, we predicted the antisense oligonucleotides by using two design methods: i) conventional antisense oligonucleotides with 100% phosphorothioate modifications (ASO); ii) antisense locked nucleic acids GapmeR. After binding the viral RNA target, the hetero-duplexes antisense oligonucleotide-RNA are cleaved by RNAse H1. Nine potent ASO candidates were found and we selected five of them targeting ORF1a (3), ORF1b (1) and N (1). Nine GapmeR candidates were predicted with excellent properties and we retained four of them targeting 5’-UTR (1), ORF1a (3), ORF1b (1) and N (1). The most potent GapmeR candidate targets the 5’-UTR, a key genomic domain with multiple functions in the viral cycle. By this open publication, we are pleased to share these in silico results with the scientific community in hopes of stimulating innovation in translational research in order to fight the unprecedented COVID-19 pandemic. These antisense oligonucleotide candidates should be now experimentally evaluated.
REVIEW | doi:10.20944/preprints202004.0395.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: coronavirus disease 2019; chloroquine; drug repurposing; HIV; Africa
Online: 22 April 2020 (08:33:34 CEST)
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2, has been declared by the World Health Organization (WHO) as a pandemic. Unfortunately, finding a vaccine or developing drugs from the scratch is a time-consuming luxury given the widespread and high fatality rates of the virus. In the short term, repurposing of drugs already in use seem to be the most rational step to quickly and effectively curb the virus. Several antiviral agents had been proposed as possible remedies, but the 4-aminoquinolines, Chloroquine (CHQ) and hydroxychloroquine (HCHQ) appear to be generating more interest. They are generic, cheaply available and have proven efficacy against malaria parasites in Africa. The human immunodeficiency virus (HIV), on the other hand, targets the immune system thereby reducing the patient’s ability to fight infections. Sadly, 68% of the global HIV burden occur in Africa. It is therefore anticipated that incidence of severe forms of COVID-19 could occur in Africa because of associated endemic conditions that compromise the immune system. With CHQ and HCHQ being considered for clinical use against COVID-19, there is a need to highlight their potential merits and confounding variables in the subgroup of patients with or without HIV.
COMMUNICATION | doi:10.20944/preprints202004.0379.v1
Subject: Keywords: coronavirus; statistical analysis; extrapolation; parameter estimation; pandemic spreading
Online: 21 April 2020 (08:14:23 CEST)
The Gauss model for the time evolution of the first corona pandemic wave allows to draw conclusions on the dark number of infections, the amount of heard immunization, the used maximum capacity of breathing apparati and the effectiveness of various non-pharmaceutical interventions in different countries. In Germany, Switzerland and Sweden the dark numbers are 7.4 +/- 6.1, 11.1 +/- 8.5 and 25 +/- 25, respectively. Our method of estimating dark numbers from modeling both, infection and death rates simultaneously spares these countries the laborious, time-consuming and costly medical testing for antibodies of large portions of the population. In Germany the total number of infected persons, including the dark number of infections by the first wave is estimated to be 1.06 +/- 0.60 million, corresponding to 1.28 +/- 0.72 percent of the German population. We work out direct implications from these predictions for managing the 2nd and further corona waves.
REVIEW | doi:10.20944/preprints202004.0283.v1
Subject: Medicine & Pharmacology, Other Keywords: Covid-19; coronavirus; SARS-CoV-2; review; pandemic
Online: 16 April 2020 (15:55:12 CEST)
Coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. The current classification of coronaviruses recognizes 39 species in 27 subgenera that belong to the family Coronaviridae. From those, at least seven coronaviruses are known to cause respiratory infections in humans. Four of these viruses can cause common cold-like symptoms, while others that infect animals can evolve and become infectious to humans. Three recent examples of this viral jumps include SARS CoV, MERS-CoV and SARS CoV-2 virus. They are responsible for causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the most recently discovered coronavirus disease during 2019 (COVID-19).COVID-19, a respiratory disease caused by the SARS-CoV-2 virus, was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. The rapid spread of the disease has taken the scientific and medical community by surprise. Latest figures from 14 April 2020 show more than 2 million people had been infected with the virus, causing more than 120,000 deaths in over 210 countries worldwide. The large amount of information we receive every day concerning this new disease is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. In order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the SARS CoV-2 Virus and the Coronavirus Diseases 2019 (COVID-19).
HYPOTHESIS | doi:10.20944/preprints202003.0435.v1
Subject: Medicine & Pharmacology, Other Keywords: coronavirus; fevers; pneumonia; nutrients; sauna baths; physical exercise
Online: 29 March 2020 (11:25:23 CEST)
The recent outbreak and spread of the COVID-19 virus infection across the world has seen a massive global system-wide shutdown of human social and economic activity. Both developed and developing nations have been forced to contain and isolate their citizens as much as possible. However, the continuous rising cases in both categories of nations, especially those with poor or nonexistent testing facilities and healthcare systems pose a hidden danger. The seemingly lack of and access to a truly global concerted research effort in both temporary but effective symptom mitigation may lead to more deaths in infected cases. We propose that a fusion of both technological and home-grown solutions can be utilized effectively to manage symptoms. This would add to the preventive methods of social distancing, isolation, quarantine and frequent handwashing to halt the impact of the disease. We also hope to spur further research in such drug/non-drug combination therapy-based methods with emphasis on effectiveness based on quality of nutrient sources.
HYPOTHESIS | doi:10.20944/preprints202003.0415.v1
Subject: Keywords: coronavirus; self-defense mechanisms of the human body
Online: 29 March 2020 (03:12:09 CEST)
Social distancing, washing hands and good hygiene are essential and currently the most potent methods available to curb down the unprecedented speed by which the new coronavirus is spreading across the globe. Even under lockdown, which is necessary to significantly reduce the number of people that get infected by an ill person, are there additional measures that each of us can embrace to even further reduce the risk of infection and the severity of the COVID-19 disease? Given the lack of licensed drugs that target SARS-CoV-2 specifically, we have to look into additional non-specific defense mechanisms that animals and humans evolved to protect themselves from pathogen invasions. The goal of this article is to describe how various of our non-specific defense mechanisms work, which actually precede the inflammatory response, and to discuss whether we can exploit the unique features of the coronavirus envelope and the self-cleaning machinery of the human respiratory tract to strengthen our self-defense. The challenge is to actively interfere with supportive measures during the short time window between getting exposed and before an inflammatory response gets initiated.
ARTICLE | doi:10.20944/preprints202003.0291.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: co-infection; coronavirus disease 2019; COVID-19; influenza
Online: 19 March 2020 (02:00:47 CET)
Background: On late December 2019, a viral pneumonia known as coronavirus disease 2019 (COVID-19), was originated from China and spread very rapidly in the world. Therefore, COVID-19 became a global concern and health problem. Methods: We presented four patients in this study. They were selected from patients who presented with pneumonia symptoms and were suspicious for COVID-19 and referred to the intended centers for COVID-19 diagnosis and management of Shiraz University of Medical Sciences in the south of Iran. Two nasopharyngeal and oropharyngeal throat swab samples were collected from each patient and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse-transcriptase–polymerase-chain-reaction (RT-PCR), and also samples were sent for influenza viruses and all the respiratory panel. Results: In the present report, four patients were diagnosed in the starting days of COVID-19 disease in our center in south of Iran with co-infection of SARS-CoV-2 and influenza virus. Conclusions: This co-infection of COVID-19 and influenza highlights the importance of considering SARS-CoV-2 PCR assay regardless of other positive findings for other pathogens in the primary test during the epidemic.
Subject: Keywords: novel coronavirus infection; renal transplant; acute kidney injury
Online: 12 March 2020 (03:02:03 CET)
Novel coronavirus infection is a recent infective agent that causes severe potentially fatal pneumonia. The clinical presentation includes asymptomatic infection, severe pneumonia, and acute respiratory failure. Data pertaining to the clinical presentation of solid organ transplant recipients are scarce. Two cases of novel coronavirus infection in two recipients of renal transplant with variable clinical presentations and outcomes are reported. The first patient presented with progressive respiratory symptoms, acute renal failure, and passed away, whereas the second one, although presented with respiratory tract symptoms and hypoxemia remained stable and exhibited an excellent clinical recovery despite recent reception of thymoglobulin induction. This paper reports rare cases of novel coronavirus infection in renal transplant recipients. For an enhanced insight of the novel coronavirus infection and acute kidney injury on the clinical presentation, severity, and outcome in solid organ transplant recipients, further investigations are required.
ARTICLE | doi:10.20944/preprints202002.0220.v2
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: coronavirus; COVID-19 pneumonia; pathology; SARS-CoV-2
Online: 2 March 2020 (01:34:58 CET)
There is currently a lack of pathologic data on the novel coronavirus (SARS-CoV-2) pneumonia, or COVID-19, from autopsy or biopsy. Two patients who recently underwent lung lobectomies for adenocarcinoma were retrospectively found to have had COVID-19 at the time of surgery. These two cases thus provide important first opportunities to study the pathology of COVID-19. Pathologic examinations revealed that, apart from the tumors, the lungs of both patients exhibited edema, proteinaceous exudate, focal reactive hyperplasia of pneumocytes with patchy inflammatory cellular infiltration, and multinucleated giant cells. Hyaline membranes were not prominent. Since both patients did not exhibit symptoms of pneumonia at the time of surgery, these changes likely represent an early phase of the lung pathology of COVID-19 pneumonia.
Subject: Medicine & Pharmacology, Allergology Keywords: Coronavirus; SARS-CoV-2; COVID-19; Thalidomide; pneumonia
Online: 26 February 2020 (12:31:47 CET)
A novel coronavirus strain (severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first appeared in December 2019 and can cause acute respiratory distress syndrome and death. However, there are only limited therapy choices and no vaccine for SARS-CoV-2 is currently available. Here we report about a case of a SARS-CoV-2 caused pneumonia successfully treated with thalidomide. Thalidomide is an immunomodulatory and anti-inflammatory agent and was combined with a low-dose glucocorticoid. We suggest, that the effects of thalidomide might be related to regulating immunity, inhibiting the inflammatory cytokine surge, alleviating anxiety to reduce oxygen consumption, relieving vomit and lung exudation.
ARTICLE | doi:10.20944/preprints202002.0385.v1
Subject: Life Sciences, Virology Keywords: Coronavirus; SARS-CoV-2; enrichment; next-generation sequencing
Online: 26 February 2020 (02:27:21 CET)
SARS-CoV-2 is a novel betacoronavirus and the aetiological agent of the current COVID-19 outbreak that originated in Hubei Province, China. While polymerase chain reaction is the front-line tool for SARS-CoV-2 surveillance, application of amplification-free and culture-free methods for isolation of SARS-CoV-2 RNA, partnered with next-generation sequencing, would provide a useful tool for both surveillance and research of SARS-CoV-2. We here release into the public domain a set of bait capture hybridization probe sequences for enrichment of SARS-CoV-2 RNA from complex biological samples. These probe sequences have been designed using rigorous bioinformatics methods to provide sensitivity, accuracy, and minimal off-target hybridization. Probe design was based on existing, validated approaches for detecting antimicrobial resistance genes in complex samples and it is our hope that this SARS-CoV-2 bait capture platform, once validated by those with samples in hand, will be of aid in combating the current outbreak.
REVIEW | doi:10.20944/preprints202003.0343.v1
Subject: Medicine & Pharmacology, Other Keywords: coronavirus; 2019-nCoV; SARS-CoV-2; animal coronaviruses; COVID-19; bat coronavirus; zoonoses; epidemiology; transmission; diagnosis; antivirals; prevention and control
Online: 23 March 2020 (07:19:35 CET)
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.