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Preprint ARTICLE | doi:10.20944/preprints202003.0455.v1

Eucalyptol (1,8 cineole) from Eucalyptus Essential Oil a Potential Inhibitor of COVID 19 Corona Virus Infection by Molecular Docking Studies

Arun Dev Sharma, inderjeet kaur

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; Essential oil; Eucalyptol; Molecular docking

Online: 31 March 2020 (10:16:13 CEST)

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Working Paper CASE REPORT

First Case of COVID-19 Complicated with Fulminant Myocarditis: A case Report and Insights

Jia Hui Zeng, Ying-Xia Liu, Jing Yuan, Fu-Xiang Wang, Wei-Bo Wu, Jin-Xiu Li, Li-Fei Wang, Hong Gao, Yao Wang, Chang-Feng Dong, Yi-Jun Li, Xiao-Juan Xie, Cheng Feng, Lei Liu

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; coronavirus; fulminant myocarditis; infection; echocardiography.

Online: 7 April 2020 (01:03:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202003.0346.v1

The Molecular Story of COVID-19; NAD⁺Depletion Addresses All Questions in this Infection

Shirin Kouhpayeh, Laleh Shariati, Maryam Boshtam, Ilnaz Rahimmanesh, Mina Mirian, Mehrdad Zeinalian, Azhar Salari-jazi, Negar Khanahmad, Mohammad Sadegh Damavandi, Parisa Sadeghi, Hossein Khanahmad

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; nCoV 19; oxidative stress; PARP; PARG; TRPM2

Online: 23 March 2020 (07:40:50 CET)

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Preprint REVIEW | doi:10.20944/preprints202007.0613.v3

Review of Infective Dose, Routes of Transmission, and Outcome of COVID-19 Caused by the SARS-CoV-2 Virus: Comparison with Other Respiratory Viruses

Sedighe Karimzadeh, Raj Bhopal, Huy Nguyen Tien

Subject: Biology And Life Sciences, Virology Keywords: infective dose; SARS-CoV-2; COVID-19; respiratory viruses; viral load; viral dynamics

Online: 7 December 2020 (11:36:05 CET)

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Preprint REVIEW | doi:10.20944/preprints202002.0283.v1

Emerging Understanding of Etiology and Epidemiology of the Novel Coronavirus (COVID-19) infection in Wuhan, China

Daibing Zhou, Peng Zhang, Chen Bao, Youzhi Zhang, Ning Zhu

Subject: Biology And Life Sciences, Virology Keywords: Etiology; Epidemiology; COVID-19; Wuhan

Online: 19 February 2020 (11:58:13 CET)

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Working Paper SHORT NOTE

Understanding the Origin of ‘BatCoVRaTG13’, a Virus Closest to SARS-CoV-2

Monali C. Rahalkar, Rahul A. Bahulikar

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RATG13; BtCoV/4991; SARS-like (SL-) corona virus; pneumonia

Online: 24 May 2020 (20:02:22 CEST)

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Genomic analysis indicates that SARS-CoV-2 is most related to RaTG13, a beta corona virus derived from bats by 96% ¹. At present, RaTG13 is only available on the public database in the form of a genome sequence. The genome of RaTG13 (MN996532.1) was sequenced from the RNA of a bat faecal swab collected in 2013 from Yunnan, China, however the exact location is not mentioned. Since RaTG13 is one of the main supports for SARS-CoV-2 to have a natural origin, it is of utmost importance to understand the sample location. RNA dependent RNA polymerase (RdRp) sequence of RaTG13 shows that it is 100% similar to that of bat corona virus BtCoV/4991 and 98.7-98.9% similar to SARS-CoV-2 RdRp ². BtCoV/4991 was described to be a SARS-like (SL-) corona virus from bat faeces sampled in an abandoned mine from Mojiang ². Both the publications ^1,2 are authored by Dr. Zheng-li Shi (Z-L Shi), who is described as the bat woman of China ³. However, BtCoV/4991 has not been mentioned by Zhou et al 2020 ¹ where novel corona virus was first described. Based on the RdRp sequence similarities, similarities in sample collection dates, sample locations, and the fact that RaTG13 is mentioned synonymous to BtCoV/4991 on the Chinese bat database, it is predicted that RaTG13 and BtCoV/4991 originate from the same sample. The sample, bat faecal swab was collected in 2013 from an abandoned mineshaft in Mojiang by Dr. Shi and her work group. In 2012, in a Mojiang mineshaft, six mine workers suffered from atypical pneumonia and three of them died. These workers were engaged in the work of clearing debris from a mineshaft which had a lot of bats and bat faeces ³^,4. A detailed health investigation indicated that the miners suffered from atypical pneumonia mostly of the viral origin ⁴. Therefore, in the light of the present Covid-19 caused by SARS-CoV-2, the fact that its phylogenetic neighbour RaTG13 originated from bat faeces collected from a mineshaft, which was also the origin of pneumonia-like disease in miners in 2012, should be noted.

Preprint REVIEW | doi:10.20944/preprints202003.0197.v3

2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission

Leslie Dietz, Patrick F. Horve, David Coil, Mark Fretz, Jonathan Eisen, Kevin Van Den Wymelenberg

Subject: Biology And Life Sciences, Virology Keywords: Built Environment (BE); building operations; novel coronavirus; COVID-19; SARS-CoV-2

Online: 2 April 2020 (05:19:41 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0138.v1

Medical Countermeasures Analysis of 2019-nCoV and Vaccine Risks for Antibody-Dependent Enhancement (ADE)

Darrell O. Ricke, Robert W. Malone

Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; SARS-CoV-2; COVID-19; ADE; antibody depedendent enhancement

Online: 8 March 2020 (15:35:27 CET)

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Background: In 80% of patients, COVID-19 presents as mild disease^1,2. 20% of cases develop severe (13%) or critical (6%) illness. More severe forms of COVID-19 present as clinical severe acute respiratory syndrome, but include a T-predominant lymphopenia³, high circulating levels of proinflammatory cytokines and chemokines, accumulation of neutrophils and macrophages in lungs, and immune dysregulation including immunosuppression⁴. Methods: All major SARS-CoV-2 proteins were characterized using an amino acid residue variation analysis method. Results predict that most SARS-CoV-2 proteins are evolutionary constrained, with the exception of the spike (S) protein extended outer surface. Results were interpreted based on known SARS-like coronavirus virology and pathophysiology, with a focus on medical countermeasure development implications. Findings: Non-neutralizing antibodies to variable S domains may enable an alternative infection pathway via Fc receptor-mediated uptake. This may be a gating event for the immune response dysregulation observed in more severe COVID-19 disease. Prior studies involving vaccine candidates for FCoV^5,6 SARS-CoV-1^7-10 and Middle East Respiratory Syndrome coronavirus (MERS-CoV) ¹¹ demonstrate vaccination-induced antibody-dependent enhancement of disease (ADE), including infection of phagocytic antigen presenting cells (APC). T effector cells are believed to play an important role in controlling coronavirus infection; pan-T depletion is present in severe COVID-19 disease³ and may be accelerated by APC infection. Sequence and structural conservation of S motifs suggests that SARS and MERS vaccine ADE risks may foreshadow SARS-CoV-2 S-based vaccine risks. Autophagy inhibitors may reduce APC infection and T-cell depletion¹² ¹³. Amino acid residue variation analysis identifies multiple constrained domains suitable as T cell vaccine targets. Evolutionary constraints on proven antiviral drug targets present in SARS-CoV-1 and SARS-CoV-2 may reduce risk of developing antiviral drug escape mutants. Interpretation: Safety testing of COVID-19 S protein-based B cell vaccines in animal models is strongly encouraged prior to clinical trials to reduce risk of ADE upon virus exposure.

Preprint ARTICLE | doi:10.20944/preprints202003.0308.v1

Potential Pathogenesis of Multiple Organ Injury in COVID-19

Ling Guo, Kuipeng Yu, Dengren Li, Huimin Yang, Lei Liu, Jiahui Fan, Nan Sun, Xiangdong Yang

Subject: Biology And Life Sciences, Virology Keywords: AGTR2; ACE2; COVID-19

Online: 20 March 2020 (07:01:44 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202003.0295.v1

DNA Methylation Analysis of the COVID-19 Host Cell Receptor, Angiotensin I Converting Enzyme 2 Gene (ACE2) in the Respiratory System Reveal Age and Gender Differences

Michael J. Corley, Lishomwa C. Ndhlovu

Subject: Biology And Life Sciences, Virology Keywords: Wuhan 2019-nCoV; ACE2; DNA methylation; epigenetics; profiling; lung tissue; age; gender; COVID-19; coronavirus

Online: 19 March 2020 (02:51:45 CET)

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Preprint REVIEW | doi:10.20944/preprints202004.0341.v1

Myths and Facts: Chloroquine May Be A Potential Supportive/Therapeutic Drug in COVID-19 Treatment

Muhammad Kashif, Muhammad Aamir, Sadia Minhas, Romeeza Tahir, Shah Jahan, Nadeem Afzal

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; Outbreak; nCoV-19; Quinine; Chloroquine; Hydroxychloroquine

Online: 19 April 2020 (08:36:55 CEST)

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Preprint ESSAY | doi:10.20944/preprints202004.0484.v1

CoVID-19: Where We Are, What We Should Do and What We Should Learn

Jörg Eppinger, Magnus Rueping

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; CoVID-19; pandemic control; research policy

Online: 28 April 2020 (07:50:12 CEST)

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There were warnings before; nevertheless the current CoVID-19 pandemic took the world by surprise: within just four month, it conquered the globe and claimed over 200'000 lives. Unprecedented governmental actions put about half of the population under curfew or lock-down. The resulting economic meltdown is expected to eliminate globally 9’000’000’000’000 (9 trillion) USD in 2020 and 2021 alone, a value roughly the size of the yearly GDP of the world’s 150 smallest economies. The resulting crises might cause mass-unemployment and a hunger pandemic later this year. This Essay analyses current statistical data of the CoVID-19 pandemic to develop a guideline for a path through the crisis, minimizing both loss of lives and economic costs. Part 1 details the current situation; part 2 develops a small set of measures, allowing a near normal life until a future vaccination campaign has reached sufficient numbers of people; and part 3 provides some important lessons for the future beyond SARS-CoV-2. The Essay leads to the following key-messages: 1) The CoVID-19 pandemic will stay for at least two more years. This is the minimum time required for a vaccination campaign to reach sufficient numbers of people. 2) The crucial element to control the pandemic is keeping case numbers under the threshold required for a functional tracing, testing & isolation (TTI) strategy. That threshold differs from country to country and strongly depends on culture and the applied tracing technology as well as available testing capacities. 3) The economic burden of a TTI strategy is moderate while fatalities are also reduced. Hence, such an approach is strongly recommended. Its implementation requires a set of simple and cost-effective measures (see figure below), which in combination seem to be sufficient to keep CoVID-2’s reproductive rate at or below 1. 4) Implementing international coordination of actions will be necessary for effective infection-chain tracing5) If case numbers are above the TTI threshold, shutdown measures remain the only option until tracing of infection chains becomes feasible again.6) In the future, neglected pandemic-related research requires a funding boost. Just 1% of the bill of the current crisis could support the research of 45’000 scientist for 20 years.

Preprint HYPOTHESIS | doi:10.20944/preprints202003.0392.v1

In silico Comparative Genomics of the Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) and Designing of a Cost-effective RFLP-PCR Based Mass Screening Diagnostic Protocol

Aditya Singh, Prateek Bhatia

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; diagnosis; comparative genomics

Online: 26 March 2020 (14:58:35 CET)

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SARS-CoV 2 also known as COVID-19 is a fast spreading coronavirus related disease that emerged from China in December 2019 and is currently attained the status of a pandemic. There are currently no drugs/ vaccines against the same and moreover limited diagnostic tests to identify the infection. Additionally, these tests are expensive and hence are exclusive for very highly suspected cases of the disease especially in developing countries. This is causing an under-diagnosis which is an alarming state of affairs, as even a single missed SARS-CoV 2 case would spread the disease exponentially and keep it in the community. Through this entirely in silico study, we have developed a cheaper and faster diagnostic method based on simple PCR and restriction enzyme digestion, commonly used in restriction fragment length polymorphism (RFLP) tests. Through comparative genomics, we found the closest neighbours of SARS-CoV 2 then found the highly conserved regions of the genome which were absent in SARS-CoV 1, its closest neighbour. Then we found restriction sites for various enzymes followed by designing of PCR primers flanking those sites. We have found the primer pair to produce a 401 bp amplicon and when digested by SwaI enzyme, it produces two fragments of lengths 216 bp and 185 bp. As an internal control, GAPDH primers are pooled with the SARS-CoV 2 primers as the patient sample will also include human RNA mixed with the viral RNA. This primer pair gives an amplicon of 131 bp and hence a negative sample should show a single band of 131 bp while a positive digested sample will give three bands of 401 bp, 216 bp and 131 bp. The primers are specific to SARS-CoV 2 only and can additionally be used for SYBR green based real time quantification of viral load. The developed tests have not yet been tested in vitro due to stressed out working hours in the only pathogenic virus handling laboratory in our institute. Nonetheless, this study works as a head start for other laboratories to rapidly test the suggested protocols in vitro and make available a cheaper alternative test for SARS-CoV 2 which would especially be beneficial for the lower to middle income countries.

Preprint ARTICLE | doi:10.20944/preprints202004.0281.v2

Mutation Hot Spots in Spike Protein of SARS-CoV-2 Virus

Feroza Begum, Arup Kumar Banerjee, Upasana Ray

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; S protein; RBD; S1; S2

Online: 7 September 2020 (04:15:59 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202003.0077.v4

The Ongoing COVID-19 Epidemic Curves Indicate Initial Point Spread in China With Log-Normal Distribution of New Cases per Day With a Predictable Last Date of the Outbreak Version 4: Predictions for Selected European Countries, USA and the World as a Whole and Try to Predict the End of the Outbreak Including a Discussion of a Possible “New Normal”

Stefan Olsson, Jing Zhang

Subject: Biology And Life Sciences, Virology Keywords: epidemiology; COVID-19

Online: 19 April 2020 (08:15:10 CEST)

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During an epidemic outbreak it is useful for planners and responsible authorities to be able to plan ahead to estimate when an outbreak of an epidemic is likely to ease and when the last case can be predicted in their area of responsibility. Theoretically this could be done for a point source epidemic using epidemic curve forecasting. The extensive data now coming out of China makes it possible to test if this can be done using MS Excel a standard spreadsheet program available to most offices. The available data is divided up for whole China and the different provinces. This and the high number of cases makes the analysis possible. Data for new confirmed infections for Hubei, Hubei outside Wuhan, China excluding Hubei as well as Zhejiang and Fujian provinces all follow a log-normal distribution that can be used to make a rough estimate for the date of the last new confirmed cases in respective areas. In the version 2 continuation work, 9 additional days were added for the Chinese data to evaluate the previous predictions. The extra data then available from China follows the previous predicted trend supporting the usefulness of this simple technique. In the version 2 we also tested the feasibility for a non-specialist to make similar predictions using additional data from S Korea now available. In this third continuation the predictions for Version 2 are evaluated for S Korea and fits well the beginning of the decline but it seems to be difficult to bring down numbers of cases per day under about 100 new cases per day, potential reasons for this is discussed. To further evaluate when in a prediction becomes reliable the Chinese data was used to evaluate to make predictions for each day around the peak in number of cases and after2-3 consecutive days of decreasing new cases per day the prediction becomes reliable. In version 3 data for Italy just reaching this point was used to make further predictions for that country. A second new analysis was also added to use the fitted equation to detect when the acceleration of new cases per day stopped increasing exponentially. In the Chinese case this measured point coincides with the date of the complete Hubei lockdown and in the new Italian analysis it coincides with the mandatory Italian lockdown. Predicted dates for the end of the Italian outbreak is also added. In version 4 we expand the analysis to selected European countries, USA and the World as a whole and try to predict the end of the outbreak. We further discuss the apparent success of the used techniques that might work to introduce a “new normal” not very different to the previous to stop secondary outbreaks of COVID19 and future COVIDs that are sure to come.

Working Paper ARTICLE

COVID-19 Evolves in Human Hosts

Yanni Liu, Bing Liu, Jiangtao Cui, Zhi Wang, Yulong Shen, Yueshen Xu, Kaicheng Yao, Yuanfang Guan, Xiaoke Ma

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; divergence

Online: 21 July 2020 (13:46:45 CEST)

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Working Paper HYPOTHESIS

Could Unconventional Immunomodulatory Agents Help Alleviate COVID-19 Symptoms and Severity?

Stephen Mamber, Steven Krakowka, Jeffrey Osborn, Lloyd Saberski, Ryan Rhodes, Albert Dahlberg, Kara Fitzgerald, Neal Wright, Sarah Beseme, John McMichael

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2, Immunomodulators

Online: 27 April 2020 (09:55:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201911.0330.v1

Identifying Early-Warning Signals for the Sudden Transition from Mild to Severe Tobacco Rtch Disease by Dynamical Network Biomarkers

Adrián Tarazona, Javier Forment, Santiago F. Elena

Subject: Biology And Life Sciences, Virology Keywords: complex systems; DNB; phase transitions; plant-virus interaction; Potyvirus; protein-protein interaction networks; response to infection; systems biology; Tobacco etch virus

Online: 27 November 2019 (04:42:28 CET)

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Preprint REVIEW | doi:10.20944/preprints202009.0395.v1

V483a – an Emerging Mutation Hotspot of Sars-Cov-2

Omar Ashwaq, Pratibha Manickavasagam, Sk Manirul Haque

Subject: Biology And Life Sciences, Virology Keywords: Spike protein, V483A, substitution mutation, virus-host cell interaction, high transmission, infectivity.

Online: 17 September 2020 (10:43:02 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202003.0184.v2

Serological Test is an Efficient Supplement for Detecting RNA to Confirm SARS-CoV-2 Infection

Ning-Shao Xia, Gui-Qiang Wang, Wen-Feng Gong

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; diagnosis; antibody; serology; screening

Online: 6 April 2020 (14:09:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0386.v1

Accelerated Production of Hesperidin-rich Citrus Pectin from Waste Citrus Peel for Prevention and Therapy of COVID-19

Francesco Meneguzzo, Rosaria Ciriminna, Federica Zabini, Mario Pagliaro

Subject: Biology And Life Sciences, Virology Keywords: hesperidin; COVID-19; pectin; flavonoids; hydrodynamic cavitation; IntegroPectin

Online: 26 March 2020 (13:59:28 CET)

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Preprint SHORT NOTE | doi:10.20944/preprints202006.0225.v1

CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation

Joshua Singer, Robert Gifford, Matthew Cotten, David Robertson

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; web application; virus genome; lineage assignment; amino acids

Online: 18 June 2020 (06:24:20 CEST)

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Working Paper COMMUNICATION

Evidence That Quinine Exhibits Antiviral Activity against SARS-CoV-2 Infection In Vitro

Maximilian Große, Natalia Ruetalo, Ramona Businger, Sascha Rheber, Christian Setz, Pia Rauch, Janina Auth, Ekkehard Brysch, Michael Schindler, Ulrich Schubert

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Quinine; Hydroxy-Chloroquine; Chloroquine; COVID-19; antiviral

Online: 6 July 2020 (09:19:06 CEST)

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Preprint REVIEW | doi:10.20944/preprints202003.0362.v1

Leveraging Open Hardware to Alleviate the Burden of COVID-19 on Global Health Systems

Andre Maia Chagas, Jennifer Molloy, Lucia Prieto Godino, Tom Baden

Subject: Biology And Life Sciences, Virology Keywords: Free and Open Source Hardware; COVID-19; pandemic

Online: 24 March 2020 (14:46:29 CET)

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Working Paper ARTICLE

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Daniele Mercatelli, Federico Manuel Giorgi

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; genomics coronavirus; COVID-19 evolution

Online: 3 July 2020 (09:45:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0440.v1

COVID-19: A Drug Repurposing and Biomarker Identification by Using Comprehensive Gene-Disease Associations through Protein-Protein Interaction Network Analysis

Suresh Kumar

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; 2019-nCoV; novel corona virus; drug repurposing; chloroquine; high-risk group; asymptomatic

Online: 30 March 2020 (07:24:16 CEST)

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COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.

Working Paper ARTICLE

Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?

Martina Bianchi, Domenico Benvenuto, Marta Giovanetti, Silvia Angeletti, Massimo Ciccozzi, Stefano Pascarella

Subject: Biology And Life Sciences, Virology Keywords: Sars-CoV-2; homology modelling; envelope membrane glycoprotein; Bat; Pangolin; Sars-CoV

Online: 9 May 2020 (08:43:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0376.v1

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, René Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria J. Martin, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric Nawrocki, Áine Niamh O'Toole, Nancy Palacios-Ontiveros, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz

Subject: Biology And Life Sciences, Virology Keywords: virus bioinformatics; SARS-CoV-2; sequencing; epidemiology; drug design; tools

Online: 23 May 2020 (11:01:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0010.v1

Identifying Hotspots of Peoples Diagnosed with Tuberculosis and Drug Addiction of Alcohol, Tobacco and other Drugs through a Geospatial Intelligence Application on Communities from Southern Brazil

Alessandro Rolim Scholze, Felipe Mendes Delpino, Luana Seles Alves, Josilene Dália Alves, Thaís Zamboni Berra, Antônio Carlos Vieira Ramos, Miguel Fuentealba-Torres, Inês Fronteira, Ricardo Alexandre Arcêncio

Subject: Biology And Life Sciences, Virology Keywords: Tuberculosis; Alcoholism; Illicit drugs; Tobacco use disorder; Spatial analysis

Online: 4 April 2022 (07:22:45 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0597.v1

An Analysis Review, Detection Coronavirus Disease 2019 (COVID-19) based on Biosensor Application

Bakr Taha, Norhana Arsad, Yousif Al Mashhadany

Subject: Biology And Life Sciences, Virology Keywords: COVID-19 detection; biosensor application; COVID-19 transmission styles; sensors interaction; artificial intelligence

Online: 27 August 2020 (08:01:55 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202004.0006.v1

COVID-19 Pandemic: Can Maintaining Optimal Zinc Balance Enhance Host Resistance?

Mohammed S. Razzaque

Subject: Biology And Life Sciences, Virology Keywords: zinc; antiviral; COVID-19; pandemic; host resistance

Online: 1 April 2020 (09:30:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0710.v1

Evaluation of the Effect of D614G, N501Y and S477N Mutation in SARS-CoV-2 through Computational Approach

Sarmilah Mathavan, Suresh Kumar

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; D614G; N501Y; S477N; mink; VOC 202012/01; B.1.1.7

Online: 28 December 2020 (17:00:23 CET)

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an outbreak of COVID-19 disease in humans with the aid of spike protein. It consists of a receptor-binding domain (RBD) that recognizes and binds to the host receptor angiotensin-converting enzyme 2 (ACE2). The aim of this study was to examine the mutational effect of spike protein on the sequence through an interaction study of the mutant spike protein and the human ACE2 protein at the structural level. A total of 17,227 spike proteins from Asia, Africa, Europe, Oceania, South America, and North America were compared to the Wuhan spike protein reference sequence (Wuhan-Hu-1). The structural and stability implications of D614G, N501Y, and S477N mutations were evaluated. The binding affinity between mutated RBD and human ACE2 protein was also studied. The D614G mutation may have originated in Germany, Europe based on the date of the first sample collection report. It is now widely circulated all over the world with most occurrences in North America. The mutations N501Y and S477N may have originated from Oceania based on the date of the first sample collection report and also have the highest occurrences in Oceania. Based on the computational analysis of mutational effects, the D614G, N501Y, and S477N mutations decreased stability and were tolerated. For disease propensity prediction, N501Y was more prone to disease compared to D614G, while S477N was not prone to disease. The mutation of D to G at position 614 and S to N at position 477 for secondary structure prediction shows no changes in secondary structure while remaining in the coil region, whereas the mutation of N to Y at position 501 changes from coil structure to extended strand. N501Y mutation has a higher affinity to human ACE2 protein compared to D614G and S477N based on a docking study. D614G spike mutation was identified to exist between the two hosts based on a comparison of SARS-CoV-2 derived between the mink and human. Further research is needed on the link between the mink mutation N501T and the mutation N501Y in humans, which has evolved as a separate variant.

Preprint REVIEW | doi:10.20944/preprints202009.0500.v1

A Deep Analysis on the Impact and Statistics of Covid-19 in Kerala, India – A Meta-Analysis Study

Merin Dickson, Anjana Abhilash, Gayathri G Menon, Sapna Chandran

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; impact on society during COVID-19; behavioral impact of COVID-19; government policies against COVID-19; measures adopted by the government; COVID-19 Statistics; Infection rate and Data analysis

Online: 21 September 2020 (11:09:11 CEST)

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Working Paper REVIEW

Marine Red Alga Porphyridium sp. as a Source of Sulfated Polysaccharides (SPs) for Combating Against COVID-19

Vinod Nagle, Mahadev Gaikwad, Yogesh Pawar, Santanu Dasgupta

Subject: Biology And Life Sciences, Virology Keywords: Anti-viral; Carrageenan; Coronavirus; COVID-19; Porphyridium; sulfated polysaccharides (SPs)

Online: 10 April 2020 (07:49:11 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202005.0084.v1

Nsp7 and Spike Glycoprotein of SARS-CoV-2 Are Envisaged as Potential Targets of Vitamin D and Ivermectin

Jhimli Dasgupta, Udayaditya Sen, Abhisek Bakshi, Abhijit Dasgupta, Krishnendu Manna, Chinmay Saha, Rajat K. De, Satinath Mukhopadhyay, Nitai P. Bhattacharyya

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Vitamin D; Ivermectin; RNA-dependent-RNA polymerase; Spike glycoprotein; Knowledge based docking

Online: 5 May 2020 (15:18:30 CEST)

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COVID-19 has emerged as deadly pandemic worldwide with no vaccine or suitable antiviral drugs to prevent or cure the disease. Because of the time-consuming process to develop new vaccines or antiviral agents, there has been a growing interest in repurposing some existing drugs to combat SARS-CoV-2. Vitamin D is known to be protective against acute respiratory distress syndrome (ARDS), pneumonia and cytokine storm. Recently it has been used as a repurposed drug for the treatment of H5N1 virus-induced lung injury. Circumstantial evidences indicate that people with low level of vitamin D are more susceptible to SARS-CoV-2. Although, vitamin D was suggested to interfere with viral replication, its interaction with any SARS-CoV-2 protein is unexplored yet. Beside this, ivermectin, a well-known anti-parasitic agent, exhibits potent anti-viral activities in vitro against viruses such as HIV-1 and dengue. Very recently, ivermectin has been found to reduce viral load of SARS-CoV-2 in vitro. We have analyzed available structures of SARS-CoV-2 proteins to identify probable binding partner(s) of vitamin D and ivermectin through knowledge-based docking studies and figured out possible implication of their binding in SARS-CoV-2 infection. Our observations suggest that the non-structural protein nsp7 possesses a potential site to house 25-hydroxyvitamin D3 (VDY) or the active form of Vitamin D, calcitrol. Binding of vitamin D with nsp7 likely to hamper the formation of nsp7-nsp8 complex which is required to bind with RNA dependent RNA polymerase (RdRP), nsp12 for optimal function. On the other hand, potential binding site of ivermectin has been identified in the S2 subunit of trimeric spike(S) glycoprotein of SARS-CoV-2. We propose that deeply inserted mode of ivermectin binding at three inter-subunit junctions may restrict large scale conformational changes of S2 helices which is necessary for efficient fusion of viral and host membrane. Our study, therefore, opens up avenues for further investigations to consider vitamin D and ivermectin as potential drugs against SARS-CoV-2.

Preprint REVIEW | doi:10.20944/preprints202004.0005.v1

SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions

Mohammed Uddin, Farah Mustafa, Tahir A. Rizvi, Tom Loney, Hanan Al Suwaidi, Ahmad Al Marzouqi, Afaf Kamal Eldin, Nabeel Alsabeeha, Thomas E. Adrian, Cesare Stefanini, Norbert Nowotny, Alawi Alsheikh-Ali, Abiola C. Senok

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Coronavirus; Pandemic; Viral Genomics

Online: 1 April 2020 (09:22:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0091.v1

COVID-19: A Review on Molecular Basis, Pathogenic Mechanisms, Therapeutic Aspects and Future Projections

Muneeb Faiq, Ashutosh Kumar, Himanshu Singh, Vikas Pareek, Rizwana Qadri, Khursheed Raza, Chiman Kumari, Ravi Narayan, Pavan Kumar, Maheswari Kulandhasamy, Sada Pandey

Subject: Biology And Life Sciences, Virology Keywords: Coronavirus; Pneumonia; COVID-19; Virus; Flu; Vaccine; Epidemic; Pandemic

Online: 7 April 2020 (11:15:55 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0024.v1

Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

Takahiko Koyama, Dilhan Weeraratne, Jane L. Snowdon, Laxmi Parida

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-nCoV-2; vaccine; antibody; immune escape; variant; spike protein; genomic drift; convalescent plasma

Online: 3 April 2020 (04:24:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0085.v1

Structural Elucidation of SARS-CoV-2 Vital Proteins: Computational Methods Reveal Potential Drug Candidates Against Main Protease, Nsp12 RNA-dependent RNA Polymerase and Nsp13 Helicase

Muhammad Usman Mirza, Matheus Froeyen

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; CoV-Mpro; CoV-Nsp12 polymerase; CoV-Nsp13 helicase

Online: 5 March 2020 (11:50:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0337.v1

Reporting Two SARS-CoV-2 Strains Based on A Unique Trinucleotide-Bloc Mutation and Their Potential Pathogenic Difference

Mustak Ibn Ayub

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; strains of SARS-CoV-2

Online: 19 April 2020 (07:14:52 CEST)

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SARS-CoV-2, the novel coronavirus behind COVID-19 pandemic is acquiring new mutations in its genome. Although some mutations provide benefits to the virus against human immune response, a number of them may result in their reduced pathogenicity and virulence. By analyzing more than 3000 high-coverage, complete genome sequences deposited in the GISAID database, here I report a unique 28881-28883:GGG>AAC trinucleotide-bloc mutation in the SARS-CoV-2 genome that results in two sub-strains, described here as SARS-CoV-2g (28881-28883:GGG genotype) and SARS-CoV-2a (28881-28883:AAC genotype). Computational analysis and literature review suggest that this bloc mutation would bring 203-204:RG(arginine-glycine)>KR(lysine-arginine) amino acid changes in the nucleocapsid (N) protein affecting the SR (serine-arginine)-rich motif of the protein, a critical region for the transcription of viral RNA and replication of the virus. Thus, 28881-28883:GGG>AAC bloc-mutation is expected to modulate the pathogenicity of the SARS-CoV-2. Remarkably, SARS-CoV-2g and SARS-CoV-2a strains can be linked with the heterogeneity of COVID-19 cases across different regions within and between countries by analyzing existing data. Sequence analysis suggests that severely affected cities, such as Milan, Lombardy, New York, Paris have the predominant presence of SARS-CoV-2g strains, whereas less affected places like Abruzzo, Lyon, Valencia have a relatively higher presence of SARS-CoV-2a, an indication that the latter strain may contribute to the reduced cases of COVID-19. A similar relationship is observed when Netherlands, Portugal are compared with Spain, France and Germany. These analyses suggest that the SARS-CoV-2 has already evolved into a less infective SARS-CoV-2a affecting COVID-19 cases in different regions. The time a country or region needs to acquire SARS-CoV-2a strains may be indicative to the time it would need to overcome the peak of the COVID-19 cases. To confirm these assumptions, prompt retrospective and prospective epidemiological studies should be conducted in different countries to understand the course of pathogenicity of the SARS-CoV-2a and SARS-CoV-2g. Potential drugs can be designed targeting 28881-28883 region of the N protein to modulate virus pathogenicity.

Preprint REVIEW | doi:10.20944/preprints202004.0040.v3

COVID-19 Virus Infection and Transmission are Observably Less in Highly Dengue-endemic Countries: Can Dengue Vaccines be “Repurposed” to Prevent COVID-19?

Subhajit Biswas, Soumi Sukla

Subject: Biology And Life Sciences, Virology Keywords: Dengue; COVID-19; SARS-CoV-2; epidemiology; infection; mortality; cross-protection; Dengue vaccine; ELISA; Dengvaxia

Online: 5 May 2020 (03:00:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0327.v1

Transmission of SARS-CoV-2 in Northern Ghana; Insights from Whole Genome Sequencing

Augustina Angelina Sylverken, Philip El-Duah, Michael Owusu, Julia Schneider, Richmond Yeboah, Ayisi-Boateng Ayisi-Boateng, Richmond Gorman, Eric Adu, Alexander Kwarteng, Michael Frimpong, Sherihane Aryeetey, Jesse Addo Asamoah, Yaw Ampem Amoako, John Humphrey Amuasi, Jörn Beheim-Schwarzbach, Ellis Owusu-Dabo, Yaw Adu-Sarkodie, Kwasi Obiri-Danso, Victor Max Corman, Christian Drosten, Richard Phillips

Subject: Biology And Life Sciences, Virology Keywords: Ghana; SARS-CoV-2; transmission; Phylogenetics

Online: 15 September 2020 (04:24:17 CEST)

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In regions lacking genomic data, analysis of sequences from the early stages of an outbreak can provide important insights into the diversity of pathogens present. Following the detection of the first imported case of COVID-19 in the Northern sector of Ghana on 13^th March 2020, we have now molecularly characterized and phylogenetically analysed sequences including three (3) complete genomes of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) isolated from nine (9) patients observed in Ghana. Eight (8) of these patients reported with a recent history of foreign travel and one (1) with no history of foreign travel. We performed high throughput sequencing for 9 samples following the determination of high concentration of viral RNA. In addition, we estimated the potential impact that long distance transportation of samples to testing centres may have on sequencing outcomes. Here, two samples that were closest in terms of viral RNA concentration but transported from sites which are over 400km apart were assessed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Complete genomes were obtained for three (3) sequences and with another near complete genome with a coverage of 95.6%. Sequences with coverage in excess of 80% were found to belong to three lineages namely A, B.1 and B.2. Our sequences clustered in two different clades with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23 which was collected 9km compared with sample TTH6 which was collected and transported over a distance of 400km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be the need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.

Preprint ARTICLE | doi:10.20944/preprints202005.0413.v1

Characterization of Nucleocapsid (N) Protein from Novel Coronavirus SARS-CoV-2

Abhishek Kumar, Alisha Parveen, Narendra Kumar, Sneha Bairy, Vibha Kaushik, Chetan Chandola, Jyoti Sharma, Phulwanti Sharma, Akhil Agarwal, Akhilesh Pandey, Pankaj Goyal, Muniasamy Neerathilingam

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; nucleocapsid (N); genomics; coronavirus; Wuhan; Pandemic

Online: 25 May 2020 (17:45:40 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints202004.0384.v1

Tackling the Pandemic COVID-19: The Bangladesh Perspective

Md. Taimur Islam, Anup Kumar Talukder, Md. Nurealam Siddiqui, Tofazzal Islam

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Bangladesh; Pandemic; stimulus package

Online: 21 April 2020 (09:34:19 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0018.v1

Preparedness and Response to COVID-19 in Saudi Arabia: Lessons Learned from MERS-CoV

Abdullah Algaissi, Naif Alharbi, Mazen Hassanain, Anwar Hashem

Subject: Biology And Life Sciences, Virology Keywords: COVID-19 response; MERS-CoV; Saudi Arabia; travel restrictions; Pandemic preparedness

Online: 2 April 2020 (12:08:33 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0042.v2

Virtual Screening of Inhibitors Against Spike Glycoprotein of SARS-CoV-2: A Drug Repurposing Approach

Kanishka Senathilake, Sameera Samarakoon, Kamani Tennekoon

Subject: Biology And Life Sciences, Virology Keywords: Flue; Virus; COVID19; SARS CoV-2; Spike Protein; Virtual Screening; dgitoxin; anthracycline; rolitetracycline; E-155

Online: 23 March 2020 (10:19:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0385.v1

Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2

Jalees A. Nasir, David J. Speicher, Robert A. Kozak, Hendrik N. Poinar, Matthew S. Miller, Andrew G. McArthur

Subject: Biology And Life Sciences, Virology Keywords: Coronavirus; SARS-CoV-2; enrichment; next-generation sequencing

Online: 26 February 2020 (02:27:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints202006.0293.v1

Doxycycline and Pentoxifylline for Mild and Mild-To-Moderate Covid-19

Emil Toma

Subject: Biology And Life Sciences, Virology Keywords: Covid-19; SARS-CoV-2; doxycycline; pentoxifylline; treatment; proposal

Online: 24 June 2020 (09:47:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0071.v1

Drug and Vaccine Design against Novel Coronavirus (2019-nCoV) Spike Protein through Computational Approach

Suresh Kumar

Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; novel corona virus; Wuhan virus; drug; vaccine; spike protein; epitope; vaccine design

Online: 5 February 2020 (15:34:15 CET)

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Preprint REVIEW | doi:10.20944/preprints201910.0144.v6

Discovery and Development of Safe-in-Man Broad-Spectrum Antiviral Agents

Petter I. Andersen, Aleksandr Ianevski, Hilde Lysvand, Astra Vitkauskiene, Valentyn Oksenych, Magnar Bjoras, Kaidi Telling, Irja Lutsar, Uga Dumpis, Yasuhiko Irie, Tanel Tenson, Anu Kantele, Denis E. Kainov

Subject: Biology And Life Sciences, Virology Keywords: virus; antiviral drug; drug discovery; drug development; broad-spectrum antivirals

Online: 14 February 2020 (02:27:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0689.v2

The INDIA Mutations and B.1.617 Variant: Is There a Global "Strategy" for Mutations and Evolution of Variants of The SARS-CoV2 Genome?

Jean-claude Perez

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV2; Biomathematics; vaccine; variants; mRNA; Fibonacci; Indian variants; B.1.617

Online: 28 April 2021 (17:18:50 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0341.v1

The AI-Discovered Aetiology of COVID-19 and Rationale of the Irinotecan+Etoposide Combination Therapy for Critically Ill COVID-19 Patients

Bragi Lovetrue

Subject: Biology And Life Sciences, Virology Keywords: Aetiology; Treatment; Cytokine Storm; ICU; COVID-19; ACE2; Irinotecan; Etoposide

Online: 23 March 2020 (06:56:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202003.0433.v1

Design of a Peptide-Based Subunit Vaccine against Novel Coronavirus SARS-CoV-2

Parismita Kalita, Aditya K. Padhi, Kam Y.J. Zhang, Timir Tripathi

Subject: Biology And Life Sciences, Virology Keywords: adjuvant; COVID-19; immunogenic epitopes; peptide vaccine; subunit vaccine; molecular dynamics simulation

Online: 29 March 2020 (11:14:42 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0070.v2

Possible Effects of Air Temperature on COVID-19 Disease Severity and Transmission Rates

Dominique Kang, Clifford Ellgen, Erik Kulstad

Subject: Biology And Life Sciences, Virology Keywords: Covid; covid-19; sars-cov-2; temperature; heat; body temperature; air temperature; viral decay; viral stability; transmission; severity; virology; thermodynamics

Online: 6 September 2021 (13:23:23 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0004.v1

Transmission Potential and Severity of COVID-19 in Pakistan

Sohail Raza

Subject: Biology And Life Sciences, Virology Keywords: COVID-19, Pakistan, Economic Losses, Disease Spread, SARS-CoV-2

Online: 1 April 2020 (09:19:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0003.v2

Computational Screening for Potential Drug Candidates Against SARS-CoV-2 Main Protease

Bruno Andrade, Preetam Ghosh, Debmalya Barh, Sandeep Tiwari, Raner José Santana Silva, Wagner Rodrigues de Assis Soares, Tarcisio Silva Melo, Andria dos Santos Freitas, Patrícia González-Grande, Lucas Sousa Palmeira, Luiz Carlos Junior Alcantara, Marta Giovanetti, Aristóteles Góes-Neto, Vasco Ariston de Carvalho Azevedo

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; protease; virtual screening; pharmacophore; inhibitors; natural compounds

Online: 17 April 2020 (11:00:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0407.v1

The SARS-CoV-2 Spike Protein D614G Mutation Shows Increasing Dominance and May Confer a Structural Advantage to the Furin Cleavage Domain

Leyan Tang, Allison Schulkins, Chun-Nan Chen, Kurt Deshayes, John S. Kenney

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling

Online: 24 May 2020 (20:31:16 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202004.0381.v1

Hydroxychloroquine for the Treatment of COVID-19: Evidence, Possible Mode of Action and Industrial Supply of the Drug

Mario Pagliaro, Francesco Meneguzzo

Subject: Biology And Life Sciences, Virology Keywords: hydroxychloroquine; COVID-19; immunomodulator; cytokine storm; flow chemistry

Online: 21 April 2020 (08:26:31 CEST)

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Working Paper ARTICLE

A Preceding Low-virulence Strain Pandemic Inducing Immunity Against COVID-19

Hagai Perets, Ruth Perets

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; low-virulence; high-virulence; pandemic; T-cell; immunity; virus; SARS-CoV-2

Online: 16 July 2020 (13:02:40 CEST)

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Abstract The COVID-19 pandemic is thought to began in Wuhan, China in December 2019. Mobility analysis identified East-Asia and Oceania countries to be highly-exposed to COVID-19 spread, consistent with the earliest spread occurring in these regions. However, here we show that while a strong positive correlation between case-numbers and exposure level could be seen early-on as expected, at later times the infection-level is found to be negatively correlated with exposure-level. Moreover, the infection level is positively correlated with the population size, which is puzzling since it has not reached the level necessary for population-size to affect infection-level through herd immunity. These issues are resolved if a low-virulence Corona-strain (LVS) began spreading earlier in China outside of Wuhan, and later globally, providing immunity from the later appearing high-virulence strain (HVS). Following its spread into Wuhan, cumulative mutations gave rise to the emergence of an HVS, known as SARS-CoV-2, starting the COVID-19 pandemic. We model the co-infection by an LVS and an HVS, and show that it can explain the evolution of the COVID-19 pandemic and the non-trivial dependence on the exposure level to China and the population-size in each country. We find that the LVS began its spread a few months before the onset of the HVS, and that its spread doubling-time is

\sim 1.59 \pm 0.17

times slower than the HVS. Although more slowly spreading, its earlier onset allowed the LVS to spread globally before the emergence of the HVS. In particular, in countries exposed earlier to the LVS and/or having smaller population-size, the LVS could achieve herd-immunity earlier, and quench the later-spread HVS at earlier stages. We find our two-parameter (the spread-rate and the initial onset time of the LVS) can accurately explain the current infection levels (R^2

=0.74

; correlation p-value (p) of 5x10^-13

). Furthermore, countries exposed early should have already achieved herd-immunity. We predict that in those countries cumulative infection levels could rise by no more than 2-3 times the current level through local-outbreaks, even in the absence of any containment measures. We suggest several tests and predictions to further verify the double-strain co-infection model and discuss the implications of identifying the LVS.

Preprint REVIEW | doi:10.20944/preprints202004.0160.v2

The human-COVID-19 Tango: Connecting the Dots

Hamdi Hamdi, Ensaf Abdaldayem

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; ACE; ACE2; Angiotensin II; Bradykinin; RAS inhibitors; ACE inhibitors; AT1 receptor blockers; Losartan; Bradykinin Antagonists; Ang II loading; Giapreza; Icatibant.

Online: 14 April 2020 (14:34:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0242.v1

A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS‐COV‐2 by Comprehensive Immunoinformatic and Molecular Modelling Approach

Hafiz Muzzammel Rehman, Muhammad Usman Mirza, Mahjabeen Saleem, Matheus Froeyen, Sarfraz Ahmad, Roquyya Gul, Muhammad Shahbaz Aslam, Muhammad Sajjad, Munir Ahmad Bhinder

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; spike protein; multiepitope vaccine; molecular modeling

Online: 15 March 2020 (12:45:54 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202005.0359.v1

Entry of SARS-CoV2 through the Basal Surface of Alveolar Endothelial Cells – A Proposed Mechanism Mediated by CD147 in COVID-19

Francia Acosta Saltos, Alejandro David Acosta Saltos

Subject: Biology And Life Sciences, Virology Keywords: Covid-19; Endothelial; CD147; SARS-CoV2

Online: 23 May 2020 (05:26:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0201.v1

Detecting the COVID-19

Pravin Pokhrel, Changpeng Hu, Hanbin Mao

Subject: Biology And Life Sciences, Virology Keywords: diagnosis; detection kits; RT-PCR; immunoassay; false negative; false positive; sensitivity; point-of-care (POC)

Online: 12 April 2020 (16:50:05 CEST)

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Preprint REVIEW | doi:10.20944/preprints202011.0558.v1

Recombinant Protein Vaccines, a Proven Approach Against Coronavirus Pandemics

Jeroen Pollet, Wen-Hsiang Chen, Ulrich Strych

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Adjuvants; Vaccine Production; Vaccine Delivery; Clinical Trials; Neutralizing Antibodies; Th1

Online: 22 November 2020 (11:57:51 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0216.v2

Detection and Survival of SARS-coronavirus in Human Stool, Urine, Wastewater and Sludge

Andrew Singer, Rachel Wray

Subject: Biology And Life Sciences, Virology Keywords: SARS-coronavirus; Severe Acute Respiratory Syndrome; COVID-19; Stool; Urine; Wastewater; Wastewater-based epidemiology

Online: 18 June 2020 (09:29:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0325.v1

A Retrospective Analysis of Influence of Environmental/Air Temperature and Relative Humidity on SARS-CoV-2 Outbreak

Md. Arifur Rahman, Md. Golzar Hossain, Atul Chandra Singha, Md Sayeedul Islam, Md Ariful Islam

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; infectivity; temperature; humidity

Online: 23 March 2020 (01:30:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0719.v1

Long-term Existence of SARS-CoV-2 in COVID-19 Patients: Host Immunity, Viral Virulence, and Transmissibility

Meilin Jin, Xingyu Wang, Haini Jiang, Lijuan Hua, Weiwei Yu, dan ding, ke wang, Xiaopan Li, Kun Huang, Zhong zou, Shuyun Xu

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; long-term; neutralization antibody; lymphocyte functionality; viral pathogenicity.

Online: 30 July 2020 (12:16:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201610.0119.v1

Resistance to Rose Rosette Virus and Transmission Attributes

Patrick L. Di Bello, Thanuja Thekke-Veetil, Tobiasz Druciarek, Ioannis E. Tzanetakis

Subject: Biology And Life Sciences, Virology Keywords: transmission; resistance; detection, Emaravirus

Online: 27 October 2016 (11:50:52 CEST)

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Working Paper REVIEW

The Mother of All Battles: Viruses vs. Humans. Can Humans Avoid Extinction in 50-100 Years?

Eleftherios Diamandis

Subject: Biology And Life Sciences, Virology Keywords: pandemics; contagious diseases; human race extinction; viruses; microbiome; COVID-19; blindness

Online: 14 April 2021 (17:53:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0377.v1

The Dynamics of Humoral Immune Responses Following SARS-CoV-2 Infection and the Potential for Reinfection

Paul Kellam, Wendy Barclay

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; immune response; antibodies

Online: 21 April 2020 (06:56:12 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0340.v1

The Lysosome: A Potential Therapeutic Juncture between the COVID-19 Pandemic and Niemann-Pick Type C Disease

Rami Ballout

Subject: Biology And Life Sciences, Virology Keywords: coronavirus; SARS-CoV-2; lysosomal storage diseases; lipid rafts; cholesterol; angiotensin-converting enzyme-2 (ACE2); cathepsins

Online: 24 March 2020 (03:07:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0125.v1

Photodynamic Inactivation of Herpes Simplex Viruses

Andrea L.-A. Monjo, Eric S. Pringle, Mackenzie Thornbury, Brett A. Duguay, Susan M. A. Monro, Marc Hetu, Danika Knight, Colin G. Cameron, Sherri McFarland, Craig McCormick

Subject: Biology And Life Sciences, Virology Keywords: HSV-1; HSV-2; photodynamic inactivation; plaque assay; natural product; antiviral

Online: 7 September 2018 (05:26:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0145.v1

Lessons for SARS-CoV-2 Study (COVID-19 Disease) From Its Exosome Relatives

Pierre Arsene

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Exosome; Extracellular Vesicle; Diagnostics; Vaccine; Treatment

Online: 12 June 2020 (09:01:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0346.v1

A Hundred Lives Lost: Doctor Deaths in India During the Times of COVID-19

Rajeev Jayadevan

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; deaths; doctor; nurse; pharmacist; healthcare worker; frontline; occupational risk; suicide; violent death; accident; pandemic; SARS-CoV-2

Online: 16 July 2020 (08:28:55 CEST)

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Preprint REVIEW | doi:10.20944/preprints201608.0054.v1

Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction

Sandra Söderholm, Yu Fu, Lana Gaelings, Sergey Belanov, Laxmana Yetukuri, Mikhail Berlinkov, Anton V. Cheltov, Simon Anders, Tero Aittokallio, Tuula A. Nyman, Sampsa Matikainen, Denis E. Kainov

Subject: Biology And Life Sciences, Virology Keywords: influenza virus; antiviral agent; proteomics; phosphoproteomics; metabolomics; transcriptomics; genomics; virtual ligand screening

Online: 5 August 2016 (12:41:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0234.v1

Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

David G. Karlin

Subject: Biology And Life Sciences, Virology Keywords: adeno-associated virus; protein sequence analysis; overlapping genes; amino acid depletion; cysteine depletion; tyrosine depletion; capsid design; membrane-binding amphipathic helix

Online: 17 February 2020 (02:42:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0450.v1

Novel Mutations in the S1 domain of COVID 19 Spike Protein of Isolate from Gujarat Origin, Western India

Arup Kumar Banerjee, Feroza Begum, Dluya Thagriki, Prem Prakash Tripathi, Upasana Ray

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; S protein; RBD; S1; S2; Mutation

Online: 24 April 2020 (14:19:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202002.0007.v1

CRISPR-Cas Systems for Diagnosing Infectious Diseases

Anastasiya Kostyusheva, Sergey Brezgin, Yurii Babin, Irina Vasil'eva, Dmitry Kostyushev, Vladimir Chulanov

Subject: Biology And Life Sciences, Virology Keywords: molecular diagnostics; molecular epidemiology; HIV; HBV; HCV; HPV; Zika virus; Dengue virus; tuberculosis; SARS; MERS; nCov-2019

Online: 3 February 2020 (03:47:27 CET)

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

Preprint ARTICLE | doi:10.20944/preprints201609.0014.v1

Decreasing Trends in HIV Testing among Adults in Georgia: Analysis of the 2010-2014 BRFSS Data

Benjamin E. Ansa, Sashia White, Yunmi Chung, Selina A. Smith

Subject: Biology And Life Sciences, Virology Keywords: HIV/AIDS; testing; trends; Behavioral Risk Factor Surveillance System; socio-demographic; Georgia

Online: 5 September 2016 (11:21:36 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202003.0091.v1

Predicting the Angiotensin Converting Enzyme 2 (ACE2) Utilizing Capability as the Receptor of SARS-CoV-2

Ye Qiu, Yuan-Bo Zhao, Qiong Wang, Jin-Yan Li, Zhi-JIan ZHou, Ce-Heng Liao, Xing-Yi Ge

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; coronavirus; angiotensin converting enzyme 2 (ACE2); receptor utilization; phylogenetic analysis.

Online: 5 March 2020 (12:12:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0276.v1

Investigating the Factors Affecting SARS-COV-2 Transmission and Mortality Rate in Sub-Saharan Africa

Obuks Ejohwomu, Noor Al-Saffar, Samuel Adeniyi Adekunle, Majeed Oladokun, Judy Too, Clinton Aigbavboa

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; coronavirus; transmission; meteorological impact

Online: 19 July 2022 (04:05:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0165.v2

Conserved Sequence Features in the Spike Protein Provide Evidence Suggesting the Origin of SARS-CoV-2 (COVID-19)-Related Viruses by Recombination between SARS virus and Another Sarbecovirus

Radhey S. Gupta, Bijendra Khadka

Subject: Biology And Life Sciences, Virology Keywords: Conserved signature indels (CSIs) specific for SARS and SARS-CoV-2-related viruses. Molecular markers distinguishing different clades of Sarbecovirus, Evolutionary relationships between SARS and SARS-CoV-2-related viruses, Origin of SARS-CoV-2 and Pangolin CoV_MP789 viruses, Novel sequence and structural features of spike and nucleocapsid proteins. Genetic recombination.

Online: 26 August 2020 (10:17:16 CEST)

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Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, protein sequences from sarbecoviruses were analyzed to identify highly-specific molecular markers consisting of conserved inserts or deletions (termed CSIs) in the spike (S) and nucleocapsid (N) proteins that are specific for either particular clusters/lineages of these viruses or are commonly shared by specific lineages. Three novel CSIs in the N-terminal domain of the spike protein S1-subunit (S1-NTD) are uniquely shared by the SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs, distinguishing this cluster of viruses (SARS-CoV-2r) from all others. In the same positions, where these CSIs are found, related CSIs are also present in two other sarbecoviruses (viz. CoVZXC21 and CoVZC45 forming CoVZC cluster), which form an out group of the SARS-CoV-2r cluster. These three CSIs are not found in the SARS-CoVs. However, both SARS and SARS-CoV-2r CoVs contain two large CSIs in the C-terminal domain of S1 (S1-CTD), which binds the human ACE-2 receptor, that are absent in the CoVZC cluster of CoVs. These results indicate that while the S1-NTD of the SARS-CoV-2r viruses possesses the sequence characteristics of the CoVZC cluster of CoVs, their S1-CTD resembles the SARS viruses. Thus, the spike protein of SARS-CoV-2r viruses has likely originated from a recombination event between the S1-NTD of the CoVZC viruses and the S1-CTD of SARS viruses. This inference is also supported by the amino acid sequence similarity of the S1-NTD and S1-CTD from SARS-CoV-2 compared to the CoVZC and SARS CoVs. We also present evidence that one of the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2, is also derived by a recent recombination between the S1-NTD of the CoVZC CoVs and the S1-CTD of a SARS-CoV-2 related virus. Several other identified CSIs are specific for others clusters of sarbecoviruses including a clade consisting of bat SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mappings studies show that the identified CSIs are located within surface-exposed loops and form distinct patches on the surface of the spike protein. These surface loops/patches are predicted to interact with other host components and play important role in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for the SARS-CoV-2r clade provide novel means for development of new diagnostic and therapeutic targets for these viruses.

Preprint ARTICLE | doi:10.20944/preprints202002.0221.v1

Single Cell Analysis of ACE2 Expression Reveals the Potential Targets for 2019-nCoV

Yanyan Zhu, Miaomiao Jiang, Liang Gao, Xiaoyun Huang

Subject: Biology And Life Sciences, Virology Keywords: ACE2; single cell; 2019-nCoV

Online: 16 February 2020 (14:56:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0063.v1

A Proposal for Isotherm World Maps to Forecast the Seasonal Evolution of the SARS-CoV-2 Pandemic

Nicola Scafetta

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Pandemic geographical distribution; Epidemic forecasting; Weather conditions; Climatic zones.

Online: 6 April 2020 (14:11:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0260.v2

COVID-19 Pandemic: Insights into Structure, Function, and hACE2 Receptor Recognition by SARS-CoV-2

Anshumali Mittal, Kavyashree Manjunath, Rajesh Kumar Ranjan, Sandeep Kaushik, Sujeet Kumar, Vikash Verma

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV; SARS-like coronavirus; 2019-nCoV; SARS-CoV-2; angiotensin-converting enzyme 2 (ACE2); RdRp; Remdesivir; and neutralizing antibody

Online: 10 July 2020 (16:21:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0033.v1

Establish and Apply a Safe and Convenient Pseudovirus-Based Assay to Detect Neutralizing Antibodies against Influenza A (H7N9) Virus

Li Zhang, Jing Lu, Jingxing Li, Rong Tang, Haiyan Peng, Fanyue Meng, Yuemei Hu

Subject: Biology And Life Sciences, Virology Keywords: H7N9 avian influenza; pseudovirus; neutralization assay; relative luminescence units (RLU)

Online: 6 January 2017 (10:21:52 CET)

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Working Paper ARTICLE

Virtual Screening of Approved Clinic Drugs with Main Protease (3CL^pro) Reveals Potential Inhibitory Effects on SARS-CoV-2

Qiang Wang, Ying Zhao, Xiaojia Chen, An Hong

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; 3CLpro; approved drugs; virtual screening

Online: 8 March 2020 (17:14:57 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202004.0133.v2

The Airborne and Gastrointestinal Coronavirus SARS-COV-2 Pathways

Tomás Santa-Coloma

Subject: Biology And Life Sciences, Virology Keywords: ACE2, airborne; coronavirus; COV-2; COVID-19; food chain; intestinal infection; Kepler conjecture; rebound epidemic; packaging; particle size; SARS; surgical masks.

Online: 13 April 2020 (10:12:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints201707.0045.v1

Fighting Cancer with Mathematics and Viruses

Daniel N. Santiago, Johannes P. W. Heidbuechel, Wendy M. Kandell, Rachel Walker, Christine E. Engeland, Daniel Abate-Daga, Heiko Enderling

Subject: Biology And Life Sciences, Virology Keywords: oncolytic virotherapy; combination therapy; mathematical model; immune system; cancer; immunotherapy

Online: 17 July 2017 (13:01:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0462.v1

Theoretical Analysis of the Induction of Forced Resonance Mechanical Oscillations to Virus Particles by Microwave Irradiation:Prospects as an Anti-virus Modality

Nikolaos Uzunoglu

Subject: Biology And Life Sciences, Virology Keywords: coronavirus; virus sterilization

Online: 25 April 2020 (11:18:57 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0478.v1

Risk Assessment of SARS-CoV-2 in Antarctic Wildlife

Andrés Barbosa, Arvind Vansani, Virginia Morandini, Wray Grimaldi, Ralph E.T. Vanstreels, Julia I. Diaz, Thierry Boulinier, Meagan Dewar, Daniel Gonzalez-Acuña, Rachel Gray, Clive R. McMahon, Gary Miller, Michelle Power, Amandine Gamble, Michelle Wille

Subject: Biology And Life Sciences, Virology Keywords: Antarctica; coronavirus; COVID-19; mitigation measures; reverse zoonoses; risk assessment; SARS-CoV-2; wildlife

Online: 21 August 2020 (09:21:25 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0179.v2

Prevalence of COVID-19: A Look behind the Scenes

Samir Haj Bloukh, Annis A. Shaikh, Habib M. Pathan, Zehra Edis

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; human coronavirus; control; vitamin D; antibiotic resistance; antimicrobial agents; BCG; malaria; climate; latitude

Online: 15 April 2020 (08:25:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0372.v1

Structural Genomics and Interactomics of 2019 Wuhan Novel Coronavirus, SARS-CoV-2, Indicate Evolutionary Conserved Functional Regions of Viral Proteins

Hongzhu Cui, Ziyang Gao, Ming Liu, Senbao Lu, Winnie Mkandawire, Oleksandr Narykov, Suhas Srinivasan, Mo Sun, Dmitry Korkin

Subject: Biology And Life Sciences, Virology Keywords: structural genomics; protein-protein interactions; structural bioinformaticscomparative modeling; functional annotation; antiviral design; SARS-CoV-2; 2019-nCoV

Online: 25 February 2020 (11:24:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0264.v1

Rapid Quantification and Neutralization Assays for Novel Coronavirus SARS-CoV-2 Using Avicel RC-591 Semi-Solid Overlay

Anna N. Honko, Nadia Storm, David J. Bean, Jhonatan Henao Vasquez, Sierra N. Downs, Anthony Griffiths

Subject: Biology And Life Sciences, Virology Keywords: plaque assay; neutralization; SARS; SARS-CoV-2; coronavirus; Avicel; methylcellulose; COVID

Online: 16 May 2020 (15:51:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0471.v1

Fecal Shedding of SARS-CoV-2 and Its Potential Role in Person-To-Person Transmission and the Environment-Based Spread of COVID-19

Davey Jones, Marcos Quintela Baluja, David Graham, Alexander Corbishley, James McDonald, Shelagh Malham, Luke Hillary, Thomas Connor, William Gaze, Ines Moura, Mark Wilcox, Kata Farkas

Subject: Biology And Life Sciences, Virology Keywords: bathing waters; coronavirus; environmental transmission; faecal-oral route; infection risk; waterborne illness

Online: 20 July 2020 (12:02:45 CEST)

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The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). Overall, severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 10²-10⁵ gc/ml) and feces (ca. 10²-10⁷ gc/ml) is much lower than in nasopharyngeal fluids (ca. 10⁵-10¹¹ gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the GI tract and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that over eight million global cases of COVID-19 have occurred, but exposure to feces or wastewater has never been implicated as a transmission vector.

Preprint COMMUNICATION | doi:10.20944/preprints201802.0134.v1

Arbidol (Umifenovir): A Broad-spectrum Antiviral Drug that Inhibits Medically Important Arthropod-borne Flaviviruses

Jan Haviernik, Michal Stefanik, Martina Fojtikova, Sabrina Kali, Noël Tordo, Ivo Rudolf, Zdenek Hubalek, Ludek Eyer, Daniel Ruzek

Subject: Biology And Life Sciences, Virology Keywords: flavivirus; arbidol; umifenovir; antiviral activity; cytotoxicity; cell-type dependent antiviral effect

Online: 21 February 2018 (14:44:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0459.v1

SARS-CoV-2 Infections - Gene Expression Omnibus (GEO) Data Mining, Pathway Enrichment Analysis, and Prediction of Repurposable Drugs/Compounds

Srilakshmi Chaparala, Carrie L Iwema, Ansuman Chattopadhyay

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; coronavirus; drug repositioning; pathway enrichment

Online: 19 September 2020 (11:34:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0320.v1

Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention

Salma Jamal, Jasdeep Singh, Javaid Ahmad Sheikh, Hina Singh, Mohd Khubaib, Sunil Kohli, Ulrich Dobrindt, Syed Asad Rahman, Nasreen Zafar Ehtesham, Seyed Ehtesham Hasnain

Subject: Biology And Life Sciences, Virology Keywords: envelope protein; furin cleavage site; hydrophobic aggregation and rapid transmission; immediate ancestor; pangolins coronaviruses; SARS-CoV-2; spike protein

Online: 23 March 2020 (00:42:35 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202007.0398.v1

New SARS-CoV-2 Infection in a Pet Cat with Severe Lung Disease in Italy

Nicolò Musso, Angelita Costantino, Sebastiano La Spina, Alessandra Finocchiaro, Francesca Andronico, Stefano Stracquadanio, Luigi Liotta, Rosanna Visalli, Giovanni Emmanuele

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; pet cat; RNA-extraction; pneumonia

Online: 17 July 2020 (16:02:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201703.0232.v1

The Transmembrane Morphogenesis Protein gp1 of Filamentous Phages Contains Walker A and Walker B Motifs Essential for Phage Assembly

Belinda Loh, Maximilian Haase, Lukas Mueller, Andreas Kuhn, Sebastian Leptihn

Subject: Biology And Life Sciences, Virology Keywords: Filamentous phage; M13; gp1; Zonula occludens toxin (Zot); phage assembly; assembly 27 complex; ATPase; membrane protein; molecular hinge; secretion; Walker motifs

Online: 31 March 2017 (11:13:40 CEST)

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