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Preprint REVIEW | doi:10.20944/preprints202005.0070.v1

The Role of Temperature in COVID-19 Disease Severity and Transmission Rates

Dominique Kang, Clifford Ellgen

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

Online: 5 May 2020 (10:47:18 CEST)

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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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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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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 CASE REPORT | doi:10.20944/preprints202003.0180.v1

First Case of COVID-19 Infection with Fulminant Myocarditis Complication: 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: 11 March 2020 (04:57:10 CET)

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Preprint REVIEW | doi:10.20944/preprints202003.0197.v1

2019 Novel Coronavirus (COVID-19) Outbreak: A Review of the Current Literature and Built Environment (BE) Considerations to Reduce Transmission

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

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

Online: 12 March 2020 (04:18:26 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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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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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 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 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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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 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/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 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 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 REVIEW | doi:10.20944/preprints202003.0197.v2

2019 Novel Coronavirus (COVID-19) Outbreak: A Review of the Current Literature and Built Environment (BE) 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: 20 March 2020 (05:02:44 CET)

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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/preprints202004.0377.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 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.

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.

Working Paper REVIEW

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: 25 July 2020 (16:21:53 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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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 ARTICLE | doi:10.20944/preprints202004.0529.v1

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: 30 April 2020 (11:15:17 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/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 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 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/preprints202005.0188.v2

SARS-CoV-2 S1 and N-Based Serological Assays Reveal Rapid Seroconversion and Induction of Specific Antibody Response in COVID-19 Patients

Abdullah Algaissi, Mohamed A. Alfaleh, Sherif Hala, Turki S. Abujamel, Sawsan S. Alamri, Sarah A Almahboub, Khalid A. Alluhaybi, Haya I. Hobani, Reem M. Alsulaiman, Rahaf H. Alharbi, M-Zaki El-Assouli, Rowa Y Alhabbab, Ahdab A. AlSaieedi, Wesam H. Abdulaal, Afrah A. AL-Somali, Fadwa S. Alofi, Asim A. Khogeer, Ahmad Bakur Mahmoud, Almohanad A Alkayyal, Naif A.M. Almontashiri, Arnab Pain, Anwar M. Hashem

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 serology; ELISA; N protein; COVID-19; serosurvey

Online: 2 July 2020 (07:19:44 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202005.0322.v1

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

Online: 20 May 2020 (07:08:38 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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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/preprints202008.0312.v1

Virion Structure and Mechanism of Propagation of Coronaviruses including SARS-CoV 2 (COVID -19 ) and some Meaningful Points for Drug or Vaccine Development

Swapan Ghosh

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2(COVID-19); + ssRNA; ribosomal – framshift; Pseudoknot; replication; model; drug; vaccine

Online: 14 August 2020 (08:26:31 CEST)

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SARS-CoV-2 or COVID-19, a new seventh human corona virus, has out-broken in Wuhan, China since 31^st December 2019, and quickly escalated to take the form of pandemic which killed many human beings throughout almost all countries across continents. The rapidity of its transmission from human to human is far greater than all previous human corona viruses which came into existence like SARS-CoV, MERS-CoV, etc. The nucleotide sequence of SARS-CoV-2 (isolates Wuhan-Hu-1) is 29,875 bp in ss-RNA. Symptoms of SARS-CoV-2 infected pneumonia include from asymptomatic to high fever and/or respiratory illnesses. Coronavirus virion (spherical/round /elliptical in shape) consists of three parts- outer membrane or envelope, nucleocapsid and genome (RNA). SARS-CoV-2 was shown to use receptor, angiotensin converting enzyme 2 (ACE2) for attachment to the cells through its surface spike (S) protein (S1), and the virion enters into the host cell through two routes- direct membrane fusion and endocytotic pathway. The RNA of SARS-CoV acts directly as mRNA and here minus(-) 1 programmed ribosomal frameshift (-1PRF) is being operated by slippery sequence and pseudoknot, so it translates 16 nonstructural proteins including RNA dependent RNA replicase. Then genomic RNA replicated continuously on – strand RNA template and subgenomic RNA transcribed discontinuously on –RNA template to sgmRNA. Subgenomic RNAs/sgmRNAs synthesize all structural proteins. This article takes into consideration the details of established theories of viral structure, viral attachment, mode of entry into human cells, different models of replication and transcription of virus genome proposed by eminent scientists over the years, and makes an in depth examination highlighting meaningful points or important target cites of viral propagation or synthesis, which are conserved, for prompt development of potent drugs or vaccine to counter COVID-19 for which human race is anxiously and eagerly waiting.

Preprint COMMUNICATION | doi:10.20944/preprints202003.0184.v1

Serological Test is an Efficient Supplement of RNA Detection for Confirmation of 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: 11 March 2020 (10:40:09 CET)

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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 ARTICLE | doi:10.20944/preprints202004.0281.v1

Mutation Hot Spots in Spike Protein of COVID-19

Arup Kumar Banerjee, Feroza Begum, Upasana Ray

Subject: Biology And Life Sciences, Virology Keywords: COVID 19; spikme; S1; mutations

Online: 16 April 2020 (15:30:56 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 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 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/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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Preprint ARTICLE | doi:10.20944/preprints202002.0232.v1

Terahertz Detection of Zika Viruses

Subhashish Dolai, Massood Tabib-Azar

Subject: Biology And Life Sciences, Virology Keywords: electromagnetic properties of viruses; terahertz sensors; label-free detection of viruses; nanotechnologies

Online: 17 February 2020 (01:56:06 CET)

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Preprint SHORT NOTE | doi:10.20944/preprints202004.0089.v1

Sars-CoV-2 Envelope and Membrane Proteins: Differences from Closely Related Proteins Linked to Cross-species Transmission?

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: 7 April 2020 (11:09:23 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 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.v1

Virtual Screening of Inhibitors Against Spike Glycoprotein of 2019 Novel Corona Virus: A Drug Repurposing Approach

Kanishka Senathilake, Sameera Samarakoon, Kamani Tennekoon

Subject: Biology And Life Sciences, Virology Keywords: COVID -19; 2019-nCoV; spike (S) protein; zorubicin; aclarubicin

Online: 3 March 2020 (11:41:51 CET)

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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/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 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 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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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 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/preprints201611.0125.v1

Up-regulation of Lamin A/C Expression in Epstein-Barr Virus Immortalized B Cells and Burkitt Lymphoma Cell Lines of Activated B Cell Phenotype

Ferenc Bánáti, Anita Koroknai, Kálmán Szenthe, Tamás Tereh, Nóra Kovács, Anita Hidasi, Barbara Bánkuti, Krisztina Buzás, Frederic Lemnitzer, Zsolt Ruzsics, Susan Szathmary, Hans Wolf, Dániel Salamon, János Minárovits, Hans-Helmut Niller

Subject: Biology And Life Sciences, Virology Keywords: Lamin, EBV latency, transformation, epigenetic regulation, activated B cell

Online: 24 November 2016 (17:53:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints201903.0012.v1

First Description of a Natural Infection with Shrimp Hemocyte Iridescent Virus in Farmed Giant Freshwater Prawn, Macrobrachium Rosenbergii

Liang Qiu, Xing Chen, Ruo-Heng Zhao, Chen Li, Wen Gao, Qing-Li Zhang, Jie Huang

Subject: Biology And Life Sciences, Virology Keywords: SHIV; Macrobrachium rosenbergii; Macrobrachium nipponense; Procambarus clarkii; white head; Histopathology; Susceptible species; Viral load

Online: 1 March 2019 (12:49:53 CET)

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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 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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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 ARTICLE | doi:10.20944/preprints201703.0087.v1

Inhibition of Zika Virus by Marine Algae

Claudio Cirne-Santos, Caroline De Souza Barros, Caio Cesar Richter Nogueira, Renata Mendonça Campos, Valéria Teixeira, Davis Ferreira, Izabel Christina Nunes De Palmer Paixão

Subject: Biology And Life Sciences, Virology Keywords: Zika Virus, Antiviral, Marine Algae

Online: 14 March 2017 (18:34:37 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/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 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 REVIEW | doi:10.20944/preprints201608.0043.v1

Arms Race between Enveloped Viruses and the Host ERAD Machinery

Dylan A. Frabutt, Yong-Hui Zheng

Subject: Biology And Life Sciences, Virology Keywords: enveloped viruses; viral glycoproteins; endoplasmic reticulum-associated degradation; ERAD; unfolded protein response; UPR; ER stress

Online: 4 August 2016 (11:44:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0003.v1

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

Bruno Andrade, Preetam Ghosh, Debmalya Barth, 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: 1 April 2020 (09:16:14 CEST)

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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 REVIEW | doi:10.20944/preprints202004.0469.v1

Pandemic Coronavirus Disease (COVID-19): Challenges and A Global Perspective

Yashpal Singh Malik, Naveen Kumar, Shubhankar Sircar, Rahul Kaushik, Sudipta Bhatt, Kuldeep Dhama, Parakriti Gupta, Kapil Goyal, Mini P. Singh, Ujjala Ghoshal, Mohamed Ezzat Mahmoud El Zowalaty, O.R. Vinodh Kumar, Mohd. Iqbal Yatoo, Ruchi Tiwari, Mamta Pathak, Shailesh Kumar Patel, Ranjit Sah, Alfonso J. Rodriguez-Morales, Balasubramanian Ganesh, Prashant Kumar, Raj Kumar Singh

Subject: Biology And Life Sciences, Virology Keywords: severe acute respiratory syndrome coronavirus-2; COVID-2019; epidemiology; pathobiology; clinical profile; phyloanalysis; artificial intelligence; diagnosis; vaccines; therapeutics

Online: 26 April 2020 (08:15:23 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202203.0010.v1

Analytical Sensitivity of Five SARS-CoV-2 Rapid Antigen Tests for Omicron Versus Delta Variant

Jean-Louis Bayart, Jonathan Degosserie, Julien Favresse, Constant Gillot, Marie Didembourg, Happy Phanio Djokoto, Valérie Verbelen, Gatien Roussel, Celine Maschietto, François Mullier, Jean-Michel Dogné, Jonathan Douxfils

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; variant; Omicron; Delta; antigen; RT-qPCR

Online: 1 March 2022 (09:01:19 CET)

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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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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/preprints202201.0416.v1

Athletes and Coaches Through COVID-19 Pandemic: A Qualitative View of Goal Management

Sergio Costa, Eugenio De Gregorio, Lisa Zurzolo, Giampaolo Santi, Edoardo Giogio Ciofi, Francesco Di Gruttola, Luana Morgilli, Cristina Montesano, Francesca Cavallerio, Maurizio Bertollo, Selenia di Fronso

Subject: Biology And Life Sciences, Virology Keywords: Goal setting; goal adjustment; lockdown; qualitative survey; reflexive thematic analysis

Online: 27 January 2022 (11:27:26 CET)

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Preprint REVIEW | doi:10.20944/preprints202002.0358.v3

Coronavirus Disease 2019 Assosiated Pneumonia in China: Current Status and Future Prospects

Temoor Ahmed, Muhammad Noman, Ahmad Almatroudi, Muhammad Shahid, Mohsin Khurshid, Farheen Tariq, Muhammad Tahir ul Qamar, Rongrong Yu, Bin Li

Subject: Biology And Life Sciences, Virology Keywords: Infectious diseases; Coronavirus; SARS-CoV-2; COVID-19; Pneumonia; China

Online: 28 February 2020 (13:21:43 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202008.0661.v1

What Is Life? Are Viruses Living Entities?

Jaime Gomez-Marquez

Subject: Biology And Life Sciences, Virology Keywords: life definition; living being definition; robot definition; living viruses; extraterrestrial life

Online: 30 August 2020 (11:33:48 CEST)

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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 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 HYPOTHESIS | doi:10.20944/preprints202004.0151.v1

Ace Inhibitors and AT1R Blockers for COVID-2019: Friends or Foes ?

Daniele Focosi, Marco Tuccori, Fabrizio Maggi

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; ACEI; ARB; SARS; ALI; ARDS

Online: 9 April 2020 (12:34:46 CEST)

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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 REVIEW | doi:10.20944/preprints202004.0326.v1

Antibodies to SARS-CoV-2 and Their Potential for Therapeutic Passive Immunization

P.J. Klasse, John P. Moore

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; neutralizing antibodies; immunotherapy; vaccine

Online: 19 April 2020 (04:52:17 CEST)

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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 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 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 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 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/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 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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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/preprints202003.0433.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 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 COMMUNICATION | doi:10.20944/preprints202005.0270.v1

Use of Isoelectric Point for Fast Identification of Anti-SARS CoV-2 Coronavirus Proteins

Kanad Mallik

Subject: Biology And Life Sciences, Virology Keywords: isoelectric point; anti-viral; SARS CoV-2

Online: 16 May 2020 (16:51:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202202.0224.v1

Omicron Variant: Secrets Behind the Great Escape Artist

Henry Sutanto, Djoko Santoso

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; pandemic; SARS-CoV-2; Omicron variant; emerging disease; global health; virus; genome; mutation

Online: 18 February 2022 (05:23:18 CET)

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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/preprints202003.0316.v1

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

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

Online: 20 March 2020 (12:57:10 CET)

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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/preprints201909.0076.v2

Immunoinformatics-Guided Designing of Peptide Vaccine against Lassa Virus with Dynamic and Immune Simulation Studies

Sifat Bin Sayed, Zulkar Nain, Faruq Abdullah, Md. Shakil Ahmed khan, Zahurul Haque, S.M. Raihan Rahman, Rubaia Tasmin, Utpal Kumar Adhikari

Subject: Biology And Life Sciences, Virology Keywords: Lassa fever; immunoinformatics; peptide vaccine; immune simulation

Online: 9 September 2019 (08:46:04 CEST)

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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 COMMUNICATION | doi:10.20944/preprints202202.0158.v1

Comparison of Auto Sampling and Passive Sampling Methods for SARS-CoV-2 Detection in Wastewater

Melissa Wilson, Yuanyuan Qiu, Jiaao Yu, Bonita E. Lee, David T. McCarthy, Xiaoli Pang

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; wastewater; passive sampler; autosampler; RT-qPCR

Online: 11 February 2022 (08:38:07 CET)

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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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Working Paper REVIEW

Reactive Oxygen Species (ROS) Homeostasis in Influenza Virus Infection

Ker-Kong Chen, Moeko Minakuchi, Kenly Wuputra, Chia-Chen Ku, Jia-Bin Pan, Kung-Kai Kuo, Ying-Chu Lin, Shigeo Saito, Chang-Shen Lin, kazunari K. Yokoyama

Subject: Biology And Life Sciences, Virology Keywords: antioxidation; aryl hydrocarbon receptor; cellular oxidation; nuclear factor E2-related factor 2; reactive oxygen species

Online: 27 November 2019 (04:20:30 CET)

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Preprint REVIEW | doi:10.20944/preprints202202.0261.v1

Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging more Transmissible and Vaccine-Resistant Strains

Anacleto S. de Souza, Vitor Martins de Freitas Amorim, Gabriela D. A. Guardia, Filipe F dos Santos, Henning Ulrich, Pedro A. F. Galante, Robson Francisco de Souza, Cristiane Rodrigues Guzzo

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 variants; transmissibility; viral load; sensitivity to antisera

Online: 22 February 2022 (02:59:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0240.v1

Characterisation of Particle size and Viability of SARS-CoV-2 Aerosols from a Range of Nebuliser Types Using a Novel Sampling Technique

Susan Paton, Simon Clark, Antony Spencer, Isobel Garratt, Ikshitaa Dinesh, Katy-Anne Thompson, Allan Bennett, Thomas Pottage

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; aerosols; particles; viable; respirable; sizing; sampling

Online: 21 February 2022 (01:48:14 CET)

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Preprint REVIEW | doi:10.20944/preprints202004.0040.v1

COVID-19 Infection and Transmission are Observably Less in Highly Dengue-endemic Countries

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: 3 April 2020 (15:48:36 CEST)

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Biology and Life Sciences