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Working Paper REVIEW

Immunogenicity of Clinically Relevant SARS-CoV-2 Vaccines in Non-human Primates and Humans

P.J. Klasse, D. F. Nixon, J. P. Moore

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; S-protein; RBD; COVID-19; neutralizing antibodies; serology; T-cells; vaccines; animal models; Operation Warp Speed

Online: 27 October 2020 (11:25:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0199.v1

Revealing SARS-CoV-2 Functional Druggability Through Multi-Target Cadd Screening of Repurposable Drugs

Yash Gupta, Dawid Maciorowski, Raman Mathur, Catherine M. Pearce, David J. Ilc, Hamza Husein, Ajay Bharti, Daniel Becker, Rathi Brijesh, Steven B Bradfute, Ravi Durvasula, Prakasha Kempaiah

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: SARS-CoV-2; COVID-19; CADD; virtual screening; approved drugs; drug repurposing; essential targets; molecular docking; molecular dynamics simulations

Online: 11 May 2020 (13:14:18 CEST)

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The emergence of SARS/MERS drug resistant COVID-19 with high transmission and mortality has recently been declared a deadly pandemic causing economic chaos and significant health problems. Like all coronaviruses, SARS-CoV-2 is a large virus that has many druggable components within its proteome. In this study, we focused on repurposing approved and investigational drugs by identifying potential drugs that are predicted to effectively inhibit critical enzymes within SARS-CoV-2. We shortlisted seven target proteins with enzymatic activities known to be essential at different stages of the virus life cycle. For virtual screening, the energy minimization of a crystal structure or modeled protein was carried out using Protein Preparation Wizard (Schrödinger LLC, 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs (n=5903) that are already approved by worldwide regulatory bodies including the FDA, using the ZINC database. Screening was performed against viral targets using three sequential docking modes (i.e. HTVS, SP and XP). Our in-silico virtual screening identified ~290 potential drugs based on the criteria of energy, docking parameters, ligand and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. A top lead from each target group was further subjected to molecular dynamics simulation (MDS) using the Desmond module to validate the efficacy of the screening pipeline. All of the simulated hit-target complexes were predicted to strongly interact and with highly stable binding. Thus, we have identified a number of approved and investigational drugs with high likelihood of inhibiting a variety of key SARS-CoV-2 proteins. Follow-up studies will continue to identify inhibitors suitable for combination therapy based on drug-drug synergy to thwart resistance. In addition, the screening hits that we have identified provide excellent probes for understanding the binding properties of the active sites of all seven targets, further enabling us to derive consensus molecules through computer-aided drug design (CADD). While infections are expanding at a rampant pace, it must be recognized that resistance will grow commensurately through either genetic shift and/or genetic drift to all small molecule drugs identified. Vaccines should provide a more permanent solution through prevention, but resistivity is still a possible scenario. Nevertheless, a persistent multi-target drug development program is essential to curb this ongoing pandemic and to keep reemergence in check.

Preprint ARTICLE | doi:10.20944/preprints202308.1546.v1

SARS-CoV-2 Epidemic in a Small-Sized Municipality in Ceará State, Brazil: Temporal and Spatial Evolution

Jaliana Holanda Nascimento dos Santos, Carlos Henrique Alencar, Jorg Heukelbach

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Brazil; control measures; COVID-19; spatial analysis; temporal analysis

Online: 22 August 2023 (09:39:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0020.v1

Impact of SARS-Cov-2 on Clinical Trial Unit Workforce in the United Kingdom: An Observational Study

Gayathri Delanerolle, Jintong Hu, Heitor Cavalini, Lucy Yardley, Katharine Barnard-Kelly, Kathryn Elliot, Vanessa Raymont, Shanaya Rathod, Jian Qing Shi, Peter Phiri

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: COVID-19; Clinical trials; Mental health; Vaccination; CTU workforce

Online: 1 March 2023 (10:44:52 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202003.0394.v2

Understanding the Role of Key Point Mutations in Receptor Binding Domain of SARS-CoV-2 Spike Glycoprotein

Bipin Singh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Covid-19; SARS-CoV-2; ACE2; Coronavirus; 2019-nCoV

Online: 30 March 2020 (08:25:51 CEST)

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Preprint REVIEW | doi:10.20944/preprints202304.0767.v1

Functional Foods: A Promising Strategy for Restoring Gut Microbiota Diversity Impacted by SARS-CoV-2 Variants

Antara Banerjee, Indumathi Somasundaram, Diptimayee Das, Samatha Jain M, Husaina Banu, Pavane MS, Sujay Paul, Atil Bisgin, Hong Zhang, Xiao-Feng Sun, Asim K Duttaroy, Surajit Pathak

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: COVID-19; SARS-CoV-2; Gut microbiota; Variants; Probiotics; gut microbiota metabolites

Online: 23 April 2023 (04:34:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202209.0390.v1

Determination of SARS-CoV-2 Variants and Seroprevalence in Accra, Ghana during the Delta-Omicron Waves

Irene Owusu Donkor, Elvis Suatey Lomotey, Jewelna Akorli, Millicent Opoku, Emmanuel Frimpong Gyekye, Kojo M. Sedzro, Nana Efua Andoh, Yvonne Ashong, Benjamin Abuaku, Kwadwo Ansah Koram, Vincent Munster

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; asymptomatic; seroprevalence; Delta variant; Omicron variant; vaccination

Online: 26 September 2022 (09:41:01 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0428.v1

A Furin Cleavage Site Inserted into the Spike Protein of SARS-CoV-2: A Structural Implication?

Wei Li

Subject: Biology And Life Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; furin cleavage site (FCS); salt bridging analysis

Online: 29 March 2020 (08:54:42 CEST)

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Working Paper ARTICLE

Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia

Ngoc Minh Hien Phan, Helen Faddy, Robert Flower, Kirsten Spann, Eileen Roulis

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; novel severe acute respiratory syndrome coronavirus 2; ancestral reconstruction; clonality; source of entry; dispersal routes

Online: 28 June 2020 (09:21:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0008.v1

KERRA, Mixed Medicinal Plant Extracts, Inhibits SARS-CoV-2 Targets Enzymes and Feline Corona Virus

Supaphorn Seetaha, Phatcharin Khamplong, Panatda Wanaragthai, Thitinan Aiebchun, Siriluk Ratanabunyong, Sucheewin Krobthong, Yodying Yingchutrakul, Jatuporn Rattanasrisomporn, Kiattawee Choowongkomon

Subject: Medicine And Pharmacology, Pharmacy Keywords: COVID-19 pandemic; KERRA; SARS-CoV-2 main protease; RNA-dependent RNA polymerase; anti-FIPV activity

Online: 1 April 2022 (14:53:44 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202005.0177.v1

Interference of SARS-CoV-2 with the Homeostasis of Ventilation and Perfusion in the Lung

Clemente F. Arias, Francisco J. Acosta, Federica Bertocchini, Cristina Fernández-Arias

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; COVID-19; homeostasis; hypoxic pulmonary vasoconstriction; renin-angiotensin system; hydrostatic edema; permeability edema

Online: 10 May 2020 (17:22:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0390.v1

A Novel Purification Procedure for Active Recombinant Human DPP4 and the Inability of DPP4 to Bind SARS-CoV-2

Cecy Xi, Arianna Arianna Di Fazio, Naveed Nadvi, Karishma Patel, Michelle Xiang, Hui Emma Zhang, Chandrika Deshpande, Jason Low, Xiaonan Trixie Wang, Yiqian Chen, Brenna Osborne, Ana Julia Vieira de Ribeiro, Geoffrey McCaughan, Bret Church, Joel Mackay, Mark Gorrell

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Recombinant protein; Protease; DPP4; Covid-19

Online: 17 September 2020 (08:44:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1276.v1

Genomic analysis and tracking of SARS-CoV-2 variants in Gwangju, South Korea from 2020 to 2022

Yeong-Un Lee, Kwangho Lee, Hongsu Lee, Jung wook Park, Sun-Ju Cho, Ji-Su Park, Jeongeun Mun, Sujung Park, Cheong-mi Lee, Juhye Lee, Mihee Seo, Eunju Kim, Jinjong Seo, Yonghwan Kim, Sun-Hee Kim, Yoon-Seok Chung

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; whole-genome sequencing; variants; lineages

Online: 19 October 2023 (11:25:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.0196.v1

“When”, “Where”, and “How” of SARS-CoV-2 Infection Affects the Human Cardiovascular System: a Narrative Review

Nicholas G. Kounis, Christos Gogos, Cesare de Gregorio, Ming-Yow Hung, Sophia N. Kouni, Efthymios P. Tsounis, Stelios F. Assimakopoulos, Soheila Pourmasumi, Virginia Mplani, George Servos, Periklis Dousdampanis, Panagiotis Plotas, Marina A. Michalaki, Grigorios Tsigkas, Gerasimos Grammatikopoulos, Dimitrios Velissaris, Ioanna Koniari

Subject: Biology And Life Sciences, Life Sciences Keywords: ACE2 receptors; COVID-19; cardiac complications, kinin-kallikrein; Kounis syndrome

Online: 2 August 2023 (10:07:00 CEST)

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The novel severe acute respiratory coronavirus-2 (SARS-Cov-2) constitutes the causative agent of coronavirus disease-2019 (COVID-19). Several mechanisms have been proposed regarding the development of cardiovascular complications during and after acute COVID-19 infection. COVID-19, caused by SARS-CoV-2, has emerged as one of the deadliest pandemics in modern history. Several clinical and pathophysiologic mechanisms have been proposed for development of cardiovascular complications during and after acute COVID-19 infection. The myocardial injury in patients with COVID-19 has been attributed to coronary spasm, microthrombi formation, plaque rupture, hypoxic injury or cytokine storm disposing the same pathophysiology with the three clinical variants of Kounis syndrome. One of the main proposed mechanisms for development of cardiovascular complications is the angiotensin converting enzyme 2 (ACE2) and its interactions with the renin-aldosterone system (RAAS) and the kinin-kallikrein system (KKS). The ACE2 receptors are expressed throughout the human body located mainly in heart, blood vessels endothelium, lungs, intestines, testes and neurons. The SARS-CoV-2 directly invades the endothelial cells that contain ACE2 receptors and constitutes the main pathway through which the virus enters the endothelial cells. This leads to downregulation of the ACE2 receptors and causes angiotensin II accumulation leading to prothrombotic effects such as hemostatic imbalance via activation of the coagulation cascade, impaired fibrinolysis, thrombin generation, vasoconstriction, endothelial and platelet activation, and pro-inflammatory cytokine release. Indeed, angiotensin I exerts no direct biological function except that its high levels can stimulate catecholamine production. It is metabolized to its biologically active byproduct angiotensin II, a potent vasoconstrictor, by angiotensin converting enzyme (ACE) through cleavage of the two terminal amino acids. SARS-CoV-2 infection prevents the counterbalancing action of the KKS system that normally causes vasodilation and regulates tissue repair, inflammation, cell proliferation, and platelet aggregation. All this cascade leads to the following cardiovascular events: cardiac arrhythmias, cardiac arrest, cardiomyopathy, cytokine storm, heart failure, ischemic myocardial injuries and microvascular disease, Kounis syndrome, long COVID, myocardial fibrosis, myocarditis, new onset hypertension, pericarditis, postural orthostatic tachycardia syndrome (POTS), pulmonary hypertension, stroke, Takotsubo Syndrome, venous thromboembolism and thrombocytopenia. In this narrative review we describe and elucidate when and how the COVID-19 affects the human cardiovascular system, in various areas on the human body that are vulnerable in every category of patients including children and athletes.

Preprint REVIEW | doi:10.20944/preprints202305.1219.v1

Biology and Behavior of SARS-COV-2 Contagion with Emphasis on Treatment Strategies, Risk Assessment, and Resilience

James Baldwin, Samina Noorali, Ashok Vaseashta

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; risk assessment; mitigation; resilience; pandemic modeling; lessons learned

Online: 17 May 2023 (09:59:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0861.v1

Prevalence of SARS-CoV-2 Infections and the Percentage of Deaths Among Infected Healthcare Workers in Poland

Marek Wojczyk, Ewa Niewiadomska, Małgorzata Kowalska

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; healthcare workers; pandemics; SARS-CoV-2; vaccination coverage

Online: 24 April 2023 (13:51:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0586.v1

Experimental Lung Inflammation Induced by Inactivated SARS-CoV-2 is Controlled by Intranasal Instillation of Vitamin D

William Danilo Fernandes de Souza, Sofia Fernanda Gonçalves Zorzella-Pezavento, Marina Caçador Ayupe, Caio Loureiro Salgado, Bernardo de Castro Oliveira, Francielly Moreira, Guilherme William da Silva, Stefanie Primon Muraro, Gabriela Fabiano de Souza, José Luiz Proença-Módena, Joao Pessoa Araujo-Junior, Denise Fonseca, Alexandrina Sartori

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; lung; inflammation; mice; vitamin D

Online: 31 January 2023 (12:04:19 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202208.0081.v1

Pathological Evidence for Residual SARS-CoV-2 in the Micrometastatic Niche of a Patient with Ovarian Cancer

Takuma Hayashi, Kenji Sano, Nobuo Yaegashi, Ikuo Konishi

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; micrometastatic niche; Patient with Cancer

Online: 3 August 2022 (10:22:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0258.v1

Prevalence of Co-Infections With Respiratory Viruses in Individuals Investigated for Sars-Cov-2 in Ontario, Canada

Adriana Peci, Vanessa Tran, Jennifer L Gurtherie, Ye Li, Paul Nelson, Kevin L Schwartz, Sara A Buchan, Jonathan B Gubbay

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: co-infection; SARS-CoV-2; Covid-19; seasonal respiratory viruses

Online: 10 December 2020 (12:53:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0174.v1

Homologous or Heterologous COVID-19 Boosters Regimens Significantly Impact Sero-neutralization of SARS-CoV-2 Virus and Variants

Rome Buathong, Taweewun Hunsawong, Supaporn Wacharapluesadee, Suriya Guharat, Ratthapat Jirapipatt, Sasiprapa Ninwattana, Nattakarn Thippamom, Anusara Jitsatja, Anthony R. Jones, Kamonthip Rungrojchareonkit, Jindarat Lohachanakul, Rungarun Suthangkornkul, Kedsara Tayong, Chonticha Klungthong, Stefan Fernandez, Opass Putcharoen

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; vaccine; booster; variants of concern; neutralization

Online: 12 July 2022 (07:43:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0021.v2

Expression and Clinical Significance of SARS-CoV-2 Human Targets in Lung Tissues: Normal, Primary Tumor and Metastasis

Karthikeyan Subbarayan, Kamatchi Ulagappan, Claudia Wickenhauser, Barbara Seliger

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: COVID-19; metastasis; lung adenocarcinoma; smoking; aging; ACE2

Online: 6 July 2020 (10:14:03 CEST)

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Preprint REVIEW | doi:10.20944/preprints202401.1910.v1

Cytokine Storm Fatal Acute Kidney Infection Triggered by COVID-19 (SARS CoV-2) Infection: A Review

Hailemeleak Regassa, Kasahun Gudeta, Ankeet Bhagat, Rachna Chaturvedi

Subject: Medicine And Pharmacology, Internal Medicine Keywords: cytokine storm, COVID-19, Acute kidney infection, SARS-CoV-2, pro-inflammatory cytokines

Online: 29 January 2024 (02:10:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.2087.v1

SARS-CoV-2 and Influenza Vaccine Hesitancy during the COVID-19 Pandemic in a Dynamic Perspective

Valentina Gerussi, Maddalena Peghin, Alvisa Palese, Maria De Martino, Elena Graziano, Stefania Chiappinotto, Federico Fonda, Giulia Bontempo, Tosca Semenzin, Luca Martini, Miriam Isola, Carlo Tascini

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Influenza; COVID-19; SARS-CoV-2; Green-Pass; Vaccination; Immunization; Vaccine-hesitancy; Pandemic

Online: 29 June 2023 (10:23:58 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0481.v1

Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance

Warish Ahmed, Stuart Simpson, Paul Bertsch, Kyle Bibby, Aaron Bivins, Linda Blackall, Silvia Bofill-Mas, Albert Bosch, Joao Brandao, Phil Choi, Mark Ciesielski, Erica Donner, Nishita D'Souza, Andreas Farnleitner, Daniel Gerrity, Raul Gonzalez, John Griffith, Pradip Gyawali, Charles Haas, Kerry Hamilton, Chanditha Hapuarachchi, Valerie Harwood, Rehnuma Haque, Greg Jackson, Stuart Khan, Wesaal Khan, Masaaki Kitajima, Asja Korajkic, Giuseppina La Rosa, Blythe Layton, Erin Lipp, Sandra McLellan, Brian McMinn, Gertjan Medema, Suzanne Metcalfe, Wim Meijer, Jochen Mueller, Heather Murphy, Colleen Naughton, Rachel Noble, Sudhi Payyappat, Susan Petterson, Tarja Pitkanen, Veronica Rajal, Brandon Reyneke, Fernando Roman, Joan Rose, Marta Rusinol, Michael Sadowsky, Laura Sala-Comorera, Yin Xiang Setoh, Samendra Sherchan, Kwanrawee Sirikanchana, Wendy Smith, Joshua Steele, Rosalie Sabburg, Erin Symonds, Phong Thai, Kevin Thomas, Josh Tynan, Simon Toze, Janelle Thompson, Andy Whiteley, Judith Wong, Daisuke Sano, Stefan Wuertz, Irene Xagoraraki, Qian Zhang, Amity Zimmer-Faust, Orin Shanks

Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: COVID-19; SARS-CoV-2; Wastewater; Surveillance; False-positive; False-negative; RT-PCR

Online: 19 April 2021 (13:08:13 CEST)

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Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.

Working Paper REVIEW

A Critical Review of Disinfection Processes to Control SARS-CoV-2 Transmission in the Food Industry

Adrián Pedreira, Yeşim Taşkın, Míriam R. García

Subject: Biology And Life Sciences, Food Science And Technology Keywords: SARS-CoV-2; COVID-19 pandemic; food industry; disinfection trade-offs; one-health

Online: 15 December 2020 (12:58:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0439.v1

Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

Umesh Kalathiya, Monikaben Padariya, Marcos Mayordomo, Małgorzata Lisowska, Judith Nicholson, Ashita Singh, Maciej Baginski, Robin Fåhraeus, Neil Carragher, Kathryn Ball, Juergen Haas, Alison Daniels, Ted R. Hupp, Javier Antonio Alfaro

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; spike glycoprotein; variability; molecular docking; molecular dynamics; inhibitors

Online: 24 April 2020 (11:42:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0308.v1

Pharmacoinformatics and Molecular Dynamic Simulation Studies Reveal Potential Inhibitors of SARS-CoV-2 Main Protease 3CL^pro

Mubarak A. Alamri, Muhammad Tahir ul Qamar, Safar M. Alqahtani

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: SARS-CoV-2; COVID-19; 3CL protease; molecular docking; molecular dynamics and simulations

Online: 23 February 2020 (02:17:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0815.v1

The Anti-SARS-CoV-2 IgG1 and IgG3 Antibody Isotypes with Limited Neutralizing Capacity against Omicron Elicited in a Latin Population Switch toward IgG4 after Multiple Doses with the mRNA Pfizer-BioNTech Vaccine.

Ana M Espino, Albersy Armina-Rodriguez, Laura Alvarez, Carlimar Ocasio, Riseilly Ramos-Nieves, Esteban I Rodríguez-Martinó, Paola López-Marte, Esther A. Torres, Carlos A. Sariol

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Covid-19; IgG4; Switch class; ELISA; neutralizing antibody

Online: 10 January 2024 (11:06:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.1945.v1

Cognitive Profile of SARS-cov-2 Recovered Patients: A Comprehensive Analysis of Persistent Dysfunctions in Long COVID

Alisson Rafael Oliveira Lima, Beatriz Cavendish, Bianca Silva Pinto, Rebeca Pelosof, Juliana Pereira de Sousa, Pedro Henrique Rodrigues da Silva, Laiss Bertola, Mariana Pita Batista, Adriano Augusto Domingos Neto, Andre Russowsky Brunoni, Kallene Summer Moreira Vidal, Dora Fix Ventura

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: memory loss; long COVID; post COVID; depression; mental confusion; COVID-19

Online: 27 July 2023 (13:28:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0647.v1

Nanomaterials Used in the Preparation of Personal Protective Equipment (PPE) in the Fight against SARS-CoV-2

Pierantonio De Luca, Anastasia Macario, Janos B.Nagy

Subject: Chemistry And Materials Science, Nanotechnology Keywords: Covid-19; Coronaviruses; Personal protective equipment; Nanomaterials; PPE; SARS-CoV-2

Online: 8 June 2023 (13:19:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0558.v2

Small Molecule Stabilization of Non-native Protein-Protein Interactions of SARS-CoV-2 N Protein as a Mechanism of Action against COVID-19

Martin Lavecchia, Julian Fernandez

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; protein protein interactions; virtual screening; docking; molecular dynamics; zinc

Online: 2 September 2020 (09:48:48 CEST)

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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/preprints202004.0052.v1

Estimation of Unreported Novel Coronavirus (SARS-CoV-2) Infections from Reported Deaths: a Susceptible Exposed Infectious Recovered Dead Model

Andrea Maugeri, Martina Barchitta, Sebastiano Battiato, Antonella Agodi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: novel coronavirus; epidemiology; COVID-19; epidemic model

Online: 6 April 2020 (12:30:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0387.v1

Acquisition of Humoral Immune Responses in Convalescent Japanese People with SARS-CoV-2 (COVID-19) Infection in 2021

Koshiro Monzen, Takanori Watanabe, Toshihiro Okabe, Hisakuni Sekino, Hironori Nakagami, Ryuichi Morishita

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-CoV-2; Convalescent serum; Neutralizing antibody

Online: 4 August 2023 (12:35:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0319.v1

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-Cov-2 Spike Protein

Rico Ballmann, Sven-Kevin Hotop, Federico Bertoglio, Stephan Steinke, Philip Alexander Heine, M.-Zeeshan Chaudhry, Dieter Jahn, Boas Pucker, Fausto Baldanti, Antonio Piralla, Maren Schubert, Luka Čičin-Šain, Michael Hust, Stefan Dübel

Subject: Biology And Life Sciences, Virology Keywords: phage display; epitope mapping; COVID-19; genomic library; NGS

Online: 24 May 2022 (04:20:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0319.v1

SARS-CoV-2 Impact on the Central Nervous System: Are Astrocytes and Microglia Main Players or Merely Bystanders?

Veronica Murta, Alejandro Villarreal, Alberto Javier Ramos

Subject: Biology And Life Sciences, Virology Keywords: glia; central nervous system; COVID-19; SARS; MERS; coronavirus

Online: 26 June 2020 (17:32:55 CEST)

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With confirmed COVID-19 cases surpassing the 8.5 million mark around the globe, there is an imperative need to deepen the efforts from the international scientific community to gain comprehensive understanding of SARS-CoV-2. Although the main clinical manifestations are associated with respiratory or intestinal symptoms, reports of specific and non-specific neurological signs and symptoms, both at presentation or during the course of the acute phase, are increasing. Approximately 25-40% of the patients present neurological symptoms. The etiology of these neurological manifestations remains obscure, and probably involves several direct pathways, not excluding the direct entry of the virus to the Central Nervous System (CNS) through the olfactory epithelium, circumventricular organs, or disrupted blood-brain barrier (BBB). Furthermore, neuroinflammation might occur in response to the strong systemic cytokine storm described for COVID-19, or due to dysregulation of the CNS angiotensin system. Descriptions of neurological manifestations in patients in the previous coronavirus (CoV) outbreaks have been numerous for the SARS-CoV and lesser for MERS-CoV. Strong evidence from patients and experimental models suggests that some human variants of CoV have the ability to reach the CNS and that neurons, astrocytes and/or microglia can be target cells for CoV. A growing body of evidence shows that astrocytes and microglia have a major role in neuroinflammation, responding to local CNS inflammation and/or to dysbalanced peripheral inflammation. This is another potential mechanism for SARS-CoV-2 damage to the CNS. In this work we will summarize the known neurological manifestations of SARS-CoV-2, SARS-CoV and MERS-CoV, explore the potential role for astrocytes and microglia in the infection and neuroinflammation, and compare them with the previously described human and animal CoV that showed neurotropism. We also propose possible underlying mechanisms by focusing on our knowledge of glia, neurons, and their dynamic intricate communication with the immune system.

Preprint CASE REPORT | doi:10.20944/preprints202004.0446.v1

Central Disequilibrium Could be an Early Sign and Symptom of Rapidly Progressive SARS-CoV-2 related Respiratory Failure

Ali Zreik, Ali Ammar, Charles. Hunley, Mario Madruga, Rumi Khan

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Central Disequilibrium; CNS; covid-19 coronavirus; SARS-CoV-2

Online: 24 April 2020 (14:07:43 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202004.0090.v1

Hydroxychloroquine as an Aerosol Might Markedly Reduce and Even Prevent Severe Clinical Symptoms after SARS-CoV-2 Infection

Ansgar Klimke, Gudrun Hefner, Bianca Will, Ursula Voss

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: COVID-19: hydroxychloroquine aerosol; pharmacotherapy; prevention; SARS-CoV-2

Online: 7 April 2020 (11:11:09 CEST)

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Covid-19 is a new coronavirus disease first described in December 2019. This respiratory illness is severe and potentially fatal. Severe cases make up to 15%, lethality ranges between 1.5 and more than 10 %. What is urgently needed is an efficient pharmacological treatment for the treatment of severe cases. During the infection of alveolar epithelial cells of the lung, the ACE2 receptor has a central function. The antimalarial drugs chloroquine phosphate (CQ) and hydroxychloroquine (HCQ) impair in vitro the terminal glycosylation of ACE2 without significant change of cell-surface ACE2 and, therefore, might be potent inhibitors of SARS-CoV-2 infections. Starting inhibition at 0.1 µM, CQ completely prevented in vitro infections at 10 µM, suggesting a prophylactic effect and preventing the virus spread 5 hours after infection. In a first clinical trial, CQ was effective in inhibiting exacerbation of pneumonia, improving lung imaging findings, promotion of virus-negative conversion, and shortening the disease. In addition, HCQ, which is three times more potent than CQ in SARS-CoV-2 infected cells (EC50 0.72 µM), was significantly associated with viral load reduction/disappearance in COVID-19 patients compared to controls. Theoretically, CQ and HCQ could thus be effectively used in the treatment of SARS-CoV pneumonia. From a pharmacological standpoint, however, the major problems of oral treatment with these drugs are possible severe side effects and toxicity. Concretely, this relates to (a) the inconsistent individual bioavailability of these drugs at the alveolar target cells, depending on intestinal resorption, hepatic first-pass metabolism and accumulation in liver, spleen and lung, and (b) the need for a relatively high concentration of 1-5 µM at the alveolar surface. Therefore, we propose in a first dose estimation the use of HCQ as an aerosol in a dosage of 2-4 mg per inhalation in order to reach sufficient therapeutic levels at the alveolar epithelial cells. By using a low-dose non-systemic aerosol, adverse drug reactions will markedly be reduced compared with oral application. This increase in tolerability enables a broader use for prevention and after contact with an infected person, which would be an advantage especially for the high-risk, often multi-morbid and elderly patients. Empirical data on self-medication with a one-week aerosol application by two of the authors is presented. Inhalation was well tolerated without relevant side effects.

Preprint REVIEW | doi:10.20944/preprints202009.0361.v2

Foodborne Transmission of SARS-CoV-2 Is More Evident Than It Has Been Before

Hamada Aboubakr, Sagar Goyal

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; foodborne viruses; enteric viruses; fecal-oral transmission; fresh produce, berries, fruits, hepatitis A virus, Norovirus, ready-to-eat foods.

Online: 18 September 2020 (10:35:33 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202304.1127.v1

Metformin Therapy Changes Gut Microbiota Alpha-Diversity in COVID-19 Patients with Type 2 Diabetes: The Role of SARS-CoV-2 Variants and Antibiotic Treatment

Pavlo Petakh, Iryna Kamyshna, Valentyn Oksenych, Denis Kainov, Aleksandr Kamyshnyi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; gut microbiota; diversity; diabetes; metformin

Online: 28 April 2023 (07:06:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0171.v2

Systems Biology Approach to Characterize Potential SARS-CoV-2 Pathways Based on Protein Functional Motifs

Haitham Sobhy

Subject: Biology And Life Sciences, Virology Keywords: protein functional domains; short linear motifs; coronaviruses; COVID-19; severe acute respiratory syndrome-related coronavirus; 2019-nCoV; virus outbreak

Online: 16 May 2020 (18:54:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0040.v1

Augmented Sensitivity of At-Home Rapid SARS-CoV-2 Antigen Test (RAT) Kits with Computer Vision

Kim Miikki, Lars Miikki, Jenny Wiklund, Alp Karakoç

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; rapid antigen test; RT-PCR test; COVID-19; image processing; Raspberry Pi

Online: 2 March 2022 (08:06:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0473.v1

Summarize of the Available Molecular Methods for Detection of Sars-Cov-2 During the Ongoing Pandemic

Fabio Arena, Simona Pollini, Gian Maria Rossolini, Maurizio Margaglione

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: molecular methods; virus; pandemic; Coronaviridae; COVID-19, diagnosis; UK variant; B.1.1.7 variant; 501Y.V2 variant

Online: 25 January 2021 (10:32:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0050.v1

Biological Cloth Face Coverings - The Reduction of SARS-CoV-2 and Influenza (H1N1) Infectivity by Viruferrin^TMTreatment

Emily Medina Magues, Anna Stedman, Paul Hope, Jorge E. Osorio

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; face masks; Personal Protective Equipment; Personal Protective Material; droplet; aerosols

Online: 2 April 2021 (11:28:19 CEST)

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Preprint ESSAY | doi:10.20944/preprints202012.0730.v1

Model Estimation for Sars-Cov-2 Peak Contagion (Mespc): Brazil’s Case for the First and Second Wave

Guilherme Asai

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Monte Carlo Simulation; Bayesian statistics; SARS-CoV-2; Covid-19; model estimation

Online: 29 December 2020 (14:34:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0655.v1

SARS-CoV-2 and Rohingya Refugee Camp, Bangladesh: Uncertainty and How the Government Took Over the Situation

Md. Kamrujjaman, MD. Shahriar Mahmud, Shakil Ahmed, Md. Omar Qayum, Mohammad Morshad Alam, Md Nazmul Hassan, Md Rafiul Islam, Kaniz Fatema Nipa, Ummugul Bulut

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; Rohingya Refugee camp; Mathematical model; Numerical results; Basic reproduction number.

Online: 25 December 2020 (12:06:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202102.0588.v1

Inactivating SARS-CoV-2 Using 275nm UV-C LEDs through a Spherical Irradiation Box: Design, Characterization and Validation

Nicola Trivellin, Matteo Buffolo, Francesco Onelia, Alberto Pizzolato, Marco Barbato, Viviana Teresa Orlandi, Claudia Del Vecchio, Fabrizio Dughiero, Enrico Zanoni, Gaudenzio Meneghesso, Andrea Crisanti, Matteo Meneghini

Subject: Engineering, Automotive Engineering Keywords: SARS-CoV-2; Covid-19; LED; UVC; disinfection; inactivation; virucide

Online: 25 February 2021 (14:44:22 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 CONCEPT PAPER | doi:10.20944/preprints202004.0412.v1

Think Different with RNA Therapy: Can Antisense Oligonucleotides Be Used to Inhibit Replication and Transcription of SARS-Cov-2?

Eric Barrey, Veronica Burzio, Sophie Dhorne-Pollet, Jean-François Eléouët, Bernard Delmas

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: coronavirus; COVID-19; antisense oligonucleotide; ASO; LNA GapmeR

Online: 23 April 2020 (11:30:39 CEST)

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The severity of the global COVID-19 pandemic, with a high transmission rate, 2.6-4.7% lethality and a huge economic impact, poses an urgent need for efficient medical treatments and vaccines. Currently, there are only non-specific treatments to assist the patients in acute respiratory distress during the inflammatory step following the preliminary infection by SARS-CoV-2. Clinical trials of drug repurposing were quickly launched at the international level. Specific treatments such as the transfusion of plasma from patients who have recovered into infected patients or the use of specific inhibitors of the viral RNA-polymerase complex are promising strategies to block infection. To complete the therapeutic arsenal, we believe that the opportunity of targeting the SARS-CoV-2 genome by RNA therapy should be deeply investigated. In the present paper, we propose to design specific antisense oligonucleotides targeting transcripts encoding viral proteins associated to replication and transcription of SARS-CoV-2, aiming to block infection. We designed antisense oligonucleotides targeting the genomic 5’ untranslated region (5’-UTR), open reading frames 1a and 1b (ORF1a and ORF1b) governing expression of the replicase/transcriptase complex, and the gene N encoding the nucleoprotein that is genome-associated. To maximize the probability of efficiency, we predicted the antisense oligonucleotides by using two design methods: i) conventional antisense oligonucleotides with 100% phosphorothioate modifications (ASO); ii) antisense locked nucleic acids GapmeR. After binding the viral RNA target, the hetero-duplexes antisense oligonucleotide-RNA are cleaved by RNAse H1. Nine potent ASO candidates were found and we selected five of them targeting ORF1a (3), ORF1b (1) and N (1). Nine GapmeR candidates were predicted with excellent properties and we retained four of them targeting 5’-UTR (1), ORF1a (3), ORF1b (1) and N (1). The most potent GapmeR candidate targets the 5’-UTR, a key genomic domain with multiple functions in the viral cycle. By this open publication, we are pleased to share these in silico results with the scientific community in hopes of stimulating innovation in translational research in order to fight the unprecedented COVID-19 pandemic. These antisense oligonucleotide candidates should be now experimentally evaluated.

Preprint ARTICLE | doi:10.20944/preprints202401.1449.v1

COVID-19–Sensitive Tumour Response – 2-Year Assessment of the SARS-CoV-2 Humoral Response in Cancer Patients in Oncology Hospital in Poland

Piotr Kosiorek, Bożena Mikołuć, Samuel Stróż, Anna Hryniewicz, Dorota Elżbieta Kazberuk, Robert Milewski, Anna Grzeszczuk, Magdalena Joanna Borkowska, Anna Stasiak-Barmuta

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: breast cancer; lung cancer; colon cancer; SARS-CoV-2; COVID-19

Online: 19 January 2024 (04:45:55 CET)

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Background: So far, vaccination has been considered the most crucial defense against viral infection, including SARS-CoV-2. Numerous reports have demonstrated the effectiveness of the above vaccines in oncology patients. It has also been proven that, apart from vaccinations and oncological therapy, the course of the cancer process itself influences the magnitude of the humoral response, especially in people after infection with SARS-CoV-2. Objective: This study aimed to answer the question about the impact of the cancer process on the humoral response in oncological patients vaccinated against SARS-CoV-2 infection and in patients after COVID-19. Material and methods: 1,668 people were observed. Over two years, 5,082 SARS-CoV-2 IgG and IgM antibody samples were determined. The concentration of antibodies was assessed in three groups of oncological patients: those undergoing anticancer therapy after contracting COVID-19 and those after vaccination against the SARS-CoV-2 infection. Results: The obtained results indicate a naturally more significant humoral response in oncological patients who have not been vaccinated and have not undergone anticancer therapy, such as radiotherapy, chemotherapy, or surgical intervention. The above observation applies to patients with breast, lung, and colon cancer, although the response varies significantly depending on the type of cancer. Summary: The size of the humoral response and the presence of specific antibodies directed against the SARS-CoV-2, IgM, and IgG, in response to the supply of the vaccine antigen or assessed after COVID-19, is an indicator of adequate immune protection against reinfection. This study highlights for the first time the phenomenon of increased humoral response in response to a viral infection in patients with certain types of cancer that are assumed to be sensitive to oncological therapy, the initiation of which, according to generally accepted principles, was blocked by infection with the SARS-CoV-2. The phenomenon we observe seems to confirm the presence of a "natural" defence potential in a cancer patient's body, in this case, directed against infection with a viral pathogen. A "stronger" antiviral response also seems to explain the asymptomatic course of SARS-CoV-2 infection in some of the above patients. It remains an open question to what extent the SARS-CoV-2 infection weakened the "natural" potential of the anticancer response in these patients.

Preprint COMMUNICATION | doi:10.20944/preprints202004.0130.v1

Challenges in Controlling SARS-CoV-2 in a Lower-middle Income Country and the Potential Unintended Effects due to Aggressive Restrictions

Lincoln Lau, Peng Wu, Daryn Go, Warren Dodd, Charles Yu

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: COVID-19; LMIC; Quarantine Measures

Online: 8 April 2020 (12:03:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0192.v1

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Jake Gazeley, Terence Lee, Daniel R Knight, Alexander Shivarev, Cameron Gordon, David Speers, Dylan D Barth, Jelena Maticevic, Meredith Hodge, Paul Armstrong, Paul Knight, Sandra Sjollema, Avram Levy

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Wastewater-based epidemiology; SARS-CoV-2; COVID-19; surveillance system; correlation analysis; genomics

Online: 5 March 2024 (09:07:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.0871.v1

María Gónzalez, Miriam Al-Adib, Ana Beatriz Rodríguez, Cristina Carrasco

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: women’s health; COVID-19 vaccine; menstrual-related disturbances; formerly menstruating women; secondary amenorrhea

Online: 13 June 2023 (03:38:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0334.v1

Molecular Docking and Molecular Dynamic Study of Two Viral Proteins Associated with SARS-CoV-2 with Ivermectin

Lenin Andres Gonzalez Paz, Carla A. Lossada, Luis S. Moncayo, Freddy Romero, J. L. Paz, Joan Vera-Villalobos, Aleivi E. Perez, Ernesto San-Blas, Ysaias J. Alvarado

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: SARS-COV-2; folding/unfolding; antiparasitic; molecular docking; molecular dynamics; COVID-19; Ivermectin

Online: 19 April 2020 (06:56:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0161.v2

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2

Olujide O. Olubiyi, Maryam Olagunju, Monika Keutmann, Jennifer Loschwitz, Birgit Strodel

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: COVID-19; docking; drug repurposing; natural products; in silico drug design; viral replication inhibition

Online: 1 June 2020 (02:42:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0369.v1

On the Essential Role of SARS-CoV-2 Localization in the Nasopharynx and Intestines in the Pathogenesis of COVID-19

Vasily Afonyushkin, Ilya Akberdin, Yulia Kozlova, Ivan Shchukin, Tatyana Mironova, Anna Bobikova, Nikolay Donchenko, Viktoria Cherepushkina, Yulia Poletaeva, Fedor Kolpakov

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; immunology; nasopharynx; intestines; lungs; mathematical modeling; modular approach; pathophysiology of COVID-19

Online: 28 March 2022 (14:40:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0360.v1

SARS-CoV-2 in Domestic UK Cats from Alpha to Omicron: Swab Surveillance and Case Reports

Sarah Jones, Grace B. Tyson, Richard J. Orton, Katherine Smollett, Federica Manna, Kirsty Kwok, Nicolás M Suárez, Nicola Logan, Michael McDonald, Andrea Bowie, Ana Filipe, Brian J. Willett, William Weir, Margaret J. Hosie

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; pets; companion animals; reverse zoonosis; veterinary; animal welfare; feline; One Health

Online: 4 August 2023 (14:48:06 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/preprints202310.1719.v2

Demographic Characteristics of Pre-Vaccinated Asymptomatic and Symptomatic SARS-CoV-2 Cases in Barwon South West Victoria, Australia

Shinae C Tobin-Salzman, Darcie Cooper, Bridgette J McNamara, Eugene Athan, Catherine M Bennett

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; asymptomatic; COVID-19; symptom profile; demographic; testing; ethnicity

Online: 4 December 2023 (04:21:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202205.0247.v1

Description of a One-Year Succession of Variants of Interest and Concern of SARS-Cov-2 in Venezuela

Rossana C. Jaspe, Carmen L. Loureiro, Yoneira F. Sulbaran, Zoila C. Moros, Pierina D´Angelo, Mariana Hidalgo, Lieska Rodriguez, Victor Alarcon, Marwan Aguilar, Doneyla Sanchez, Jesus Ramirez, Domingo J. Garzaro, Jose Luis Zambrano, Ferdinando Liprandi, Hector Rafael Rangel, Flor H. Pujol

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Variants of Concern; Rapid screening; Mutations

Online: 19 May 2022 (03:31:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0511.v1

COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-COV-2

Ameh S. James, John I. Al-alawneh

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: point of care testing; novel coronavirus; COVID-19; rapid testing; LAMP

Online: 29 April 2020 (13:43:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0151.v1

Dynamics of Anti-SARS-CoV-2 Antibodies in the Albanian Population: Impact of Infection and Vaccine-Induced Immunity during the COVID-19 Pandemic Year from August 2021 to August 2022

Genc Sulcebe, Alban Ylli, Fabian Cenko, Margarita Kurti-Prifti, Erkena Shyti, Jonida Dashi-Pasholli, Erina Lazri, Irena Seferi-Qendro, Melissa J. Perry

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-CoV-2 Seroprevalence; Vaccination Status; SARS-CoV-2; anti-SARS-CoV-2 antibodies; Albanian population

Online: 2 August 2023 (10:10:13 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202311.1268.v1

The Naturally Occurring m¹A RNA Modification Can Be Efficiently Incorporated into RNA by SARS-CoV-2 RdRp

Alexander Apostle, Reed Arneson, Yinan Yuan, Shiyue Fang

Subject: Biology And Life Sciences, Life Sciences Keywords: SARS-CoV-2; COVID-19; RdRp; m¹A triphosphate; Antiviral Drug

Online: 21 November 2023 (07:19:23 CET)

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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 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 ARTICLE | doi:10.20944/preprints202301.0404.v1

XBB.1.5 Kraken Cracked: Gibbs Energies of Binding and Biosynthesis of the XBB.1.5 Variant of SARS-Cov-2

Marko Popovic

Subject: Biology And Life Sciences, Virology Keywords: Omicron variant; Infectivity; Pathogenicity; Biothermodynamics; COVID-19; Viral evolution

Online: 23 January 2023 (08:53:40 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202105.0187.v1

Detection of Fecal SARS-CoV-2 RNA in a Prospective Cohort of Children with Multisystem Inflammatory Syndrome (MIS-C)

Emilia Parodi, Andrea Carpino, Elena Franchitti, Giulia Pruccoli, Marco Denina, Federica Pagliero, Ugo Ramenghi, Deborah Traversi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; stools; COVID-19; MIS-C; children

Online: 10 May 2021 (13:00:43 CEST)

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Working Paper ARTICLE

Raising Concern About Cross-Infection Between Humans and Companion Animals by Evolutionary Analysis of Receptors for SARS-CoV-2

Huihao Tang, Mayan Ali, Lina Zhang, Cheng Deng

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; companion animals; cross-infection

Online: 17 May 2020 (15:27:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202105.0549.v1

What Could Explain the Lower COVID-19 Burden in Africa Despite Considerable Circulation of the SARS-CoV-2 Virus?

Richard G. Wamai, Jason L. Hirsch, Wim Van Damme, David Alnwick, Robert C. Bailey, Stephen Hodgins, Uzma Alam, Mamka Anyona

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19 pandemic; Africa; SARS-CoV-2 virus spread; lower COVID-19 disease burden; African populations; demographic pyramid; trained immunity; government measures

Online: 24 May 2021 (09:56:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0961.v1

Whole Genome Sequence Analysis of SARS-COV-2 Isolated from COVID-19 Patients in Duhok Province, Iraq

Sherzad Majeed Taher, Jassim Mohammed Abdo, Muayad Aghali Merza

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19 patient; whole Genome sequence; Of SARS-COV-2; phylogenetic analysis and Transmission supported

Online: 26 April 2023 (05:15:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0426.v1

Predicting the Cross-Coordinated Immune Response Dynamics in Sars-Cov-2 Infection: Implications for Disease Pathogenesis

Dmitry Grebennikov, Antonina Karsonova, Marina Loginova, Valentina Casella, Andreas Meyerhans, Gennady Bocharov

Subject: Computer Science And Mathematics, Applied Mathematics Keywords: SARS-CoV-2 infection; innate immune response; antigen-specific immune response; kinetic coordination; mathematical model; pathogenesis, long COVID-19

Online: 27 July 2022 (15:11:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0380.v1

Molecular Mimicry between SARS-CoV-2 and Human Endocrinocytes: A Prerequisite of Post-COVID Endocrine Autoimmunity

Leonid P. Churilov, Muslimbek G. Normatov, Vladimir J. Utekhin

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; COVID-19; autoantibodies; autoimmune endocrinopathies; long-COVID syndrome; molecular mimicry; thyroid gland; adrenals; pituitary; Langerhans’ islets

Online: 26 July 2022 (03:42:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.2238.v1

Omicron Variant Reinfection Risk Among Individuals with Previous SARS-CoV-2 Infections within One Year in Shanghai, China: A Cross-sectional Study

Chuchu Ye, Anran Zhang, Ge Zhang, Hualei Xin, Kang Wu, Zhongjie Li, Yilin Jia, Lipeng Hao, Caoyi Xue, Yuanping Wang, Hongmei Xu, Yixin Zhou, Weiping Zhu

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: reinfection; COVID-19; vaccination; Omicron

Online: 31 May 2023 (11:38:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0439.v1

One Possible Reinfection with SARS-CoV-2 Validated by 205-days Interval of Re-detection in Sapporo City, Japan

Toshiaki Asakura, Akiko Tamakoshi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; reinfection; re-detected positive; Japan

Online: 16 April 2021 (11:09:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1536.v1

Evolution of Collective Sars-Cov-2 Humoral Immunity among the Population of the Republic of Belarus

Anna Y. Popova, Viacheslav Smirnov, Svetlana A. Egorova, Alexander A. Tarasenko, Alla M. Dashkevich, Angelika M. Milichkima, Angela L. Scuranovich, Irina V. Drozd, Iruna N. Glinskaya, Elena V. Zueva, Elena O. Samoilovich, Valery A. Ivanov, Edward S. Ramsay, Alexandra V. Gubanova, Victoria G. Drobyshevskaya, Oyuna B. Zhumbaeva, Olga A. Petrova, Alexandra P. Razumovskaya, Inna A. Karaban, Tamara V. Amvrosieva, Natalya P. Shmeleva, Ludmila V. Rubanic, Alina M. Dronina, Areg A. Totolian

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Republic of Belarus; population; SARS-CoV-2; COVID-19; seromonitoring; herd immunity; antibodies; nucleocapsid; receptor binding domain; vaccination; hybrid immunity

Online: 23 May 2023 (02:47:10 CEST)

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Background. The course of the COVID-19 epidemic process depends on population immunity which prevents pathogen spread among the population. Aim: to study the evolution of SARS-CoV-2 humoral immunity in the Belarusian population relative to COVID-19 pandemic dynamics. Materials and methods. The work was carried out according to a methodology for assessing population immunity developed by Rospotrebnadzor (Russia) and the Belarusian Ministry of Health with the participation of the St. Petersburg Pasteur Institute (SPPI), taking into account WHO recommendations. The study was approved by the Bioethics Committee of Belarus and the SPPI Bioethics Committee. Participant selection was carried out by questionnaire using a cloud (internet server) service. To monitor population immunity, a cohort of 4,661 people (participating in all stages of seromonitoring) was formed from the overall volunteer group. Volunteers were randomized by age group (1-17, 18-29, 30-39, 40-49, 50-59, 60-69, 70+ years), region, and professional group. For the detection of antibodies (Abs) to nucleocapsid (Nc) and S glycoprotein receptor-binding domain (RBD), corresponding assay systems were used following manufacturer instructions. The study was conducted in 4 stages according to a single scheme. Results. In the 1st stage (pandemic month 15), collective immunity was due mainly to Nc+RBD+ Ab status alone. By the 2nd stage (carried out after 4 months), their share decreased 1.2-fold, while the share of volunteers who had only RBD Abs increased 1.7-fold. In the 3rd and 4th stages (carried out after 9 and 19 months), the share of persons with RBD+Nc‒ compared to the 2nd stage decreased by 3.5%; the proportion of persons with Nc+RBD‒ Abs increased by 1.5-fold. The most important factor in population immunity was vaccination of the population, the coverage of which reached 70% by the 4th stage. Among vaccines, the Sputnik V and Sputnik Light vector designs were used most often. The whole-virion, inactivated BIBP-CorV vaccine was used less often. Conclusion. The evolution of collective SARS-CoV-2 humoral immunity included a set of changes in circulating Ab levels (Nc, RBD). The hybrid immunity formed helped to reduce the incidence to nearly zero.

Preprint ARTICLE | doi:10.20944/preprints202008.0092.v1

COVID-19 Vaccine Candidates by Identification of B and T Cell Multi-Epitopes Against SARS-COV-2

Suresh Kumar, Sarmilah Mathavan, Wee Jia Jin, Nur Azznira Bt Azman, Devindren Subramanaiam, Nur Afiqah Binti Zainalabidin, Dhivashini Lingadaran, Zainah Binti Abdul Sattar, Danniya Lakshmi Manickam, Priscilla Sheba Anbananthan, Johan Ahmad Taqiyuddin, Yuvapriya Thevarajan

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: COVID-19; SARS-CoV-2; epitopes; B-cell; T-cell; immuno informatics; MHC-I; MHC-II

Online: 4 August 2020 (11:18:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0576.v1

Neutralization of Different Variants of SARS-CoV-2 by a F(ab’)2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain

Mariajosé Rodriguez-Nuñez, Mariana del Valle Cepeda, Carlos Bello, Miguel Angel Lopez, Yoneira Sulbaran, Carmen Luisa Loureiro, Ferdinando Liprandi, Rossana Celeste Jaspe, Héctor Rafael Rangel, Flor Helene Pujol

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; variants; equine sera; neutralizing antibodies; immune escape; evolution

Online: 8 September 2023 (09:37:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0240.v1

Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife

Marcelo González-Aravena, Cristobal Galban-Malagon, Eduardo Castro-Nallar, Gonzalo P. Barriga, Victor Neira, Lucas Krüger, Aiko D. Adell, Jorge Olivares-Pacheco

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Antarctica; wastewater-based epidemiology; COVID-19; Antarctic wildlife; environmental surveillance

Online: 5 February 2024 (07:58:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0486.v1

A Meta-analysis of Comorbidities in COVID-19: Which Diseases increase the Susceptibility of SARS-CoV-2 Infection?

Srinivasan Ramachandran, Manoj Kumar Singh, Ahmed Mobeen, Amit Chandra, Sweta Joshi

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; comorbidity; SARS-CoV-2; leukemia; NAFLD; psoriasis; cancer; type II diabetes

Online: 21 September 2020 (03:32:58 CEST)

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Background: Comorbidities have been frequently reported in COVID-19 patients, which often lead to more severe outcomes. The underlying molecular mechanisms behind these clinical observations have not yet been explained. Herein, we investigated the disease-specific gene expression signatures that may induce susceptibility to SARS-CoV-2 infection. Methods: We studied 30 frequently occurring acute, chronic, or infectious diseases of recent times that have shown comorbidity in one or another respiratory disease(s) caused by pathogenic human infecting coronaviruses, especially SARS-CoV-2. We retrieved array-based gene expression data for each disease and control from relevant datasets. Subsequently, all the datasets were quantile normalized, and log-2 transformed data was used for analysis. Results The expression of ACE2 receptor and host proteases, namely FURIN and TMPRSS2 that are essential for cellular entry of SARS-CoV-2, was upregulated in all six studied subtypes of leukemia (hereafter, referred as leukemia). The expression of ACE2 was also increased in psoriasis, lung cancer, Non-alcoholic fatty liver disease (NAFLD), breast cancer, and pulmonary arterial hypertension patients. The expression of FURIN was higher in psoriasis, NAFLD, lung cancer, and in type II diabetic liver, whereas it was lowered in breast cancer. Similarly, the expression of TMPRSS2 was increased during lung cancer and type II diabetes; it was decreased during psoriasis, NAFLD, lung cancer, breast cancer, and cervical cancer.Furthermore, a heightened expression of genes that are involved in immune response was observed in leukemia patients, as shown by the higher expression of IFNA2, IFNA8, IFNA10, IFNA14, IFNA16, IFNA21, IFNB1, CXCL10, and IL6. The expression of JAK1, STAT1, IL6, and CXCL10 was higher in NAFLD. Besides, JAK1 and STAT1 were upregulated in type II diabetic muscles. In addition, most of the upregulated genes in COVID-19 patients showed a similar trend in leukemia, NAFLD, and psoriasis. Furthermore, SARS-CoV-2, SARS-CoV and MERS CoV, were found to commonly alter two genes, namely, CARBONIC ANHYDRASE 11 and CLUSTERIN.Conclusions: The genes that may confer susceptibility to SARS-CoV-2 infection are mostly upregulated in leukemia patients; hence, leukemia patients are relatively more susceptible to develop COVID-19, followed by other chronic disorders, such as, NAFLD, type II diabetes, psoriasis, and hypertension. This study identifies key genes that are altered in the studied diseases types, which may aid in the infection of SARS-CoV-2 and underlie COVID-19 associated comorbidities.

Preprint ARTICLE | doi:10.20944/preprints202402.0200.v1

SARS-CoV-2-Specific Immune Responses in Vaccination and Infection during the Pandemic in 2020–2022

Wakana Inoue, Yuta Kimura, Shion Okamoto, Takuto Nogimori, Akane Sakaguchi-Mikami, Takuya Yamamoto, Yasuko Tsunetsugu-Yokota

Subject: Medicine And Pharmacology, Other Keywords: SARS-CoV-2; COVID-19; infection and vaccination; serum and saliva; RBD and N-specific; IgG and IgA; T-cell responses

Online: 5 February 2024 (03:43:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202402.1094.v1

Development and Evaluation of an In-House Real-Time Rt-Pcr Targeting nsp10 Gene for SARS-CoV-2 Detection

Cyril Chik-Yan Yip, Jane Hau-Ching Poon, Kit-Hang Leung, Wan-Mui Chan, Jonathan Daniel Ip, Allen Wing-Ho Chu, Vincent Chi-Chung Cheng, Kwok-Yung Yuen, Kelvin Kai-Wang To

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; nsp10; real-time RT-PCR; diagnostic

Online: 20 February 2024 (06:07:31 CET)

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Preprint REVIEW | doi:10.20944/preprints202310.0001.v2

Xenosialylation: Role in SARS/CoV-2 Post-infectious and Post-vaccination Complications and Common Cause of Hyperimmune/Autoimmune Diseases

Fiorella Carnevali, Sara Mangiaterra, Giacomo Rossi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: sialic acid; sialylation; xeno-sialic acid; COVID-19; SARS-CoV-2

Online: 14 December 2023 (05:56:10 CET)

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The host glycosylation mechanism synthesizes the carbohydrates of glycoproteins of viral envelopes. Due to the loss of the Cytidine Monophospho-N-Acetylneuraminic Acid Hydroxylase gene by some mammalian species, including humans (negative-CMAH), Neu5Gc is no longer synthesized. Uptake of Neu5Gc by negative-CMAH species, through the intake of food products derived from positive-CMAH mammals, leads to incorporating Neu5Gc-glycans in the glycocalyx (xenosialylation). Neu5Gc, being a Mammalian-associated Carbohydrate Antigen (MCA), acts as a non-self-antigen, inducing an inflammatory reaction (Xenosialitis), and triggering the production of circulating antiNeu5Gc antibodies to attack/remove all incorporated Neu5Gc. In the state of Xenosialitis, the virus-neutralizing antibodies produced by a heavily xenosialylated patient following exposure to viral infection (including SarsCoV2) or anti SarsCoV2 vaccination cross-react against all incorporated non-self Neu5Gc-MCA glycans due to their resemblance with viral envelope antigens synthesized by the host glycosylation mechanism. In addition, the circulating anti-XeSias antibodies determine the massive removal of the circulating neutralizing FC-xeno-contaminated antibodies by the serum, living only the hyper-inflammatory agalattosylated antiviral IgG antibodies. Therefore, we hypothesize that the combination of antibody cross-reaction against non-self Neu5Gc-MCA glycans and the massive removal of the xeno-contaminated newly formed neutralizing antibodies in favor of hyper reactive antibodies, could be the cause of the massive inflammatory reaction (cytokine storm, coagulopathies, neuropathies) observed in Covid 19 patients or after anti-SarsCoV2 vaccination. This analysis is an invitation to investigate the post-infectious and/or post-vaccination adverse phenomena in the light of xenosialization as a key to understanding the severe post viral and post vaccine complications, including SARS-CoV2 infection or related vaccination.

Preprint ARTICLE | doi:10.20944/preprints202008.0530.v1

Antiviral phytochemicals identified in Rhododendron arboreum petals exhibited strong binding to SARS-CoV-2 M^Pro and Human ACE2 receptor

Maneesh Lingwan, Shagun Shagun, Yogesh Pant, Bandna Kumari, Ranjan Nanda, Shyam K Masakapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: R. arboreum, Antiviral phytochemicals, SARS-CoV-2, MPro, ACE2, COVID-19

Online: 24 August 2020 (11:14:07 CEST)

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Background: Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) affects human respiratory function causing COVID-19 disease. Safe natural products with potential antiviral phytochemicals with benefits to control high-altitude sickness could be adopted as adjunct therapy for COVID-19. The red petals of Rhododendron arboreum, commonly available and consumed in the Himalayan region may have phytochemicals with potential antiviral properties against COVID-19 targets.Purpose: This study was aimed to profile the secondary metabolites of R. arboreum petals, to assess their absorption, distribution, metabolism and elimination (ADME) properties and evaluate their antiviral potential by docking against COVID-19 targets such as SARS-CoV-2 main protease (M^pro PDB ID: 6LU7) and Human Angiotensin Converting Enzyme 2 (ACE2) receptor (PDB ID: 1R4L) that mediates the viral replication and entry into the host respectively.Methods: The phytochemicals of R. arboreum petals were mainly profiled using Gas Chromatography-Mass Spectroscopy (GC-MS) and ¹H-NMR. In addition, the phytochemicals reported from the literature were tabulated. The ADME properties of the phytochemicals were predicted using SwissADME tool. Molecular docking simulation of the phytochemicals against SARS-CoV-2 main protease (M^pro PDB ID: 6LU7) and Human Angiotensin converting enzyme 2 (ACE2) receptor (PDB ID: 1R4L) were carried out using PyRx.Results: R. arboreum petals were found to be rich in appreciable proportions of secondary metabolites such as Quinic acid, 3-Caffeoyl-quinic acid, 5-O-Coumaroyl-D-quinic acid, 5-O-Feruloylquinic acid, 2,4-Quinolinediamine, Coumaric acid, Caffeic acid, Epicatechin, Catechin, 3-Hydroxybenzoic acid, Shikimic acid, Protocatechuic acid, Epicatechin gallate, Quercetin, Quercetin-O-pentoside, Quercetin-O-rhamnoside, Kaempferol-O-pentoside and Kaempferol. Several of these phytochemicals were reported to exhibit inhibitory activities against a range of viruses. From the molecular docking studies, 5-O-Feruloylquinic acid, 3-Caffeoyl-quinic acid, 5-O-Coumaroyl-D-quinic acid, Epicatechin and Catechin showed strong binding affinity with SARS-CoV-2 M^pro and human ACE2 receptor.Conclusion: This report showed that R. arboreum petals are rich in several antiviral phytochemicals that also docked against SARS-CoV-2 M^Pro and Human ACE2 receptor. This is the first report highlighting R. arboreum petals as a reservoir of antiviral phytochemicals with potential for synergetic activities. The outcomes merit further in vitro, in vivo and clinical studies on R. arboreum phytochemicals to develop natural formulations against COVID-19 disease for therapeutic benefits.

Preprint REVIEW | doi:10.20944/preprints202007.0262.v1

Epidemiological Models of SARS-CoV-2 (COVID-19) to Control the Transmission Based on Current Evidence: A Systematic Review

Swati Arora, Rishabh Jain, Harendra Pal Singh

Subject: Public Health And Healthcare, Health Policy And Services Keywords: SARS-COV-2; COVID-19; Lockdown; Epidemiological Models; Machine Learning; Transmission

Online: 12 July 2020 (15:18:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1684.v1

High Exposure to SARS-CoV-2 among Pregnant Women after the First and Second Waves of COVID-19 in Senegal

Abou Abdallah Malick Diouara, Fatou Thiam, Seynabou Coundoul, Noël Magloire Manga, Halimatou Diop Ndiaye, Assane Senghor, Sophie Deli Tene, Sarbanding Sané, Betty Kane, Habibou Sarr, Yakhya Dieye, Seynabou Lo, Fodé Danfakha, Marie Edouard Faye Dieme, Babacar Biaye, Cheikh Momar Nguer, Martine Peeters, Coumba TOURE KANE, Ahidjo Ayouba

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: SARS-CoV-2; Seroprevalence; Pregnancy and COVID-19; Senegal

Online: 26 October 2023 (09:09:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0078.v1

Inactivation of Human Coronavirus by Fathhome’s Dry Sanitizer Device: Rapid and Eco-friendly Ozone-based Disinfection of SARS-CoV-2

Timsy Uppal, Amir Khazaieli, Antoine Snijders, Subhash C. Verma

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: FATHHOME, SARS-CoV-2; COVID-19; Virus decontamination, PPEs

Online: 2 February 2021 (09:34:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0251.v1

RNA-Dependent RNA Polymerase and Spike Protein Mutant Variants of SARS-CoV-2 Predominate in Severely Affected COVID-19 Patients

Subrata K. Biswas, Sonchita R. Mudi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; Spike protein; Mutant; Genome

Online: 12 July 2020 (12:03:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0108.v1

Bioinformatics-Based Design Strategy and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein

Partha Ray, Melissa Ledgerwood-Lee, Howard Brickner, Alex E. Clark, Aaron Garretson, Rishi Graham, Westley Van-Zant, Aaron F. Carlin, Eliah S. Aronoff-Spencer

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Nucleocapsid protein; Monoclonal and Polyclonal Antibodies; Enzyme-Linked Immunoassay; Peptide epitope mapping; Viral Quality Assurance; RADx; COVID-19 diagnostics

Online: 1 April 2024 (17:21:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0108.v1

Physical Effectiveness of Safety Interventions in Fire Engines to Reduce Potential Airborne Transmission of SARS-CoV-2 (COFIRE)

Elmar Bourdon, Thomas Schaefer, Maximilian Kittel, Matthias Raedle, Alexandra Heininger

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Safety Interventions; Fire Engine; Vehicle, Aerosol; Fine Dust Measurement

Online: 6 May 2021 (15:24:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0032.v1

Emergence of RBD and D614G Mutations in Spike Protein: An Insight from Indian SARS-CoV-2 Genome Analysis

VINAYAGAM SAMYUKTHA, VENKATESAN NAVEEN KUMAR

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Spike protein; COVID-19; Mutation; hACE2 Receptor; Real-time PCR; Vaccine

Online: 4 June 2020 (08:48:03 CEST)

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Currently, entire world is crumbled due to COVID-19 caused by novel SARS-CoV-2. Globally, over 5 million people are infected by SARS-CoV-2 with 6% fatality rate. The surface spike (S) protein plays a key role in the pathogenesis of SARS-CoV-2 by mediating viral entry through human angiotensin converting enzyme 2 (hACE2) receptors on the host cell and there is a big global race to find viral neutralizing antibodies and vaccine against S protein of SARS-CoV-2. Since SARS-CoV-2 evolved into 10 different clades in a very short span, a study on sipke protein mutation is essential to have effective vaccine coverage globally. Based on the mutation analysis of S protein from 166 Indian SARS-CoV-2 genome, a total of 40 different SNPs comprising of 14 synonymous and 26 non-synonymous mutations were observed, and notably, Indian S protein diverged into two major clusters, D614 and G614, with 11 different types. Majority of Indian strains fall in A2a and O clusters. Alarmingly, we have observed six SNPs at RBD and notably two of them at RBM (S438F and S494P). S494P SNP, similar to Bat–SARS like-CoV, may indicate a low ACE2 binding affinity. Interestingly 38% of Indian strains harbor a characteristic D614G SNP which was found predominantly in A2a cluster, mostly comprising USA and European strains with high disease severity. The association of disease severity with D614G SNP is well-correlated in states with high death rate except Maharashtra. Notably, more than 50% of D614G mutation were observed in Northern part of India and 14% in Southern part but not in Kerala and Tamil Nadu strains. Highly conserved motif, D614 (608-VAVLYQDVNCT-618) in upstream and also few downstream, of S1/S2 furin cleavage site may indicate specific key role in efficient interaction with host proteases in pathogenesis. Further studies are warranted to clarify the impact of SD614G SNP association to disease severity . Interestingly, C2367T (Y789Y) synonymous SNP is observed in 37% of Indian strains and notably similar SNPs with degeneracy bases were observed which is a key indication for the possibility of misdiagnosis by Real-Time PCR and revised strategies are needed for the precise diagnosis. Circulation of high number of signature SNPs [D614G and C2367T (Y789Y)] in certain states may be an early indication of emergence of community transmission in India. Further large genome sequence data from India will aid in deep understanding on the diversity of circulating SASR-Cov-2 and its impact on disease severity, origin of imported cases to India, community spread, effect on diagnosis and vaccine coverage.

Preprint ARTICLE | doi:10.20944/preprints202209.0297.v1

Effectiveness and Tolerability of Early Treatment with Monoclonal Antibodies against SARS-Cov-2: Results from A Real-Life Study before Omicron Surge

Riccardo Scotto, Antonio Riccardo Buonomo, Giulia Zumbo, Antonio Di Fusco, Nunzia Esposito, Isabella Di Filippo, Mariano Nobile, Biagio Pinchera, Nicola Schiano Moriello, Riccardo Villari, Ivan Gentile

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Mabs; VoC; COVID-19; real-life

Online: 20 September 2022 (07:15:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202203.0338.v1

COVID-19 Test Frequency Versus Test Sensitivity in Disrupting SARS-CoV-2 Transmission: A Review of Statistical Modeling Simulations

Justin Rogers, Laurel Jackson, Adam Buss, Susan Gawel

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: COVID-19; rapid testing; test sensitivity; test frequency; testing programs; compartmental models

Online: 25 March 2022 (03:50:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0154.v1

SARS-CoV-2 (COVID-19 Pandemic) in Nigeria: Multi-institutional Survey of Knowledge, Practices and Perception Amongst Undergraduate Veterinary Medical Students

Oluwawemimo Adebowale, Olubukola Adenubi, Hezekiah Adesokan, Abimbola Oloye, Noah Bankole, Oladotun Fadipe, Patience Ayo-Ajayi, Adebayo Akinloye

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; Knowledge; Practices; Perception; Veterinarians students; Nigeria

Online: 7 September 2020 (03:52:58 CEST)

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Background: The novel Coronavirus SARS-CoV-2 (COVID-19) is a global pandemic with an increasing public health concern. Due to the non-availability of a vaccine against the disease, non-pharmaceutical interventions constitute major preventive and control measures. However, inadequate knowledge about the disease and poor perception might limit compliance. Aim: This study examined COVID-19-related knowledge, practices, perceptions and associated factors amongst undergraduate veterinary medical students in Nigeria. Methods: A cross-sectional web survey was employed to collect data from 437 consenting respondents using pre-tested self-administered questionnaire (August 2020). Demographic factors associated with the knowledge and adoption of recommended preventive practices towards COVID-19 were explored using multivariate logistic regression at P ≤ 0.05.Results: The respondents’ mean knowledge and practice scores were 22.7 (SD ± 3.0) and 24.1 (SD ± 2.9), respectively with overall 63.4% and 88.8% displaying good knowledge and satisfactory practice levels. However, relatively lower proportions showed adherence to avoid touching face or nose (19.5%), face mask-wearing (58.1%), and social distancing (57.4%). Being in the 6^th year of study (OR = 3.18, 95%CI: 1.62-6.26, P = 0.001) and female (OR = 2.22, 95% CI = 1.11-4.41, P = 0.024) were significant positive predictors of good knowledge and satisfactory practices, respectively. While only 30% of the respondents perceived the pandemic as a scam or a disease of the elites (24.0%), the respondents were worried about their academics being affected negatively (55.6%). Conclusion: The study revealed good knowledge and satisfactory preventive practices towards COVID-19 among Nigerian Veterinary students; albeit with essential gaps in the key non-pharmaceutical preventive measures recommended by the WHO. Therefore, there is a need to step up enlightenment and targeted campaigns about COVID-19 pandemic.

Preprint ARTICLE | doi:10.20944/preprints202005.0022.v1

Structural and Genetic Analysis of Coronaviruses Spike Proteins Suggest Pangolin as a Proximate Intermediate Host of SARS-CoV-2 (COVID-19)

Sohail Raza, Muhammad Asif Rasheed, Wajeeha Zahir, Muhammad Tariq Navid, Rana Aamir Diwan, Muhammad Awais, Tahir Yaqub, Masood Rabbani, Muhammad Rashid

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

Online: 2 May 2020 (16:29:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0075.v1

SARS-CoV-2/COVID-19 and Advances in Developing Potential Therapeutics and Vaccines to Counter this Emerging Pandemic Virus – A Review

Ali A. Rabaan, Shamsah H. Al-Ahmed, Ranjit Sah, Ruchi Tiwari, Mohd. Iqbal Yatoo, Shailesh Kumar Patel, Mamta Pathak, Yashpal Singh Malik, Kuldeep Dhama, Karam Pal Singh, D. Katterine Bonilla-Aldana, Shafiul Haque, Alfonso J. Rodriguez-Morales

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; immunotherapeutics; therapeutics; vaccines

Online: 7 April 2020 (02:01:34 CEST)

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A novel coronavirus (SARS-CoV-2), causing an emerging coronavirus disease (COVID-19), first detected in Wuhan City, Hubei Province, China has resulted in an outbreak in China which has taken a catastrophic turn with high toll rates in China and subsequently spreading across the globe. The rapid spread of this virus to more than 175 countries while affecting nearly 500,000 persons and causing more than 22,000 human deaths, it has resulted in a pandemic situation in the world. The SARS-CoV-2 virus belongs to the genus Betacoronavirus, like MERS-CoV and SARS-CoV, all of which originated in bats. It is highly contagious, causing symptoms like fever, dyspnea, asthenia and pneumonia, thrombocytopenia and the severely infected patients succumb to the disease. Coronaviruses (CoVs) among all known RNA viruses have the largest genomes ranging from 26 to 32 kb in length. Extensive research has been conducted to understand the molecular basis of the SARS-CoV-2 infection and evolution, develop effective therapeutics, antiviral drugs and vaccines, and to design rapid and confirmatory viral diagnostics as well as adopt appropriate prevention and control strategies. Till date, no clinically proclaimed, proven therapeutic antibodies or specific drugs and therapeutics, and vaccines have turned up. Several molecular diagnostic tests such as Real Time-PCR, isothermal loop-mediated amplification of coronavirus (i-LACO), full genome analysis by next-generation sequencing (NGS), multiplex nucleic acid amplification, and microarray-based assays are in use currently for the laboratory confirmation of this CoV infection. In this review article, we describe the basic molecular organization and phylogenetic analysis of the coronaviruses, including the SARS-CoV-2, and recent advances in diagnosis and vaccine development in brief and focusing mainly on developing potential therapeutic options that can be explored to manage this pandemic virus infection, which would help in valid countering of COVID-19.

Preprint ARTICLE | doi:10.20944/preprints202203.0290.v3

New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells

Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: host-virus interactions; tissue-specific model; COVID-19; SARS-CoV-2; antiviral targets; flux balance analysis; flux variability analysis; reaction knockout; host-derived enforcement; metabolic modeling; virus mutations; software engineering; Python

Online: 17 January 2023 (01:50:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202404.1101.v1

The Impact of Resistance Training on Equilibrium Abilities and Quality of Life in Older Adults after SARS-cov-2 Surviving

Patrycja Bobowik, Jan Gajewski, Ida Wiszomirska, Agnieszka Maciejewska-Skrendo, Katarzyna Leźnicka, Katarzyna Kaczmarczyk

Subject: Public Health And Healthcare, Physical Therapy, Sports Therapy And Rehabilitation Keywords: COVID-19; elderly; postural stability; resistance training; post-covid symptoms

Online: 17 April 2024 (12:17:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0084.v1

In silico Repositioning for Dual Inhibitor Discovery of SARS-CoV-2 (COVID-19) 3C-like Protease and Papain-like Peptidase

Kowsar Bagherzadeh, Kourosh Daneshvarnejad, Mohammad Abbasinazari, homa azizian

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: in silico repositioning; dual inhibitor; Covid-19; 3CLpro; PLpro; remdesivir

Online: 7 April 2020 (10:44:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0161.v1

The Small Intestine, an Underestimated Site of SARS-CoV-2 Infection: From Red Queen Effect to Probiotics

Zhijie Feng, Yan Wang, Wei Qi

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: coronaviruses receptors; angiotensin-converting enzyme 2 (ACE2); COVID-19; SARS-Cov-2; the Red Queen hypothesis; segmented filamentous bacteria

Online: 10 March 2020 (08:45:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202403.0572.v1

Link Between the G Protein-Coupled Receptor (GPCR), SARS-CoV-2 Spike Protein, ACE2, Vaccines, and Long COVID

Marcos Altable

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: G Protein-Coupled Receptor; SARS-CoV-2 Spike (S) Protein; Vaccines; Long COVID; ACE2; COVID-19

Online: 11 March 2024 (05:33:53 CET)

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