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Preprint COMMUNICATION | doi:10.20944/preprints202008.0253.v1

Prediction and Analysis of SARS-CoV-2-Targeting microRNA in Human Lung Epithelium

Jonathan Tak-Sum Chow, Leonardo Salmena

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: microRNA; SARS-CoV-2; coronavirus; lung epithelia; cellular antiviral defence

Online: 11 August 2020 (06:05:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0375.v1

Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19

Hayder O. Hashim, Mudher K. Mohammed, Mazin J. Mousa, Hadeer H. Abdulameer, Alaa T.S. Alhassnawi, Safa A. Hassan, Mohammed Baqur S. Al-Shuhaib

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: co-infection; SARS-CoV-2; pike glycoprotein; stop mutations

Online: 17 September 2020 (05:33:59 CEST)

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There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection way also suggested. To the best of our knowledge, this is the first report to describe the co-infection of multiple strains of SARS-CoV-2 in patients with COVID-19.

Preprint REVIEW | doi:10.20944/preprints202008.0020.v1

SARS-CoV-2 and Covid-19 Immunopathogenesis

Antonio Luiz Boechat, Beatriz Pessoa, Carlos Soares, Cecília Barroso, David Vila, Emanuelly Barbosa, Isabela Seffair, João Victor Melo, Julia Becil, Maria Polyanna Rebouças, Natascha Rodrigues, Pedro Henrique Freitas, Rebeka Rocha, Thaise Rodrigues, Vanessa Ferreira, Rosmery Ubiera, Maria Cristina Dos-Santos

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; COVID-19; Immunopathogenesis; Cytokine storm; IL-6; macrophages; neutrophils

Online: 2 August 2020 (11:53:17 CEST)

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Working Paper ARTICLE

Genomic Characterization and Phylogenetic Analysis of SARS-CoV-2 during the early phase of the pandemic in Asia

Jale Moradi, Mohsen Moghoofei, Mohammad Doroudian, Ramin Abiri

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; Phylogenetics; Asia

Online: 15 January 2021 (13:14:15 CET)

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Preprint REVIEW | doi:10.20944/preprints202204.0118.v1

SARS-CoV-2-Infection (COVID-19): Clinical Course and Cause(s) of Death

Giuliano Ramadori

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2-infection; dehydration; hypoalbuminemia; pulmonary hypoxia; hyaline memrane; pulmonary engorgement; lung weight; acute respiratory distress syndrome; diffuse alveolar damage (DAD)

Online: 13 April 2022 (08:27:30 CEST)

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ABSTRACT Two years after first patients approached the emergency rooms of hospitals in Wuhan becouse of respiratory distress,thousend of SARS-CoV-2 infected persons continue to die every day worldwide.SARS-CoV-2-infected patients undergo a process of dehydration and malnutrition before they develop respiratory problems and approach the emergency room of a hospital.This is,in many cases, the consequence of high fever which causes massive loss of fluids. In addition loss of appetite, is responsible for the deficit of protein intake.Most of the virus-infected patients admitted to the emergency room are therefore hypovolemic and hypoproteinemic and suffer of respiratory distress accompanied by ground grass opacities at CT-scan of the lungs.Critically ill patients are treated following the guidelines for treatment of septic shock but with „conservative“ fluid replacement and administration of diuretics to assure sufficient hourly urine production. The combination of conservative fluid administration with reduced protein content in the enterally administered diet, together with administration of diuretics, has severe hemodynamic consequenses in mostly aged,dehydrated,critically ill patients. Many of them will develop acute kidney injury in the next 24 hours.In most of the cases, patients continue to loose weight by loosing skeletal muscle mass. Ischemic damage in the lung capillaries is responsible for the acute respiratory distreass syndrome (ARDS) and for the hallmark of autoptic findings,diffuse alveolar damage (DAD) characterized by hyaline membrane formation,fluid invasion of the alveoli recruitment of some inflammatory cells and progressive arrest of blood flow in the pulmonary vessels.The consequence is progressive congestion , increase of lung weight and progressive hypoxia (progressive severity of ARDS).Sequestration of blood in the lungs worsen hypovolemia and ischemia in different organs.This is most probably responsible for recruitment of inflammatory cells and for persistance of elevated serum levels of positive acute-phase markers and of hypoalbuminemia. Autoptic studies have been performed mostly in patients who died in the ICU after SARS-CoV-2-infection because of progessive ARDS.In those patients, tubulus epithelium necrosis in the kidney is a frequent finding as it has been the case in the first SARS-CoV-1 pandemic.In the death certification charts, many times weeks after first symptoms have started ,cardiac arrest is the cause of death after respitatory insufficiency.Replacement therapy with sufficient amount of fluid and albumin should be part of the early individualized life-saving supportive measures avoiding mechanical ventilation.

Preprint REVIEW | doi:10.20944/preprints202005.0060.v3

Fighting the SARS CoV-2 (COVID-19) Pandemic with Soap

Narendra Kumar Chaudhary, Nabina Chaudhary, Manis Dahal, Biswash Guragain, Sumie Rai, Rahul Chaudhary, K.M. Sachin, Reena Lamichhane-Khadka, Ajaya Bhattarai

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: COVID-19; SARS-Cov-2; soap; hand washing; WHO

Online: 6 July 2021 (11:30:53 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202005.0061.v1

Lysosomotropic Active Compounds—Hidden Protection against COVID-19 / SARS-CoV-2 Infection?

Markus Blaess, Lars Kaiser, Martin Sauer, Hans-Peter Deigner

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: SARS-CoV-2; COVID-19; Lysosomotropism; Chloroquine

Online: 5 May 2020 (04:29:48 CEST)

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Preprint REVIEW | doi:10.20944/preprints202102.0319.v2

Factors Associated with Mortality Among Elderly People in the COVID-19 Pandemic (SARS-CoV-2): A Systematic Review and Meta-Analysis

Vicente Alves, Francine Casemiro, Bruno Araujo, Marcos Lima, Rayssa Oliveira, Fernanda Fernandes, Ana Vitória Gomes, Dario Gregori

Subject: Public Health And Healthcare, Other Keywords: SARS-CoV-2; COVID-19; Non-Communicable Chronic Diseases (NCCDs); Clinical features; Institucionalized or hospitalized elderly; meta-analisys.

Online: 1 July 2021 (11:21:00 CEST)

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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 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/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 REVIEW | doi:10.20944/preprints202210.0292.v1

SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with Covid-19

Zeinab Mohseni Afshar, Ali Tavakoli Pirzaman, Bardia Karim, Rezvan Hosseinzadeh, Arefeh Babazadeh, Dariush Hosseinzadeh, Seyed Rouhollah Miri, Terence T. Sio, Mark J. M. Sullman, Mohammad Barary, Soheil Ebrahimpour

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Omicron; Covid-19; SARS-CoV-2; Variants of concern

Online: 20 October 2022 (02:16:05 CEST)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202305.0568.v1

Financial Burden of SARS-CoV-2 Infected Pregnancy in a Tertiary Exclusive COVID-19 Maternity

Tina-Ioana Bobei, Romina Marina Sima, Gabriel-Petre Gorecki, Anca Bobircă, Mihai Popescu, Bashar Haj Hamoud, Liana Ples

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: COVID-19; SARS-COV-2; pregnancy

Online: 9 May 2023 (04:51:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202012.0663.v1

Ciliary Dysfunction Secondary to COVID-19. Explanation of the Pathogenesis From Analysis of Human Interactome With Sars-Cov-2 Proteome

Alejandro Jesús Bermejo-Valdés, Alexander Ariel Padrón-González, Jessica Archer-Jiménez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; interactome; ciliary-flagellar dysfunction; infertility; pathogenicity

Online: 25 December 2020 (13:18:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0085.v1

Myocarditis and Pericarditis Following the SARS-CoV-2 Infection and COVID-19 Vaccination

Zeinab Mohseni Afshar, Jackson Liang, Mohammad Amin Habib, Mohamad Ali Taghizadeh Moghadam, Arefeh Babazadeh, Elham Ramzani, Rezvan Hosseinzadeh, Erfan Hashemi, Terence T. Sio, Amirreza Allahgholipour, Mohammad Barary, Soheil Ebrahimpour

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Vaccines; Myocarditis; Pericarditis

Online: 6 February 2023 (07:51:04 CET)

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Preprint REVIEW | doi:10.20944/preprints202008.0353.v1

Rethinking Aptamers as Nanotheranostic Tools for SARS-COV-2 and COVID-19 Infection

christian Dzuvor

Subject: Biology And Life Sciences, Virology Keywords: aptamers; theranostics; SARS-COV-2; COVID-19; bioaffinity

Online: 17 August 2020 (08:01:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0449.v2

An Updated Primer on SARS-CoV-2 and the Evolving Covid-19 Pandemic

Subramani Mani

Subject: Public Health And Healthcare, Health Policy And Services Keywords: SARS-CoV-2; Covid-19; pandemic; primer; India; mortality rate; evolution; updated primer; evolving pandemic

Online: 1 June 2020 (11:08:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0409.v2

YoungJoon Park, Ju Won Ahn, Sojung Hwang, Kyoung Su Sung, Jaejoon Lim, KyuBum Kwack

Subject: Biology And Life Sciences, Virology Keywords: angiotensin-converting enzyme 2; SARS-CoV-2; spike protein; COVID-19

Online: 9 April 2020 (09:59:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0962.v1

The Impact of SARS-CoV-2 Immune Status and Societal Restrictions in Controlling COVID-19 Across the World

Jasmijn Stroo, Michaëla Lepolder, Jean-Luc Murk, Ger T. Rijkers

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID pass; SARS-CoV-2 antigen test; SARS-CoV-2 antibodies; societal restrictions

Online: 14 July 2023 (05:20:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0448.v1

Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening

Riccardo Cecchetto, Emil Tonon, Nicoletta Medaina, Giona Turri, Erica Diani, Pier Paolo Piccaluga, Angela Salomoni, Michela Conti, Evelina Tacconelli, Anna Lagni, Virginia Lotti, Mosè Favarato, Davide Gibellini

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; genomic surveillance; NGS; deletion; variants.; clusters

Online: 4 August 2023 (13:34:25 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/preprints202403.0473.v1

A tiny viral protein, SARS-CoV-2-ORF7b: Functional molecular mechanisms.

Gelsomina Mansueto, Giovanna Fusco, Giovanni Colonna

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2-ORF7b, COVID-19, Interactomics, Topological analysis, Cluster analysis, Co-regulation network, Transcription Factors, microRNA, SARS-CoV-2 inter-tissue diffusion, programmed death.

Online: 8 March 2024 (09:02:28 CET)

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Preprint REVIEW | doi:10.20944/preprints202004.0082.v1

Update on the SARS-CoV-2 (COVID-19) Outbreak: A Global Pandemic Challenge

Abhishek Kumar Soni

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; global pandemic; global health emergency; SARS-CoV-2

Online: 7 April 2020 (10:08:47 CEST)

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Preprint REVIEW | doi:10.20944/preprints202304.0038.v1

Serological Response to SARS-CoV-2 after COVID-19 Vaccination in Lung Cancer patients: Short Review

Ananda Rodilla, Sooyun Tavolacci, Jazz Cagan, Tanay Shah, Sandeep Mittan, Philip C. Mack, Fred R. Hirsch

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: lung cancer; SARS-CoV-2 vaccine; immunogenicity

Online: 4 April 2023 (04:58:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0396.v1

Phylogenetic and Variant Analysis of 1,040 SARS-CoV-2 Genomes

Eric C. Rouchka, Julia H. Chariker, Donghoon Chung

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; variant analysis; phylogenetic analysis; viral evolution

Online: 24 May 2020 (18:25:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0522.v1

A Tiny Viral Protein, SARS-CoV-2-ORF7b: Structural Features.

Giovanni Colonna

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ORF7b; SARS-CoV-2; COVID-19; 3D-structure; molecular dynamics; dipole vector; Electrostatic properties of alpha-helix.

Online: 18 April 2023 (11:14:01 CEST)

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ORF7b-2 is an accessory protein of the SARS-CoV-2 virus of only 43 amino acids. It has been implicated in various functional hypotheses, some of which predict its involvement as a trans-membrane protein. In this study, ORF7b-2 has often been compared to ORF7b-1 of the SARS virus to highlight differences and similarities with a protein that should have a similar biological role. Structural analysis of ORF7b-2 and its electrostatic characteristics show a polypeptide with both ends negatively charged and a diffuse negative charge over the entire structure. Therefore, its behavior in solution is like that of a weak negative polyelectrolyte, more precisely a polyanion with a net charge of – 4 at neutral pH. Its structure was modeled with two different modeling systems, one of which was ab initio. The two best models are similar, as confirmed by the Ramachandran plot, and show a central alpha-helical structure with two disordered and mobile ends. A normal mode analysis characterized the low-frequency dynamic aspects of the protein. The analysis of the structural shows a rigid central segment with mobile and fluctuating extremities, involved in a conformational equilibrium of the helix ↔ coil type. The calculation of the dipole moment shows its vector is not aligned with the main axis of the structure with an outward tilt of 24°. Molecular dynamics simulations were also conducted and the one in water is in good agreement with the previous results. While, the simulation performed by inserting a pre-oriented dimer (OMP) into a solvated lipid showed the low tendency of the protein to solvate in the apolar environment of the membrane. ORF7b-2 also shows a widespread distribution of negative surfaces that dynamically adjust to changes in structural organization. The BioGrid platform's [Biological General Repository for Interaction Datasets] through the BioGrid COVID-19 Coronavirus Curation Project shows a very large number of experimentally proven physical interactions unique to ORF7b-2, some of them with cytoplasmic proteins. These features of ORF7b-2, evaluated together, suggest a remarkable propensity of ORF7b-2 to interact with multiple molecular partners on both an electrostatic and hydrophobic basis. All this makes it unreasonable that the only biological function of this protein should be that exerted as an intramembrane protein.

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

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

Pierre Arsene

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

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

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Preprint REVIEW | doi:10.20944/preprints202404.1316.v1

SARS-CoV-2 and Influenza Co-Infection: Fair Competition or Sinister Combination?

Narasaraju Teluguakula, Vincent TK Chow, Pandareesh MD, Venkatesha Dasegowda, Vidyasagar Kurrapotula, Shivaramu MG, Marko Radic

Subject: Pulmonary And Respiratory Medicine, Medicine And Pharmacology Keywords: influenza; SARS-CoV-2; co-infection; inflammation; lung pathology

Online: 19 April 2024 (08:05:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0196.v1

SARS-CoV-2 PCR Persistence and Duration of COVID-19 Symptoms in Health Professionals

Tatiana Schäffer Gregianini, Ludmila Fiorenzano Baethgen, Richard Steiner Salvato, Ivone Andreatta Menegolla, CEVS COVID-19 Team, Ana Beatriz Gorini da Veiga

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; PCR persistent positive; respiratory infection; COVID-19

Online: 12 December 2022 (09:04:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202205.0234.v1

Physical Analysis of SARS-CoV-2 Routes: from Primary Production and Emissions to Exposures and COVID-19 Infection

Gjalt Huppes, Ruben Huele

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; virions mass balance; spatial modelling of toxics concentrations; human exposure to airborne substances; Substance Flow Analysis (SFA); environmental routes of toxic viruses; primary production of SARS-2 virions

Online: 17 May 2022 (14:19:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0340.v1

Altered microRNA Transcriptome in Cultured Human Airway Cells upon Infection with SARS-CoV-2

Idrissa Diallo, Rajesh Abraham Jacob, Elodie Vion, Robert A. Kozak, Karen Mossman, Patrick Provost

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RNA-Seq; miRNA; miR-1246; ACE2; Calu-3

Online: 18 August 2022 (10:45:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0641.v1

Persistence of SARS-CoV-2 Viral RNA in Nasopharyngeal Swabs after Death: An Observational Study

Francesca Servadei, Silvestro Mauriello, Manuel Scimeca, Bartolo Caggiano, Marco Ciotti, Lucia Anemona, Manuela Montanaro, Erica Giacobbi, Michele Treglia, Sergio Bernardini, Luigi Tonino Marsella, Nicoletta Urbano, Orazio Schillaci, Alessandro Mauriello

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; pandemic; autopsy; medico-legal procedures

Online: 25 March 2021 (16:14:21 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202203.0185.v1

Would New SARS-CoV-2 Variants Change the War Against COVID-19?

Elrashdy M. Redwan, Fatma Elrashdy, Alaa A. A. Aljabali, Wagner Baetas-da-Cruz, Debmalya Barh, Adam M. Brufsky, Sk. Sarif Hassan, Kenneth Lundstrom, Ángel Serrano-Aroca, Kazuo Takayama, Murtaza M. Tambuwala, Bruce D. Uhal, Vladimir N Uversky

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: SARS-CoV-2; COVID-19; variant; sublineage; transmission; immunity; infection; vaccination; non-pharmaceutical interventions

Online: 14 March 2022 (11:19:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0394.v1

Factors Associated with SARS-CoV-2 Infection in Resident Physicians and Fellows in New York City During the First COVID-19 Wave

Kate R Pawloski, Betty Kolod, Rabeea F Khan, Vishal Midya, Tania Chen, Adeyemi Oduwole, Bernard Camins, Elena Colicino, I. Michael Leitman, Ismail Nabeel, Kristin Oliver, Damaskini Valvi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; physician trainee; resident; fellow; risk factors

Online: 14 April 2021 (17:42:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0060.v1

COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies

Renuka Raman, Krishna J. Patel, Kishu Ranjan

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; COVID-19; variants; vaccines; immune dysregulated; comorbidities; antibody; Spike protein; biomolecules; coronavirus

Online: 2 June 2021 (09:56:14 CEST)

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Preprint REVIEW | doi:10.20944/preprints202310.0217.v1

Comparative Analysis of Immune-response in Humans Infected by Alpha, Delta and Omicron Strains of SARS-CoV-2

Mihieka Bose, Chayan Munshi

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2, Immune response, Pandemic

Online: 4 October 2023 (07:54:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0097.v1

Efficacy of COVID-19 Vaccines Against the Omicron Variant of SARS-CoV-2

Kritika Srinivasan Rajsri, Meena Singh, Mana Rao

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Bivalent COVID-19 vaccine; COVID-19 vaccination booster; COVID-19; Omicron; SARS-CoV-2

Online: 6 March 2023 (07:00:00 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0086.v2

An Overview of Basic Molecular Biology of SARS-CoV-2 and Current COVID-19 Prevention Strategies

Ankur Das, Raja Ahmed, Suraiya Akhtar, Khaleda Begum, Sofia Banu

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Genome organisation and expression; Polyproteins; Prevention strategies

Online: 14 June 2020 (16:49:10 CEST)

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

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

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

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

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

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Preprint REVIEW | doi:10.20944/preprints202007.0587.v1

SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

Sameer Mohammad, Abderrezak Bouchama, Bothina Mohammad Alharbi, Mamoon Rashid, Tanveer Saleem Khatlani, Nusaibah S Gaber, Shuja Shafi Malik

Subject: Biology And Life Sciences, Virology Keywords: Keywords: COVID-19; SARS-CoV-2; SARS-CoV; Accessory Protein; ORF8; ORF8ab

Online: 24 July 2020 (13:51:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints202310.0889.v1

Postural Orthostatic Tachycardia Syndrome Following SARS-CoV-2 Infection and COVID-19 Vaccination: A Comparative Review

Zeinab Mohseni Afshar, Homa Mazaherinia, Hosein Nazari rostami, Arefeh Babazadeh, Mohammad Barary, Erfan Hashemi, Soheil Ebrahimpour

Subject: Public Health And Healthcare, Primary Health Care Keywords: Postural Orthostatic Tachycardia Syndrome (POTS); COVID-19; SARS-CoV-2; Vaccination

Online: 13 October 2023 (10:58:23 CEST)

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Preprint REVIEW | doi:10.20944/preprints202102.0432.v1

Biomedical Research During the COVID-19 Pandemic: Success in Sars-Cov-2 and Other Infectious Diseases

Nuno S. Osório, Maria Isabel Veiga

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; SARS-CoV-2; Infectious disease; Pandemics; Epidemics; Biomedical Research

Online: 19 February 2021 (10:03:47 CET)

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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/preprints202003.0325.v1

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202101.0024.v1

Serological Testing for COVID-19 in the Fertility Setting: The Lockdown Impact and Subsequent Dynamics Reflected in the Seroprevalence of Sars-Cov-2 Antibodies

Corina Manolea, andrei capitanescu, anca pop, roxana bors, ioana rugescu, melihan bechir, claudia mehedintu, valentin varlas

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2 antibodies; COVID-19; infertility; lockdown; IVF; SARS-CoV-2 serological testing

Online: 4 January 2021 (12:07:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0307.v1

Bioinformatic Analysis Reveals That the Reproductive System is Potentially at Risk from SARS-CoV-2

Jiawei Zhang, Yuqi Wu, Rui Wang, Keshi Lu, Menjiang Tu, Huan Guo, Weijie Xie, Zizhen Qin, Shulin Li, Pei Zhu, Xiangwei Wang

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; ACE2; reproductive system; single-cell RNA-seq

Online: 21 February 2020 (08:09:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0333.v1

An In Silico Analysis of Potential SARS-CoV-2 Interactions with Proteins Involved in Placental Functions

Ashikh A. Seethy, Sunil Singh, Indrani Mukherjee, Karthikeyan Pethusamy, Kakali Purkayastha, Jai Bhagwan Sharma, Ruby Dhar, Subhradip Karmakar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; pregnancy; trophoblasts; interactome; placenta

Online: 21 May 2020 (03:38:05 CEST)

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COVID-19 is a rapidly evolving medical emergency that has drawn global attention, unprecedented in any disease of its kind in recent times. The magnitude of the health crisis emerging from this pandemic has overwhelmed health care workers worldwide and called in for extraordinary measures to contain this virus. A simple Pubmed query on “COVID-19” returned with 12214 articles (as on May 17^th, 2020), published just within a few months. A detailed survey revealed around 250 clinical reports, 8 clinical trials, 9 meta-analyses, and 906 reviews that were published during this time span. Combining the strings “COVID-19 and Pregnancy” yielded a total of 132 reports while querying “COVID-19 and Placenta” returned with just 11 articles Even taking into considerations that few materials are in the PrePrint Server, we still have a gross under-representation of studies addressing the effect of this disease on pregnancy outcome and maternal & child health. An essential aspect of a successful pregnancy is proper placentation, where transiently invasive placental trophoblast cells invade the maternal endometrium to establish a functional feto-maternal communication. Based on the elegant study by David. E. Gordon, et al. published in Nature (April 30, 2020), which identified 332 human host proteins interacting with SARS-nCoV2 using an affinity-based purification, we interrogated several gene expression data sets available at NCBI-GEO related to trophoblast invasion and differentiation. Both of these processes are indispensable for placentation and fetal survival. Our analysis showed several overlaps with the interactome proteins implying that SARS-CoV-2 infection can affect several proteins, which are crucial for trophoblasts function. GeneMANIA and STRING based functional analysis further revealed that several of that SARS-CoV-2 interacting trophoblast proteins as a hub for the protein-protein interaction network. Our study thus elucidates the possible effect of SARS-CoV-2 infection on placenta formation and pregnancy outcome.

Preprint ARTICLE | doi:10.20944/preprints202207.0384.v1

Clinical and Evolutionary Features of SARS Cov-2 Infection (COVID-19) in Children, A Romanian Perspective

George Jugulete, Daniela Pacurar, Mirela Luminita Pavelescu, Mihaela Safta, Elena Gheorghe, Bianca Borcos, Carmen Pavelescu, Mihaela Oros, Madalina Merisescu

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: SARS-CoV-2; COVID-19; children; clinical features; comorbidities; male genderSARS-CoV-2, COVID-19, children, clinical features, comorbidities, male gender

Online: 26 July 2022 (04:43:02 CEST)

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Background: Given the potential for additional development to clarify a better knowledge of the overall impact of COVID-19 on the pediatric population, the clinical symptoms of SARS-CoV-2 infection in children and adolescents are still being explored. Morbidity in children is characterized by a variable clinical course. Our study's goal was to compare clinical aspects of 230 pediatric patients who tested positive for SARS-CoV-2 and were hospitalized between April 2020 and March 2022. Methods: In a retrospective analysis, we compared two groups hospitalized in the infectious diseases clinical ward IX at the National Institute for Infectious Diseases "Prof. Dr. Matei Bals," Bucharest, Romania. The first group of 88 patients was admitted between (April–December 2020) and their clinical manifestations were compared with the second group of 142 children followed between July 2021 and March 2022. Results: Of 230 children, the median age was 4.5 (interquartile range 0.6-17) years, 53.9% were male. 88 (36.21%) patients (first group) were admitted during the second wave in Romania, mostly aged < 5 years old, and experienced digestive manifestations like fever (p=0.001), and diarrhoea (p=0.004). The second group experienced different clinical signs when compared with the first group, with higher temperature and increased respiratory symptoms analogous to those of acute respiratory viral infections. The proportion in the second group increased, and 64.5% had symptoms for a median interval of 5 days; age (0-4 -years old) and length of stay were both proportionally inversely (p<0.01) and with correlation with hospital admission (p = 0.04). We report two Paediatric Inflammatory Multisystem Syndrome (PIMS) in the second group, with favourable evolution under treatment. Comorbidities were risk factors for complications appear (p < 0.001) in both groups. All paediatric cases admitted to our clinic evolved favourably and no death was recorded. Conclusions: In the first group children experienced digestive symptoms, whereas the second group experienced mild and moderate respiratory symptoms. We confirmed risk factors for severe cases as manifestations across the age spectrum, 0-4 (digestive symptoms) and 5-12 years old (for respiratory symptoms), associated comorbidities, fever, and male gender. The potential effects of COVID-19 infection in children older than 5 years should encourage caregivers to vaccinate and improve the prognosis among pediatric patients at risk.

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

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

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

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

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

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Preprint BRIEF REPORT | doi:10.20944/preprints202307.0613.v1

Discriminative Identification of SARS-CoV-2 Variants Based on Mass Spectrometry Analysis

Liron Feldberg, Anat Zvi, Yfat Yahalom Ronen, Ofir Schuster

Subject: Biology And Life Sciences, Virology Keywords: COVID19; SARS-CoV-2; Variants of Concern; Diagnosis; LC-MS/MS; Mass-Spectrometry; Spike; Nucleocapsid

Online: 11 July 2023 (03:01:19 CEST)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202210.0320.v1

A Time-series Metabolomic Analysis of SARS-CoV-2 Infection in a Ferret Model

Avinash V. Karpe, Thao V. Nguyen, Rohan Shah, Gough G. Au, Alexander J. McAuley, Glenn A. Marsh, Sarah Riddell, Seshadri S. Vasan, David J. Beale

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID19; SARS-CoV-2; metabolomics; omics; animal models; ferret; host metabolic responses

Online: 21 October 2022 (03:55:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0515.v1

An Analysis of the Neutralizing Antibodies Against the Main SARS-CoV-2 Variants in Healthcare Workers (HCWs) Vaccinated Against or Infected by SARS-CoV-2

Palmira Immordino, Vincenzo Pisciotta, Emanuele Amodio, Celestino Bonura, Floriana Bonura, Federica Cacioppo, Giuseppe Calamusa, Giuseppina Capra, Alessandra Casuccio, Simona De Grazia, Dario Genovese, Davide Graci, Guido Lacca, Giuseppa Luisa Sanfilippo, Maria Gabriella Verso, Giovanni Maurizio Giammanco, Donatella Ferraro

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; healthcare workers; vaccine; COVID-19; neutralizing antibodies; variants of concern

Online: 10 October 2023 (02:50:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0155.v1

Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-Analysis

Kaiming Tao, Philip L. Tzou, Sergei L. Kosakovsky Pond, John P.A. Ioannidis, Robert W. Shafer

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Omicron variant; Monoclonal antibody; Neutralization; Spike protein

Online: 10 March 2022 (14:30:25 CET)

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Preprint REVIEW | doi:10.20944/preprints202002.0399.v1

Preliminary Case Report on the SARS-CoV-2 Cluster in the UK, France, and Spain

Emma B. Hodcroft

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19 SARS-CoV-2 hCOV-19 coronavirus epidemiology contact-tracing cluster outbreak epidemic

Online: 27 February 2020 (11:08:56 CET)

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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 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/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/preprints202209.0439.v1

SARS-CoV-2 Detection in Fecal Samples in Sym-asymptotic Patients with Typical Findings of COVID-19 on Ag-RDT and SARS-CoV-2 RT-PCR Tests

Richard Odongo Magwanga, Benson Onyango, Alfred Ochieng, Shehu Shagari Awandu, Pamela Were, Joy Nyangasi Kirungu, Marceline Adhiambo Oloo, Erick Muok, Stephen Munga, Fredrick Ogutu, Angeline Orwa, Fredrick Okumu, Clayton Onyango, Dorothy Awuor, Francis Orata, Justine Ochieng’-Midega, Bonface Oure, Regina Nyunja, Fredrick Ade, Sharley Indechi, Erick Okuto, Benson Estambale

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID19; SARS-CoV-2 virus; Oro-nasopharyngeal; fecal; vaccination; asym-symptomatic; rapid diagnostic test

Online: 28 September 2022 (11:51:21 CEST)

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Coronavirus is a disease caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged as a global pandemic in 2019 from Wuhan, China. Since its emergence, it has caused immense suffering to human life, 6.27 million lives have been lost, movement curtailed and social dynamics disrupted. The golden standard for getting samples for SARS-CoV-2 detection is through oral- nasopharyngeal swab, this method of sample collection is invasive and uncomfortable, thus stigmatized the general population, and thereby impeded the progress of controlling the spread through mass testing. Being a contact disease, mechanisms to encourage mass testing is key to reduce the spread. This study thus developed a complimentary sample type to test for SARS-CoV-2, the use of human feces. Fecal samples were collected from 100 asym-symptomatic individuals suspected to be infected with COVID-19, virus RNA was then extracted and profiled through Real Time Polymerase Chain Reaction (RT-qPCR). The antigen rapid diagnostic test revealed high positivity rate of 44%, but the real time polymerase chain reaction results on nasopharyngeal and fecal samples revealed a significant variation, high number of the patients tested positive with stool samples compared to the nasopharyngeal swabs, with 43 and 37%, respectively. SARS-CoV-2 virus was detected in both symptomatic and asymptomatic individuals; however, the symptomatic registered a higher positivity of 25% compared to 20% among the asymptomatic patients. Vaccination only lowered the risk of infection, fully and partially vaccinated lowered the infection level to 10% compared to 20% among the unvaccinated. Finally, gender parity in relation to COVID19 was evaluated, more females (56%) compared to males were recruited in this study, out of which (20; 43.4%) were positive, and 26 (56.6%) were negative based on fecal RT-qPCR outcomes. Based on the outcome of this study, rapid diagnostic test (Ag-RDT) however cheap and or fast does not provide accurate information, moreover, the virus does not stay longer within the Oro-nasopharyngeal region, thus the invalid or negative results, thus use of feces should be adopted as a confirmatory test to ascertain the COVID19 status of an individual.

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/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/preprints202104.0534.v1

AuNP Coupled Rapid Flow-Through Dot-Blot Immuno-Assay for COVID-19 (SARS-CoV-2) Explicit IgG Antibody Revelation

Bijon Kumar Sil, Mohd. Raeed Jamiruddin, Md. Ahsanul Haq, Mohib Ullah Khondoker, Nowshin Jahan, Shahad Saif Khandker, Tamanna Ali, Mumtarin Jannat Oishee, Taku Kaitsuka, Masayasu Mie, Kazuhito Tomizawa, Eiry Kobatake, Mainul Haque, Nihad Adnan

Subject: Biology And Life Sciences, Virology Keywords: COVID-19, SARS-CoV-2, Serological test, Sensitivity, Specificity, Serosurveillance.

Online: 20 April 2021 (11:36:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0570.v1

Seven Epidemic Waves of COVID-19 in a Hospital in Madrid. Analysis of Severity and Associated Factors

Juan V. San Martín, Nieves Mesa, David Bernal-Bello, Alejandro Morales-Ortega, Marta Rivilla, Marta Guerrero, Ruth Calderón, Ana I. Farfán, Luis Rivas, Guillermo Soria, Aída Izquierdo, Elena Madroñal, Miguel Duarte, Sara Piedrabuena, María Toledano-Macías, Jorge Marrero, Cristina De Ancos, Begoña Frutos, Rafael Cristóbal, Laura Velazquez, Belén Mora, Paula Cuenca, José Á. Satué, Ibone Ayala-Larrañaga, Lorena Carpintero, Celia Lara, Álvaro R. Llerena, Virginia García, Vanesa García de Viedma, Santiago Prieto, Natalia González-Pereira, Cristina Bravo, Carolina Mariño, Luis Antonio Lechuga, Jorge Tarancón, Sonia Gonzalo, Santiago Moreno, José M. Ruiz-Giardin

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-CoV-2; waves; mortality

Online: 10 July 2023 (09:47:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0345.v1

ACEII Gene Analysis Exposes SARS-CoV-2 As A Potential Threat to Agricultural and National Security

Michael Ruhl, Tracie Jenkins

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: food safety; SARS-CoV-2; coronavirus; ACEII; agricultural security; national security

Online: 16 September 2020 (03:57:36 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202004.0339.v1

SARS-CoV-2 infection and Cardiology: Beware of Myocarditis

Marco Antonio Machado Schlindwein, Letícia Caroline Breis, Isabelle Pastor Bandeira, Rafael M. Ronsoni, Clizenaldo Torres, Marcus Vinicius Magno Gonçalves

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: SARS-COV-2; COVID-19; myocarditis

Online: 19 April 2020 (08:22:24 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 ARTICLE | doi:10.20944/preprints202201.0315.v2

Biosafety in Dental Care Facing Highly Transmissible SARS-CoV-2 Variants: Introduction of Prospective Setting Protocol in Prevention of COVID-19

Andrej Thurzo, Alexandra Bražinová, Neda Markovská, Iveta Waczulíková, Martin Smatana, Wanda Urbanová, Martin Strunga, Veronika Kurilová, Jana Kaiferová, Peter Sabaka, Helena Kosnáčová, Bela Mriňáková, Ivan Varga, Ladislav Czakó, Branislav Gális, Georgia Fountoulaki, Bohuslav Novák

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: SARS-CoV-2; Omicron; biosafety protocol; dentistry; orthodontics; sustainability

Online: 8 April 2022 (03:58:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0544.v1

Co-ultraPEALut in Subjective Cognitive Impairment Following SARS-CoV-2 Infection: An Exploratory Retrospective Study

Valentina Cenacchi, Giovanni Furlanis, Alina Menichelli, Alberta Lunardelli, Valentina Pesavento, Paolo Manganotti

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Long-COVID; neuro-long-COVID; SARS-CoV-2; Cognitive impairment; Co-ultraPEALut

Online: 9 February 2024 (10:52:46 CET)

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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/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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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 ARTICLE | doi:10.20944/preprints202007.0189.v1

Is Japan Succeeding in Suppressing COVID-19? Estimation of Infection Rate and the Size of the Population Potentially Exposed to SARS-CoV-2

Motohiko Naito

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; NESID; Japan; infection

Online: 9 July 2020 (12:18:46 CEST)

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Working Paper ARTICLE

Analysis of Two Choir Outbreaks in Germany in 2020 Characterizes Long- range Transmission Risks Through SARS-CoV-2

Felix Reichert, Oliver Stier, Anne Hartmann, Claudia Ruscher, Annika Brinkmann, Marica Grossegesse, Markus Neumann, Dirk Werber, Marius Hausner, Mareike Kunze, Bettina Weiß, Janine Michel, Andreas Nitsche, Martin Kriegel, Victor M. Corman, Terry C. Jones, Christian Drosten, Tobias Brommann, Udo Buchholz

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; Singing; Disease Outbreaks; Aerosols; Dose-Response Model

Online: 21 June 2021 (14:49:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0087.v1

An In-Silico Analysis of Drugs Potentially Modulating the Cytokine Storm Triggered by SARS-CoV-2 Infection

Laura Sanchez-Burgos, Gonzalo Gómez-López, Fatima Al-Shahrour, Oscar Fernandez-Capetillo

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; CMap; Cytokine Storm; NF-kB; Glucocorticoids; MEK; Estrogens

Online: 7 June 2020 (12:04:46 CEST)

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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 HYPOTHESIS | doi:10.20944/preprints202004.0286.v1

Comparative Domain-Fold Analysis of the SARS-CoV-2 ORF1ab Polyprotein: Insight into Co-Evolution, Conservation of Folding Patterns, Potential Therapeutic Strategies, and the Possibility of Reemergence

Srijeeb Karmakar, Sachin Kumar, Vimal Katiyar

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; domain-fold; evolutionary fingerprint; conserved domain; point mutation; recombination

Online: 16 April 2020 (16:13:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0577.v1

Effects of Toll Like Receptor Agonists and SARS-Cov-2 Antigens on Interferon (IFN) Expression by Peripheral Blood CD3+ T Cells in COVID-19 Patients

Samaneh A Abdolmohammadi-Vahid, Behzad Baradaran, Armin Sadeghi, Gilina Bezemer, Fatemeh K Kiaee, Ian Adcock, Gert Folkerts, Johan Garssen, Esmaeil Mortaz

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

Online: 30 December 2022 (09:13:21 CET)

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Background: Signaling by toll like receptors (TLRs) initiates important immune responses against viral infection. The role of TLRs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is not well elucidated. Thus, we investigated the interaction of TLRs agonists and SARS-COV-2 antigens with immune cells in vitro. Material & methods: 30 coronavirus disease 2019 (COVID-19) patients (15 severe and 15 moderate) and 10 age and sex matched control (HC) were enrolled. Peripheral blood mononuclear cells (PBMCs) were isolated and activated with TLR3, 7, 8 and 9 agonists, the spike protein (SP) of SARS-CoV-2 and the Receptor Binding Domain (RBD) unit of SP. Frequencies of CD3⁺IFN-β⁺ T cells, and CD3⁺IFN-g⁺ T cells was evaluated by flow cytometry. Interferon (IFN)-b gene expression was assessed by qRT-PCR. Results: The frequency of CD3+IFN-β+ T cells was higher in moderate and severe patients at baseline in comparison with HCs. Stimulation of PBMCs from moderate patients with SP and TLR8 agonist significantly upregulated the frequency of CD3+IFN-β+ T cells (P=0.0005 and 0.0024, respectively) when compared to non-stimulated (NS) samples. The greatest increase in CD3⁺IFN-b⁺ T cell frequency in PBMCs from severe patients was seen with TLR8 and TLR7 agonists when compared to NS (P= 0.003 and 0.0167, respectively). TLR stimulation did not significantly enhance the frequency of CD3+IFN-g+ T cells generated from PBMCs from moderate and severe patients compared with unstimulated controls. However, the frequency of CD3+IFN-ɣ+ T cells in PBMCs from moderate patients was upregulated by agonists of TLR3, 8 and 9, SP and RBD when compared with NS samples from HCs. The expression of the IFN-β gene after stimulation of CD3⁺T cells with the TLR8 agonist was also up-regulated in moderate than severe patients (moderate vs. severe: p=0.0006). In addition, stimulation of CD3⁺ T cells with SP, up-regulated the expression of IFN-β gene expression in cells from patients with moderate disease (moderate vs. severe: p=0.01). Conclusion: Stimulation of PBMCs from COVID-19 patients with a TLR8 agonist and with SP enhanced IFN-b protein and gene levels. This may potentiate immune responses against SARS-CoV-2 infection and prevent viral replication and spread.

Preprint REVIEW | doi:10.20944/preprints202003.0348.v1

An Update on SARS-COV-2/COVID-19 with Particular Reference on Its Clinical Pathology, Pathogenesis, Immunopathology and Mitigation Strategies – A Review

Kuldeep Dhama, Shailesh Kumar Patel, Mamta Pathak, Mohd. Iqbal Yatoo, Ruchi Tiwari, Yashpal Singh Malik, Rajendra Singh, Ranjit Sah, Ali A. Rabaan, D. Katterine Bonilla-Aldana, Alfonso J. Rodriguez-Morales

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-COV-2; COVID-19; clinical pathology; pathogenesis; immunopathology

Online: 23 March 2020 (07:51:17 CET)

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Coronavirus Disease 2019 (COVID-19), caused by a novel coronavirus named Severe Acute Respiratory Syndrome - Coronavirus-2 (SARS-CoV-2), emerged in early December 2019 in China and attained a pandemic situation worldwide by its rapid spread to nearly 167 countries with 287.239 confirmed cases and 11.921 human deaths with a case fatality rate (CFR) of around 4 per cent. Bats were considered as the reservoir host, and the search of a probable intermediate host is still going on. Animals have anticipated culprit of SARS-CoV-2 as of now. The disease is mainly manifested by pneumonia and related respiratory signs and symptoms, but the involvement of the gastrointestinal system and nervous system is also suggested. The severe form of the disease associated with death is mainly reported in older and immune-compromised patients with pre-existing disease history. Death in severe cases is attributed to respiratory failure associated with hyperinflammation. Cytokine storm syndrome associated with rampant inflammation in response to SARS-CoV-2 infection is considered as the leading killer of COVID-19 patients. COVID-19 patients were reported with higher levels of many pro-inflammatory cytokines and chemokines like IFN-g, IL-1b, IP-10, and MCP-1. Furthermore, severe cases of COVID-19 revealed higher levels of TNF-α, G-CSF, and MIP-1A. Blood profile of the COVID-19 patients exhibits lymphopenia, leucopenia, thrombocytopenia and RNAaemia along with increased levels of aspartate aminotransferase. SARS-CoV-2 infection in pregnant women does not lead to fetus mortalities unlike other zoonotic coronaviruses like SARS-CoV and MERS-CoV, with no evidence of intrauterine transmission to neonates. Rapid and confirmatory diagnostics have been developed, and high efforts are being made to develop effective vaccines and therapeutics. In the absence of any virus-specific therapeutic, internationally health care authorities are recommending adoption of effective prevention and control measures to counter and contain this pandemic virus. This paper is an overview of this virus and the disease with a particular focus on SARS-COV-2 / COVID-19 clinical pathology, pathogenesis and immunopathology along with a few recent research developments.

Preprint REVIEW | doi:10.20944/preprints202004.0045.v1

The Conceptual Framework for SARS-CoV-2 Related Lymphopenia

Ilnaz Rahimmanesh, Shirin Kouhpayeh, Hossein Khanahmad

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: SARS-CoV-2; lymphopenia; NAD+ depletion; CD38

Online: 6 April 2020 (09:28:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints202202.0187.v1

Endothelial Dysfunction in SARS CoV-2 Infection

Francesco Nappi, Sanjeet Singh Avtaar Singh

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: endothelial dysfunction; SARS-CoV-2 infection; thrombosis, angiotensin-converting enzyme-2; angiogenesis

Online: 15 February 2022 (11:05:22 CET)

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

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

Radhey S. Gupta, Bijendra Khadka

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

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

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

Preprint ARTICLE | doi:10.20944/preprints202004.0184.v1

Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs

Ujjwal Neogi, Kyle J. Hill, Anoop T. Ambikan, Xiao Heng, Thomas P. Quinn, Siddappa N. Byrareddy, Anders Sönnerborg, Stefan G. Sarafianos, Kamal Singh

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Coronavirus; SARS-CoV; MERS-CoV; SARS-CoV-2; COVID-19; RNA polymerase; nsp12

Online: 12 April 2020 (05:36:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0216.v1

Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation

Evangelia Georgia Kostaki, Ioulia Tseti, Sotirios Tsiodras, George N. Pavlakis, Petros P. Sfikakis, Dimitrios Paraskevis

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; variants; co-circulation; dominance; vaccines

Online: 7 April 2021 (17:24:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0456.v1

Winter is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19

Albertus Smit, Jennifer Fitchett, Francois Engelbrecht, Robert Scholes, Godfrey Dzhivhuho, Neville Sweijd

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; environmental influences; humidity; SARS-CoV-2; seasonality; temperature

Online: 20 July 2020 (07:41:44 CEST)

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SARS-CoV-2 virus infections in humans were first reported in December 2019, the boreal winter. The resulting COVID-19 pandemic was declared by the WHO in March 2020. By July 2020 COVID-19 is present in 213 countries and territories, with over 12 million confirmed cases and over half a million attributed deaths. Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally-varying environmental factors such as temperature and humidity. Many studies on the environmental sensitivity of COVID-19 are appearing online, and some have been published in peer-reviewed journals. Initially, these studies raised the hypothesis that climatic conditions would subdue the viral transmission rate in places entering the boreal summer and that southern hemisphere countries would experience enhanced disease. For the latter, the COVID-19 peak would coincide with the peak of the influenza season, increasing misdiagnosis and placing an additional burden on health systems. In this review, we assess the evidence that environmental drivers are a significant factor in the trajectory of the COVID-19 pandemic, globally and regionally. We critically assessed 42 peer-reviewed and 80 preprint publications that met qualifying criteria. Since the disease has been prevalent for only half a year in the northern, and a quarter of a year in the southern hemisphere, datasets capturing a full seasonal cycle in one locality are not yet available. Analyses based on space-for-time substitutions, i.e. using data from climatically distinct locations as a surrogate for seasonal progression, have been inconclusive. The reported studies present a strong northern bias. Socio-economic conditions peculiar to the ‘Global South’ have been omitted as confounding variables, thereby weakening evidence of environmental signals. We explore why research to date has failed to show convincing evidence for environmental modulation of COVID-19, and discuss directions for future research. We conclude that the evidence thus far suggests a weak modulation effect, currently overwhelmed by the scale and rate of the spread of COVID-19. Seasonally-modulated transmission, if it exists, will be more evident in 2021 and subsequent years.

Preprint ARTICLE | doi:10.20944/preprints202005.0188.v2

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

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

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

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

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Preprint REVIEW | doi:10.20944/preprints202101.0002.v1

Animal Coronaviruses and SARS-COV-2 in Animals, What Do We Actually Know?

Paolo Bonilauri, Gianluca Rugna

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; animals; veterinary

Online: 4 January 2021 (08:27:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0145.v1

Mouth Washing Impaired SARS-CoV-2 Detection in Saliva

Monique Melo Costa, Nicolas Benoit, Hervé Tissot-Dupont, Matthieu Million, Bruno Pradines, Samuel Granjeaud, Lionel Almeras

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: saliva; COVID-19 diagnosis; coronavirus; SARS-CoV-2

Online: 6 July 2021 (12:26:41 CEST)

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Preprint REVIEW | doi:10.20944/preprints202010.0214.v1

Endothelial Cells and SARS-CoV-2: An Intimate Relationship

Lucas Barbosa, Thaynan Lopes, Luanna Araujo, Luciane Rosario, Valeria Ferrer

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: endothelial cells; SARS-CoV-2; ACE2; inflammation; coagulation

Online: 12 October 2020 (09:41:20 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0009.v5

A Flexible Genome-Scale SARS-CoV-2 Clone Resource

Dae-Kyum Kim, Jennifer J. Knapp, Da Kuang, Aditya Chawla, Patricia Cassonnet, Hunsang Lee, Dayag Sheykhkarimli, Payman Samavarchi-Tehrani, Hala Abdouni, Ashyad Rayhan, Oxana Pogoutse, Etienne Coyaud, Sylvie van der Werf, Caroline Demeret, Anne-Claude Gingras, Mikko Taipale, Brian Raught, Yves Jacob, Frederick P. Roth

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; coding sequence collection; gateway-compatible

Online: 7 July 2020 (18:09:21 CEST)

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Working Paper ARTICLE

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Daniele Mercatelli, Federico Manuel Giorgi

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

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

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Preprint REVIEW | doi:10.20944/preprints202004.0192.v2

An Overview of SARS‐CoV‐2 and Animal Infection

Mohamed Mahdy

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: animal; COVID-19; intermediate host; SARS-COV-2

Online: 16 May 2020 (18:06:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0220.v2

Pulmonary Pathology of Early Phase 2019 Novel Coronavirus (COVID-19) Pneumonia in Two Patients with Lung Cancer

Sufang Tian, Weidong Hu, Li Niu, Huan Liu, Haibo Xu, Shu-Yuan Xiao

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: coronavirus; COVID-19 pneumonia; pathology; SARS-CoV-2

Online: 2 March 2020 (01:34:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0026.v1

Sequence Analysis and Amino Acid Variations of Structural Proteins Deduced From Novel Coronavirus SARS-CoV-2 Strains, Isolated in Different Countries

Tarlan Mamedov, Inanc Soylu, Gunay Mammadova, Gulnara Hasanova

Subject: Biology And Life Sciences, Virology Keywords: coronavirus; SARS-CoV-2; Spike protein; Nucleocapsid protein; MSA

Online: 3 May 2020 (06:27:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0524.v1

From Cell to Symptoms: The Role of SARS-CoV-2 Cytopathic Effects in the Pathogenesis of COVID-19 and Long COVID

Pablo Gonzalez-Garcia, Ornella Fiorillo Moreno, Eloina Zarate Peñate, Alejandro Calderón-Villalba, Lisandro Pacheco Lugo, Antonio Acosta Hoyos, Jose Luis Villarreal Camacho, Roberto Navarro Quiroz, Leonardo Pacheco Londoño, Gustavo Aroca Martinez, Noelia Moares, Antonio Gabucio, Cecilia Fernandez-Ponce, Francisco Garcia-Cozar, Elkin Navarro Quiroz

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: COVID-19; SARS-CoV-2; Long COVID; Cytopathy; cytokine storm; sequelae; PASC; coronavirus; angiotensin-converting enzyme 2; cell dysfunction

Online: 30 March 2023 (05:09:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0286.v1

Network Bioinformatics Analysis Provides Insight into Drug Repurposing for COVID-2019

Xu Li, Jinchao Yu, Zhiming Zhang, Jing Ren, Alex E. Peluffo, Wen Zhang, Yujie Zhao, Kaijing Yan, Daniel Cohen, Wenjia Wang

Subject: Medicine And Pharmacology, Pharmacy Keywords: COVID-2019; SARS-CoV-2; repurposing; network bioinformatics

Online: 18 March 2020 (08:50:10 CET)

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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 BRIEF REPORT | doi:10.20944/preprints202305.1332.v1

Mycophenolate Interruption Restores Anti-SARS-CoV-2 Vaccine Immunogenicity in Unresponsive Liver Transplant Recipients

Pierluigi Toniutto, Annarosa Cussigh, Sara Cmet, Martina Fabris, Francesco Curcio, Davide Bitetto, Ezio Fornasiere, Elisa Fumolo, Edmondo Falleti

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: Sars-CoV-2 infection; mycophenolate mofetil, liver transplantation, anti-SARS-CoV-2 vaccine.

Online: 18 May 2023 (10:39:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0250.v1

Low Prevalence of SARS-CoV-2 Antibodies in Canine and Feline Serum Samples Collected during the Covid-19 Pandemic in Hong Kong and Korea

Yun Young Go, Maura Carrai, Yan Ru Choi, Christopher J. Brackman, Karina W.S. Tam, Pierra Y.T. Law, Fiona Woodhouse, Jane Gray, Ji Hun Kim, Joohyung Park, Chae Won Jeon, Hyomi Jang, Ioannis Magouras, Nicola Decaro, Samuel MS Cheng, Malik Peiris, Julia A. Beatty, Vanessa R. Barrs

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Feline; Canine; seroprevalence; zoonosis

Online: 13 January 2023 (10:21:53 CET)

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