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Preprint REVIEW | doi:10.20944/preprints202402.0212.v1

The Effects of SARS-CoV-2 on Angiopoietin/Tie Axis and Vascular Endothelium

Dolgormaa Janchivlamdan, Maitreyi Shivkumar, Harprit Singh

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: SARS-CoV-2; Endothelial cell; Angiopoietin; Tie1/2; ACE2; inflammatory cytokines

Online: 5 February 2024 (10:53:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0174.v1

SARS-CoV-2 Intra-host Evolution Is Not Favoured by Immune System Deficiencies

Laura Manuto, Martina Bado, Marco Cola, Elena Vanzo, Maria Antonello, Giorgia Mazzotti, Monia Pacenti, Giampaolo Cordioli, Lolita Sasset, Anna Maria Cattelan, Stefano Toppo, Enrico Lavezzo

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 genomic variability; viral quasispecies; immunocompromised subjects; intra-host

Online: 4 December 2023 (10:04:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1272.v1

Evaluation of Blood Cultures of SARS-CoV-2 Positive and Negative Adult Patients

Bahar Akgün Karapınar, İlvana Çaklovica Küçükkaya, Yasemin Bölükbaşı, Sertaç Küçükkaya, Gonca Erköse Genç, Zayre Erturan, Ali Ağaçfidan, Betigül Öngen

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: blood culture; SARS-CoV-2; COVID-19; co-infection; antimicrobial resistance

Online: 17 August 2023 (10:34:23 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202203.0035.v1

Biocompatible Films of Calcium Alginate Inactivate Enveloped Viruses such as SARS-CoV-2

Alba Cano-Vicent, Rina Hashimoto, Kazuo Takayama, Ángel Serrano-Aroca

Subject: Chemistry And Materials Science, Biomaterials Keywords: calcium alginate; SARS-CoV-2; bacteriophage; phi 6; biomaterials; films; hydrogels

Online: 2 March 2022 (07:17:08 CET)

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

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

Pierre Arsene

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

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

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Preprint 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/preprints202209.0241.v1

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy

Alessia Lai, Annalisa Bergna, Carla Della Ventura, Stefano Menzo, Bianca Bruzzone, Fabio Sagradi, Francesca Ceccherini-Silberstein, Alessandro Weisz, Nicola Clementi, Gaetano Brindicci, Ilaria Vicenti, Lolita Sasset, Sara Caucci, Benedetta Corvaro, Silvia Ippoliti, Carla Acciarri, Vanessa De Pace, Leonardo Lanfranchi, Maria Concetta Bellocchi, Giorgio Giurato, Roberto Ferrarese, Antonella Lagioia, Daniela Francisci, Martina Laura Colombo, Samuel Lazzarin, Matilde Ogliastro, Maria Rosa Cappelletti, Marco Iannetta, Francesca Rizzo, Carmen Rita Santoro, Chiara Fraccalvieri, Sophie Testa, Luca Carioti, Teresa Rocco, Annalisa Saracino, Annamaria Cattelan, Massimo Clementi, Loredana Sarmati, Agostino Riva, Spinello Antinori, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Virology Keywords: variants circulation; SARS-CoV-2; Italy; epidemiology

Online: 16 September 2022 (08:07:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0430.v1

Anticipating the Next Chess Move: Blocking SARS-CoV-2 Replication and Simultaneously Disarming Viral Escape Mechanisms

Samir Mansour Moraes Casseb, André Salim Khayat, Jorge Estefano Santana de Souza, Edivaldo Herculano Correa de Oliveira, Sidney Emanuel Batista dos Santos, Pedro Fernando da Costa Vasconcelos, Paulo Pimentel de Assumpção

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

Online: 25 August 2022 (10:00:27 CEST)

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The COVID-19 pandemic initiated a race to determine the best measures to control the disease and to save as many people as possible. Efforts to implement social distancing, the use of masks, and massive vaccination programs turned out to be essential in reducing the devastating effects of the pandemic. Nevertheless, the high mutation rates of SARS-CoV-2 challenge the vaccination strategy and maintain the threat of new outbreaks due to the risk of infection surges and even lethal variations able to resist the effects of vaccines and upset the balance. Most of the new therapies tested against SARS-CoV-2 came from already available formulations developed to treat other diseases, so they were not specifically developed for SARS-CoV-2. In parallel, the knowledge produced regarding the molecular mechanisms involved in this disease was vast due to massive efforts worldwide. Taking advantage of such a vast molecular understanding of virus genomes and disease mechanisms, a targeted molecular therapy based on siRNA specifically developed to reach exclusive SARS-CoV-2 genomic sequences was tested in a non-transformed human cell model. Since coronavirus can escape from siRNA by producing siRNA inhibitors, a complex strategy to simultaneously strike both the viral infectious mechanism and the capability of evading siRNA therapy was developed. The combined administration of the chosen produced siRNA proved to be highly effective in successfully reducing viral load and keeping virus replication under control, even after many days of treatment, unlike the combinations of siRNAs lacking this anti-anti-siRNA capability. Additionally, the developed therapy did not harm the normal cells, which was demonstrated because, instead of testing the siRNA in nonhuman cells or in transformed human cells, a non-transformed human thyroid cell was specifically chosen for the experiment. The proposed siRNA combination deeply reduced the viral load throughout the experiment and allowed cellular recovery, thus representing a potential innovation, to be considered as an additional weapon for therapy of COVID-19 and even other infectious diseases.

Preprint REVIEW | doi:10.20944/preprints202104.0193.v2

SARS-CoV-2 Portrayed Against HIV: Contrary Viral Strategies in Similar Disguise

Ralf Duerr, Keaton M. Crosse, Ana Mayela Valero Jimenez, Meike Dittmann

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; HIV; zoonotic viruses; COVID-19 and AIDS pandemics; viral entry

Online: 8 April 2021 (10:51:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0372.v1

A Review of Evidence: Using Respirators to prevent Sars-Cov-2 Transmission

Adam Nulty

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: sars-cov-2, covid, covid-19, masks, dentistry, respirator, n99, n95, ffp2, ffp3,

Online: 18 August 2020 (04:30:45 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/preprints202003.0214.v1

Revealing the Potency of Citrus and Galangal Constituents to Halt SARS-CoV-2 Infection

Rohmad Yudi Utomo, Muthi' Ikawati, Edy Meiyanto

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: SARS-Cov-2; Citrus sp.; Galangal; Curcuma sp.; Sappan wood

Online: 12 March 2020 (13:59:40 CET)

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Working Paper REVIEW

The Alterations of Cellular Signaling Pathways in the Host Cell upon the High Pathogenic Coronaviruses Infection, SARS-CoV and MERS-CoV. What Could Be Expected from the SARS-CoV-2?

Nima Hemmat, Zahra Asadzadeh, Noora Karim-ahangar, Hajar Alemohammad, Basira Najafzadeh, Afshin Derakhshani, Amir Baghbanzadeh, Hossein Bannazadeh Baghi, Darya Javadrashid, Souzan Najafi, Meriadeg Ar Gouilh, Behzad Baradaran

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration

Online: 21 September 2020 (04:17:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0059.v1

Genomic Epidemiology of SARS-Cov-2 in Western Burkina Faso, West Africa

Yacouba Sawadogo, Lokman Galal, Essia Belarbi, Arsène Zongo, Grit Schubert, Fabian Leendertz, Abdoulie Kanteh, Abdul Karim Sesay, Annette Erhart, Anne-Laure Bañuls, Zekiba Tarnagda, Sylvain Godreuil, Halidou Tinto, Abdoul-Salam Ouedraogo

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Whole Genome Sequencing; Genomic epidemiology; West Africa, Burkina Faso

Online: 2 November 2022 (11:14:27 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/preprints202406.0885.v1

TAS2R38 Genotype Does Not Affect SARS-CoV-2 Infection in Primary Ciliary Dyskinesia

Gioia Piatti, Giorgia Girotto, Maria Pina Concas, Leonardo Braga, Umberto Ambrosetti, Mirko Aldè

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: bitter taste receptors; TAS2R38; Primary Ciliary Dyskinesia; COVID-19; SARS-CoV-2

Online: 13 June 2024 (05:37:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0409.v1

Clinical Features of Hospitalized Stroke Patients Infected with SARS-CoV-2 Omicron Variant

Hiroshi Kanno, Kazuki Miyazaki, Sachiko Yamada, Shutaro Matsumoto, Yuki Sagehashi, Satoru Takahashi, Yongson Kim, Keiko Namiki, Satoshi Fujii

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Stroke; COVID-19; SARS-CoV-2 Omicron variant; modified Ranking scale; coagulopathy

Online: 9 October 2023 (09:30:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.0055.v1

Recent Advances on SARS-CoV-2 Mpro Inhibitors: From Nirmatrelvir to Future Perspectives

Andrea Citarella, Alessandro Dimasi, Davide Moi, Daniele Passarella, Angela Scala, Anna Piperno, Nicola Micale

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: COVID-19; SARS-CoV-2 Mpro; protease inhibitors; coronavirus; peptidomimetics; Paxlovid; Nirmatrelvir

Online: 2 August 2023 (05:25:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0024.v1

Potential Inhibitors Targeting RNA-Dependent RNA Polymerase Activity (NSP12) of SARS-CoV-2

Zijing Ruan, Chao Liu, Yuting Guo, Zhenqing He, Xinhe Huang, Xu Jia, Tai Yang

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; nonstructural proteins (NSP); NSP12; NSP7; NSP8; virtual screening; inhibitor

Online: 2 March 2020 (03:11:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0196.v1

The Epidemiological Scenario of the SARS-CoV-2 Omicron Emergence in the Southeast Brazilian Population

Evandra Strazza Rodrigues, Svetoslav N. Slavov, Debora Glenda Lima De La-Roque, Elaine Vieira Santos, Josiane Serrano Borges, Mariane Evaristo, Pericles Natan Mendes Da Costa, Juliana Matos, Adriana Marques, Anemarie Dinarte Baccarin, Renata Aparecida Machado Oliveira, Wilson Lau Junior, Bruno Iglesias Benincasa, Luana Martins de Andrade Da Cruz, Alex R. J. Lima, Gabriela Ribeiro, Vincent Louis Viala, Loyze Paola Oliveira De Lima, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Elaine Cristina Marqueze, Jardelina De Souza Todão Bernardino, Rejane Maria Tommasini Grotto, Jayme A. Souza-Neto, Vagner Fonseca, Maurício Lacerda Nogueira, Heidge Fukumasu, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Dimas Tadeu Covas, Marta Giovanetti, Luiz Carlos Júnior Alcantara, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Simone K. Haddad

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2 genomic surveillance; Brazilian population; omicron variant

Online: 3 January 2024 (08:01:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202304.1094.v1

Effects of Different Types of Recombinant SARS-CoV-2 Spike Protein on Circulating Monocytes Structure

Marco Vettori, Francesco Dima, Brandon Michael Henry, Giovanni Carpenè, Matteo Gelati, Giovanni Celegon, Gianluca Salvagno, Giuseppe Lippi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Monocyte; Spike protein; Morphology.

Online: 28 April 2023 (03:29:08 CEST)

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

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

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

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

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

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Preprint COMMUNICATION | doi:10.20944/preprints202202.0158.v1

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

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

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

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

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Working Paper CASE REPORT

SARS-CoV-2 Infection in the Central Nervous System of a 1-Year-Old Infant

Ismael Carlos Gomes, Karina Karmirian, Julia Oliveira, Carolina Pedrosa, Mayara Abud Mendes, Fernando Colonna Rosman, Leila Chimelli, Stevens Rehen

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2 neuroinvasion; COVID-19; infant; Choroid plexus

Online: 15 March 2021 (13:03:33 CET)

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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/preprints202006.0041.v1

SARS-CoV-2 Existence in Different Types of Biological Specimens and Leading Public Health Concern

Priyanka Yadav

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; 2019-nCOV; Shedding; Detection

Online: 4 June 2020 (17:34:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0329.v1

Identification of Pharmacophoric Features and Novel Compounds for Inhibition of SARS-Cov-2 Main Protease

Priti Jain, Rupesh Dorik, Munendra Jain

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; protease; docking; pharmacophore; Zinc15

Online: 19 April 2020 (05:33:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0366.v2

Mapping the Non-Structural Transmembrane Proteins of SARS-CoV-2

Sunil Thomas

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; coronavirus; non-structural proteins; nsps; nsp3; nsp4; nsp6; Orf1ab; Orf3a; endoplasmic reticulum; double membrane vesicle

Online: 11 October 2022 (16:19:20 CEST)

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Preprint REVIEW | doi:10.20944/preprints202406.1289.v1

Post-Acute Sequelae And Mitochondrial Aberration In SARS-CoV-2 Infection

Charles Ward, Beata Schlichtholz

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; PASC; long-Covid; mitochondria; mtDNA, autophagy; mitophagy; innate immunity; cell metabolism; reactive oxygen species

Online: 18 June 2024 (15:41:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202403.0362.v1

SARS-CoV-2 Vaccines-Related Endocrine Disorders: An Updated Narrative Review

Avraham Ishay, Kira Oleinikov, Elena Chertok Shacham

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: COVID-19; COVID-19 vaccines; SARS-CoV-2 vaccine; endocrine adverse events; thyroid; pituitary; adrenal; diabetes; gonads

Online: 6 March 2024 (12:19:04 CET)

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Preprint REVIEW | doi:10.20944/preprints202209.0429.v1

SARS-CoV-2 - The Role of Natural Immunity: A Narrative Review

Sara Diani, Erika Leonardi, Attilio Cavezzi, Simona Ferrari, Oriana Iacono, Alice Limoli, Zoe Bouslenko, Daniele Natalini, Stefania Conti, Silvano Tramonte, Alberto Donzelli, Eugenio Serravalle

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; Sars-CoV-2; Natural immunity; Cellular immunity; Vaccine-induced immunity; Hybrid immunity; Cross-reactivity; Omicron

Online: 28 September 2022 (03:38:36 CEST)

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Background: Both natural immunity and vaccine-induced immunity to COVID-19 may be useful to reduce the mortality/morbidity of this disease, but still a lot of controversy exists. Aims: This narrative review analyzes the literature about: a) the duration of natural immunity; b) cellular immunity; c) cross-reactivity; d) the duration of post-vaccination immune protection; e) the probability of reinfection and its clinical manifestations in the recovered patients; f) comparisons between vaccinated and unvaccinated in the possible reinfections; g) the role of hybrid immunity; h) the effectiveness of natural and vaccine-induced immunity against Omicron variant; i) comparative incidence of adverse effects after vaccination in recovered individuals vs. COVID-19-naïve subjects. Material and Methods: through multiple search engines we investigated COVID-19 literature related to the aims of the review, published since April 2020 through July 2022, including also the previous articles pertinent to the investigated topics. Results: nearly 900 studies were collected and 238 pertinent articles were included. It was highlighted that the vast majority of individuals after COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality. Conclusions: this narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: a) measure the durability of immunity over time; b) evaluate both the impacts of Omicron-5 on vaccinated and healed subjects and of hybrid immunity.

Preprint BRIEF REPORT | doi:10.20944/preprints202105.0526.v1

Circulating SARS-CoV-2 Variants in Italy, October 2020-March 2021

Alessia Lai, Annalisa Bergna, Stefano Menzo, Gianguglielmo Zehender, Sara Caucci, Valeria Ghisetti, Francesca Rizzo, Fabrizio Maggi, Francesco Cerutti, Giorgio Giurato, Alessandro Weisz, Chiara Turchi, Bianca Bruzzone, Francesca Ceccherini-Silberstein, Nicola Clementi, Annapaola Callegaro, Fabio Sagradi, Daniela Francisci, Emmanuele Venanzi Rullo, Ilaria Vicenti, Massimo Clementi, Massimo Galli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 virus; complete genome sequencing; COVID-19 RT-PCR testing; Spike protein; vi-ral variants

Online: 21 May 2021 (15:12:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1728.v1

Symptomatology and IgG Levels Before and After SARS-CoV-2 Omicron Breakthrough Infections in Vaccinated Individuals

Nigella M. Paula, Emerson Joucoski, Valter A. Baura, Emanuel M. Souza, Fábio O. Pedrosa, Alan G. Gonçalves, Luciano F. Huergo

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: omicron; symptoms; IgG; SARS-CoV-2; COVID-19

Online: 28 April 2024 (07:48:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202311.1976.v1

SARS‐COV‐2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms

Marilia Inês Móvio, Giovana Carneiro, Isabella Lopes Martines, Gilmara Barros de Lima, Sergio Daishi Sasaki, Alexandre Hiroaki KIhara, Emma Poole, Michael Nevels, Maria Cristina Carlan da Silva

Subject: Biology And Life Sciences, Virology Keywords: SARS CoV-2; COVID-19; ORF8, cytokine storm

Online: 30 November 2023 (10:29:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1518.v1

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Sergio Luis Aguilar-Martinez, Gustavo Adolfo Sandoval-Peña, José Arturo Molina-Mora, Pablo Tsukayama-Cisneros, Cristian Díaz-Vélez, Franklin Rómulo Aguilar-Gamboa, D. Katterine Bonilla-Aldana, Alfonso J. Rodriguez-Morales

Subject: Medicine And Pharmacology, Tropical Medicine Keywords: SARS-CoV-2; genome; sequencing; phylogenetic analysis; Peru

Online: 23 November 2023 (11:07:09 CET)

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

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

Paul Kellam, Wendy Barclay

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

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

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Preprint 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 ARTICLE | doi:10.20944/preprints202006.0184.v1

Single Amino Acid Variant (SAV) Percentage and Monomer Modeling of Spike Protein of SARS-CoV-2 in Jordan

Walid Al-Zyoud, Hazem Haddad, Ramzi Foudeh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS; spike; variants; structure

Online: 14 June 2020 (16:00:35 CEST)

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Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human endothelial cells of the respiratoty system for the virus to be engulfed causing COVID-19 disease after priming by type II transmembrane protease TMPRSS2 and then binding with the angiotensin-converting enzyme 2 (ACE2). Therefore, mutations and amino acid variants analysis are essential in understanding the mechanism of binding of spike protein with its receptor to have an insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 and to analyze the amino acid variants for protein sequences from GISAID database for samples collected from Jordan in a try to find an explanation for the low confirmed number of COVID-19 in Jordan. Our Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) findings showed four single amino acid variants (SAV) found in 20 samples of SARS-CoV-2. What is equal to 5% of samples showed tyrosine deletion at Y144 located in the SARS-CoV-like_Spike_S1_NTD (N terminal domain), 62% showed aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD (spike recognition binding site), 5% showed aspartate substitution to tyrosine at D1139Y and 5% showed glycine substitution to serine at G1167S both located in the Corona_S2 domain. The findings have shown lower mutational sensitivity in all variants that might not affect the function of spike glycoprotein except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a higher likelihood to affect the function of the spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan.

Preprint ARTICLE | doi:10.20944/preprints202210.0471.v1

High Seroprevalence of Anti-SARS-CoV-2 Antibodies in Children in Vietnam: An Observational, Hospital-based Study

Dien Minh Tran, Uyen Tu Vu, Canh Ngoc Hoang, Ha Thu Thi Nguyen, Phu Huy Nguyen, Mai Chi Thi Tran, Anh Ngoc Chu, Phuc Huu Phan

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: children; seroprevalence; antibodies; SARS-CoV-2; Vietnam

Online: 31 October 2022 (07:37:55 CET)

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Background: The robustness of sero-surveillence has delineated the high burden of SARS-CoV-2 infection in children; however, these existing data showed wide variation. This study aimed to identify the serostatus of antibodies against SARS-CoV-2 and associated factors among children following the fourth pandemic wave in Vietnam. Methods: A cross-sectional study was conducted at Vietnam National Children’s Hospital (VNCH) between March 13 and April 3, 2022. 4,032 eligible children seeking medical care for any medical condition not related to acute Covid-19 infections was tested for IgG SARS-CoV-2 Antibodies by ADVIA Centaur® SARS-CoV-2 IgG (sCOVG) assay using the residuals of routine blood samples. Results: The median age of enrolled children was 39 (IQR=14-82) months. The overall seropositive prevalence was 59.2%, and the median antibody titer was 4.78 [IQR 2.38-9.57] UI/mL. The risk of seropositivity and the median antibody titer was not related to gender (58.6% versus 60.1%, 4.9 versus 4.6 UI/mL, all p>0.05). Among age groups, the highest seroprevalence was reported in the children aged 13 to <36 months old. Children aged ≤12 months were likely to be seropositive compared to children aged 36 to <60 months (59.2% versus 57.5%, p=0.49) and those aged ≥144 months (59.2% versus 65.5%, p=0.16). Children aged ≥144 months exhibited a significantly higher titer of protective COVID-19 antibodies than other age groups (p <0.001). In multivariate logistic regression, we observed independent factors associated with SARS-CoV-2 seropositivity, including the age 13 to <36 months (OR=1.29, 95%CI=1.06-1.56, p=0.01), 60 to <144 months (OR=79, 95%CI=0.67-0.95, p=0.01), ≥144 months (OR=1.84, 95%CI=1.21-2.8, p=0.005), the presence of infected household members (OR=2.36, 95%CI=2.06–2.70, p<0.001), participants from Hanoi (OR=1.54, 95%CI=1.34-1.77, p<0.001), underlying conditions (OR=0.71, 95%CI=0.60-0.85, p<=0.001), and using corticosteroids or immunosuppressants (OR=0.64, 95%CI=0.48-0.86, p=0.003). Conclusions: This study highlights a high seroprevalence of antibodies against SARS-CoV-2 among children seeking medical care for non-COVID-19-related conditions in a tertiary children’s hospital in Hanoi, Vietnam. In the context of reopening in-person schools and future emerged COVID-19 variants, this point will also be a key message about the necessity of “rush-out” immunization coverage for children, especially those under the age of three years.

Preprint ARTICLE | doi:10.20944/preprints202402.0288.v1

SARS-CoV-2 Seroepidemiology and Antibody Levels in Children during BA.5 Predominance Period

Filippos Filippatos, Elizabeth-Barbara Tatsi, Maria-Myrto Dourdouna, Alexandra Margeli, Vasiliki Syriopoulou, Athanasios Michos

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Children; BA.5 Omicron variant; seroepidemiology

Online: 5 February 2024 (15:09:27 CET)

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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 REVIEW | doi:10.20944/preprints202010.0585.v1

The Contribution of Endothelial Dysfunction in Systemic Injury Subsequent to SARS-Cov-2 Infection

Jessica Maiuolo, Rocco Mollace, Micaela Gliozzi, Vincenzo Musolino, Cristina Carresi, Sara Paone, Miriam Scicchitano, Roberta Macrì, Saverio Nucera, Francesca Bosco, Federica Scarano, Maria Caterina Zito, Stefano Ruga, Annamaria Tavernese, Vincenzo Mollace

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; Angiotensin-converting enzyme 2; Endothelium dysfunction; Thrombosis; Vasculitis.

Online: 28 October 2020 (11:21:55 CET)

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Abstract: SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection is associated, alongside with lung infection and respiratory disease, to cardiovascular dysfunction that occurs at any stage of the disease. This includes ischemic heart disease, arrhythmias, and cardiomyopathies. The common pathophysiological link between SARS-CoV-2 infection and the cardiovascular events is represented by coagulation abnormalities and disruption of factors released by endothelial cells which contribute in maintaining the blood vessels into an anti-thrombotic state. Thus, early alteration of the functionality of endothelial cells, which may be found soon after SARS-CoV-2 infection, seems to represent the major target of SARS CoV-2 disease state and accounts for the systemic vascular dysfunction that leads to detrimental effect in terms of hospitalization and death accompanying the disease. In particular, the molecular interaction of SARS-CoV-2 with ACE2 receptor located in endothelial cell surface, either at the pulmonary and systemic level, leads to early impairment of endothelial function which, in turn, is followed by vascular inflammation and thrombosis of peripheral blood vessels. This highlights systemic hypoxia and further aggravates the vicious circle that compromises the development of the disease leading to irreversible tissue damage and death of patients with SARS CoV-2 infection. The review aims to assess some recent advances to define the crucial role of endothelial dysfunction in the pathogenesis of vascular complications accompanying SARS-CoV-2 infection. In particular, the molecular mechanisms associated to the interaction of SARS CoV-2 with ACE2 receptor located on the endothelial cells are highlighted to support its role in compromising endothelial cell functionality. Finally, the consequences of endothelial dysfunction in enhancing pro-inflammatory and pro-thrombotic effects of SARS-CoV-2 infection are assessed in order to identify early therapeutic interventions able to reduce the impact of the disease in high-risk patients.

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/preprints202305.0403.v1

SARS-CoV-2 in the Middle Ear. CovEar: A Prospective Pilot Study

Nina Rubicz, Nikolaus Poier-Fabian, Christian Paar, Markus Winkler-Zamani, Philipp Hermann, Stefan Raidl, Paul Martin Zwittag

Subject: Medicine And Pharmacology, Otolaryngology Keywords: COVID-19; Coronavirus; SARS-CoV-2; middle ear; ear surgery; middle ear surgery; otologic surgery

Online: 6 May 2023 (09:34:27 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 ARTICLE | doi:10.20944/preprints202406.1394.v1

Molecular Characterization and Genomic Surveillance of SARS-CoV-2 Lineages in Central India

Purna Dwivedi, Mukul Sharma, Afzal Ansari, Arup Ghosh, Subasa Chandra Bishwal, Suman Kumar Ray, Manish Katiyar, Kombiah Subbiah, Lalit Sahare, Mahendra Ukey, Pradip Barde, Aparup Das, Pushpendra Singh

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Genetic diversity; Whole genome sequencing; Phylogenetic tree; COVID-19; Transmission

Online: 21 June 2024 (05:04:45 CEST)

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Preprint REVIEW | doi:10.20944/preprints202206.0022.v1

Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics

Alexander Kudryavtsev, Anna V. Vakhrusheva, Valery Novoseletsky, Marine Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Omicron; bioinformatics; immune escape; RBD mutations; vaccine development

Online: 1 June 2022 (14:12:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0377.v2

A Review of SARS-CoV-2, Responsible for COVID-19: History, Biology, Infection Mechanism, Antigenic Vaccines, Their Risks and how an Alternate RBD Vaccine is Safer?

Z.M.G. Sarwar Jahangir, Arleta Helena Marnik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: aa = amino acids; ACE-2 = receptor angiotensin-converting enzyme 2; cDNA = complementary DNA; mRNA = messenger RNA; orf = open reading frame; RBD = receptor binding protein; S-protein = Spike protein; SARS-CoV-2 = severe respiratory syndrome coronavirus 2; Vaccines.

Online: 22 June 2021 (11:53:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.0703.v1

Safety and Immunogenicity of the Intranasal Vaccine Candidate Mambisa and the Intramuscular Vaccine Abdala Used as Booster Doses for COVID-19 Convalescents: A Randomized Phase 1–2 Clinical Trial

Gilda Lemos-Pérez, Yinet Barrese-Pérez, Yahima Chacón-Quintero, Rolando Uranga-Piña, Yisel Avila-Albuerne, Iglermis Figueroa-García, Osaida Calderín-Marín, Martha M. Gómez-Vázquez, Marjoris Piñera-Martínez, Sheila Chávez-Valdés, Ricardo Martínez-Rosales, Lismary Ávila-Díaz, Amalia Vázquez-Arteaga, Hany González-Formental, Giselle Freyre-Corrales, Edelgis Coizeau-Rodríguez, Miladys Limonta-Fernández, Marta Ayala-Avila, Eduardo Martínez-Díaz, Eulogio Pimentel-Vazquez, Gerardo Enrique Guillén-Nieto

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19 vaccines; convalescents; booster; intranasal; intramuscular; vaccination; Cuba

Online: 11 June 2024 (12:00:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0648.v1

Insights into the SARS-CoV-2 ORF6 Mechanism of Action

Elena Krachmarova, Peicho Petkov, Elena Lilkova, Nevena Ilieva, Miroslav Rangelov, Nadezhda Todorova, Kristina Malinova, Rossitsa Hristova, Genoveva Nacheva, Anastas Gospodinov, Leandar Litov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 ORF6 – RAE1 binding; 3D molecular structure modelling; molecular dynamics simulations; cell cycle, cyclin E; R-loops; DNA replication stress

Online: 8 June 2023 (13:52:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202010.0341.v1

SARS-CoV-2 and Environmental Samples: A Methodological Approach to Have Consistent and Comparable Results

Angelo Robotto, Paola Quaglino, David Lembo, Marcello Morello, Enrico Brizio, Luisella Bardi, Andrea Civra

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: SARS-CoV-2; airborne transmission; environmental virology; bioaerosol; wastewater samples

Online: 16 October 2020 (08:26:10 CEST)

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Since the beginning of coronavirus disease 2019 (COVID-19) pandemic, large attention has been focused on the relationship between SARS-CoV-2 diffusion and environment. As a matter of fact, clear evidence of the transmission of SARS-CoV-2 via respiratory aerosol would be of primary importance; at the same time, checking the presence of SARS-CoV-2 in wastewater can be extremely useful to control the diffusion of the disease. Up to now, many studies report SARS-CoV-2 concentrations in indoor/outdoor air samples or water/wastewater samples that can differ by order of magnitude. Unfortunately, complete information about the scientific approach of many studies is still missing, relating to: samplers and sampling materials performances, recovery tests, measurement uncertainty, robustness, detection and quantification limits, infectivity of captured virus, virus degradation during sampling, influence of sample pre-treatments (included freezing) on results, effects of inhibitors, sample alterations due to manipulation, validation of methods and processes, quality assurance according to ISO/IEC 17025 requirements.Based on the first experiences focused on the presence of SARS-CoV-2 in environmental samples such as air quality filters, air-liquid impingers and wastewater samples, the present study describes a coherent preliminary approach to SARS-CoV-2 environmental sampling in order to overcome the evident lack of standardization. Three aspects are highlighted here: the first solution to assure quality and consistency to environmental sampling relies on the development of recovery tests using standard materials and investigating sampling materials, sampling techniques, sampling durations, sample conservation and pre-treatments; secondly, in order to overcome the shortcomings of every single sampling technique, coupling different samplers in parallel sampling could be an efficient strategy to collect more information and make data more reliable, in particular for air samples; finally, with regards to airborne virus sampling, the results could be confirmed by simplified emission and dilution models.

Preprint ARTICLE | doi:10.20944/preprints202003.0360.v2

TMPRSS2 Transcriptional Inhibition as a Therapeutic Strategy for COVID-19

Xinchen Wang, Ryan Dhindsa, Gundula Povysil, Anthony Zoghbi, Joshua Motelow, Joseph Hostyk, Nicholas Nickols, Matthew Rettig, David B. Goldstein

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; transcriptional inhibition; COVID-19; drug repurposing; TMPRSS2

Online: 28 April 2020 (09:39:02 CEST)

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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 REVIEW | doi:10.20944/preprints202202.0261.v1

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

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

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

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

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Preprint COMMUNICATION | doi:10.20944/preprints202306.2007.v1

Ct-Value from qRT-PCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success

Dominik Hadzega, Klaudia Babisova, Michaela Hyblova, Nikola Janostiakova, Peter Sabaka, Pavol Janega, Gabriel Minárik

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RNA genome assembly; RT-qPCR; SPAdes

Online: 29 June 2023 (02:12:07 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202010.0308.v1

Potential Role of Children in the Household Transmission of SARS-CoV-2 Infection in Catalonia (Spain)

Antoni Soriano-Arandes, Berta Ferran, Magda Campins, Juliana Esperalba-Esquerra, Juliana Reyes-Urueña, Uxue Lazcano, Anna Gatell, Pepe Serrano, Xavier Bruna, Ramon Capdevila, Maria Esteller, Andres Anton, Jordi Gómez i Prat, Gloria Ruiz, Anna Fàbrega, Neus Rius, Marina Fenoy, Núria López, Almudena Sánchez, Miriam Poblet, Anton Foguet, Guillermo García, Teresa Riera, Elisenda Martínez-Carbonell, Yesika Díaz, Valentí Pineda, Pere Soler-Palacin

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; children; household; contact tracing

Online: 14 October 2020 (13:33:49 CEST)

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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/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 ARTICLE | doi:10.20944/preprints202308.0123.v1

Novel Entropy-Based Phylogenetic Algorithm: A New Approach for Classifying SARS-CoV-2 Variants

Vladimir Perovic, Sanja Glisic, Milena Veljkovic, Slobodan Paessler, Veljko Veljkovic

Subject: Biology And Life Sciences, Other Keywords: Entropy; Electron-Ion Interaction Potential; COVID-19; Phylogenetic analysis; SARS-CoV-2

Online: 2 August 2023 (03:29:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0219.v1

SARS-CoV-2 Positivity and Viral Load during Three Viral Waves in Mumbai, India

Chaitali Nikam, Wilson Suraweera, Sze Hang Fu, Patrick E Brown, Nico Nagelkerke, Prabhat Jha

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 pandemic; PCR positivity; Aleph Delta Omicron waves; Mumbai; India

Online: 13 March 2023 (06:31:08 CET)

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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/preprints202106.0472.v1

Non-Uniform Aspects of SARS-CoV-2 Intraspecies Evolution Reopen Questions on Its Origin

Sk Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Ángel Serrano-Aroca Aroca, Gajendra Kumar Azad, Alaa A.A. Aljabali, Giorgio Palu, Tarek Mohamed Abd El-Aziz, Debmalya Barh, Bruce D. Uhal, Parise Adadi, Kazuo Takayama, Nicolas G. Bazan, Murtaza Tambuwala, Samendra P. Sherchan, Amos Lal, Gaurav Chauhan, Wagner Baetas-da-Cruz, Vladimir N. Uversky

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; Mutations; Furin Cleavage Site (FCS); Evenly-uneven; Invariant regions

Online: 18 June 2021 (09:22:08 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 ARTICLE | doi:10.20944/preprints202206.0086.v1

Leveraging Geographically Distributed Data for Influenza and SARS-CoV-2 Non-Parametric Forecasting

Pablo Boullosa, Adrián Garea, Iván Carlos Area-Carracedo, Juan Nieto, Jorge Mira

Subject: Computer Science And Mathematics, Computational Mathematics Keywords: non-parametric modeling; flu; influenza; COVID-19; SARS-CoV-2; Empirical Dynamic Modeling; forecasting

Online: 6 June 2022 (10:24:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0369.v2

Repurposing of Approved Drugs with Potential to Interact with SARS-CoV-2 Receptor

Abu Sajib

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; spike protein; ACE1; ACE2; host-virus interaction; drug repurposing

Online: 2 August 2020 (09:23:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1603.v1

Perioperative Analgesia in Crisis Situation SARS-CoV-2. Patient Characteristics in COVID-19 in Pain Out Registry

María A. Pérez-Herrero, Manuel Carrasco, Berta Velasco, Sara Cocho, Carla del Rey, Hermann Ribera

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: analgesia; COVID-19; pain; postoperative pain; SARS-CoV2

Online: 22 July 2024 (03:10:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0300.v1

Sars-Cov-2 Inactivation by a Panel of Commercialized Buffers and by Traditional Protocols (Heat or SDS)

Grégory Quéromès, Emilie Frobert, Maude Bouscambert-Duchamp, Martine Valette, Geneviève Billaud, Vanessa Escuret, Antoine Oblette, Bruno Lina, Florence Morfin, Alexandre Gaymard

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; inactivation; commercial buffer; heat; SDS

Online: 22 March 2022 (11:21:05 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0049.v1

Mutational Screening of the Proteome of Sars-Cov-2 Isolates: Mutability of ORF3a, Nucleocapsid and Nsp2 Proteins

Martina Bianchi, Domenico Benvenuto, Massimo Ciccozzi, Stefano Pascarella

Subject: Biology And Life Sciences, Virology Keywords: Sars-CoV-2; proteome; mutation; ORF3a; Nucleoprotein; Nsp2

Online: 5 July 2020 (06:54:01 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/preprints202307.0375.v1

Serological Assay for SARS-CoV-2 in Domestic and Wild Animals in Middle and Southeast Regions in Brazil

Julia Maldi Dias, Mariana Oliveira Costa, Amanda Oliveira De Souza, Majela Lima Faria, Daniel Hofman Golcman, Mariana Baroni Selim, Emília Patrícia Medici, Guilherme Shin Iwamoto Haga, Adriana Hellmeister de Campos Nogueira Romaldini, Liria Hiromi Okuda

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; pandemic; animals; antibodies; seroprevalence

Online: 6 July 2023 (07:17:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0042.v1

Viral Targets in Human Interactome with Comprehensive Centrality Analysis: SARS-CoV-2, A Case Study

Nilesh Kumar, M. Shahid Mukhtar

Subject: Biology And Life Sciences, Life Sciences Keywords: comprehensive human interactome; SARS-CoV-2 targets; network metrices; centrality analyses

Online: 1 May 2024 (07:24:25 CEST)

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Preprint REVIEW | doi:10.20944/preprints202305.0103.v1

Novel Antiviral Therapeutic Against SARS-CoV-2 and its Variants: Recent Developments and Future Perspectives

Amit Gupta, Ashish P. Singh, Vinay K. Singh, Rajeshwar P. Sinha

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; antiviral agents; Omicron variant; mutant; vaccines; clinical studies

Online: 3 May 2023 (06:04:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0086.v1

Evaluation of Serological Tests to Determine Postvaccinal Immunity to SARS-Cov-2 by Mrna Vaccines

Graciela Iglesias García, Ángel Díaz Rodíguez, Beatriz Díaz Rodríguez, Carmela Cuello Estrada, Tania Ferreiro García, Noelia Crespo García, Jesús Seco-Calvo

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: automated immunoassays; COVID-19; lateral flow immunoassay; performance; SARS-CoV-2

Online: 4 November 2022 (01:59:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0647.v1

First Description of Natural SARS-CoV-2 Infection in Two Wild American Minks (Neovison vison)

Jordi Aguiló-Gisbert, Miguel Padilla-Blanco, Victor Lizana, Elisa Maiques, Marta Muñoz Baquero, Eva Chillida-Martínez, Jesús Cardells, Consuelo Rubio-Guerri

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: American Mink; COVID-19; Neovison vison; SARS-CoV-2; Spike; wildlife

Online: 25 March 2021 (16:39:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0356.v1

Clinical and Pathological Correlation between SARS-CoV-2 Infection with Coexisting Health Conditions: A Review

Rituparna Saha, Mainak Mukhopadhyay, Debalina Bhattacharya

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Comorbidities; Clinical characteristics; Pathobiology; 2019-nCov

Online: 14 December 2020 (18:16:00 CET)

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Preprint REVIEW | doi:10.20944/preprints202009.0565.v1

Immunobiochemical Aspects in the Pathogenesis, Diagnosis, and Management of Novel Coronavirus (SARS-Cov-2) Infection

Venkata Bharat Kumar Pinnelli, Mangala N. Sirsikar, W. Vishnu Vandana, Shrabani Mohanty, Wilma Delphine Silvia CR, Ranjan Kumar Mohapatra, Sabitha Vadakedath, Venkataramana Kandi

Subject: Biology And Life Sciences, Virology Keywords: Coronavirus; SARS-CoV-2; COVID-19; Immunobiochemical aspects; pathogenesis; diagnosis; management

Online: 24 September 2020 (04:39:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0512.v6

The Structure of the Membrane Protein of SARS-CoV-2 Resembles the Sugar Transporter semiSWEET

Sunil Thomas

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Coronavirus; Virus; sugar transporter; SemiSWEET; Membrane glycoprotein, Pandemic

Online: 19 October 2020 (10:48:05 CEST)

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes are at risk of the disease. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include, membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N) and the spike protein (S). The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein. The M protein of SARS-CoV-2 is 98.6% similar to the M protein of bat SARS-CoV, maintains 98.2% homology with pangolin SARS-CoV, and has 90% homology with M protein of SARS-CoV; whereas, the similarity was only 38% with the M protein of MERS-CoV. In silico analyses showed that the M protein of SARS-CoV-2 has a triple helix bundle, form a single 3-transmembrane domain (TM), and are homologous to the prokaryotic sugar transport protein semiSWEET. SemiSWEETs are related to the PQ-loop family that function as cargo receptors in vesicle transport, mediates movement of basic amino acids across lysosomal membranes, and is also involved in phospholipase flippase function. The advantage and role of the M protein having a sugar transport-like structure is not clearly understood. The M protein of SARS-CoV-2 interacts with S, E and N protein. The S protein of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein influences glycosylation of the S protein. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the semiSWEET sugar transporter-like structure of the M protein may be involved in multiple functions that may aid in the rapid proliferation, replication and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the semiSWEET sugar transporter.

Preprint REVIEW | doi:10.20944/preprints202004.0272.v1

Anosmia and Ageusia as Initial or Unique Symptoms after SARS-COV-2 Virus Infection

Calixto Machado, Joel Victor Gutierrez

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2 (CoV-2); COVID-19; coronavirus; pandemic; smell; anosmia; taste; ageusia

Online: 16 April 2020 (12:42:44 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/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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Working Paper BRIEF REPORT

Identification of Novel Missense Mutations in a Large Number of Recent SARS-CoV-2 Genome Sequences

Hugh Y. Cai, Kimberly K. Cai, Julang Li

Subject: Biology And Life Sciences, Virology Keywords: COVI-19; SARS-CoV-2; virus; mutation; polymorphism; genome sequence

Online: 21 May 2020 (04:09:53 CEST)

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Background: SARS-CoV-2 infection has spread to over 200 countries since it was first reported in December of 2019. Significant country-specific variations in infection and mortality rate have been noted. Although country-specific differences in public health response have had a large impact on infection rate control, it is currently unclear as to whether evolution of the virus itself has also contributed to variations in infection and mortality rate. Previous studies on SARS-CoV-2 mutations were based on the analysis of ~ 160 SARS-CoV-2 sequences available until mid-February 2020.^{2, 3, 4, 5} By mid-April, > 550 SARS-CoV-2 sequences had been deposited in GenBank, and over 8,200 in the GISAID database. Methods: We performed a sequence analysis on 474 SARS-CoV-2 genomes submitted to GenBank up to April 11, 2020 by multiple alignment using Map to a Reference Assembly and Variants/SNP identification. The results were verified on a larger scale, 8,126 hCoV-19 (SARS-CoV-2) sequences from GISAID database. Results: We identified 5 recently emerged mutations in many isolates (up to 40%). Our analysis highlights 5 frequent new mutations that have emerged since late February 2020. These mutations are: one each missense (non-synonymous) mutation in orf1ab (C1059T), orf3 (G25563T) and orf8 (C27964T), one in 5’UTR (C241T), one in a non-coding region (G29553A). The final mutation (G29553A) was found to be almost exclusive to the US isolates. The first 3 mutations are non-synonymous, leading to amino acid substitutions in the viral protein sequence. Except for C241T, all the novel mutations identified are absent in the isolates from Italy and Spain in the SARS-CoV-2 genomes deposited in GenBank and GISAID by April 13, 2020. Conclusion: The results of current study indicate that new mutations are emerging as COVID-19 pandemic are spreading to different countries and that geography specific mutants may exist. The findings of current study lay the foundation for further investigation into the impact of SARS-CoV-2 mutations on disease incidence, severity, and host immune response. In addition, it may also provide insights into vaccine development and serological response detection for the virus.

Preprint REVIEW | doi:10.20944/preprints202004.0510.v1

A Structural View at SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping

Maria Romano, Alessia Ruggiero, Flavia Squeglia, Giovanni Maga, Rita Berisio

Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID19; RNA replication; protein structure; infectious disease

Online: 29 April 2020 (12:52:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0425.v1

Non-Coding RNAs and Innovative Therapeutic Strategies to Target the 5’UTR of SARS-CoV-2

Antonella Baldassarre, Alessandro Paolini, Stefania Paola Bruno, Cristina Felli, Alberto Eugenio Tozzi, Andrea Masotti

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; 5’UTR; miRNAs; RNAi; GapmeRs

Online: 24 April 2020 (04:16:20 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 REVIEW | doi:10.20944/preprints202212.0418.v2

Cellular and Humoral Immunity and Infection Responses to SARS-CoV-2:Immune Biomolecular Mechanisms by Case Study within SARS-CoV-2 Pathogenesis and Other Infections

Brent Brown, Vanshika Ojha, Ingo Fricke, Michael Green, Chinua Imarogbe, Suhaila A. Al-Sheboul, Tanya Gravier, Lori Peterson, Ivoyl Koutsaroff

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; B Cells; Neutrophils; T Cells; NK Cells; Innate; Adaptive; Cytokines; Chemokines; Adhesion Molecules; Antibody; Cluster of Differentiation; Receptors; Proteins; SARS-CoV-2; Serology

Online: 27 December 2022 (03:19:48 CET)

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The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist, of which Middle East Respiratory Syndrome (MERS) and SARS-CoV (SARS) showed higher mortality rates without causing a pandemic. As of December 2022, SARS-CoV-2 has resulted in over 6.6 million deaths worldwide through an array of acute to chronic pathologies. Historical pandemics include smallpox and influenza with efficacious therapeutics utilized to reduce overall disease burden. Therefore, immune system process analysis is required to compare innate and adaptive immune system interactions. Lymphatic system organs include bone marrow and thymus using a network of nodes throughout which white blood cells traverse glycolipid membranes utilizing cytokines and chemokine gradients that affect cell development, differentiation, proliferation, and migration processes as well as genetic factors affecting cell receptor expression. Innate processes involve antigen-presenting cells and B lymphocyte cellular responses to pathogens relevant to other viral and bacterial infections but also in oncogenic diseases. Such processes utilize cluster of differentiation (CD) marker expression, major histocompatibility complexes (MHC), pleiotropic interleukins (IL) and chemokines. The adaptive immune system consists of Natural Killer (NK) and T cells. Other viruses are also contributory to cancer including human papillomavirus (cervical carcinoma ), Epstein-Barr virus (EBV) ( lymphoma), hepatitis B and C (hepatocellular carcinoma) and human T cell leukemia virus-1 (adult T-cell leukemia). Bacterial infections also increase the risk of developing cancer( e.g. H. pylori). Therefore, as the above factors can cause both morbidity and mortality along-side being transmitted within clinical and community settings, it is appropriate to now examine advances in single cell sequencing, FACS analysis and many other laboratory techniques that allow insights into discoveries of newer cell types. These developments offer improved clarity and understanding that over-lap with known autoimmune conditions that could be affected by innate B cell or T cell responses to SARS-CoV-2 infection. Thus, this review quantifies and outlines the nature of specific receptors and proteins relevant to clinical laboratories and medical research by documenting both innate and adaptive immune system cells within current coronavirus immunology case study data and other pathologies to date.

Preprint ARTICLE | doi:10.20944/preprints202003.0267.v1

Binding Mechanism of Remdesivir to SARS-CoV-2 RNA Dependent RNA Polymerase

Leili Zhang, Ruhong Zhou

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: COVID-19; SARS-CoV-2; RNA-dependent RNA polymerase (RdRp); remdesivir; homology model; molecular dynamics; free energy perturbation

Online: 17 March 2020 (04:07:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1507.v1

The Interaction between SARS-CoV-2 Nucleocapsid Protein and UBC9 Inhibits MAVS Ubiquitination by Enhancing Its SUMOylation

Huang Congcong, Yiping Yin, Pan Pan, Yanping Huang, Siwei Chen, Junkai Chen, Ju Wang, Guoqing Xu, Xuan Tao, Xiao Xiao, Jian Li, Jing Yang, Zhixiong Jin, Bei Li, ZhaoHui Tong, Weixing Du, Long Liu, Zhixin Liu

Subject: Biology And Life Sciences, Virology Keywords: SARS‐CoV‐2; Nucleocapsid Protein; UBC9; MAVS; SUMOylation; Ubiquitination

Online: 24 October 2023 (08:15:43 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202205.0018.v2

First Identification in Italy of SARS-CoV-2 Omicron BA.4 Harboring KSF141_del: Genomic Comparison with Omicron Sub-Variants

Cinzia Peronace, Rossana Tallerico, Manuela Colosimo, Marco De Fazio, Federica Pasceri, Ilenia Talotta, Giuseppina Panduri, Letizia Pintomalli, Rosaria Oteri, Valeria Calantoni, Maria Teresa Fiorillo, Maria Cristina Caroleo, Rosita Curcio, Vincenza Dolce, Erika Cione, Pasquale Minchella

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; Variant of Concern; BA.4; pandemic

Online: 6 May 2022 (11:55:20 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202201.0087.v1

Exploring Mitochondrial Localization of SARS-CoV-2 RNA by Padlock Assay. A Pilot Study in Human Placenta

Maria Grazia Di Certo, Francesca Gabanella, Christian Barbato, Nicoletta Corbi, Marco Fiore, Carla Petrella, Marco de Vincentiis, Antonio Greco, Giampiero Ferraguti, Alessandro Corsi, Massimo Ralli, Irene Pecorella, Cira R.T. Di Gioia, Francesco Pecorini, Roberto Brunelli, Claudio Passananti, Antonio Minni

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: COVID-19; SARS-CoV-2 RNA; mitochondria; placenta; padlock

Online: 6 January 2022 (12:35:00 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 ARTICLE | doi:10.20944/preprints202310.0429.v2

Assessing the Potential Role of Cats (Felis Catus) as Generators of Relevant SARS-CoV-2 Lineages during the Pandemic

Ninnet Gomez-Romero, Francisco Javier Basurto-Alcantara, Lauro Velazquez-Salinas

Subject: Biology And Life Sciences, Virology Keywords: cats; SARS-CoV-2; evolution; variants; phylogenomics

Online: 9 October 2023 (11:45:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0654.v1

Evolutionary Dynamics of SARS-CoV-2 in Space and Time During the First Phase of the Epidemic in Italy

Alessia Lai, Annalisa Bergna, Stefano Toppo, Marina Morganti, Stefano Menzo, Valeria Ghisetti, Bianca Bruzzone, Mauro Codeluppi, Vito Fiore, Emmanuele Venanzi Rullo, Guido Antonelli, Loredana Sarmati, Gaetano Brindicci, Annapaola Callegaro, Caterina Sagnelli, Daniela Francisci, Ilaria Vicenti, Arianna Miola, Giovanni Tonon, Daniela Cirillo, Ilaria Menozzi, Sara Caucci, Francesco Cerutti, Andrea Orsi, Roberta Schiavo, Sergio Babudieri, Giuseppe Nunnari, Claudio M. Mastroianni, Massimo Andreoni, Laura Monno, Davide Guarneri, Nicola Coppola, Andrea Crisanti, Massimo Galli, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; viral variants; molecular tracing

Online: 29 July 2021 (12:23:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1814.v1

Identification of Delta Variant-Specific Mutations of SARS-CoV-2 Genomes Found in Uzbek Patients by Amplicon Sequencing

Mirzakamol Ayubov, Zabardast Buriev, Mukhammadjon Mirzakhmedov, Abdurakhmon Yusupov, Bakhtiyor Nosirov, Dilshod Usmanov, Shukhrat Shermatov, Khurshida Ubaydullaeva, Abdusattor Abdukarimov, Ibrokhim Abdurakhmonov

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; virus; transmission; mutations; Delta strain

Online: 27 July 2023 (09:36:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202210.0245.v1

SARS-Cov-2 Spike Protein Mutation at Cysteine-488 Impairs Its Golgi Localization And Intracellular S1/S2 Processing

Yuichiro Yamamoto, Tetsuya Inoue, Mana Murae, Masayoshi Fukasawa, Mika K Kaneko, Yukinari Kato, Kohji Noguchi

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Spike; Cysteine; proteolysis; brefeldin A

Online: 18 October 2022 (03:52:19 CEST)

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Working Paper ARTICLE

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

Qiang Wang, Ying Zhao, Xiaojia Chen, An Hong

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

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

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Preprint ARTICLE | doi:10.20944/preprints202205.0381.v1

Efficacy of Licensed Monoclonal Antibodies and Antiviral Agents against the SARS-CoV-2 Omicron Sub-Lineages BA.1 and BA.2

Lia Fiaschi, Filippo Dragoni, Elisabetta Schiaroli, Annalisa Bergna, Barbara Rossetti, Federica Giammarino, Camilla Biba, Anna Gidari, Alessia Lai, Cesira Nencioni, Daniela Francisci, Maurizio Zazzi, Ilaria Vicenti

Subject: Biology And Life Sciences, Virology Keywords: Sars-Cov-2; mAbs; Paxlovid; Remdesivir; Molnupiravir; Microneutralization assay; Cell-based assay; Omicron sublineages

Online: 27 May 2022 (10:45:19 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 ARTICLE | doi:10.20944/preprints202101.0173.v1

Molecular Epidemiology Surveillance of SARS-Cov-2: Mutations and Genetic Diversity One Year After Emerging

Alejandro Flores-Alanis, Armando Cruz-Rangel, Flor Rodríguez-Gómez, James González, Carlos Alberto Torres-Guerrero, Gabriela Delgado, Alejandro Cravioto, Rosario Morales-Espinosa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; genetic diversity; molecular surveillance; natural selection; non-synonymous substitution

Online: 11 January 2021 (09:50:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202406.1845.v1

Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2

Roberto Patarca, William A. Haseltine

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Coronavirus; enhancer; long-range RNA-RNA interactions; IBV; SARS-CoV-2; viral attenuation; host immune evasion

Online: 26 June 2024 (10:45:44 CEST)

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