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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 CONCEPT PAPER | doi:10.20944/preprints202004.0412.v1

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

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

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

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

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

Preprint ARTICLE | doi:10.20944/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/preprints202212.0386.v1

Seroprevalence of SARS-CoV-2 Antibodies in French Polynesia and Perspective for Vaccine Strategies

Maite Aubry, Noémie Maset, Lloyd Chapman, Aurélie Simon, Sophie Olivier, Raphaëlle Bos, Kiyojiken Chung, Iotefa Teiti, Adam Kucharski, Henri-Pierre Mallet, Van-Mai Cao-Lormeau

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; seroprevalence; antibodies; vaccine; natural infection; French Polynesia

Online: 21 December 2022 (04:56:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.1994.v1

A Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants of Concern and Lineages from Direct Nasopharyngeal Swab Samples without RNA Isolation

Santiago Enrique Werbajh, Luciana Larocca, Carolina Carrillo, Fabiana Stolowicz, Lorena Ogas, Sergio Pallotto, Solange Cassará, Lilia Mammana, Inés Zapiola, María Belén Bouzas, Adrián Alberto Vojnov

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

Online: 28 July 2023 (13:29:56 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 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/preprints202309.0576.v1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Veronica Murta, Alejandro Villarreal, Alberto Javier Ramos

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

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

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

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

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

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

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

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

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

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

Ansgar Klimke, Gudrun Hefner, Bianca Will, Ursula Voss

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

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

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

Preprint ARTICLE | doi:10.20944/preprints202212.0232.v1

Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies

Alexandre Hassanin, Opale Rambaud

Subject: Biology And Life Sciences, Virology Keywords: coronavirus; genome; recombination; COVID-19; reservoir host; secondary host; phylogenetic support; tree reconstruction

Online: 13 December 2022 (07:44:48 CET)

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

The Airborne and Gastrointestinal Coronavirus SARS-COV-2 Pathways

Tomás Santa-Coloma

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

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

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Preprint ARTICLE | doi:10.20944/preprints202206.0410.v1

Patients with Inflammatory Bowel Disease on anti-Tumor Necrosis Factor Therapy Might be Predisposed to SARS-CoV-2 Variants Infection Even after Receiving a Third mRNA Vaccine Dose

Paola López-Marte, Alondra Soto-González, Lizzie Ramos-Tollinchi, Stephan Torres-Jorge, Mariana Ferre, Esteban Rodríguez-Martinó, Esther A. Torres, Carlos A. Sariol

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: COVID-19 variants; COVID-19 vaccine; IBD; ulcerative colitis; Crohn’s disease; anti-TNF

Online: 29 June 2022 (15:02:36 CEST)

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Working Paper BRIEF REPORT

Potential for Developing a SARS-CoV Receptor Binding Domain (RBD) Recombinant Protein as a Heterologous Human Vaccine against Coronavirus Infectious Disease (COVID)-19

Wen-Hsiang Chen, Peter J. Hotez, Maria Elena Bottazzi

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: heterologous vaccine; receptor-binding domain; subunit vaccine; coronavirus; COVID-19; SARS; SARS-CoV-2

Online: 4 March 2020 (05:19:16 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/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/preprints202310.1276.v1

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

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

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

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

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

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

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

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

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

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

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

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

James Baldwin, Samina Noorali, Ashok Vaseashta

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

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

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

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

Marek Wojczyk, Ewa Niewiadomska, Małgorzata Kowalska

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

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

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

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

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

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

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

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

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

Takuma Hayashi, Kenji Sano, Nobuo Yaegashi, Ikuo Konishi

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

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

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Preprint ARTICLE | doi:10.20944/preprints202403.0923.v1

Seroprevalence of Anti-SARS-Cov-2 Antibodies among Patients Visiting Hospital-Based Sentinel Sites in the Rift Valley Region, Kenya

Vincent Kiplangat Ruttoh, Brian Kipkoech, Ronald Tonui, Ruth Omoti John, Ibrahim Ndungu Mwangi, Ruth Wambui Gicho, Sally Wambui Kamau, Maureen Wangui Njihia, Samwel Lifumo Symekher, Timothy Muasya Mwanzia, James Murithi Gikunda, Matthew Mutinda Munyao, Caroline Wangui Njoroge, Samson Muuo Nzou

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

Online: 15 March 2024 (19:11:29 CET)

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Background: Accurate estimation of the spread of SARS-CoV-2 is crucial for guiding public health strategies. Underreporting from PCR-based testing, especially in low- and middle-income countries, often obscures the true extent of exposure and immunity to coronavirus disease 2019 (COVID-19). This study aimed to determine the seroprevalence and antibody levels against SARS-CoV-2 among patients visiting hospital-based sentinel sites in Kenya's Rift Valley region following the Omicron wave. Method: We conducted a cross-sectional study in four hospital-based sentinel sites among patients with acute respiratory infection symptoms. Patients aged six months or older visiting the sites between January 2022 and December 2022, presenting with symptoms of acute respiratory infection, were enrolled. Clinical and sociodemographic data were collected using a structured questionnaire. We used a quantitative ELISA kit to detect IgG antibodies against SARS-CoV-2 S protein in serum samples. Results: Among 557 individuals enrolled in the study, the seroprevalence of SARS-CoV-2 antibodies was 97.8% (n=545). Vaccinated individuals demonstrated significantly higher odds of seropositivity compared to unvaccinated counterparts, with an odds ratio of 3.33 (95% CI: (0.4, 27.87)). While seropositivity remained consistent across age groups, older adults exhibited the highest odds. Site-specific differences in enrolment and vaccination rates highlight potential access-related disparities. Conclusion: Our findings indicate widespread prior exposure to SARS-CoV-2 within the study region, underscoring the significant impact of both natural infection and vaccination efforts in driving SARS-CoV-2 seroprevalence within the Rift Valley region. Despite the underestimation of infections and disparities in vaccination access, this study demonstrates the effectiveness of vaccination for conferring SARS-CoV-2 immunity. Targeted interventions are crucial to address accessibility barriers and vaccine hesitancy, ensuring equitable vaccination coverage.

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 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 ARTICLE | doi:10.20944/preprints202305.0432.v1

Persistence of SARS-Cov-2 Igg Antibody Response among South African Adults: A Prospective Cohort Study

Oladele Vincent Adeniyi, Oyewole Chris Durojaiye, Charity Masilela

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: SARS-CoV-2; COVID-19; Humoral immune response; Persistence; South Africa

Online: 8 May 2023 (03:29:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0008.v1

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Selvakumar Murugesan, Chinnasamy Ragavendran, Amir Ali, Safir Ullah Khan, Velusamy Arumugam, Dinesh Kumar Lakshmanan, Palanikumar Palanichamy, Manigandan Venkatesan, Chinnaperumal Kamaraj, Zia-ur-Rehman Mashwani, Muhammad Younas, Juan Pedro Luna-Arias, Fabian Fernández-Luqueño

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; molecular docking; ADMET; marine natural products; Chrysophaentin A; Hymenidin

Online: 1 December 2022 (03:51:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0422.v1

Immunogenicity of BNT162b2 mRNA-Based Vaccine against SARS-CoV-2 in People with Cystic Fibrosis

Gianfranco Alicandro, Valeria Daccò, Lisa Cariani, Chiara Rosazza, Calogero Sathyà Sciarrabba, Federica Ferraro, Chiara Lanfranchi, Paola Medino, Daniela Girelli, Carla Colombo

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: cystic fibrosis; SARS-CoV-2; Covid-19, vaccine; antibody response; humoral response

Online: 27 July 2022 (13:29:14 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202006.0314.v2

Semen Quality as a Potential Susceptibility Indicator to SARS-CoV-2 Insults in Polluted Areas

Luigi Montano, Ian Marc Bonapace, Francesco Donato, Pietro Massimiliano Bianco, Antonino Guglielmino, Marina Piscopo

Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: air pollution; COVID-19; semen quality; environmental marker; health marker; oxidative stress

Online: 6 July 2020 (09:48:39 CEST)

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Working Paper REVIEW

Sars-Cov-2 Pandemic: A Narrative Review on Lessons and Viewpoints Arising From Both the History of Medicine and From the Biological Behaviour of Other Well-Known Viruses

Sirio Fiorino, Fabio Tateo, Dario De Biase, Claudio Giuseppe Gallo, Paolo Emilio Orlandi, Ivan Corazza, Roberta Budriesi, Matteo Micucci, Michela Visani, Elisabetta Loggi, Wandong Hong, Roberta Pica, Federico Lari, Maddalena Zippi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: coronavirus; COVID-19; Hepatitis C Virus (HCV); Human Immunodeficiency Virus (HIV); Influenza viruses ribonucleic acid (RNA); SARS-CoV-2

Online: 19 February 2021 (14:34:38 CET)

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the etiological agent of the current pandemic worldwide. The pathological condition induced by this pathogen is known as COVID-19 disease. SARS-CoV-2 associated pandemic has been defined as a “public health emergency of international concern” by the International Health Regulation Emergency Committee of the World Health Organization. To date, considerable efforts are in progress to develop more advanced strategies against SARS-CoV-2. Despite the numerous scientific studies published, our knowledge regarding this pathogen is still incomplete, as this virus has been identified only recently. Therefore, scientific investigation of the SARS-CoV-2 has been possible only for a short period of time and effective management of the serious forms of this disease is still lacking. Considerable efforts are in progress worldwide with the purpose to develop more advanced strategies against this pathogen. In this review, we have analyzed the structural and the biological SARS-CoV-2 characteristics and those of other well-known RNA viruses, with the aim to identify possible similarities and analogies between all these pathogens, may be a very useful approach. These infectious agents have been widely studied since several years ago and, a large series of scientific reports are available in the literature regarding this topic. Therefore, focusing on the Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV) and Influenza viruses (IVs), we have collected their historical data, clinical manifestations, pathogenetic mechanisms and related infections. Taking advantage of the results of our research, we have assembled this narrative review, with the aim to get useful insights and lessons from HIV, HCV and IVs characteristics and, consequently, to transfer the obtained knowledge to the study of SARS-CoV-2 biology. There are well known differences between all these pathogens. In particular, they present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne pathogens, whereas HIV and HCV are bloodborne infectious agents. However, these viruses exhibit some potential common clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2. Accordingly, we have analysed and discussed the following points: 1) the biology, the pathogenesis and the clinical manifestations of SARS-CoV-2, HIV, HCV and IVs in mankind; 2) the onset and spreading of pandemics caused by respiratory viruses according to a perspective historical point of view; 3) the possible development of a persistent SARS-CoV-2 reservoir worldwide; 4) the possibility of SARS-CoV-2 reinfection/reactivation; 5) the possible involvement and impact of climatic factors in increasing the risk of SARS-CoV-2 spreading.

Preprint ARTICLE | doi:10.20944/preprints202402.0483.v1

Using the Transactional Model of Stress and Coping to Explore Coping Strategies Adopted by Radiology Health Caregivers during the COVID-19 Pandemic.

Shillah Nyaradzo Hundah, Maureen Nokuthula Sibiya, Thandokuhle Emmanuel Khoza

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: COVID-19; pandemic; well-being; mental health; coping strategies; radiology; radiography; frontline health caregiver

Online: 8 February 2024 (10:22:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0404.v1

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

Marko Popovic

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

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

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

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

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

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

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

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Working Paper ARTICLE

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

Huihao Tang, Mayan Ali, Lina Zhang, Cheng Deng

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

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

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Preprint 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 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/preprints202211.0480.v1

Global COVID-19 Pandemic Outcomes: Dissecting a Failed Strategy

James A Thorp, Margery M. Thorp, Elise M. Thorp, Ajovi Scott-Emuakpor, K.E. Thorp

Subject: Public Health And Healthcare, Health Policy And Services Keywords: COVID-19 death rates; COVID-19 vaccines; hydroxychloroquine; ivermectin; rates of COVID-19 testing; containment measures; social distancing; travel restriction,

Online: 25 November 2022 (10:16:41 CET)

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Objectives to assess COVID-19 mortality rates per country population. To determine what if any independent country-specific variables from 9 different databases were correlated. Design population based retrospective cohort study. Setting analysis of global COVID-19 treatment and containment strategies using data from 9 worldwide websites. Participants 108 countries worldwide. Interventions none. Main Outcome Measures were COVID-19 death rates per country population analyzed by univariate and multivariate analysis. The main outcome parameters were to determine if there are any correlations between the percentage of countrywide COVID-19 deaths/population by the countries’ percent vaccinated. Secondary outcome measures include the effect of other independent variables on COVID-19 death rates per country population including: health expenditures per capita, annual income per capita, COVID-19 tests per 1000 people, stringency index (a measure of each countries containment strategies), hydroxychloroquine score (a measure of each countries use), ivermectin score (a measure of each countries use), hypertension, obesity, diabetes, and specific countries and geographic locations. Results COVID-19 vaccination rates ranged from 0-99% in 108 countries. Univariate analysis demonstrates the following independent variables to correlate with COVID-19 deaths/population (correlation coefficient, p value): countrywide COVID-19 vaccination rates (+0.2936, p=0.002); healthcare costs per capita (+0.3212, p=0.0007), income per capita (+0.3051, p=0.0013), COVID-19 tests per 1000 population (+0.6981 p=0.0307); stringency index (+0.3098, p=0.0011); hydroxychloroquine index (-0.1337, p=0.0678); and ivermectin index (-0.1383, p=0.1535). Conclusions Increasing rates of COVID-19 vaccination are associated with increase COVID-19 death rates per country population (p=0.002). Other variables associated include healthcare costs per capita (+0.3212, p=0.0007), income per capita (+0.3051, p=0.0013), COVID-19 tests per 1000 population (+0.6981 p=0.0307); and stringency index (+0.3098, p=0.0011).

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

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

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

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

Online: 25 February 2021 (14:44:22 CET)

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

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

Mustak Ibn Ayub

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

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

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

Preprint ARTICLE | doi:10.20944/preprints202211.0516.v1

Discovery of Polyphenolic Natural Products as SARS-CoV-2 Mpro Inhibitors for COVID-19

Nadine Krüger, Thales Kronenberger, Hang Xie, Cheila Rocha, Stefan Pöhlmann, Haixia Su, Yechun Xu, Stefan A. Laufer, Thanigaimalai Pillaiyar

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Antivirals; coronavirus; COVID-19; covalent drugs; dynamic light scattering; inhibitors; main protease; natural products

Online: 28 November 2022 (13:40:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0114.v1

Two SARS-CoV-2 IgG Immunoassays Comparison and Time-Course Profile of Antibodies Response

Ruggero Dittadi, Haleh Afshar, Paolo Carraro

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Immune response; SARS-CoV-2 antibodies response; Covid-19 management; Maglumi; Architect; method comparison.

Online: 5 August 2020 (08:09:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0321.v1

Hesperidin and SARS-CoV-2: New Light on the Healthy Functions of Citrus Fruit

Paolo Bellavite, Alberto Donzelli

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Citrus fruits; Citrus sinensis; hesperidin; COVID-19; vitamin C; SARS-CoV-2; sweet orange

Online: 28 June 2020 (08:45:24 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202006.0250.v1

Evolution of Nucleotide Composition in the SARS-CoV-2 Lineage: Implications for Vaccine Design

Sankar Subramanian

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Nucleotide composition; mutational change; GC to AT; COVID-19; SARS-CoV-2; Vaccine design

Online: 21 June 2020 (10:16:01 CEST)

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

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

Marcos Altable

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

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

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

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

Pierantonio De Luca, Anastasia Macario, Janos B.Nagy

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

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

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

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

Martin Lavecchia, Julian Fernandez

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

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

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Preprint ARTICLE | doi:10.20944/preprints202103.0320.v1

Exploring the Air Pollution Control Direction of Two Typical Cities, Beijing and Wuhan, from the Air Pollution under Emergency Responses during COVID-19

Ada Tsan Qin

Subject: Environmental And Earth Sciences, Environmental Science Keywords: COVID-19; air pollution; PM2.5; NOx; MERRA-2; OMNO2

Online: 11 March 2021 (14:51:22 CET)

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

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

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

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

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

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

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

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

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

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

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

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

Wei Li

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Subrata K. Biswas, Sonchita R. Mudi

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

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

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Preprint ARTICLE | doi:10.20944/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 TECHNICAL NOTE | doi:10.20944/preprints202008.0659.v1

Noisy Genome Data and Faulty Clade Statistics Undermine Conclusions on SARS-CoV-2 Evolution and Strain Typing in the Brazilian Epidemy: A Technical Note

Marcelo R. S. Briones, Fernando Antoneli, Renata C. Ferreira, Isabel M. V. G. Carvalho, Luiz M. R. Janini

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

Online: 30 August 2020 (11:22:12 CEST)

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

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

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

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

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

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Preprint HYPOTHESIS | doi:10.20944/preprints202003.0247.v1

Prediction of Potential 3CLpro-Targeting Anti-SARS-CoV-2 Compounds from Chinese Medicine

Ning Sun, Wing-Leung Wong, Jiao Guo

Subject: Medicine And Pharmacology, Pharmacy Keywords: SARS-CoV-2; COVID-19; molecular docking; Chinese medicine; lithospermic acid B; specnuezhenide; neonuezhenide; rutin; neodiosmin

Online: 15 March 2020 (15:11:22 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 COMMUNICATION | doi:10.20944/preprints202205.0330.v1

Variant Allele of ALDH2, rs671 Associates with Attenuated Post-Vaccination Response in Anti-SARS-CoV-2 Spike Protein IgG: A Prospective Study in the Japanese General Population

Akiko Matsumoto, Megumi Hara, Mohammad Said Ashenagar, Mikiko Tokiya, Takeshi Sawada, Chiharu Iwasaka, Takuma Furukawa, Kyoko Kitagawa, Yasunobu Miyake, Yoshio Hirota

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: ALDH2; rs671; COVID-19; vaccine; immunogenicity

Online: 24 May 2022 (10:08:35 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/preprints202104.0439.v1

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

Toshiaki Asakura, Akiko Tamakoshi

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

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

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Preprint ARTICLE | doi:10.20944/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 REVIEW | doi:10.20944/preprints202308.1547.v1

Unravelling Insights into the Evolution and Management of SARS-CoV-2: A Comprehensive Review

Aganze Mushebenge, Samuel C. Ugbaja, Nonkululeko Avril Mbatha, Rene M. Khan, Hezekiel M. Kumalo

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Main Protease Inhibitors; SARS-CoV-2; COVID-19; mutations; vaccines; therapeutics; drug repurposing; management strategies

Online: 22 August 2023 (09:31:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0847.v1

The Mental Burden of the COVID-19 Pandemic in Romania- a Retrospective Post-pandemic View

Adriana Mitrea, Anca Hăisan, Ani Cǎșǎricǎ, Rodica Gabriela Enache, Elena Danteș

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID-19; mental health; anxiety; depression; stress

Online: 15 February 2024 (10:04:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1719.v2

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

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

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

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

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

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

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

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

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

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

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

Ameh S. James, John I. Al-alawneh

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

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

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Preprint ARTICLE | doi:10.20944/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 ARTICLE | doi:10.20944/preprints202309.0139.v4

A Recombinant Protein XBB.1.5 RBD/Alum/CpG Vaccine Elicits High Neutralizing Antibody Titers against Omicron Subvariants of SARS-CoV-2

Syamala Rani Thimmiraju, Rakesh Adhikari, Maria J Villar, Jungsoon Lee, Zhuyun Liu, Rakhi Kundu, Yi-Lin Chen, Suman Sharma, Karm Ghei, Brian Keegan, Leroy Versteeg, Portia M Gillespie, Allan Ciciriello, Nelufa Yesmin, Cristina Poveda, Nestor Uzcategui, Wen-Hsiang Chen, Jason T Kimata, Bin Zhan, Ulrich Strych, Maria Elena Bottazzi, Peter Hotez, Jeroen Pollet

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Immune escape; Vaccine efficacy; COVID-19; SARS-CoV-2

Online: 30 September 2023 (07:44:51 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202004.0143.v1

Inflamm-Aging: Why Older Men Are the Most Susceptible to SARS-Cov-2 Complicated Outcomes

Massimiliano Bonafè, Francesco Prattichizzo, Angelica Giuliani, Gianluca Storci, Jacopo Sabbatinelli, Fabiola Olivieri

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; COVID-19; IL-6; inflamm-aging; immune senescence; host-directed therapies

Online: 9 April 2020 (08:38:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0025.v1

CRISPR-Based Assays for Rapid Detection of SARS-CoV-2

Vivek S. Javalkote, Nagesh Kancharla, Bhaskar Bhadra, Manish Shukla, Badrish Soni, Ajit Sapre, Michael Goodin, Anindya Bandyopadhyay, Santanu Dasgupta

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: CRISPR; Covid detection

Online: 4 June 2020 (06:03:16 CEST)

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

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

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

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

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

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

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

Guilherme Asai

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

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

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202205.0243.v1

A Comparative Analysis of a Self-Reported Adverse Events Analysis After Receiving one of the Available SARS-CoV-2 Vaccine Schemes in Ecuador

Esteban Ortiz-Prado, Juan Sebastian Izquiero-Condoy, Raul Fernandez-Naranjo, Katherine Simbana-Rivera, Jorge Eduardo Vasconez, Eddy P Lincango-Naranjo, Simone Cordovez, Barbara Coronel, Karen Delgado-Moreira, Ruth Jimbo-Sotomayor

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID-19; Vaccines; Adverse Events; Self-reporting; Pandemic

Online: 18 May 2022 (11:06:19 CEST)

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The COVID-19 pandemic has put a lot of pressure on health systems worldwide. Mass vaccination against SARS-CoV-2 has reduced morbidity and mortality worldwide. Despite their safety profiles, vaccines like any other medical product can cause adverse events. Yet, in countries with poor epidemiological surveillance and monitoring systems, reporting vaccine-related adverse events is scarce. The objective of this study was to describe self-reported vaccine adverse events after receiving one of the available COVID-19 vaccine schemes in Ecuador. A cross-sectional analysis based on an online self-reporting 32-questionnaire was conducted in Ecuador from April 1st to July 15th, 2021. Participants were invited by social media, radio, and TV to voluntarily participate in our study. A total of 6,654 participants were included in this study. A 38.2% of the participants reported having at least one comorbidity. Patients received AstraZeneca, Pfizer, and Sinovac vaccines, and these were distributed 38.4%, 31.1%, and 30.5%, respectively. Pain, inflammation at the injection site (20,01%), and headache (16,91%) were the most reported adverse events. Women addressed ESAVIs (64%), more often than men (36%). After receiving the first dose of any available COVID-19 vaccine, a total of 19,481 self-reported ESAVIs were informed (86.9% were mild, 11.6% moderate and 1.5% severe). In terms of vaccine type and brand, the most reactogenic vaccine was AstraZeneca with 57.8%, followed by Pfizer (24.9%) and Sinovac (17, 3 %). After the second dose, 6,757 self-reported ESAVIs were reported (87.0% mild, 10.9% moderate, and 2.1% severe). AstraZeneca vaccine users reported a higher proportion of ESAVIs (72.2%) in comparison to Pfizer/BioNTech (15.9%) and Sinovac Vaccine (11.9%). Swelling at the injection site, headache, muscle pain, and fatigue were the most common ESAVIs for the first as well as second dose. In conclusion, most ESAVIs were mild. AstraZeneca users were more likely to report adverse events. Participants without a history of COVID-19 infection, as well as those who receive the first dose, were more prone to report ESAVIs.

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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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 REVIEW | doi:10.20944/preprints202104.0481.v1

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

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

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

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

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

Working Paper REVIEW

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

Adrián Pedreira, Yeşim Taşkın, Míriam R. García

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

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

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

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

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

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

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

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202103.0258.v1

Potent Antiviral Activity Against HSV-1 and SARS-CoV-2 by Antimicrobial Peptoids

Gill Diamond, Natalia Molchanova, Claudine Herlan, John A. Fortkort, Jennifer S. Lin, Erika Figgins, Nathan Bopp, Lisa K. Ryan, Donghoon Chung, Robert Scott Adcock, Michael Sherman, Annelise E. Barron

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Antivirals; peptoids; LL-37; air-liquid interface; cytotoxicity; membrane disruption; COVID-19; HSV-1; SARS-CoV-2

Online: 9 March 2021 (10:25:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202009.0526.v1

Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls

Avinash Premraj, Abi George Aleyas, Binita Nautiyal, Thaha Jamal Rasool

Subject: Biology And Life Sciences, Virology Keywords: COVID-19 testing; molecular diagnostics; immunological testing; RT-qPCR; ELISA; pool PCR; lateral flow assay; rapid assay

Online: 23 September 2020 (03:33:12 CEST)

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

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

Kowsar Bagherzadeh, Kourosh Daneshvarnejad, Mohammad Abbasinazari, homa azizian

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

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

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Preprint SHORT NOTE | doi:10.20944/preprints202106.0117.v1

Medical Waste Management during COVID-19 Situation: Perspective Towards Safe Environment

MANOJ KUMAR JINDAL, Dr. Santosh Kumar Sar

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: COVID-19; Medical Waste; Sustainability; Environment.

Online: 3 June 2021 (13:22:55 CEST)

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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 ARTICLE | doi:10.20944/preprints202402.1094.v1

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

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

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

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

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

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

Fiorella Carnevali, Sara Mangiaterra, Giacomo Rossi

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

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

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

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

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

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

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

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

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

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

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

Swati Arora, Rishabh Jain, Harendra Pal Singh

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

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

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Preprint REVIEW | doi:10.20944/preprints202104.0078.v1

Influence Factors Psychological and Stigma During the COVID-19 Pandemic: Literature Review

Joko Susanto, Moses Glorino Rumambo Pandin

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Psychological; Stigma; Covid-19

Online: 2 April 2021 (17:02:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0420.v1

SARS-CoV-2 S Protein Binding hACE2: Viral Entry, Pathogenesis, Prognosis, and Potential Therapeutic Targets

Lobna Al-Zaidan, Sarra Mestiri, Afsheen Raza, Maysaloun Merhi, Varghese Inchakalody, Queenie Fernandez, Nassiba Taib, Shahab Uddin, Said Dermime

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID-19; SARS-CoV-2; ACE2 receptor; spike glycoprotein; S glycoprotein immunogenic sequences; ACE2 polymorphism

Online: 18 September 2020 (04:56:02 CEST)

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