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Microorganisms
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Advances in SARS-CoV-2 Infection and Variants
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Advances in SARS-CoV-2 Infection and Variants

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (15 February 2023) | Viewed by 31265

Special Issue Editor

Dr. Linda Houhamdi

E-Mail Website
Guest Editor
Assistance Publique - Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
Interests: COVID-19; molecular and genomic genotyping; reinfection; vaccination; infective endocarditis medical microbiology; infectious diseases; antibiotic resistance

Special Issue Information

Dear Colleagues,

Since 2020, the Coronavirus Disease 2019 (COVID-19) pandemic has been spreading worldwide, causing health, social, and economic distress. This infectious disease is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is an RNA, constantly evolving, virus. The emergence of variants over time is therefore an expected phenomenon and can have an impact on the dynamics of the epidemic or the effectiveness of preventive measures including screening tests, vaccines and therapeutic molecules.

Molecular and genomic surveillance of SARS-CoV-2 variants is now one of the pillars of the fight against COVID-19 on a global scale. The aim of this Special Issue is to ultimately identify the share of the different variants circulating in different countries worldwide in order to describe and monitor their circulation and their evolution over time, whatever the clinical indication (clusters of infected people, reinfection, persistence, infection following vaccination, etc).

SARS-CoV-2 variants are currently classified as variants of interest (VOI) or variants of concern (VOC). A variant is considered a VOI when it has mutations that are suspected or known to cause significant changes and it is circulating widely. The World Health Organization continuously monitors the VOIs in case they spread more easily, cause more severe disease, escape the body’s immune response regarding natural defense mechanisms or vaccines, change clinical presentation with increased transmissibility, infectivity, severity of infection, or decrease effectiveness of known tools, such as public health measures, diagnostics, treatments and vaccines. Several VOCs have been detected, including the Alpha variant (B.1.1.7) first identified in the UK, Beta variant (B.1.351) in South Africa, Gamma variant (P.1/B.1.1.28.1) in Brazil, Delta variant (B.1.617.2) in India and more recently the Omicron variant (B.1.1.529) in South Africa in November 2021.

From this perspective, we are pleased to invite you to present submissions on the topic, “Advances in SARS-CoV-2 Infection and Variants“, which deserves a Special Issue in Microorganisms. Original research articles and reviews are welcome.

We look forward to receiving your contributions.

Dr. Linda Houhamdi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • variant of concern (VOC)
  • variant of interest (VOI)
  • genomic genotyping
  • phylogeny
  • molecular genotyping
  • screening
  • GISAID (Global Initiative on Sharing Avians Influenza Data)
  • Pangolin (Phylogenetic Assignment of Named Outbeak LINeages)

Published Papers (12 papers)

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Research

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18 pages, 3097 KiB  
Article
Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant
by Wenwen He, Huan Cui, Shen Wang, Bo Liang, Cheng Zhang, Weiqi Wang, Qi Wang, Wujian Li, Yongkun Zhao, Tiecheng Wang, Zhuoran Liu, Bin Liu, Feihu Yan, Songtao Yang and Xianzhu Xia
Microorganisms 2023, 11(2), 431; https://doi.org/10.3390/microorganisms11020431 - 08 Feb 2023
Cited by 1 | Viewed by 1875
Abstract
The frequent emergence of SARS-CoV-2 variants thwarts the prophylactic and therapeutic countermeasures confronting COVID-19. Among them, the Delta variant attracts widespread attention due to its high pathogenicity and fatality rate compared with other variants. However, with the emergence of new variants, studies on [...] Read more.
The frequent emergence of SARS-CoV-2 variants thwarts the prophylactic and therapeutic countermeasures confronting COVID-19. Among them, the Delta variant attracts widespread attention due to its high pathogenicity and fatality rate compared with other variants. However, with the emergence of new variants, studies on Delta variants have been gradually weakened and ignored. In this study, a replication-competent recombinant virus carrying the S protein of the SARS-CoV-2 Delta variant was established based on the vesicular stomatitis virus (VSV), which presented a safe alternative model for studying the Delta variant. The recombinant virus showed a replication advantage in Vero E6 cells, and the viral titers reach 107.3 TCID50/mL at 36 h post-inoculation. In the VSV-vectored recombinant platform, the spike proteins of the Delta variant mediated higher fusion activity and syncytium formation than the wild-type strain. Notably, the recombinant virus was avirulent in BALB/c mice, Syrian hamsters, 3-day ICR suckling mice, and IFNAR/GR−/− mice. It induced protective neutralizing antibodies in rodents, and protected the Syrian hamsters against the SARS-CoV-2 Delta variant infection. Meanwhile, the eGFP reporter of recombinant virus enabled the visual assay of neutralizing antibodies. Therefore, the recombinant virus could be a safe and convenient surrogate tool for authentic SARS-CoV-2. This efficient and reliable model has significant potential for research on viral-host interactions, epidemiological investigation of serum-neutralizing antibodies, and vaccine development. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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14 pages, 1952 KiB  
Article
Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes
by Igor B. Rogozin, Andreu Saura, Anastassia Bykova, Vyacheslav Brover and Vyacheslav Yurchenko
Microorganisms 2023, 11(1), 229; https://doi.org/10.3390/microorganisms11010229 - 16 Jan 2023
Cited by 4 | Viewed by 2342
Abstract
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of [...] Read more.
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a “sequence space” of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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15 pages, 863 KiB  
Article
One-Year Surveillance of SARS-CoV-2 Exposure in Stray Cats and Kennel Dogs from Northeastern Italy
by Laura Bellinati, Mery Campalto, Elisa Mazzotta, Letizia Ceglie, Lara Cavicchio, Monica Mion, Laura Lucchese, Angela Salomoni, Alessio Bortolami, Erika Quaranta, Jacopo Magarotto, Mosè Favarato, Laura Squarzon and Alda Natale
Microorganisms 2023, 11(1), 110; https://doi.org/10.3390/microorganisms11010110 - 31 Dec 2022
Cited by 4 | Viewed by 2136
Abstract
Dogs and cats are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During the pandemic, several studies have been performed on owned cats and dogs, whereas limited data are available on the exposure to stray animals. The objective of this study was [...] Read more.
Dogs and cats are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During the pandemic, several studies have been performed on owned cats and dogs, whereas limited data are available on the exposure to stray animals. The objective of this study was to investigate the exposure to SARS-CoV-2 of feral cats and kennel dogs in northeastern Italy, through serological and molecular methods. From May 2021 to September 2022, public health veterinary services collected serum, oropharyngeal, and rectal swab samples from 257 free-roaming dogs newly introduced to shelters, and from 389 feral cats examined during the routinely trap–neutered–return programs. The swabs were analyzed for viral RNA through a real-time reverse transcriptase PCR (rRT-PCR), and sera were tested for the presence of the specific antibody against SARS-CoV-2 (enzyme-linked immunosorbent assay). Serology was positive in nine dogs (9/257) and three cats (3/389), while two asymptomatic cats tested positive to rRT-PCR. One cat turned out to be positive both for serology and molecular analysis. In addition, this study described the case of a possible human-to-animal SARS-CoV-2 transmission in a cat that travelled in close contact to a COVID-19-positive refugee from Ukraine. This study shows that SARS-CoV-2 can infect, in natural conditions, stray cats and kennel dogs in northeastern Italy, although with a low prevalence. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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15 pages, 2659 KiB  
Article
Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein
by Puja Adhikari, Bahaa Jawad, Rudolf Podgornik and Wai-Yim Ching
Microorganisms 2022, 10(10), 1999; https://doi.org/10.3390/microorganisms10101999 - 10 Oct 2022
Cited by 4 | Viewed by 1265
Abstract
The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2′) cleavage sites play a pivotal [...] Read more.
The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2′) cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2’ cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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9 pages, 1361 KiB  
Communication
Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy
by José María González Alba, Zulema Pérez-Martínez, José A. Boga, Susana Rojo-Alba, Juan Gómez de Oña, Marta E. Alvarez-Argüelles, Garbriel Martín Rodríguez, Isabel Costales Gonzalez, Ismael Huerta González, Eliecer Coto and Santiago Melón García
Microorganisms 2022, 10(10), 1954; https://doi.org/10.3390/microorganisms10101954 - 30 Sep 2022
Cited by 5 | Viewed by 1266
Abstract
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of [...] Read more.
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. Methods: From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. Results: The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. Conclusions: The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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15 pages, 1904 KiB  
Article
A Quantitative ELISA to Detect Anti-SARS-CoV-2 Spike IgG Antibodies in Infected Patients and Vaccinated Individuals
by Ji Luo, Jennifer Klett, Jörg Gabert, Thomas Lipp, Julia Karbach, Elke Jäger, Stephan Borte, Ralf Hoffmann and Sanja Milkovska-Stamenova
Microorganisms 2022, 10(9), 1812; https://doi.org/10.3390/microorganisms10091812 - 09 Sep 2022
Cited by 3 | Viewed by 2747
Abstract
There is an ongoing need for high-precision serological assays for the quantitation of anti-SARS-CoV-2 antibodies. Here, a trimeric SARS-CoV-2 spike (S) protein was used to develop an ELISA to quantify specific IgG antibodies present in serum, plasma, and dried blood spots (DBS) collected [...] Read more.
There is an ongoing need for high-precision serological assays for the quantitation of anti-SARS-CoV-2 antibodies. Here, a trimeric SARS-CoV-2 spike (S) protein was used to develop an ELISA to quantify specific IgG antibodies present in serum, plasma, and dried blood spots (DBS) collected from infected patients or vaccine recipients. The quantitative S-ELISA was calibrated with international anti-SARS-CoV-2 immunoglobulin standards to provide test results in binding antibody units per mL (BAU/mL). The assay showed excellent linearity, precision, and accuracy. A sensitivity of 100% was shown for samples collected from 54 patients with confirmed SARS-CoV-2 infection more than 14 days after symptom onset or disease confirmation by RT-PCR and 58 vaccine recipients more than 14 days after vaccination. The assay specificity was 98.3%. Furthermore, antibody responses were measured in follow-up samples from vaccine recipients and infected patients. Most mRNA vaccine recipients had a similar response, with antibody generation starting 2–3 weeks after the first vaccination and maintaining positive for at least six months after a second vaccination. For most infected patients, the antibody titers increased during the second week after PCR confirmation. This S-ELISA can be used to quantify the seroprevalence of SARS-CoV-2 in the population exposed to the virus or vaccinated. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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14 pages, 1955 KiB  
Article
Uninvited Guest: Arrival and Dissemination of Omicron Lineage SARS-CoV-2 in St. Petersburg, Russia
by Anna Gladkikh, Vladimir Dedkov, Alena Sharova, Ekaterina Klyuchnikova, Valeriya Sbarzaglia, Tatiana Arbuzova, Majid Forghani, Edward Ramsay, Anna Dolgova, Anna Shabalina, Nadezhda Tsyganova and Areg Totolian
Microorganisms 2022, 10(8), 1676; https://doi.org/10.3390/microorganisms10081676 - 20 Aug 2022
Cited by 4 | Viewed by 1785
Abstract
Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze [...] Read more.
Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia’s second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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Review

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13 pages, 644 KiB  
Review
Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations
by Théophile Cocherie, Karen Zafilaza, Valentin Leducq, Stéphane Marot, Vincent Calvez, Anne-Geneviève Marcelin and Eve Todesco
Microorganisms 2023, 11(1), 30; https://doi.org/10.3390/microorganisms11010030 - 22 Dec 2022
Cited by 10 | Viewed by 2188
Abstract
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its [...] Read more.
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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18 pages, 722 KiB  
Review
SARS-CoV-2 as a Zooanthroponotic Infection: Spillbacks, Secondary Spillovers, and Their Importance
by Georgios Pappas, Despoina Vokou, Ioannis Sainis and John M. Halley
Microorganisms 2022, 10(11), 2166; https://doi.org/10.3390/microorganisms10112166 - 31 Oct 2022
Cited by 8 | Viewed by 5147
Abstract
In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, [...] Read more.
In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, exhibit considerable animal-to-animal transmission resulting in potential endemicity, mutation pressure, and possible secondary spillover to humans. We attempt a comprehensive review of the available data on animal species infected by SARS-CoV-2, as presented in the scientific literature and official reports of relevant organizations. We further evaluate the lessons humans should learn from mink outbreaks, white-tailed deer endemicity, zoo outbreaks, the threat for certain species conservation, the possible implication of rodents in the evolution of novel variants such as Omicron, and the potential role of pets as animal reservoirs of the virus. Finally, we outline the need for a broader approach to the pandemic and epidemics, in general, incorporating the principles of One Health and Planetary Health. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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21 pages, 2726 KiB  
Review
COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development
by Giau Van Vo, Eva Bagyinszky and Seong Soo A. An
Microorganisms 2022, 10(3), 598; https://doi.org/10.3390/microorganisms10030598 - 10 Mar 2022
Cited by 13 | Viewed by 4841
Abstract
In the two years since the SARS-CoV-2 pandemic started, it has caused over 5 million deaths and 400 million infected cases, and the world continues to be on high alert for COVID-19. Among the variants of interest and concern of SARS-CoV-2, the current [...] Read more.
In the two years since the SARS-CoV-2 pandemic started, it has caused over 5 million deaths and 400 million infected cases, and the world continues to be on high alert for COVID-19. Among the variants of interest and concern of SARS-CoV-2, the current Omicron (B.1.1.529) and stealth Omicron (BA.2) raised serious concerns due to rapid rates of infection caused by numerous mutations in the spike protein, which could escape from the antibody-mediated neutralization and increase the risk of reinfections. Hence, this work aims to describe the most relevant mutations in the SARS-CoV-2 spike protein, discuss vaccine against variant of concerns, describe rare adverse events after COVID-19 vaccination, introduce the most available promising COVID-19 vaccine candidates, and provide few perspectives of the future variants. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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Other

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4 pages, 187 KiB  
Brief Report
SARS-CoV-2 Omicron BA.2.75 Variant May Be Much More Infective than Preexisting Variants Based on In Silico Model
by Aki Sugano, Yutaka Takaoka, Haruyuki Kataguchi, Mika Ohta, Shigemi Kimura, Masatake Araki, Yoshitomo Morinaga and Yoshihiro Yamamoto
Microorganisms 2022, 10(10), 2090; https://doi.org/10.3390/microorganisms10102090 - 21 Oct 2022
Cited by 3 | Viewed by 1469
Abstract
Previously, we developed a mathematical model via molecular simulation analysis to predict the infectivity of six SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on our previous research. We subjected Omicron [...] Read more.
Previously, we developed a mathematical model via molecular simulation analysis to predict the infectivity of six SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on our previous research. We subjected Omicron BA.4/5 and BA.2.75 variants of SARS-CoV-2 to the analysis to determine the evolutionary distance of the spike protein gene (S gene) of the variants from the Wuhan variant so as to appreciate the changes in the spike protein. We performed molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) to understand the docking affinities of these variants. We then compared the evolutionary distances and the docking affinities of these variants with those of the variants that we had analyzed in our previous research. As a result, BA.2.75 has both the highest docking affinity (ratio per Wuhan variant) and the longest evolutionary distance of the S gene from the Wuhan variant. These results suggest that BA.2.75 infection can spread farther than can infections of preexisting variants. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
12 pages, 1401 KiB  
Case Report
First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco
by Philippe Colson, Christian Lavagna, Jérémy Delerce, Guillaume Groshenry, Nouara Yahi, Jacques Fantini, Bernard La Scola and Thomas Althaus
Microorganisms 2022, 10(10), 1952; https://doi.org/10.3390/microorganisms10101952 - 30 Sep 2022
Cited by 3 | Viewed by 1858
Abstract
The Omicron BA.5/22B variant has been designated as a “variant of concern” by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination [...] Read more.
The Omicron BA.5/22B variant has been designated as a “variant of concern” by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination of non-BA.5/22B signature amino acid changes. SARS-CoV-2 neutralizing antibodies were measured with a surrogate virus neutralization test. SARS-CoV-2 genotype screening was performed on nasopharyngeal samples with a multiplex qPCR assay. The SARS-CoV-2 genome was obtained by next-generation sequencing with the Illumina COVID-seq protocol, then assembly using bioinformatics pipelines and software was performed. The BA.5/22B spike protein structure was obtained by molecular modeling. Two spouses were SARS-CoV-2-diagnosed the day they returned from a one-week trip in the Republic of Seychelles. SARS-CoV-2 qPCR screening for variant-specific mutations identified an Omicron variant BA.1/21K, BA.4/22A, or BA.5/22B. A SARS-Co-2 BA.5/22B variant genome was recovered from one of the spouses. Aside from BA.5/22B-defining amino acid substitutions, four other amino acid changes were encoded including Q556K in ORF1a, K2557R in ORF1b, and A67V and A829T in spike; only 13 genomes in sequence databases harbored these four mutations concurrently. Structural analysis of this BA.5/22B variant predicted that A829T in spike may result in a compaction that may affect conformational plasticity. Overall, our findings warrant performing genome-based genotypic surveillance to survey accurately the emergence and circulation of SARS-CoV-2 variants worldwide and point out that their first occurrence in a country is often through international travel despite implemented countermeasures. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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