The Emergence and Escape of SARS-CoV-2 Variants: Molecular Perspectives

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 2756

Special Issue Editor


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Guest Editor
Department of Physiology, Ajou University, Suwon, Republic of Korea
Interests: immunology; virology; bioinformatics; drug designing

Special Issue Information

Dear Colleagues,

In late 2020, SARS-CoV-2 began to evolve, as characterized by the rapid emergence of many viral variants that has been associated with the increased transmissibility and immune escape. Neutralizing antibodies (nAbs) are proven to be the most effective COVID-19 combating solutions due to their higher specificity and lower biosafety risks; however, the transient emergence of new variants caused a swift failure of vaccines and put the fate of COVID-19 therapeutic drugs, particularly nAbs, in danger. In addition, diagnostic procedures faced issues that caused economical and health concerns.

In the fight to bring an end to the pandemic, this Special Issue aims to comprehend the current and future mutational landscape of SARS-CoV-2 and its impact on the increased transmission of the emerging variants and potential immune escape. Additionally, this issue invites studies that delineate strategies that could help toward the diagnosis of mutated variants and therapeutics of COVID-19. Studies that computationally/empirically address molecular aspects of de-escalated and emerging SARS-CoV-2 variants with respect to the immune response are highly encouraged for submission.

Dr. Masaud Shah
Guest Editor

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Keywords

  • SARS-CoV-2
  • variants of concern
  • immune escape
  • COVID-19
  • monoclonal antibodies therapy
  • protein-protein interaction
  • therapeutics
  • vaccine
  • antiviral drugs

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Published Papers (1 paper)

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Research

14 pages, 1626 KiB  
Article
Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients
by Daniele Lombardo, Cristina Musolino, Valeria Chines, Giuseppe Caminiti, Claudia Palermo, Irene Cacciola, Giuseppina Raffa and Teresa Pollicino
Microorganisms 2024, 12(1), 2; https://doi.org/10.3390/microorganisms12010002 - 19 Dec 2023
Cited by 2 | Viewed by 2126
Abstract
Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of the RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate [...] Read more.
Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of the RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate natural mutations that could affect the efficacy of antiviral drugs. To this aim, SARS-CoV-2 genomic sequences isolated from 4155 drug-naive individuals from southern Italy were analyzed using the Illumina MiSeq platform. Sequencing of the 4155 samples showed the following viral variant distribution: 71.2% Delta, 22.2% Omicron, and 6.4% Alpha. In the Nsp12 sequences, we found 84 amino acid substitutions. The most common one was P323L, detected in 3777/4155 (91%) samples, with 2906/3777 (69.9%) also showing the G671S substitution in combination. Additionally, we identified 28, 14, and 24 different amino acid substitutions in the Nsp5, Nsp7, and Nsp8 genomic regions, respectively. Of note, the V186F and A191V substitutions, affecting residues adjacent to the active site of Nsp5 (the target of the antiviral drug Paxlovid), were found in 157/4155 (3.8%) and 3/4155 (0.07%) samples, respectively. In conclusion, the RdRp complex subunits and the Nsp5 genomic region exhibit susceptibility to accumulating natural mutations. This susceptibility poses a potential risk to the efficacy of antiviral drugs, as these mutations may compromise the drug ability to inhibit viral replication Full article
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