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The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron

In late December of 2019, high-throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we provide a short retrospecti...

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Autores principales: Wiegand, Tanner, Nemudryi, Artem, Nemudraia, Anna, McVey, Aidan, Little, Agusta, Taylor, David N., Walk, Seth T., Wiedenheft, Blake
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505243/
https://www.ncbi.nlm.nih.gov/pubmed/36146815
http://dx.doi.org/10.3390/v14092009
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author Wiegand, Tanner
Nemudryi, Artem
Nemudraia, Anna
McVey, Aidan
Little, Agusta
Taylor, David N.
Walk, Seth T.
Wiedenheft, Blake
author_facet Wiegand, Tanner
Nemudryi, Artem
Nemudraia, Anna
McVey, Aidan
Little, Agusta
Taylor, David N.
Walk, Seth T.
Wiedenheft, Blake
author_sort Wiegand, Tanner
collection PubMed
description In late December of 2019, high-throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we provide a short retrospective analysis of SARS-CoV-2 variants by analyzing a subset (n = 97,437) of all publicly available SARS-CoV-2 genomes (n = ~11.9 million) that were randomly selected but equally distributed over the course of the pandemic. We plot the appearance of new variants of concern (VOCs) over time and show that the mutation rates in Omicron (BA.1) and Omicron sub-lineages (BA.2–BA.5) are significantly elevated compared to previously identified SARS-CoV-2 variants. Mutations in Omicron are primarily restricted to the spike and nucleocapsid proteins, while 24 other viral proteins—including those involved in SARS-CoV-2 replication—are generally conserved. Collectively, this suggests that the genetic distinction of Omicron primarily arose from selective pressures on the spike, and that the fidelity of replication of this variant has not been altered.
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spelling pubmed-95052432022-09-24 The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron Wiegand, Tanner Nemudryi, Artem Nemudraia, Anna McVey, Aidan Little, Agusta Taylor, David N. Walk, Seth T. Wiedenheft, Blake Viruses Review In late December of 2019, high-throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we provide a short retrospective analysis of SARS-CoV-2 variants by analyzing a subset (n = 97,437) of all publicly available SARS-CoV-2 genomes (n = ~11.9 million) that were randomly selected but equally distributed over the course of the pandemic. We plot the appearance of new variants of concern (VOCs) over time and show that the mutation rates in Omicron (BA.1) and Omicron sub-lineages (BA.2–BA.5) are significantly elevated compared to previously identified SARS-CoV-2 variants. Mutations in Omicron are primarily restricted to the spike and nucleocapsid proteins, while 24 other viral proteins—including those involved in SARS-CoV-2 replication—are generally conserved. Collectively, this suggests that the genetic distinction of Omicron primarily arose from selective pressures on the spike, and that the fidelity of replication of this variant has not been altered. MDPI 2022-09-10 /pmc/articles/PMC9505243/ /pubmed/36146815 http://dx.doi.org/10.3390/v14092009 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Wiegand, Tanner
Nemudryi, Artem
Nemudraia, Anna
McVey, Aidan
Little, Agusta
Taylor, David N.
Walk, Seth T.
Wiedenheft, Blake
The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title_full The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title_fullStr The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title_full_unstemmed The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title_short The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
title_sort rise and fall of sars-cov-2 variants and ongoing diversification of omicron
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505243/
https://www.ncbi.nlm.nih.gov/pubmed/36146815
http://dx.doi.org/10.3390/v14092009
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