Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1784796423548567552 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9505243 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT wiegandtanner theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT nemudryiartem theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT nemudraiaanna theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT mcveyaidan theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT littleagusta theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT taylordavidn theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT walksetht theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT wiedenheftblake theriseandfallofsarscov2variantsandongoingdiversificationofomicron AT wiegandtanner riseandfallofsarscov2variantsandongoingdiversificationofomicron AT nemudryiartem riseandfallofsarscov2variantsandongoingdiversificationofomicron AT nemudraiaanna riseandfallofsarscov2variantsandongoingdiversificationofomicron AT mcveyaidan riseandfallofsarscov2variantsandongoingdiversificationofomicron AT littleagusta riseandfallofsarscov2variantsandongoingdiversificationofomicron AT taylordavidn riseandfallofsarscov2variantsandongoingdiversificationofomicron AT walksetht riseandfallofsarscov2variantsandongoingdiversificationofomicron AT wiedenheftblake riseandfallofsarscov2variantsandongoingdiversificationofomicron |