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Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant

A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of vir...

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Autores principales: Ma, Wentai, Yang, Jing, Fu, Haoyi, Su, Chao, Yu, Caixia, Wang, Qihui, de Vasconcelos, Ana Tereza Ribeiro, Bazykin, Georgii A., Bao, Yiming, Li, Mingkun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8791331/
https://www.ncbi.nlm.nih.gov/pubmed/35033679
http://dx.doi.org/10.1016/j.gpb.2022.01.001
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author Ma, Wentai
Yang, Jing
Fu, Haoyi
Su, Chao
Yu, Caixia
Wang, Qihui
de Vasconcelos, Ana Tereza Ribeiro
Bazykin, Georgii A.
Bao, Yiming
Li, Mingkun
author_facet Ma, Wentai
Yang, Jing
Fu, Haoyi
Su, Chao
Yu, Caixia
Wang, Qihui
de Vasconcelos, Ana Tereza Ribeiro
Bazykin, Georgii A.
Bao, Yiming
Li, Mingkun
author_sort Ma, Wentai
collection PubMed
description A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (median: 62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of these mutations were rarely observed in public databases and had a low mutation rate. In addition, the linkage disequilibrium between these mutations was low, with a limited number of mutations concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner.
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spelling pubmed-87913312022-01-27 Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant Ma, Wentai Yang, Jing Fu, Haoyi Su, Chao Yu, Caixia Wang, Qihui de Vasconcelos, Ana Tereza Ribeiro Bazykin, Georgii A. Bao, Yiming Li, Mingkun Genomics Proteomics Bioinformatics Original Research A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (median: 62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of these mutations were rarely observed in public databases and had a low mutation rate. In addition, the linkage disequilibrium between these mutations was low, with a limited number of mutations concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner. Elsevier 2022-02 2022-01-13 /pmc/articles/PMC8791331/ /pubmed/35033679 http://dx.doi.org/10.1016/j.gpb.2022.01.001 Text en © 2022 Beijing Institute of Genomics https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Original Research
Ma, Wentai
Yang, Jing
Fu, Haoyi
Su, Chao
Yu, Caixia
Wang, Qihui
de Vasconcelos, Ana Tereza Ribeiro
Bazykin, Georgii A.
Bao, Yiming
Li, Mingkun
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title_full Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title_fullStr Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title_full_unstemmed Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title_short Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
title_sort genomic perspectives on the emerging sars-cov-2 omicron variant
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8791331/
https://www.ncbi.nlm.nih.gov/pubmed/35033679
http://dx.doi.org/10.1016/j.gpb.2022.01.001
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