Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
- Author:
Ma WENTAI
1
,
2
;
Yang JING
;
Fu HAOYI
;
Su CHAO
;
Yu CAIXIA
;
Wang QIHUI
;
Ana Tereza Ribeiro de Vasconcelos
;
A.Bazykin GEORGII
;
Bao YIMING
;
Li MINGKUN
Author Information
1. CAS Key Laboratory of Genomic and Precision Medicine,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China
2. University of Chinese Academy of Sciences,Beijing 100049,China
- Keywords:
Omicron;
Genomics;
Mutation;
Variant of concern;
SARS-CoV-2
- From:
Genomics, Proteomics & Bioinformatics
2022;20(1):60-69
- CountryChina
- Language:Chinese
-
Abstract:
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 sequenc-ing 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 muta-tion 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 vari-ant 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.
