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

作　　者：Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A.Bazykin Yiming Bao Mingkun Li 

机构地区：[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 [3]CAS Key Laboratory of Pathogenic Microbiology and Immunology,Institute of Microbiology,Chinese Academy of Sciences,Beijing 100101,China [4]National Genomics Data Center,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China [5]Laboratorio de Bioinformatica,Laboratorio Nacional de Computacao Cientıfica,Petropolis 25651-075,Brazil [6]Skolkovo Institute of Science and Technology,Moscow 121205,Russia [7]Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences,Moscow 127051,Russia [8]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650201,China

出　　处：《Genomics, Proteomics & Bioinformatics》2022年第1期60-69,共10页基因组蛋白质组与生物信息学报（英文版）

基　　金：funded by the National Natural Science Foundation of China(Grant No.82161148009);the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB38030400);the Capital Health Development and Research Special Programme(Grant No.20211G-3012);the Conselho Nacional de Desenvolvimento Cientifico e Tecnológico(CNPq)-NGS-BRICS-n°:440931/2020-7;the Russian Foundation for Basic Research(RFBR)(Grant No.20-54-80014)。

摘　　要：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.

关 键 词：Omicron GENOMICS MUTATION Variant of concern SARS-CoV-2 

分 类 号：R373[医药卫生—病原生物学]