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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| Format: | Article |
| Language: | English |
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Oxford University Press
2022-02-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S167202292200002X |
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| author | Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A. Bazykin Yiming Bao Mingkun Li |
| author_facet | Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A. Bazykin Yiming Bao Mingkun Li |
| author_sort | Wentai Ma |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-08T17:52:18Z |
| format | Article |
| id | doaj.art-8eb8293567d7418783685aeac509bf9b |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2025-03-21T00:00:59Z |
| publishDate | 2022-02-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-8eb8293567d7418783685aeac509bf9b2024-08-03T11:36:00ZengOxford University PressGenomics, Proteomics & Bioinformatics1672-02292022-02-012016069Genomic Perspectives on the Emerging SARS-CoV-2 Omicron VariantWentai Ma0Jing Yang1Haoyi Fu2Chao Su3Caixia Yu4Qihui Wang5Ana Tereza Ribeiro de Vasconcelos6Georgii A. Bazykin7Yiming Bao8Mingkun Li9CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, ChinaNational Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, ChinaCAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, BrazilSkolkovo Institute of Science and Technology, Moscow 121205, Russia; Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow 127051, RussiaUniversity of Chinese Academy of Sciences, Beijing 100049, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, ChinaCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S167202292200002XOmicronGenomicsMutationVariant of concernSARS-CoV-2 |
| spellingShingle | Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A. Bazykin Yiming Bao Mingkun Li Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant Genomics, Proteomics & Bioinformatics Omicron Genomics Mutation Variant of concern SARS-CoV-2 |
| 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 | Omicron Genomics Mutation Variant of concern SARS-CoV-2 |
| url | http://www.sciencedirect.com/science/article/pii/S167202292200002X |
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