期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 39, 期 4, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msac061
关键词
epistasis; negative selection; positive selection; coevolution
资金
- Strategic Health Innovation Partnerships Unit of the South African Medical Research Council
- South African Department of Science and Innovation [222574/Z/21/Z, R01 AI134384]
- Wellcome Trust [206298/Z/17/Z]
- MRC [MC_UU_12014/12]
- Howard Hughes Medical Institute
- European Union
- Horizon Europe research and innovation programmes [871075, 101046203]
- European Research Council under the European Union [~725422]
- NIH [R01 AI153044, U19 AI135995]
- Francis Crick Institute [FC0010218]
- MRC (UK) [FC0010218]
- Cancer Research UK [FC0010218]
- Wellcome [203135]
- Medical Research Council of South Africa
- Horizon Europe - Research Infrastructures (RIS) [101046203] Funding Source: Horizon Europe - Research Infrastructures (RIS)
- European Research Council (ERC) [725422] Funding Source: European Research Council (ERC)
This study found 13 rare mutations among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene, which may impact important regions and functions of the S-gene. The mutations were predicted to decrease the fitness of the virus they occurred in prior to the emergence of Omicron. The study also suggests that the mutations in each cluster interact cooperatively to alter the function of Spike. Understanding how these complex and highly adaptive mutation constellations were assembled in the Omicron S-gene, and why they went undetected in the early stages, is crucial.
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
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