Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution.
[en] Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains.
Disciplines :
Veterinary medicine & animal health Immunology & infectious disease
Author, co-author :
Nunes, Danilo Rosa; Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
Braconi, Carla Torres; Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
Ludwig-Begall, Louisa ; Université de Liège - ULiège > Fundamental and Applied Research for Animals and Health (FARAH) > FARAH: Santé publique vétérinaire
Arns, Clarice Weis; Laboratory of Virology, University of Campinas, Campinas, SP, Brazil
Durães-Carvalho, Ricardo ; Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
Language :
English
Title :
Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution.
FAPESP - Fundação de Amparo à Pesquisa do Estado de São Paulo [BR] CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico [BR] CAPES - Coordenação de Aperfeicoamento de Pessoal de Nível Superior [BR]
Funding text :
Funding:Thisworkwassupportedbythe Fundac ¸ãodeAmparoàPesquisadoEstado384de SãoPaulo(FAPESP),Brazil,grants2019/01255-9 and2021/03684-4(Young385Investigator Program)(RD-C),andbytheConselhoNacionalde Desenvolvimento386 Cientı ´ fico e Tecnolo ´ gico (CNPq),Brazil,grant405691/2018-1(C.T.B).DRNis387recipientofaninstitutionalscholarship fromtheCoordenac ¸ãodeAperfeic ¸oamento388de Pessoal de Nı ´vel Superior(CAPES),Brazil,grant 88887.506234/2020-00.This work was supported by the Fundação de Amparo à Pesquisa doEstado384 de São Paulo (FAPESP), Brazil, grants 2019/01255-9 and 2021/03684-4(Young385 Investigator Program) (RD-C), and by the Conselho Nacional de Desenvolvimento386 Científico e Tecnológico (CNPq), Brazil, grant 405691/2018-1 (C.T.B). DRNis387 recipient of an institutional scholarship from the Coordenação de Aperfeiçoamento388 de Pessoal de Nível Superior (CAPES), Brazil, grant 88887.506234/2020-00. We gratefully acknowledge the authors and both the originating and submitting laboratories for the sequence data in GISAID EpiCoV and GenBank on which this work is based. The authors also thank the Rede Corona-Ômica/MCTI/FINEP, the National Laboratory for Scientific Computing (LNCC/MCTI, Brazil) for providing HPC resources of the Santos Dumont supercomputer (ID #45691), and Prof. Luiz Mário Ramos Janini for fruitful discussion.
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