Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
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| Authors: | Yuri Ypez Mariana Marcano-Ruiz Rafael S Bezerra Bibiana Fam Joo PB Ximenez Wilson A Silva Jr Maria Ctira Bortolini |
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| Institution: | 1.Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil. ; 2.Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil; 3.Instituto de Pesquisa do Câncer de Guarapuava, Guarapuava, PR, Brazil. |
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| Abstract: | Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses. |
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| Keywords: | Gamma P 1 evolution COVID-19 |
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