Comparative Genomics and Characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern From Amazonas, Brazil

Ricardo Ariel Zimerman; Patrícia Aline Gröhs Ferrareze; Flavio Adsuara Cadegiani; Carlos Gustavo Wambier; Daniel do Nascimento Fonseca; Andrea Roberto de Souza; Andy Goren; Liane Nanci Rotta; Zhihua Ren; Claudia Elizabeth Thompson

doi:10.3389/fmed.2022.806611

Comparative Genomics and Characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern From Amazonas, Brazil

Front Med (Lausanne). 2022 Feb 15:9:806611. doi: 10.3389/fmed.2022.806611. eCollection 2022.

Affiliations

¹ Hospital da Brigada Militar, Porto Alegre, Brazil.
² Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.
³ Corpometria Institute, Brasília, Brazil.
⁴ Department of Dermatology, Warren Alpert Medical School of Brown University, Providence, RI, United States.
⁵ Samel and Oscar Nicolau Hospitals, Manaus, Brazil.
⁶ Applied Biology, Inc., Irvine, CA, United States.
⁷ Suzhou Kintor Pharmaceutical, Inc., Suzhou, China.
⁸ Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.

Abstract

Background: P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality, and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies.

Methods: The samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples.

Results: Forty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage.

Conclusion: P.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.

Keywords: COVID-19; NSP; P.1; SARS-CoV-2; VOC; genomic epidemiology; phylogenomics; spike.