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

• DOI: 10.3389/fmed.2022.806611
• Publication Date: 2022-02-15T06:29:13Z
• Authors: Ricardo Ariel Zim...; Patrícia Aline Gr...; Flavio Adsuara Ca...; Carlos Gustavo Wa...; Daniel do Nascime...; Andrea Roberto de...; Andy Goren; Liane Nanci Rotta; Zhihua Ren; Claudia Elizabeth...
• Keywords: Lineage (genetic); Molecular evolution; Phylogenomics

Background P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, end 2020, and has emerged as a very important variant concern (VOC) SARS-CoV-2 worldwide. been linked to increased infectivity, higher mortality, immune evasion, leading reinfections potentially reduced efficacy vaccines neutralizing antibodies. Methods The samples 276 patients from Amazonas were sent central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global regional phylogenetic analyses successfully sequenced genomes conducted maximum likelihood method. Multiple alignments obtained including previously unique human sequences. evolutionary histories spike non-structural proteins ORF1a their molecular evolution analyzed detection positive (FUBAR, FEL, MEME) negative (FEL SLAC) selective pressures. To further evaluate possible pathways emergence P.1, we performed specific analysis copy-choice recombination events. A phylogenomic with subsampled B.1.1.28 applied relationship among samples. Results Forty-four confirmed lineage. In addition characteristic mutations, find evidence continuous diversification SARS-CoV-2, rare unseen mutations detected protein ORF1a. No found. Several sites demonstrated be under selection, various identified mostly According Pango assignment, indicate all belonging Conclusion shown after its emergence. lack clear selection several suggest that this resulted mainly strong forces progressive accumulation favorable signature set mutations.