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

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

doi:10.3389/fmed.2022.806611

Abstract

BackgroundP.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.MethodsThe 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.ResultsForty-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.ConclusionP.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.

Highlights

The Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) P.1 (Gamma) lineage has accounted for the majority of the genomes sequenced in Brazil during the second wave of the COVID-19 pandemic [1]
Beyond the constellation of mutations expected from the P.1 lineage, we have found some unusual and/or uncertain deletions and substitutions
After automatic alignment using MAFFT v7.475 and visual inspection, we identified six nucleotide deletions of amino acid residues N188 and L189 from the spike protein in three genomic sequences followed by the R190S substitution in two of them

Summary

Introduction

The Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) P.1 (Gamma) lineage has accounted for the majority of the genomes sequenced in Brazil during the second wave of the COVID-19 pandemic [1] It is considered one of the most relevant “Variants Of Concern” (VOC) worldwide. We have previously shown that both substitutions are under strong positive selection [5] Since these mutations are present in other VOCs around the world, their emergence is evidence of convergent SARS-CoV-2 evolution [5, 6]. An earlier study describing P.1 in northern Brazil has linked this lineage to lower Cycle Threshold (Ct) values [8] This may be of major significance, since persistent higher viral loads after 1 week of symptom initiation were independently associated with worse outcomes, as demonstrated in a testing mAb study [9]. 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

Results

Conclusion