Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Feb 15:9:806611.
doi: 10.3389/fmed.2022.806611. eCollection 2022.

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

Ricardo Ariel Zimerman  1 , Patrícia Aline Gröhs Ferrareze  2 , Flavio Adsuara Cadegiani  3 , Carlos Gustavo Wambier  4 , Daniel do Nascimento Fonseca  5 , Andrea Roberto de Souza  5 , Andy Goren  6 , Liane Nanci Rotta  2 , Zhihua Ren  7 , Claudia Elizabeth Thompson  2   8
Affiliations

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

Ricardo Ariel Zimerman et al. Front Med (Lausanne). .

Expression of concern in

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.

PubMed Disclaimer

Conflict of interest statement

ZR is an employee of Kintor Pharmaceuticals, Ltd. AG is an employee of Applied Biology, Inc. FC has served as a clinical director for Applied Biology, Inc. CW has served as an advisor to Applied Biology, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Flowchart of SARS-CoV-2 RT-qPCR and genome sequencing.
Figure 2
Figure 2
Mutations of the SARS-CoV-2 genomes from the Amazonas state, Northern Brazil sampled in February and March 2021. (A) Genome map for the 44 genomes sequenced. Nucleotide substitutions are colored in red and blank regions represent low sequencing coverage. (B) Frequency of SNPs per SARS-CoV-2 genome position along the 44 genomes. These mutations are corresponding to the red lines in (A) and only missense substitutions represented by >10 sequences have their respective amino acid changes indicated above the bars. Main Open Reading Frames (ORFs) and SARS-CoV-2 proteins are indicated at the bottom to allow a rapid visualization of the viral proteins affected.
Figure 3
Figure 3
Genetic distance plot of the 44 sequenced genomes in comparison with the NC_045512.2 reference genome (Wuhan). (A) Genomic sequence identity. (B) Sequence identity for the spike gene region.
Figure 4
Figure 4
Maximum Likelihood tree of 1,887 unique genomes from the North region—Brazil, added to the 44 sequenced samples of this study. Pangolin lineages represented by
Figure 5
Figure 5
Phylogenetic analyses of spike and non-structural proteins from ORF1a including northern Brazilian SARS-CoV-2 genomes. (A) spike, (B) NSP1, (C) NSP3, (D) NSP5, (E) NSP6, and (F) NSP9.
Figure 6
Figure 6
Collapsed tree representing the assigned lineages of the 4,997 subsampled genomes from global phylogeny.
Figure 7
Figure 7
Global phylogeny of 4,997 subsampled genomes from P.1 and B.1.1.28 lineages.
Figure 8
Figure 8
Representative subtree of the 44 sequenced samples of this study and their nearest grouped neighbors inside the P.1 clade. The branch support values are represented by the SH-aLRT and ultrafast bootstrap percentages ≥70.
See this image and copyright information in PMC

References

    1. Franceschi VB, Ferrareze PAG, Zimerman RA, Cybis GB, Thompson CE. Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020 to February 2021. Virus Res. (2021) 304:198532. 10.1016/j.virusres.2021.198532 - DOI - PMC - PubMed
    1. Golubchik T, Lythgoe KA, Hall M, Ferretti L, Fryer HR, MacIntyre-Cockett G . Early Analysis of a Potential Link Between Viral Load the N501Y Mutation in the SARS-COV-2 Spike Protein. Cold Spring Harbor Laboratory. (2021). Available online atat: 10.1101/2021.01.12.20249080 (accessed July 19, 2021). - DOI
    1. Ferrareze PAG, Franceschi VB, Mayer A de M, Caldana GD, Zimerman RA, Thompson CE. E484K as an innovative phylogenetic event for viral evolution: genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Infect Genet Evol. (2021) 93:104941. 10.1016/j.meegid.2021.104941 - DOI - PMC - PubMed
    1. Nelson G, Buzko O, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Molecular Dynamic Simulation Reveals E484K Mutation Enhances Spike RBD-ACE2 Affinity the Combination of E484K, K417N N501Y Mutations (501Y.V2 variant) Induces Conformational Change Greater Than N501Y Mutant Alone, Potentially Resulting in an Escape Mutant. Cold Spring Harbor Laboratory. (2021). Available online at: 10.1101/2021.01.13.426558 (accessed July 19, 2021). - DOI
    1. Ferrareze PAG, Zimerman RA, Franceschi VB, Thompson CE. Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of the fixation of selected mutations. Cold Spring Harbor Lab. (2021) 2021.07.16.452571. 10.1101/2021.07.16.452571 - DOI