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Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil.
Microbiol Spectr. 2022 02 23; 10(1):e0151121.MS

Abstract

The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.

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Authors+Show Affiliations

Wink PL
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico de SARS-CoV-2, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
Ramalho R
Bioinformatics Core, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil.
Monteiro FL
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico de SARS-CoV-2, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico Molecular, Universidade Franciscana, Santa Maria, Rio Grande do Sul, Brazil.
Volpato FCZ
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico de SARS-CoV-2, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
Willig JB
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico de SARS-CoV-2, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil.
Lovison OVA
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. Bioinformatics Core, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil.
Zavascki AP
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. Infectious Diseases Service, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil.
Barth AL
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Laboratório de Diagnóstico de SARS-CoV-2, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
Martins AF
LABRESIS-Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. Bioinformatics Core, Hospital de Clínicas de Porto Alegregrid.414449.8, Porto Alegre, Rio Grande do Sul, Brazil. Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil.

MeSH

AdolescentAdultAgedAged, 80 and overBrazilCOVID-19ChildChild, PreschoolFemaleGenome, ViralGenomicsHumansInfantMaleMiddle AgedMutationPhylogenySARS-CoV-2Spike Glycoprotein, CoronavirusWhole Genome SequencingYoung Adult

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

35171035

Citation

Wink, Priscila Lamb, et al. "Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil." Microbiology Spectrum, vol. 10, no. 1, 2022, pp. e0151121.
Wink PL, Ramalho R, Monteiro FL, et al. Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Microbiol Spectr. 2022;10(1):e0151121.
Wink, P. L., Ramalho, R., Monteiro, F. L., Volpato, F. C. Z., Willig, J. B., Lovison, O. V. A., Zavascki, A. P., Barth, A. L., & Martins, A. F. (2022). Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Microbiology Spectrum, 10(1), e0151121. https://doi.org/10.1128/spectrum.01511-21
Wink PL, et al. Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Microbiol Spectr. 2022 02 23;10(1):e0151121. PubMed PMID: 35171035.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. AU - Wink,Priscila Lamb, AU - Ramalho,Rafaela, AU - Monteiro,Francielle Liz, AU - Volpato,Fabiana Caroline Zempulski, AU - Willig,Julia Biz, AU - Lovison,Otávio von Ameln, AU - Zavascki,Alexandre Prehn, AU - Barth,Afonso Luís, AU - Martins,Andreza Francisco, Y1 - 2022/02/16/ PY - 2022/2/17/pubmed PY - 2022/3/5/medline PY - 2022/2/16/entrez KW - COVID-19 KW - P.1 lineage KW - SARS-CoV-2 KW - gamma KW - genomic surveillance SP - e0151121 EP - e0151121 JF - Microbiology spectrum JO - Microbiol Spectr VL - 10 IS - 1 N2 - The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM. SN - 2165-0497 UR - https://www.unboundmedicine.com/medline/citation/35171035/Genomic_Surveillance_of_SARS_CoV_2_Lineages_Indicates_Early_Circulation_of_P_1__Gamma__Variant_of_Concern_in_Southern_Brazil_ DB - PRIME DP - Unbound Medicine ER -