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Perico CP, De Pierri CR, Neto GP, Fernandes DR, Pedrosa FO, de Souza EM, Raittz RT. Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin. Front Microbiol 2022; 13:1037455. [PMID: 36620039 PMCID: PMC9814972 DOI: 10.3389/fmicb.2022.1037455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Brazil was the epicenter of worldwide pandemics at the peak of its second wave. The genomic/proteomic perspective of the COVID-19 pandemic in Brazil could provide insights to understand the global pandemics behavior. In this study, we track SARS-CoV-2 molecular information in Brazil using real-time bioinformatics and data science strategies to provide a comparative and evolutive panorama of the lineages in the country. SWeeP vectors represented the Brazilian and worldwide genomic/proteomic data from Global Initiative on Sharing Avian Influenza Data (GISAID) between February 2020 and August 2021. Clusters were analyzed and compared with PANGO lineages. Hierarchical clustering provided phylogenetic and evolutionary analyses of the lineages, and we tracked the P.1 (Gamma) variant origin. The genomic diversity based on Chao's estimation allowed us to compare richness and coverage among Brazilian states and other representative countries. We found that epidemics in Brazil occurred in two moments with different genetic profiles. The P.1 lineages emerged in the second wave, which was more aggressive. We could not trace the origin of P.1 from the variants present in Brazil. Instead, we found evidence pointing to its external source and a possible recombinant event that may relate P.1 to a B.1.1.28 variant subset. We discussed the potential application of the pipeline for emerging variants detection and the PANGO terminology stability over time. The diversity analysis showed that the low coverage and unbalanced sequencing among states in Brazil could have allowed the silent entry and dissemination of P.1 and other dangerous variants. This study may help to understand the development and consequences of variants of concern (VOC) entry.
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Affiliation(s)
- Camila P Perico
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Camilla R De Pierri
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Giuseppe Pasqualato Neto
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Danrley R Fernandes
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto T Raittz
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
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