SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

Varela, A. P. M.; Prichula, J.; Meyer, F. Q.; Salvato, R.; Sant'Anna, F. H.; Gregianini, T. S.; Martins, L. G.; Seixas, A.; Veiga, A. B. G. d.

doi:10.1101/2021.07.29.454323

bioRxiv · 10.1101/2021.07.29.454323

SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

Varela, A. P. M.·Prichula, J.·Meyer, F. Q.·Salvato, R.·Sant'Anna, F. H.·Gregianini, T. S.·Martins, L. G.·Seixas, A.·Veiga, A. B. G. d.

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Abstract

BackgroundGenomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first case of each Regional Health Coordination and cases from three epidemic peaks. MethodsNinety SARS-CoV-2 genomes from RS were sequenced and analyzed against SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis. ResultsSARS-CoV-2 lineages among the first cases in RS were B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July-August, 2020), emergence of P.2 (55.6%) in the second peak (November-December, 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February-April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences. ConclusionsThis study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil, and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities decisions to control COVID-19 in Brazil. SummaryNinety SARS-CoV-2 genomes from Rio Grande do Sul, Brazil, were sequenced, including the first cases from 15 State Health Coordination regions and samples from three epidemic peaks. Phylogenomic inferences showed SARS-CoV-2 lineages spread, revealing its genomic diversity.

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Varela, A. P. M., Prichula, J., Meyer, F. Q., Salvato, R., Sant'Anna, F. H., Gregianini, T. S., Martins, L. G., Seixas, A., Veiga, A. B. G. d.. 2021-07-30. SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1. https://doi.org/10.1101/2021.07.29.454323

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