Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

• Published in: Infection, genetics and evolution Vol. 96; p. 105134
• Main Authors: Demoliner, Meriane, da Silva, Mariana Soares, Gularte, Juliana Schons, Hansen, Alana Witt, de Almeida, Paula Rodrigues, Weber, Matheus Nunes, Heldt, Fágner Henrique, Silveira, Flávio, Filippi, Micheli, de Abreu Góes Pereira, Vyctoria Malayhka, da Silva, Francini Pereira, Mallmann, Larissa, Fink, Pietra, de Moura Valim, Andréia Rosane, Possuelo, Lia Gonçalves, Fleck, Juliane Deise, Spilki, Fernando Rosado
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-12-2021; Published by Elsevier B.V
• Subjects: Adolescent; Adult; Aged; Aged, 80 and over; B.1.1.25; Brazil - epidemiology; Child; Consensus Sequence; COVID-19; COVID-19 - epidemiology; COVID-19 - virology; Female; Gamma lineage; Health crisis; Humans; Male; Middle Aged; Mutation; P.2 lineage; Phylogeny; SARS-CoV-2 - genetics; Short Communication; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Whole Genome Sequencing; Young Adult; Brazil; COVID-19; Health crisis; Gamma lineage; B.1.1.25; P.2 lineage
• ISSN: 1567-1348; 1567-7257; 1567-7257
• DOI: 10.1016/j.meegid.2021.105134

Recently, the highest wave of SARS-CoV-2 epidemic occurred since the beginning of the pandemic in Brazil was registered in Rio Grande do Sul (RS) State, Southern Brazil, considering the number of cases, deaths and hospitalization per day caused by COVID-19. In this study we described which lineages were circulating in the first quarter of 2021 in Southern Brazil to better understand the viral factors involved in the health crisis caused by SARS-CoV-2 in the region, searching also for possible additional SARS-CoV-2 sequence mutations. A total of 70 positive SARS-CoV-2 samples collected between January 28th, 2021 until April 23rd, 2021, were selected to sequencing. Whole genome sequencing of 70 SARS-CoV-2 samples showed a predominance of Gamma lineage (67%, 47/70), followed by P.2 lineage (27%, 19/70) and B.1.1.28 (6%, 4/70). Two Gamma lineage consensus sequences presented a new S:D614A mutation. Newly mutations could be emerging due the quick SARS-CoV-2 spreading. Thus, the greater understanding about immune protection and variants vigilance is essential to the better management of the health SARS-CoV-2 crisis.
•High prevalence of SARS-CoV-2 Gamma lineage and dominance over other variants through the recent wave in Southern Brazil.•Gamma lineage related with an increase of cases, deaths, and hospitalizations.•New SARS-CoV-2 Gamma genomes showing an additional Spike D614A mutation.