Elsevier

Virus Research

Volume 311, 2 April 2022, 198702
Virus Research

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

https://doi.org/10.1016/j.virusres.2022.198702Get rights and content
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Highlights

  • Emergence, dispersion, and consolidation of the Delta variant in South Brazil.

  • Gamma variant was completely replaced by Delta variant in five months.

  • Most sequences generated were classified as AY.99.2, AY.99.2-like, and AY.101.

Abstract

The emergence of Variants of Concern (VOC) presenting an unusual number of new mutations is one of the most remarkable features of SARS-CoV-2. The Delta variant, since its appearance, replaced the VOC Gamma, which was responsible for the major COVID-19 wave in Brazil. In this study, we performed a Delta whole-genome sequencing of 183 samples as part of a major genomic surveillance study performed since the beginning of the pandemic. Here, we showed an emergence, widespread dispersion and consolidation of the Delta variant in Rio Grande do Sul State, completely replacing the Gamma variant in a four to five months period. Performing the phylogenetic and phylodynamic analysis, the majority of the sequences generated herein were classified as AY.99.2, AY.99.2-like and AY.101. AY.99.2 Delta-related lineage has been widely reported in Brazil and in the Americas as well. Altogether, our findings provided a mutational profile of the sequences and presented high substitutions per site in the root-to-tip phylogenetic tree, corroborating studies that show the high mutational rate of SARS-CoV-2 over time.

Keywords

SARS-CoV-2
B.1.617.2
AY.99.2
AY.101
Delta variant
Southern Brazil

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These authors contributed equally to this work.