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

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

Fig. 1

SARS-CoV-2 lineage's frequencies in Rio Grande do Sul State (RS), Brazil. Images show the lineages frequencies from genomic surveillance (1a), the Delta “AY.XX” 21 J frequencies (1b) and AY.XX-like sub-lineage frequencies (1c). These analyzes were performed with samples of our laboratory since the beginning of 2021.

Fig. 2

Phylogenetic and phylodynamic Delta SARS-CoV-2 variant analysis in Rio Grande do Sul State. Panel A shows the phylogenetic tree of all circulating lineages, developed through the Nextstrain server (Nextclade tool), using GISAID data. The sequences generated herein are clustered into a single Delta lineage, marked in green (21 J). Panel B shows the phylogenetic tree of 183 SARS-CoV-2 Delta variants. The phylogeny is embedded as a root-to-tip plot, in which the x axis represents the date of sample collection, and the y axis represents the number of genomewide mutations that have occurred since the phylogeny root. The regression line represents the average mutation rate of the SARS-CoV-2 sequences in the tree (34.5 substitutions/year).

Fig. 3

Mutational profile and frequency of mutations in complete genome sequences of SARS-CoV-2. Mutations with more than 10% of frequency were described. The presence of mutations along the genome of SARS-CoV-2, in each of the most prevalent sub-lineages, was described as follows: Fully painted squares correspond to 100% frequency of a given mutation. Hatched squares correspond to at least one sequence with the given mutation although it has never been found with 100% frequency.