SARS-COV-2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages

Abstract

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely-Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

Keywords: AY.43; Delta VOC; SARS-CoV-2; emerging sublineages; genomic surveillance.

Figure 1

Phylogenetic analysis of the AY.43 lineage clade containing 492 genomes. The newly identified sublineages are highlighted with boxes: AY.43.1 (purple box) and AY.43.2 (blue box), and their characterizing mutations are represented on the newly formed branches. The original tree from which the AY.43 cluster was initially can be observed in Figure S1

Figure 2

Dissemination of the AY.43 lineage and the newly identified sublineages in the state of São Paulo (A). Map of Brazil with emphasis on the state of São Paulo (B). Dissemination of the AY.43 lineage (C). Dissemination of the AY.43.1 sublineage and (D). Dissemination of the AY.43.2 sublineage. Bar: percentage of the sequenced genomes