SARS-CoV-2 genomic monitoring in the Sao Paulo State unveils new sublineages of the AY.43 strain

Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in Sao Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.