The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein

Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the SARS-CoV-2 Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. Importantly, we detected communitary transmission of four lineages bearing NTD indels: a P.1 Δ69-70 lineage (which can impact several SARS-CoV-2 diagnostic protocols), a P.1 Δ144 lineage, a P.1-like lineage carrying ins214ANRN, and the VOI N.10 derived from the B.1.1.33 lineage carrying three deletions (Δ141-144, Δ211 and Δ256-258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil is generating new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.