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

Resende, P. C.; Naveca, F. G.; Lins, R. D.; Dezordi, F. Z.; Ferraz, M. V. F.; Moreira, E. G.; Coelho, D. F.; Motta, F. C.; Paixao, A. C. D.; Appolinario, L.; Lopes, R. S.; Mendonca, A. C. d. F.; da Rocha, A. S. B.; Nascimento, V.; Souza, V.; Silva, G.; Nascimento, F.; Neto, L. G. L.; Riediger, I.; Debur, M. d. C.; Leite, A. B.; Mattos, T.; da Costa, C. F.; Pereira, F. M.; Khouri, R.; Bernardes, A. F. L.; Delatorre, E.; Graf, T.; Siqueira, M. M.; Bello, G.; Wallau, G. L.; Network, Fiocruz COVID-19 Genomic Surveillance

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. 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 neutralization than parental variants of concern.