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, Paola Cristina; Naveca, Felipe G; Lins, Roberto D; Dezordi, Filipe Zimmer; Ferraz, Matheus V. F; Moreira, Emerson G; Coêlho, Danilo F; Motta, Fernando Couto; Paixão, Anna Carolina Dias; Appolinario, Luciana; Lopes, Renata Serrano; Mendonça, Ana Carolina da Fonseca; da Rocha, Alice Sampaio Barreto; Nascimento, Valdinete; Souza, Victor; Silva, George; Nascimento, Fernanda; Neto, Lidio Gonçalves Lima; da Silva, Fabiano Vieira; Riediger, Irina; Debur, Maria do Carmo; Leite, Anderson Brandao; Mattos, Tirza; da Costa, Cristiano Fernandes; Pereira, Felicidade Mota; dos Santos, Cliomar Alves; Rovaris, Darcita Buerger; Fernandes, Sandra Bianchini; Abbud, Adriano; Sacchi, Claudio; Khouri, Ricardo; Bernardes, André Felipe Leal; Delatorre, Edson; Gräf, Tiago; Siqueira, Marilda Mendonça; Bello, Gonzalo; Wallau, Gabriel L

Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (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 the community transmission of different P.1 lineages bearing NTD indels ∆69-70 (which can impact several SARS-CoV-2 diagnostic protocols), ∆144 and ins214ANRN, and a new VOI N.10 derived from the B.1.1.33 lineage carrying three NTD deletions (∆141–144, ∆211, and ∆256–258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil generates new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.