A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. The two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved from lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). On the other hand, epidemiologically relevant B.1.1.33 deriving lineages have not been described so far. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North, and Northeast regions.

Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico

“…In Latin America, with the exception of P.1 and P.2 observed in Brazil, no other variants with the potential for rapid expansion have been reported so far [11]. Here, we report the identification of a potential VOI harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.…”

Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in Brazil

“…The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic [1][2][3][4][5][6]. In Brazil, six such lineages cocirculate, one originally from the UK (B.1.1.7) [1], one original from South Africa (B.1.351) [2], and four that emerged within different regions of the country, P.1 (Manaus) [3], P.2 (Rio de Janeiro) [4], N.9 (São Paulo) [5], and N.10 (Maranhão) [6].…”

SARS-CoV-2 reinfection: report of two cases in Southeast Brazil

“…The P. 2 variant is classified by the CDC as a Variant of Interest, a sub-clade of B.1.1.28, which harbors the E484K spike protein mutation, associated with immune evasion from neutralizing antibodies. Reinfections associated with the P. 2 variant have been previously reported 16 , 17 .…”