tetano
Editor, Senior Moderator
Mem Inst Oswaldo Cruz
. 2021 Nov 8;116:e210166.
doi: 10.1590/0074-02760210166. eCollection 2021.
SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil
Luis Fernando Lopez Tort[SUP] 1 2 [/SUP], Ieda Pereira Ribeiro[SUP] 1 [/SUP], Lidiane Souza Raphael Menezes[SUP] 1 [/SUP], Alexandre Araújo Cunha Dos Santos[SUP] 1 [/SUP], Marta Pereira Santos[SUP] 1 [/SUP], Luana Damasceno[SUP] 3 [/SUP], Paola Cristina Resende Silva[SUP] 4 [/SUP], Marilda Agudo Mendonça Teixeira de Siqueira[SUP] 4 [/SUP], Patricia Brasil[SUP] 3 [/SUP], Myrna Cristina Bonaldo[SUP] 1 [/SUP]
Affiliations
Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein.
Objective: To describe the first detection of variant N.9 in Rio de Janeiro State.
Methods: SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis.
Findings: Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K".
Main conclusions: The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.
. 2021 Nov 8;116:e210166.
doi: 10.1590/0074-02760210166. eCollection 2021.
SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil
Luis Fernando Lopez Tort[SUP] 1 2 [/SUP], Ieda Pereira Ribeiro[SUP] 1 [/SUP], Lidiane Souza Raphael Menezes[SUP] 1 [/SUP], Alexandre Araújo Cunha Dos Santos[SUP] 1 [/SUP], Marta Pereira Santos[SUP] 1 [/SUP], Luana Damasceno[SUP] 3 [/SUP], Paola Cristina Resende Silva[SUP] 4 [/SUP], Marilda Agudo Mendonça Teixeira de Siqueira[SUP] 4 [/SUP], Patricia Brasil[SUP] 3 [/SUP], Myrna Cristina Bonaldo[SUP] 1 [/SUP]
Affiliations
- PMID: 34755818
- DOI: 10.1590/0074-02760210166
Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein.
Objective: To describe the first detection of variant N.9 in Rio de Janeiro State.
Methods: SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis.
Findings: Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K".
Main conclusions: The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.