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Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil

Carolina M. Voloch, Ronaldo da Silva Francisco, Luiz G. P. de Almeida and 18 more

Journal of Virology · 2021 · CC BY

doi:10.1128/jvi.00119-21

Abstract

In this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections. Article Summary Line We identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.

Full text

From PubMed Central, U.S. National Library of Medicine, as current on Oct 18, 2026. Paragraph numbers are ours, so an answer can point at one.

LETTER

Almost simultaneously, several studies reported the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages characterized by distinct phylogenetic and genetic features. Here, we sequenced 180 complete genomes collected between April and November 2020 from the Brazilian state of Rio de Janeiro (see Table S1 in the supplemental material) and identified 37 samples composing a new variant lineage. This novel lineage, currently classified as P.2 by Pangolin (COG-UK), a descendant of the B.1.1.28 strain, is distinguished by five lineage-defining mutations: 5′ untranslated region [UTR] C100U, (ORF1ab L3468V, ORF1ab synC11824U, S E484K, and N A119S). Five other mutations were also detected in many genomes from this lineage (ORF1ab L3930F, ORF1ab synA12964G, ORF8 synC28253U, N M234I, and 3′ UTR C29754U).

We found a total of 731 single-nucleotide variants (SNVs) across the 180 samples, of which 50.3% were missense, 44.5% synonymous, 5.1% intergenic, and 0.1% nonsense. For the phylogenetic reconstruction, we gathered a global data set containing the 180 new genomes plus 1,197 high-coverage genomes from GISAID (GISAID Initiative; see Table S2), including 116 Brazilian and 1,081 worldwide genomes whose collection dates ranged from May to November (data downloaded 3 December 2020). Genomes were classified using Pangolin (COG-UK).

The phylogenetic reconstruction indicates that the vast majority (86.8%) of Brazilian genomes fall within three clades (Fig. 1). Clade I comprises B.1.1.33 strains, while clades II and III are composed of B.1.1.28 strains. We inferred that P.2 falls within clade II (Fig. 1) and emerged in July 2020.

An essential feature of the new strains recently described in the United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) is that they have a unique set of multiple spike mutations, including N501Y, which is associated with greater infectivity and transmissibility. In contrast, all P.2 genomes exhibit only E484K in addition to a varying collection of either novel or rarely found spike mutations. E484K is also present in P.1 and B.1.351 lineages, but not in B.1.1.7. Since both P.1 and P.2 lineages are descendants of B.1.1.28 and both were first detected in Brazil, we performed a phylogenetic analysis of all their genomes available in GISAID (data downloaded 11 February 2021). Figure 2 highlights the differences between them and their origin, showing that despite sharing E484K, both emerged from independent events. The localities where these two lineages were first detected have had entirely different epidemiological dynamics since the beginning of coronavirus disease 2019 (COVID-19) history in Brazil; therefore, the two variants arose independently in different epidemiological contexts.

The cases of reinfection involving the new variant lineage P.2 and the ability of viruses harboring the mutation E484K to escape from neutralizing antibodies emphasize the importance of monitoring the spread of this new strain. In about 4 months, 342 genomes classified as P.2 have become available. The emergent lineage P.2, initially detected in 37 samples from Rio de Janeiro State, is spread across all Brazilian regions and 16 other countries. Brazilian viruses are the oldest and constitute the majority (55%) of the P.2 genomes, suggesting its exportation worldwide.

The present study was approved by the National Committee of Research Ethics and by the Ethics Committee of Hospital Universitário Clementino Fraga Filho (protocol numbers 30161620.0.1001.5257 and 34025020.0.0000.5257).

Data availability.

NGS data generated in our study are publicly available in SRA-NCBI (www.ncbi.nlm.nih.gov/sra), under BioProject accession no. PRJNA686081. Genome sequences were also deposited in GISAID (https://www.gisaid.org/) and are fully accessible for registered users within the “browse” option of the EpiCoV database (see Table S1).

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