Gene

Genome

Pathology

Phylogenetic tree

Lineage (genetic)

Coronavirus

Disease

Coronavirus disease 2019 (COVID-19)

Infectious disease (medical specialty)

Genetics

Medicine

Evolutionary biology

Biology

Untranslated region

Phylogenetics

Journal of Virology

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 (1–4). 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).

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