Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020

Abstract

In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.

Keywords: 2019 novel coronavirus disease; Brazil; COVID-19; SARS-CoV-2; coronavirus disease; genomic; lineage B.1.1.7; respiratory infections; severe acute respiratory syndrome coronavirus 2; surveillance; transmission; viruses; zoonoses.

Figure

Phylogenetic context of novel severe acute respiratory syndrome coronavirus 2 B.1.1.7 genomes isolated from 2 patients in Brazil (labeled on figure), December 2020. Downsampling for the phylogenetic analysis of the B.1.1.7 SARS-CoV-2 variant (n = 4,693, December 31, 2020) was performed by selecting 1 sequence per country per day. As outgroups, we included 2 B.1.1 sequences from the United Kingdom that were closely related to the lineage of interest and sequence WH04 from Wuhan, China (GISAID identification no. EPI_ISL_406801; http://www.gisaid.org). Details on multiple alignment and phylogenetic tree reconstruction are described elsewhere (4). Tree file, aligned sequences, and GISAID acknowledgment tables are available at https://github.com/CADDE-CENTRE/VOC-Lineage-Brazil. Scale bar indicates nucleotide substitutions per site. VOC, variant of concern.