Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

• DOI: 10.1016/j.meegid.2021.105038
• Publication Date: 2021-08-14T15:08:30Z
• Authors: Katherine Laiton-...; Carlos Franco-Muñoz; Diego A. Álvarez-...; Hector Alejandro ...; José A. Usme-Ciro; Diego Andrés Prada; Jhonnatan Reales-...; Sheryll Corchuelo; María T. Herrera-...; Julian Naizaque; Gerardo Santamaría; Jorge Rivera; Paola Rojas; Juan Hernández Ortiz; Andrés Cardona; Diana Malo; Franklin Prieto-A...; Fernando Ruiz Gómez; Magdalena Wiesner; Martha Lucia Ospi...; Marcela Mercado-R...
• Keywords: 0301 basic medicine; Evolution; Short Communication; Genome, Viral; Colombia; Severity of Illness Index; Evolution, Molecular; 03 medical and health sciences; Protein Domains; Humans; Phylogeny; 0303 health sciences; SARS-CoV-2; Variants; COVID-19; High-Throughput Nucleotide Sequencing; Variantes; 3. Good health; Evolución; Phylogeography; Amino Acid Substitution; Epidemiological Monitoring; Mutation; Spike Glycoprotein, Coronavirus

SummaryThe genetic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes T95I, Y144T, Y145S and the insertion 146N in the N-terminal domain, R346K, E484K and N501Y in the Receptor-binding Domain (RBD) and P681H1 in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlántico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.HighlightsMonitoring the emergence of new variants of SARS-CoV-2 in real time is a worldwide priority.Emerging variants of SARS-CoV-2 may have high impact biological implications for public healthThe SARS-CoV-2 B.1.621 variant of interest was characterized by several substitutions: T95I, Y144T, Y145S, ins146N, R346K, E484K, N501Y and P681H in spike protein.