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. 2021 Nov:95:105038.
doi: 10.1016/j.meegid.2021.105038. Epub 2021 Aug 14.

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

Katherine Laiton-Donato  1 , Carlos Franco-Muñoz  2 , Diego A Álvarez-Díaz  3 , Hector Alejandro Ruiz-Moreno  3 , José A Usme-Ciro  4 , Diego Andrés Prada  3 , Jhonnatan Reales-González  3 , Sheryll Corchuelo  5 , María T Herrera-Sepúlveda  2 , Julian Naizaque  5 , Gerardo Santamaría  5 , Jorge Rivera  5 , Paola Rojas  3 , Juan Hernández Ortiz  6 , Andrés Cardona  6 , Diana Malo  7 , Franklin Prieto-Alvarado  7 , Fernando Ruiz Gómez  8 , Magdalena Wiesner  3 , Martha Lucia Ospina Martínez  9 , Marcela Mercado-Reyes  10
Affiliations

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

Katherine Laiton-Donato et al. Infect Genet Evol. 2021 Nov.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity 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 I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, 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.

Keywords: Emergence; Evolution; SARS-CoV-2; Variant of interest (VOI).

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Figures

Fig. 1
Fig. 1
Percent of variant B.1.621 in Spain, USA and Colombia. 1A) Gisaid registries of variant B.1.621 in 2021. Since January the continuous record has been maintained in Colombia. 1B) Lineage percentage and number of cases of COVID-19 in five departments with circulation of B.1.621 variant and the capital city. B.1.1.7 and P.1 VOC lineages are shown, others lineages circulating are represented as “others”.
Fig. 2
Fig. 2
Phylogeny and distribution of SARS-CoV-2 b.1.621 variant in Colombia 2a) Phylogenetic tree of the new lineage of SARS-CoV-2 emerging from B.1.621 lineage. The tree was reconstructed by maximum likelihood with the estimated GTR + F + I + G4 nucleotide substitution model for the dataset of 434 genomes. The interactive tree can be accessed in the following link: https://microreact.org/project/5CAiK3qCMaEgE4vYkKVpZW/b7113efc 2b) Map of distribution of lineages across the country.
See this image and copyright information in PMC

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