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. 2022 Nov:321:198907.
doi: 10.1016/j.virusres.2022.198907. Epub 2022 Aug 30.

Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage

Mariana Soares da Silva  1 , Juliana Schons Gularte  2 , Micheli Filippi  2 , Meriane Demoliner  2 , Viviane Girardi  2 , Ana Cristina Sbaraini Mosena  2 , Vyctoria Malayhka de Abreu Góes Pereira  2 , Alana Witt Hansen  2 , Matheus Nunes Weber  2 , Paula Rodrigues de Almeida  2 , Juliane Deise Fleck  2 , Andrea Gurgel Batista Leite Dal Bó  3 , Marcus Herbert Jones  4 , Frederico Friedrich  5 , Luiz Amorim Filho  6 , Fábio Klamt  7 , Fernando Rosado Spilki  2
Affiliations

Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage

Mariana Soares da Silva et al. Virus Res. 2022 Nov.

Abstract

Recently, SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in Botswana in November 2021. In a short period of time, this highly mutated variant replaced the previous dominant Delta variant, causing an exponential increase in the number of COVID-19 cases, resulting in a new wave of pandemic. This current research article aims to analyze and summarize information about the genetic characteristics, amino acid mutations and epidemiological data providing scientific findings to enrich the SARS-CoV-2 knowledge. More importantly, we describe here, for the first time, the identification of a new Omicron variant of concern: Omicron-L452R in Brazil.

Keywords: Mutational scanning; S:L452R; SARS-CoV-2; VOC.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Graphical display of (a) the proportion of SARS-CoV-2 lineages identified in sequencing data and (b) the epidemiological data on COVID-19 cases and deaths in RS state by epidemiological week for the period October 2021 to March 2022, RS state, Brazil.
Fig. 2
Fig. 2
Phylogenetic and phylodynamic of SARS-CoV-2 variant analysis in Rio Grande do Sul State. Phylogenetic tree of all circulating lineages, developed through the Nextstrain server (Nextclade tool), using GISAID data. The sequences generated herein are clustered into a Delta (21J) and Omicron lineage (21K and 21L), marked in green and orange, respectively (left). Phylogenetic tree of 126 SARS-CoV-2 Omicron variants. The phylogeny is embedded as a root-to-tip plot, in which the x axis represents the date of sample collection, and the y axis represents the number of genome wide mutations that have occurred since the phylogeny root (right). Gisaid accession numbers available at Supplementary Material 1 (Omicron) and 2 (Delta).
Fig. 3
Fig. 3
Frequency of non-synonymous mutations across the genomes of Omicron sublineages sequenced during October 2021 to March 2022, RS state, Brazil. The x axis represents the mutations along the genome and y axis represents each mutation's frequencies. The analysis was performed in all coding regions, as observed. The mutations marked with dot were also present in BA.2. Only the mutations with more than 40% at the same sub lineage were shown.
See this image and copyright information in PMC

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