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Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil
Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 var...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554242/ https://www.ncbi.nlm.nih.gov/pubmed/36250091 http://dx.doi.org/10.3389/fmed.2022.1008600 |
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author | Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante de Oliveira, Eneida de Menezes, André Luiz Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo de Oliveira, Cristina Mendes Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano do Monte-Neto, Rubens Calzavara-Silva, Carlos Eduardo Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro |
author_facet | Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante de Oliveira, Eneida de Menezes, André Luiz Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo de Oliveira, Cristina Mendes Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano do Monte-Neto, Rubens Calzavara-Silva, Carlos Eduardo Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro |
author_sort | Silva, Thaís de Souza |
collection | PubMed |
description | Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics. |
format | Online Article Text |
id | pubmed-9554242 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95542422022-10-13 Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante de Oliveira, Eneida de Menezes, André Luiz Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo de Oliveira, Cristina Mendes Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano do Monte-Neto, Rubens Calzavara-Silva, Carlos Eduardo Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro Front Med (Lausanne) Medicine Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics. Frontiers Media S.A. 2022-09-28 /pmc/articles/PMC9554242/ /pubmed/36250091 http://dx.doi.org/10.3389/fmed.2022.1008600 Text en Copyright © 2022 Silva, Salvato, Gregianini, Gomes, Pereira, de Oliveira, de Menezes, Barcellos, Godinho, Riediger, Debur, de Oliveira, Ribeiro-Rodrigues, Miyajima, Dias, Abbud, Monte-Neto, Calzavara-Silva, Siqueira, Wallau, Resende, Fernandes and Alves. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Medicine Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante de Oliveira, Eneida de Menezes, André Luiz Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo de Oliveira, Cristina Mendes Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano do Monte-Neto, Rubens Calzavara-Silva, Carlos Eduardo Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title | Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title_full | Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title_fullStr | Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title_full_unstemmed | Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title_short | Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil |
title_sort | molecular characterization of a new sars-cov-2 recombinant cluster xag identified in brazil |
topic | Medicine |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554242/ https://www.ncbi.nlm.nih.gov/pubmed/36250091 http://dx.doi.org/10.3389/fmed.2022.1008600 |
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