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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2022.1008600/full |
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| author | Thaís de Souza Silva Richard Steiner Salvato Tatiana Schäffer Gregianini Ighor Arantes Gomes Elisa Cavalcante Pereira Eneida de Oliveira André Luiz de Menezes Regina Bones Barcellos Fernanda Marques Godinho Irina Riediger Maria do Carmo Debur Cristina Mendes de Oliveira Rodrigo Ribeiro-Rodrigues Fabio Miyajima Fernando Stehling Dias Adriano Abbud Rubens do Monte-Neto Carlos Eduardo Calzavara-Silva Marilda Mendonça Siqueira Gabriel Luz Wallau Paola Cristina Resende Gabriel da Rocha Fernandes Pedro Alves |
| author_facet | Thaís de Souza Silva Richard Steiner Salvato Tatiana Schäffer Gregianini Ighor Arantes Gomes Elisa Cavalcante Pereira Eneida de Oliveira André Luiz de Menezes Regina Bones Barcellos Fernanda Marques Godinho Irina Riediger Maria do Carmo Debur Cristina Mendes de Oliveira Rodrigo Ribeiro-Rodrigues Fabio Miyajima Fernando Stehling Dias Adriano Abbud Rubens do Monte-Neto Carlos Eduardo Calzavara-Silva Marilda Mendonça Siqueira Gabriel Luz Wallau Paola Cristina Resende Gabriel da Rocha Fernandes Pedro Alves |
| author_sort | Thaís de Souza Silva |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T11:19:12Z |
| format | Article |
| id | doaj.art-40a9549dd6584b1a88a9743daf964349 |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-04-11T11:19:12Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-40a9549dd6584b1a88a9743daf9643492022-12-22T04:27:07ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2022-09-01910.3389/fmed.2022.10086001008600Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in BrazilThaís de Souza Silva0Richard Steiner Salvato1Tatiana Schäffer Gregianini2Ighor Arantes Gomes3Elisa Cavalcante Pereira4Eneida de Oliveira5André Luiz de Menezes6Regina Bones Barcellos7Fernanda Marques Godinho8Irina Riediger9Maria do Carmo Debur10Cristina Mendes de Oliveira11Rodrigo Ribeiro-Rodrigues12Fabio Miyajima13Fernando Stehling Dias14Adriano Abbud15Rubens do Monte-Neto16Carlos Eduardo Calzavara-Silva17Marilda Mendonça Siqueira18Gabriel Luz Wallau19Paola Cristina Resende20Gabriel da Rocha Fernandes21Pedro Alves22Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, BrazilLaboratório Central de Saúde Pública do Estado do Rio Grande do Sul, Porto Alegre, BrazilLaboratório Central de Saúde Pública do Estado do Rio Grande do Sul, Porto Alegre, BrazilInstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilInstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilLaboratório Municipal de Referência, Setor de Biologia Molecular, Belo Horizonte, BrazilLaboratório Municipal de Referência, Setor de Biologia Molecular, Belo Horizonte, BrazilCentro de Desenvolvimento Científico e Tecnológico, Porto Alegre, BrazilCentro de Desenvolvimento Científico e Tecnológico, Porto Alegre, BrazilLaboratório Central de Saúde Pública do Estado do Paraná, Curitiba, BrazilLaboratório Central de Saúde Pública do Estado do Paraná, Curitiba, BrazilDasa, Barueri, BrazilLaboratório Central de Saúde Pública do Estado do Espírito Santo, Vitória, BrazilFiocruz Ceará, Fundação Oswaldo Cruz, Eusébio, BrazilFiocruz Ceará, Fundação Oswaldo Cruz, Eusébio, Brazil0Instituto Adolfo Lutz, São Paulo, BrazilInstituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, BrazilInstituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, BrazilInstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil1Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilInstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilInstituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, BrazilInstituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, BrazilRecombination 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.https://www.frontiersin.org/articles/10.3389/fmed.2022.1008600/fullSARS-CoV-2recombinantgenomic surveillanceXAGvariantsomicron |
| spellingShingle | Thaís de Souza Silva Richard Steiner Salvato Tatiana Schäffer Gregianini Ighor Arantes Gomes Elisa Cavalcante Pereira Eneida de Oliveira André Luiz de Menezes Regina Bones Barcellos Fernanda Marques Godinho Irina Riediger Maria do Carmo Debur Cristina Mendes de Oliveira Rodrigo Ribeiro-Rodrigues Fabio Miyajima Fernando Stehling Dias Adriano Abbud Rubens do Monte-Neto Carlos Eduardo Calzavara-Silva Marilda Mendonça Siqueira Gabriel Luz Wallau Paola Cristina Resende Gabriel da Rocha Fernandes Pedro Alves Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil Frontiers in Medicine SARS-CoV-2 recombinant genomic surveillance XAG variants omicron |
| 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 | SARS-CoV-2 recombinant genomic surveillance XAG variants omicron |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2022.1008600/full |
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