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; Oliveira, Eneida de; Menezes, André Luiz de; Barcellos, Regina Bones; Godinho, Fernanda Marques; Riediger, Irina; Debur, Maria do Carmo; Oliveira, Cristina Mendes de; Ribeiro-Rodrigues, Rodrigo; Miyajima, Fabio; Dias, Fernando Stehling; Abbud, Adriano; Monte Neto, Rubens Lima do; Silva, Carlos Eduardo Calzavara; Siqueira, Marilda Mendonça; Wallau, Gabriel Luz; Resende, Paola Cristina; Fernandes, Gabriel da Rocha; Alves, Pedro Augusto

Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil.

Detalhes bibliográficos
Autor(a) principal:	Silva, Thaís de Souza
Data de Publicação:	2022
Outros Autores:	Salvato, Richard Steiner, Gregianini, Tatiana Schäffer, Gomes, Ighor Arantes, Pereira, Elisa Cavalcante, Oliveira, Eneida de, Menezes, André Luiz de, Barcellos, Regina Bones, Godinho, Fernanda Marques, Riediger, Irina, Debur, Maria do Carmo, Oliveira, Cristina Mendes de, Ribeiro-Rodrigues, Rodrigo, Miyajima, Fabio, Dias, Fernando Stehling, Abbud, Adriano, Monte Neto, Rubens Lima do, Silva, Carlos Eduardo Calzavara, Siqueira, Marilda Mendonça, Wallau, Gabriel Luz, Resende, Paola Cristina, Fernandes, Gabriel da Rocha, Alves, Pedro Augusto
Tipo de documento:	Artigo
Idioma:	eng
Título da fonte:	Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo:	https://www.arca.fiocruz.br/handle/icict/56337
Resumo:	Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil

Metadados do item

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spelling	Silva, Thaís de SouzaSalvato, Richard SteinerGregianini, Tatiana SchäfferGomes, Ighor ArantesPereira, Elisa CavalcanteOliveira, Eneida deMenezes, André Luiz deBarcellos, Regina BonesGodinho, Fernanda MarquesRiediger, IrinaDebur, Maria do CarmoOliveira, Cristina Mendes deRibeiro-Rodrigues, RodrigoMiyajima, FabioDias, Fernando StehlingAbbud, AdrianoMonte Neto, Rubens Lima doSilva, Carlos Eduardo CalzavaraSiqueira, Marilda MendonçaWallau, Gabriel LuzResende, Paola CristinaFernandes, Gabriel da RochaAlves, Pedro Augusto2023-01-05T19:16:31Z2023-01-05T19:16:31Z2022SILVA, Thaís de Souza et al. Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil. Front Med (Lausanne), v. 9, 1008600, 2022. doi: 10.3389/fmed.2022.1008600.2296-858Xhttps://www.arca.fiocruz.br/handle/icict/56337engFrontiers Media S.AMolecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilEstado do Rio Grande do Sul. Laboratório Central de Saúde Pública. Porto Alegre, RS, BrazilEstado do Rio Grande do Sul. Laboratório Central de Saúde Pública. Porto Alegre, RS, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrazilPrefeitura de Belo Horizonte. Laboratório de Referência. Setor de Biologia Molecular. Belo Horizonte, MG, BrazilPrefeitura de Belo Horizonte. Laboratório de Referência. Setor de Biologia Molecular. Belo Horizonte, MG, BrazilCentro de Desenvolvimento Científico e Tecnológico. Porto Alegre, RS, BrazilCentro de Desenvolvimento Científico e Tecnológico. Porto Alegre, RS, BrazilEstado do Paraná. Laboratório Central de Saúde Pública. Curitiba, PR, BrazilEstado do Paraná. Laboratório Central de Saúde Pública. Curitiba, PR, BrazilDasa. Barueri, SP, BrazilEstado do Espírito Santo. Laboratório Central de Saúde Pública. Vitória, ES, BrazilFundação Oswaldo Cruz. Eusébio, CE, BrazilFundação Oswaldo Cruz. Eusébio, CE, BrazilInstituto Adolfo Lutz. São Paulo, SP, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, 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.SARS-CoV-2recombinantgenomic surveillanceXAGvariantsomicroninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/56337/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMolecular characterization of a new SARS-CoV-2 .pdfMolecular characterization of a new SARS-CoV-2 .pdfapplication/pdf4263600https://www.arca.fiocruz.br/bitstream/icict/56337/2/Molecular%20characterization%20of%20a%20new%20SARS-CoV-2%20.pdfdffb72fb99d7447c3aff9db767f040e8MD52icict/563372023-01-05 16:16:32.392oai:www.arca.fiocruz.br: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ório 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dc.title.en_US.fl_str_mv	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.
spellingShingle	Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil. Silva, Thaís de Souza SARS-CoV-2 recombinant genomic surveillance XAG variants omicron
title_short	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_sort	Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil.
author	Silva, Thaís de Souza
author_facet	Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante Oliveira, Eneida de Menezes, André Luiz de Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo Oliveira, Cristina Mendes de Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano Monte Neto, Rubens Lima do Silva, Carlos Eduardo Calzavara Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro Augusto
author_role	author
author2	Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante Oliveira, Eneida de Menezes, André Luiz de Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo Oliveira, Cristina Mendes de Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano Monte Neto, Rubens Lima do Silva, Carlos Eduardo Calzavara Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro Augusto
author2_role	author author author author author author author author author author author author author author author author author author author author author author
dc.contributor.author.fl_str_mv	Silva, Thaís de Souza Salvato, Richard Steiner Gregianini, Tatiana Schäffer Gomes, Ighor Arantes Pereira, Elisa Cavalcante Oliveira, Eneida de Menezes, André Luiz de Barcellos, Regina Bones Godinho, Fernanda Marques Riediger, Irina Debur, Maria do Carmo Oliveira, Cristina Mendes de Ribeiro-Rodrigues, Rodrigo Miyajima, Fabio Dias, Fernando Stehling Abbud, Adriano Monte Neto, Rubens Lima do Silva, Carlos Eduardo Calzavara Siqueira, Marilda Mendonça Wallau, Gabriel Luz Resende, Paola Cristina Fernandes, Gabriel da Rocha Alves, Pedro Augusto
dc.subject.en.en_US.fl_str_mv	SARS-CoV-2 recombinant genomic surveillance XAG variants omicron
topic	SARS-CoV-2 recombinant genomic surveillance XAG variants omicron
description	Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil
publishDate	2022
dc.date.issued.fl_str_mv	2022
dc.date.accessioned.fl_str_mv	2023-01-05T19:16:31Z
dc.date.available.fl_str_mv	2023-01-05T19:16:31Z
dc.type.status.fl_str_mv	info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv	info:eu-repo/semantics/article
format	article
status_str	publishedVersion
dc.identifier.citation.fl_str_mv	SILVA, Thaís de Souza et al. Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil. Front Med (Lausanne), v. 9, 1008600, 2022. doi: 10.3389/fmed.2022.1008600.
dc.identifier.uri.fl_str_mv	https://www.arca.fiocruz.br/handle/icict/56337
dc.identifier.issn.en_US.fl_str_mv	2296-858X
identifier_str_mv	SILVA, Thaís de Souza et al. Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil. Front Med (Lausanne), v. 9, 1008600, 2022. doi: 10.3389/fmed.2022.1008600. 2296-858X
url	https://www.arca.fiocruz.br/handle/icict/56337
dc.language.iso.fl_str_mv	eng
language	eng
dc.rights.driver.fl_str_mv	info:eu-repo/semantics/openAccess
eu_rights_str_mv	openAccess
dc.publisher.none.fl_str_mv	Frontiers Media S.A
publisher.none.fl_str_mv	Frontiers Media S.A
dc.source.none.fl_str_mv	reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ
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reponame_str	Repositório Institucional da FIOCRUZ (ARCA)
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bitstream.url.fl_str_mv	https://www.arca.fiocruz.br/bitstream/icict/56337/1/license.txt https://www.arca.fiocruz.br/bitstream/icict/56337/2/Molecular%20characterization%20of%20a%20new%20SARS-CoV-2%20.pdf
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repository.name.fl_str_mv	Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv	repositorio.arca@fiocruz.br
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Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil.

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