Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2022 |
| Outros Autores: | , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/56915 |
Resumo: | Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil. |
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Sgorlon, GabriellaQueiroz, Jackson Alves da SilvaRoca, Tárcio PeixotoSilva, Ana Maisa Passos daGasparelo, Nadson Willian FelipeTeixeira, Karolaine SantosOliveira, Andreia Souza da NóbregaMendonça, Aline Linhares Ferreira de MeloMaia, Adriana Cristina SalvadorPereira, Soraya dos SantosBatista, Flávia SerranoSalcedo, Juan Miguel VillalobosRampazzo, Rita de Cassia PontelloResende, Paola CristinaSiqueira, Marilda MendonçaNaveca, Felipe GomesVieira, Deusilene2023-02-07T13:54:43Z2023-02-07T13:54:43Z2022SGORLON, Gabriella et al. Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220155, p. 1-9, 2022.0074-0206https://www.arca.fiocruz.br/handle/icict/5691510.1590/0074-02760220155engFundação Oswaldo Cruz. Instituto Oswaldo Cruz.SARS CoV-2Variante de preocupaçãoVariante gamaDeltaVigilância genômicaCOVID-19SARS CoV-2Variant of concernGamma variantDeltaGenomic surveillanceCOVID-19Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazoninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Hepatites Virais, Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil.Laboratório Central de Saúde Pública do Estado de Rondônia. Porto Velho, RO, Brasil.Laboratório Central de Saúde Pública do Estado de Rondônia. Porto Velho, RO, Brasil.Laboratório Central de Saúde Pública do Estado de Rondônia. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Agência Estadual de Vigilância em Saúde de Rondônia, Coordenação Estadual da Covid-19. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e do Sarampo. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e do Sarampo. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Virologia. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil.BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.info: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/56915/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALGabrielaSgorlan_PaolResende_etal_IOC_2022.pdfGabrielaSgorlan_PaolResende_etal_IOC_2022.pdfapplication/pdf1264500https://www.arca.fiocruz.br/bitstream/icict/56915/2/GabrielaSgorlan_PaolResende_etal_IOC_2022.pdf2c59e9405efd4b770c78fb9d9a3e2e1dMD52icict/569152023-09-04 11:17:47.373oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-04T14:17:47Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.en_US.fl_str_mv |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| title |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| spellingShingle |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon Sgorlon, Gabriella SARS CoV-2 Variante de preocupação Variante gama Delta Vigilância genômica COVID-19 SARS CoV-2 Variant of concern Gamma variant Delta Genomic surveillance COVID-19 |
| title_short |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| title_full |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| title_fullStr |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| title_full_unstemmed |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| title_sort |
Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon |
| author |
Sgorlon, Gabriella |
| author_facet |
Sgorlon, Gabriella Queiroz, Jackson Alves da Silva Roca, Tárcio Peixoto Silva, Ana Maisa Passos da Gasparelo, Nadson Willian Felipe Teixeira, Karolaine Santos Oliveira, Andreia Souza da Nóbrega Mendonça, Aline Linhares Ferreira de Melo Maia, Adriana Cristina Salvador Pereira, Soraya dos Santos Batista, Flávia Serrano Salcedo, Juan Miguel Villalobos Rampazzo, Rita de Cassia Pontello Resende, Paola Cristina Siqueira, Marilda Mendonça Naveca, Felipe Gomes Vieira, Deusilene |
| author_role |
author |
| author2 |
Queiroz, Jackson Alves da Silva Roca, Tárcio Peixoto Silva, Ana Maisa Passos da Gasparelo, Nadson Willian Felipe Teixeira, Karolaine Santos Oliveira, Andreia Souza da Nóbrega Mendonça, Aline Linhares Ferreira de Melo Maia, Adriana Cristina Salvador Pereira, Soraya dos Santos Batista, Flávia Serrano Salcedo, Juan Miguel Villalobos Rampazzo, Rita de Cassia Pontello Resende, Paola Cristina Siqueira, Marilda Mendonça Naveca, Felipe Gomes Vieira, Deusilene |
| author2_role |
author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Sgorlon, Gabriella Queiroz, Jackson Alves da Silva Roca, Tárcio Peixoto Silva, Ana Maisa Passos da Gasparelo, Nadson Willian Felipe Teixeira, Karolaine Santos Oliveira, Andreia Souza da Nóbrega Mendonça, Aline Linhares Ferreira de Melo Maia, Adriana Cristina Salvador Pereira, Soraya dos Santos Batista, Flávia Serrano Salcedo, Juan Miguel Villalobos Rampazzo, Rita de Cassia Pontello Resende, Paola Cristina Siqueira, Marilda Mendonça Naveca, Felipe Gomes Vieira, Deusilene |
| dc.subject.other.en_US.fl_str_mv |
SARS CoV-2 Variante de preocupação Variante gama Delta Vigilância genômica |
| topic |
SARS CoV-2 Variante de preocupação Variante gama Delta Vigilância genômica COVID-19 SARS CoV-2 Variant of concern Gamma variant Delta Genomic surveillance COVID-19 |
| dc.subject.other.none.fl_str_mv |
COVID-19 |
| dc.subject.en.en_US.fl_str_mv |
SARS CoV-2 Variant of concern Gamma variant Delta Genomic surveillance |
| dc.subject.en.none.fl_str_mv |
COVID-19 |
| description |
Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Virologia Molecular, Porto Velho, RO, Brasil / Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil. |
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2022 |
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2022 |
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2023-02-07T13:54:43Z |
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2023-02-07T13:54:43Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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| dc.identifier.citation.fl_str_mv |
SGORLON, Gabriella et al. Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220155, p. 1-9, 2022. |
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https://www.arca.fiocruz.br/handle/icict/56915 |
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0074-0206 |
| dc.identifier.doi.none.fl_str_mv |
10.1590/0074-02760220155 |
| identifier_str_mv |
SGORLON, Gabriella et al. Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220155, p. 1-9, 2022. 0074-0206 10.1590/0074-02760220155 |
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https://www.arca.fiocruz.br/handle/icict/56915 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. |
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Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. |
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reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ |
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