Gabriella Sgorlon, Jackson Alves da Silva Queiroz, Tárcio Peixoto Roca, Ana Maisa Passos da Silva, Nadson Willian Felipe Gasparelo, Karolaine Santos Teixeira, Andreia Souza da Nóbrega Oliveira, Aline Linhares Ferreira de Melo Mendonça, Adriana Cristina Salvador Maia, Soraya Dos Santos Pereira, Flávia Serrano Batista, Juan Miguel Villalobos Salcedo, Rita de Cassia Pontello Rampazzo, Paola Cristina Resende, Marilda Mendonça Siqueira, Felipe Gomes Naveca, Deusilene Vieira
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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.</p><p><strong>Findings: </strong>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.</p><p><strong>Main conclusions: </strong>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.</p>","PeriodicalId":18469,"journal":{"name":"Memorias do Instituto Oswaldo Cruz","volume":"117 ","pages":"e220155"},"PeriodicalIF":2.5000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9870256/pdf/","citationCount":"4","resultStr":"{\"title\":\"Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon.\",\"authors\":\"Gabriella Sgorlon, Jackson Alves da Silva Queiroz, Tárcio Peixoto Roca, Ana Maisa Passos da Silva, Nadson Willian Felipe Gasparelo, Karolaine Santos Teixeira, Andreia Souza da Nóbrega Oliveira, Aline Linhares Ferreira de Melo Mendonça, Adriana Cristina Salvador Maia, Soraya Dos Santos Pereira, Flávia Serrano Batista, Juan Miguel Villalobos Salcedo, Rita de Cassia Pontello Rampazzo, Paola Cristina Resende, Marilda Mendonça Siqueira, Felipe Gomes Naveca, Deusilene Vieira\",\"doi\":\"10.1590/0074-02760220155\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>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.</p><p><strong>Objectives: </strong>Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon.</p><p><strong>Methods: </strong>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.</p><p><strong>Findings: </strong>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.</p><p><strong>Main conclusions: </strong>This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. 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Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon.
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.
期刊介绍：
Memórias do Instituto Oswaldo Cruz is a journal specialized in microbes & their vectors causing human infections. This means that we accept manuscripts covering multidisciplinary approaches and findings in the basic aspects of infectious diseases, e.g. basic in research in prokariotes, eukaryotes, and/or virus. Articles must clearly show what is the main question to be answered, the hypothesis raised, and the contribution given by the study.
Priority is given to manuscripts reporting novel mechanisms and general findings concerning the biology of human infectious prokariotes, eukariotes or virus. Papers reporting innovative methods for diagnostics or that advance the basic research with these infectious agents are also welcome.
It is important to mention what we do not publish: veterinary infectious agents research, taxonomic analysis and re-description of species, epidemiological studies or surveys or case reports and data re-analysis. Manuscripts that fall in these cases or that are considered of low priority by the journal editorial board, will be returned to the author(s) for submission to another journal.
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