Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

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

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. Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. 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. 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. 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.