Caracterização genética de SARS-CoV-2 de amostras do Laboratório Central de Saúde Pública do estado do Pará

Abstract

Genetic sequencing plays an important role in the fight against emerging and reemerging epidemics. The analysis of its result allows to quantify and qualify the viral genetic diversity circulating in the country, despite not being a diagnostic method and not recommended for all positive cases. The aim was to detect the main mutation points that occurred between 2021 and June 2023, determining the SARS-CoV-2’s circulating strains in the state of Pará and relating them to epidemiological data. Aiming to obtain the complete genome of SARS-CoV-2 circulating in the State of Pará from 2021 to June 2023, making it possible to identify the circulating virus strains and perform a phylogenetic analysis of the SARS-CoV-2 detected, comparing it with data deposited in GISAID (Global Initiative on Sharing Avian Influenza Data). We sequenced 1,300 samples from the state of Pará from 69 municipalities. Although the highest incidence of cases was concentrated in the 20 to 60 age group and among female patients, the highest incidence of deaths was among patients aged over 60 and among males. The Zeta, Gamma, Delta and Omicron variants were detected in the 2021 samples, the Delta and Omicron variants in the 2022 samples and only the Omicron variant sublines in 2023. Despite Omicron being a variant of concern (VOC), there was a considerable decrease in the number of COVID-19 deaths. The sub-lineage that circulated the most throughout the state were those belonging to the Omicron variant, especially BA.1 and, more recently, XBB.1.5. Tracking the spread and mutations of SARS-CoV2 over time allows for a better understanding of the virus and worldwide sharing in GISAID of the sequences obtained regionally contributes greatly to monitoring the emergence of a variant with a substantially different phenotype that could cause a more severe disease or lead to large epidemic waves that could overwhelm health systems.