MONITORAMENTO EPIDEMIOLÓGICO E GENÔMICO DA COVID-19 EM INDIVÍDUOS ENCARCERADOS NO SISTEMA PRISIONAL DO ESTADO DE MATO GROSSO DO SUL, BRASIL

Abstract

With the advent of the COVID-19 pandemic, the context of Prison Units (UP) became the subject of investigation as they house a group particularly susceptible to COVID-19, incarcerated individuals. Brazil has the third largest prison population in the world, with overcrowded, poorly ventilated cells and frequent transfers, which aggravates the risk of transmission of infectious agents, with the state of Mato Grosso do Sul having the third highest incarceration rate. The objective of the study was to analyze the epidemiological and genomic characteristics and dissemination dynamics of SARS-CoV-2 to understand the mechanisms of transmission and evolution of the virus among incarcerated individuals. This is an epidemiological, cross-sectional study, carried out in two closed male prisons in Campo Grande – MS, namely: Gameleira I and II Closed Male Penitentiaries (PEMRFG I; PEMRFG II). The study involved 1,927 people deprived of their liberty – PPL (83.93% of the total prison population) in the two facilities, between May and October 2022, using nasopharyngeal swabs, RT-qPCR tests to detect SARS-CoV-2, and the genomic sequencing. As containment measures, we include isolation and a contact tracing strategy to monitor exposure within cells. Of the 2,108 samples, 66 positive molecular diagnoses were identified (3.13%), predominantly among asymptomatic individuals (77.27%). Regarding age distribution, the median age was 29 years old, ranging from 18 years old to 47 years old, vaccination status varied from not vaccinated to the third dose. Genomic analysis was performed using next generation sequencing, Oxford Nanopore, which identified the Ômicron variant (BA.2 and BA.5 lineage) with an average coverage of 99%. The phylogenetic tree was also carried out by Genome Detective in which monophyletic clades were identified, which provides robust evidence of linear and traceable transmission of the virus, emphasizing the presence of specific transmission chains within the prison environment studied. The study highlights the need for comprehensive control strategies in UP, including tracking, isolation protocols and vaccination.