Vigilância genômica do vírus SARS-CoV-2 durante a terceira onda epidêmica em Minas Gerais

Abstract

The coronavirus disease (COVID-19) emerged on December 8th, 2019, in the city of Wuhan, People's Republic of China, and was first reported to the World Health Organization (WHO) on December 30th of the same year. COVID-19, caused by the novel SARS-CoV-2 virus, is an acute respiratory infectious disease primarily transmitted through the respiratory tract. Since its emergence, the virus has demonstrated a considerable capacity for transmission and infectivity, becoming a global problem in less than three months. Thousands of mutations and alterations that could provide the virus a selective advantage, contributing to further increase transmission and the ability to evade host immune response, appeared rapidly. From this, the need for adopting measures such as genomic surveillance processes became clear to better understand virus dispersion and evolution patterns, especially in states severely affected by the disease, such as Minas Gerais (MG). At the end of 2021, the emergence of the Omicron variant propelled a third wave of infections and deaths in Brazil, with the most significant number of simultaneous cases since the beginning of the pandemic. Therefore, this dissertation aimed to carry out genomic surveillance of SARS-CoV-2 during the third epidemic wave in Minas Gerais. For this, we conducted a population-based study, along with a genomic surveillance process, in 15 Regional Health Units (RHUs)of the state, with the help of the Observatório de Vigilância Genômica do Estado de Minas Gerais network (OviGen). Between October 10th, 2021, and April 2nd, 2022, we received 2561 positive samples for the virus from the selected RHM. The samples were initially genotyped by RT-qPCR, and subsequently, 162 were selected for sequencing on the MiSeq platform (Illumina), aiming to identify and confirm virus sublineages. Of the total samples analyzed, 753 were classified as Delta VOC, 1782 as Omicron VOC, and 26 did not present any result. The Omicron variant was initially identified through genotypic analysis in week 50 of 2021 in the regions of Belo Horizonte, Montes Claros, and Varginha, four weeks after the World Health Organization (WHO) reported the first identification of the variant in the world. In the same week, a transition in the prevalence of variants was observed in the RHU of Minas Gerais. The Delta variant was replaced by Omicron, which reached dominance by the end of 2021. During the third epidemic wave in MG, the first sublineage in the sampling, called BA.2, was identified through phylogenetic analysis about 11 weeks after the identification of BA.1. The results of this study demonstrated the frequency of Omicron subvariants in the RHU of MG during the third epidemic wave and suggested the main dates and locations of variant introduction to the state. Additionally, the relevance of genomic surveillance in the early detection of new variants was highlighted.