Dinâmica de variantes de Sars-Cov-2 no Brasil e seu impacto nas taxas de transmissão e severidade da Covid-19

Abstract

The COVID-19 pandemic has had immeasurable impacts on health and the socioeconomic system worldwide. The identification and characterization of variants of concern (VOCs) and variants of interest (VOIs) of SARS-CoV-2 are fundamental to understanding the dynamics of the virus and its implication in transmission rates and severity of COVID-19 cases. In this sense, the COVID-19 Genomic Surveillance Observatory (OviGen-BR) was designed in collaboration with the Laboratory of Integrative Biology of the Federal University of Minas Gerais (LBI-UFMG), Pardini Group, Ezequiel Dias Foundation (FUNED), Secretary of State for Health of Minas Gerais (SES-MG), City Hall of Belo Horizonte (PBH), Ministry of Science and Technology and, Corona-Ômica Network MCTI (Virus Network-MCTI) on a national basis to monitor the dynamics of SARS-CoV-2 variants, mainly in times of changes in the epidemiological scenario with an increase in the average number of COVID-19 cases in the country. Thus, in this dissertation, we performed genomic and epidemiological surveillance of SARS-CoV-2 in two different scenarios of increasing cases of COVID-19. The first stage was carried out with 7,549 samples investigated for the COVID-19 molecular diagnosis (RT-qPCR) from 15 Brazilian capitals (Belém, Belo Horizonte, Boa Vista, Brasília, Campo Grande, Fortaleza, Goiânia, Macapá, Manaus, Palmas, Porto Alegre, Porto Velho, Rio de Janeiro, Salvador, and São Paulo) from April to October 2021, corresponding to the second wave of COVID-19. The second stage, a continuation of the project, was carried out with 291,571 samples investigated for the COVID-19 molecular diagnosis from 12 Brazilian capitals (Belém, Belo Horizonte, Boa Vista, Brasília, Fortaleza, Goiânia, Macapá, Manaus, Palmas, Porto Velho, Rio de Janeiro, and São Paulo) from August 2021 to March 2022, corresponding to the third wave of COVID-19. The samples were genotyped to identify the defining mutations of circulating SARS-CoV-2 variants, in addition to whole genome sequencing. To assess the transmissibility potential of circulating VOCs, the cycle threshold (Ct) values, which correlate inversely proportionally to the viral load, were evaluated in the period of dominance of each variant. The results obtained demonstrate that the Delta VOC was detected for the first time in June/2021 and it took sixteen weeks to replace the Gamma with the introduction from the Southeast region of the country. With the emergence of Omicron VOC, the Delta VOC was replaced in just three weeks, showing its transmission power corresponding to the biggest peak of COVID-19 since the beginning of the pandemic in Brazil. In addition, Delta VOC demonstrated a higher transmission rate compared to Gamma VOC, however, lower than the transmission rates of Omicron VOC. Although VOC Omicron had higher rates concerning the number of cases, it was not associated with increased hospitalization and severity of COVID-19, showing the importance of vaccination programs in preventing severe cases of COVID-19. This work reinforces the importance of surveillance programs at the national level.