Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil.
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Dantas Anna Carolina S, Oliveira Hellen B M, Gomes Camila P, Alves Daniele L, Infante Priscilla D B, Caitité Rosimara de J A, Fritsch Hegger M, Cucco Marina S, Silva Lucas S C, Oliveira Caline N T, Bittencourt Rafaela de S, Amorim Aline T, Nascimento Ana Luisa P, Marinho Francely A G C, de Medeiros Danielle S, de Oliveira Márcio G G, Mistro Sostenes, de Melo Fabricio F, Pereira Taiana T S, Guimarães Ana M S, Timenetsky Jorge, Moreira Pablo Maciel B, de Oliveira Sandra Helena P, Alcantara Luiz C J, Giovanetti Marta, Santos Luciane A, Fonseca Vagner, Barreto Fernanda K, Campos Guilherme B, Marques Lucas M
Аннотация
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study's findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions.