Análise do perfil epidemiológico e molecular do SARS-CoV-2 em dois municípios do estado da Bahia entre 2020 e 2022.

Abstract

Introduction: Coronavirus Disease 2019 (COVID-19) is a clinically diverse disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), whose spread in Brazil was heterogeneous and reflected deep social and regional inequalities. The emergence of viral variants carrying mutations in the genome, particularly in the Spike protein, has influenced transmissibility, clinical severity, and public health impact. Spatial dispersion analysis of the virus requires consideration of both biological and social factors, such as population density and structural inequalities, and is essential for effective genomic surveillance. In this context, investigating circulating viral lineages and individual responses to infection may contribute to control strategies and support the understanding of disease severity and immune responses in confirmed SARS-CoV-2 cases. Objective: To conduct a molecular epidemiological and spatial dispersion analysis of SARS-CoV-2 and evaluate its association with the immune response profile in patients from the municipalities of Vitória da Conquista and Salvador, Brazil. Methodology: Clinical and epidemiological data from patients in Vitória da Conquista (2020–2021) were obtained from the municipal SoulMV health system, while data from patients in Salvador (2022) were collected through a socio-behavioral questionnaire. Descriptive statistical analyses were conducted using Stata version 15.1. Genomic sequencing of samples from both cities was performed using Oxford Nanopore MinION technology and analyzed through bioinformatics for variant typing. In Vitória da Conquista, the expression of innate immunity inflammatory markers was evaluated using qPCR array. In Salvador, genomic dispersion analyses and 3D Spike protein mutation mapping were performed to compare vaccinated and unvaccinated individuals in terms of mutation distribution and potential structural implications. Results: In Vitória da Conquista (n=783), risk factors associated with COVID-19 mortality included being male (p = 0.037), having cardiovascular disease (p < 0.001), diabetes (p = 0.002), chronic obstructive pulmonary disease (COPD) (p = 0.001), and Ct (cycle threshold) values below 22 (p < 0.001). Stratification by disease severity (asymptomatic, mild, and moderate/severe) revealed increased activation of inflammatory pathways in severe cases, including cytokine storm induction and downregulation of anti-inflammatory responses. Genomic analysis indicated the circulation of multiple lineages, including Alpha and Gamma, suggesting successive viral introduction events. In Salvador (n=174), most participants were female (68.9%), aged up to 39 years (50.6%), without comorbidities (66.5%), and users of public transportation (66.5%). Most exhibited mild symptoms (41.5%) and had received a second booster vaccine dose (40.6%). The most prevalent Omicron subvariants were BA.5 (32.57%), BA.4 (21.71%), B (18.86%), and BQ.1 (26.2%). Viral dispersion was predominantly localized, with only a few rapid-spreading events. Mutation analysis revealed distinct profiles between vaccinated and unvaccinated individuals, particularly in the Spike protein, suggesting differential selective pressures. Conclusion: Variation in the clinical profiles of patients affected by COVID-19, influenced by both individual and contextual factors over the course of the pandemic, underscores the importance of identifying and understanding the introduction of new viral lineages. The findings of this study—by revealing circulating strains and the actual local epidemiological scenario—demonstrate that the integration of epidemiological and genomic surveillance is essential for informing more effective public health strategies and guiding targeted governmental actions to control transmission.