Dinâmica epidemiológica, genômica e espacial do SARS-CoV-2 no estado da Paraíba de 2020 a 2024

Abstract

The COVID-19 pandemic represented one of the greatest public health challenges of the 21st century, highlighting the importance of epidemiological and genomic surveillance for monitoring SARS-CoV-2 transmission dynamics and evolution. This study aimed to analyze, in an integrated manner, the epidemiological and molecular dynamics of COVID-19 in Paraíba State, Brazil, from March 2020 to December 2024. This was an observational, ecological study with a mixed design (retrospective and prospective) and a quantitative approach, based on the analysis of secondary epidemiological and genomic surveillance data, as well as the generation of primary SARS-CoV-2 genomic data. Data on cases and deaths were obtained from the SIVEP-Gripe and e-SUS Notifica systems, and genomic data were retrieved from the GISAID platform. During the study period, 727,242 confirmed COVID-19 cases and 10,690 deaths were recorded in Paraíba State. Of all confirmed cases, 591,470 (81.33%) were classified based on laboratory criteria. Among 444,069 real-time RT-PCR tests included in the study, 140,460 were positive, corresponding to a positivity rate of 31.63%. Annual cumulative incidence was 4,752.58 per 100,000 inhabitants in 2020, peaked at 6,808.34 per 100,000 in 2021, declined to 5,878.46 per 100,000 in 2022, and dropped sharply in 2023 (327.84 per 100,000) and 2024 (169.71 per 100,000). Genomic surveillance comprised 4,114 genomes from 174 municipalities (78.03% of the state), of which 96.89% achieved genome coverage above 95%. Successive replacement of B.1-related lineages by the Gamma, Delta, and later Omicron variants and their sublineages was observed. Gamma predominance coincided with the period of greatest epidemiological impact, whereas Omicron introduction, particularly BA.1, was associated with a marked increase in cases without a proportional rise in deaths. Higher lethality was observed among males, who had 41% greater odds of death than females (OR = 1.41; 95% CI: 1.33–1.48), and mortality increased markedly with age, reaching OR = 66.48 (95% CI: 56.76–77.90) among individuals aged 80 years or older. Despite broad territorial coverage and high-quality genomes, the interval between sample collection and sequence submission to GISAID was prolonged, with a mean of 113.49 days and a median of 66 days (IQR: 41–148), limiting its usefulness for timely public health action. In conclusion, the integration of epidemiological and genomic surveillance was essential to understanding COVID-19 dynamics in Paraíba State, highlighting the role of viral variants, population immunity, and operational capacity in shaping the pandemic impact. These findings reinforce the need to strengthen genomic surveillance as a strategic component of preparedness for future public health emergencies.