STROBE checklist.

<div> In the context of the COVID-19 pandemic, Benin, like other regions in sub-Saharan Africa and around the world, has been grappling with a public health crisis since march 2020. The country responded to this crisis by implementing adaptive response measures. The STREESCO project is part of this dynamic effort, strengthening epidemiological surveillance at three sentinel sites. This study thoroughly examines the determinants of SARS-CoV-2 infection. This involved strategic support based in Cotonou, Allada, and Natitingou. Data collection took place from march 1 to november 30, with individuals voluntarily undergoing COVID-19 screening at dedicated health units. Before participation, free and informed consent was obtained. The collected data included sociodemographic information, clinical details, and the results of COVID-19 tests. A multivariate logistic regression model was used to identify factors associated with SARS-CoV-2 infection. Surveillance included 4178 participants, with a male/female ratio of 0.98 and a median age of 33 (IQR: 25-45). Across all sites, 13.12% of participants tested positive for SARS-CoV-2, and 85.40% of them had a SARS-CoV-2 infection.of participants were symptomatic at baseline. The proportion of positivity was 6%, 11% and 28% respectively during phases 1, 2 and 3 of the national strategy. Identified risk factors included the Allada site (aOR 2.04, 95%CI 1.59-2.62), phase 3 (aOR 3.16, 95%CI 2.34-4.27), phase 2 (aOR 1.67, 95%CI 1.12-2.51), secondary (aOR 1.67, 95%CI 1.12-2.51) and higher level of education (aOR 1.83, 95%CI 1.22-2.74), respiratory symptoms (aOR 1.88, 95%CI 1.40-2.53), and/or anosmia/ageusia (aOR 1.88, 95%CI 1.48-2.38). Conversely, the Natitingou site (aOR = 0.29, 95%CI: 0.20-0.42), group living (aOR = 0.75, 95%CI: 0.60-0.94), and digestive symptoms (aOR = 0.70, 95%CI: 0.54-0.91) were associated with a reduced risk of infection. These results underscore the importance of active surveillance during crisis situations, ensuring the acquisition of reliable and persuasive data to enhance individual care and guide health policies. Trial registration NCT06170320 (retrospectively registered on December 21, 2023). </div>