Factors associated with laboratory-confirmed SARS-Cov-2 infection among patients with severe respiratory illness (SRI): Findings from the COVID-19 vaccine effectiveness evaluation in Kenya and Mali, 2022-2023

Background: Understanding the epidemiology of SARS-CoV-2 infection in settings with limited data, especially given the dynamic nature of the virus and the reported epidemiological heterogeneity across countries, is important. We used data from the COVID-19 Vaccine effectiveness evaluation to determine factors associated with SARS-COV-2 infection among patients (≥ 12 years) with severe respiratory illness (SRI) in Kenya and Mali. Methods: SRI was defined as acute onset (≤ 14 days) of at least two of the following: cough, fever, chills, rigors, myalgia, headache, sore throat, fatigue, congestion or runny nose, loss of taste or smell, or pneumonia diagnosis. We collected demographic and clinical characteristics of the patients, and nasopharyngeal and oropharyngeal specimens for SARS-CoV-2 testing using RT-PCR. We used a mixed effect logistic regression to determine factors associated with SARS-CoV-2 infection adjusting for age and sex while controlling for clustering by site and month of illness onset. Results: Between July 2022 and October 2023, a total of 9941 patients with SRI were enrolled, of whom, 588 (5.9 %) tested positive for SARS-CoV-2. Compared to patients aged 12-24 years, those who were aged >64 years were more likely to have SARS-CoV-2 infection (adjusted Odds Ratio [aOR] = 1.60; 95 % Confidence Interval [95 % CI] 1.07-2.40). Additionally, SRI patients presenting with cough (aOR = 1.37; 95 % Confidence Interval [95 % CI] 1.05-1.80), sore throat (aOR = 1.56; 95 % CI 1.23-1.99), runny nose (aOR = 1.51; 95 % CI 1.18-1.94), and ear pain discharge (aOR = 2.58; 95 % CI 1.43-4.66) were more likely to have SARS-CoV-2 infection compared to those who did not. SRI patients who had HIV were also more likely to have SAR-CoV-2 infection compared to those who did not (aOR =1.32; 95 % CI 1.04-1.67). Conclusion: Older adults and HIV patients were at increased-risk of SARS-CoV-2 infection consistent with WHO guidelines highlighting the need for targeted prevention and management strategies focused on them.