Respiratory Viral Co‐Infections in SARS‐CoV‐2 Positive Patients in Burkina Faso: A Cross‐Sectional Study

Abstract

ABSTRACT Background The burden of viral co‐infections among COVID‐19 patients is underexplored in low‐resource settings such as Burkina Faso. This study aimed to determine the prevalence and associated factors of respiratory viral co‐infections among laboratory‐confirmed COVID‐19 patients. Methods A cross‐sectional study was conducted from January 1 to December 31, 2023, across 13 sentinel sites in Burkina Faso. Patients presenting with influenza‐like illness or severe acute respiratory infection had nasopharyngeal and/or oropharyngeal swabs collected and tested for SARS‐CoV‐2 and other respiratory viruses using multiplex real‐time RT‐PCR. Descriptive statistics, univariate, and multivariate logistic regression analyses were performed to identify predictors of viral co‐infections. Results Among 201 SARS‐CoV‐2‐positive patients enrolled (median age: 1 year; interquartile range: 0.5–7). Co‐infections was identified in 48.8% (95% CI: 41.8–55.6) of cases and a single co‐infections was detected in 33.8% (95% CI: 27.5–40.6) of patients. Human rhinovirus (17.9%), adenovirus (14.4%), respiratory syncytial virus (11.4%), and influenza A/B (9.9%) were most frequently detected. In multivariate analysis, children aged 6 months to 14 years had higher odds of co‐infection (aOR 2.7; 95% CI: 1.2–5.9; p = 0.013). Fever (aOR 2.6; 95% CI: 1.3–5.5; p = 0.008) and hospitalization (aOR 4.3; 95% CI: 1.6–12.0; p = 0.005) were also independently associated with co‐infection. Conclusion Viral co‐infections were frequent among SARS‐CoV‐2 positive patients, particularly in children and hospitalized individuals. Strengthening multiplex diagnostic capacity and integrated respiratory virus surveillance in resource‐limited settings may improve clinical management and inform public health response strategies.