High prevalence of SARS-CoV-2 detected by reverse transcription polymerase chain reaction at the Laboratoire des Grandes Épidémies Tropicales in N’Djamena, Chad

The COVID-19 pandemic, caused by SARS-CoV-2, posed a significant challenge to global public health systems, particularly in resource-limited settings. Accurate molecular diagnosis is critical for effective disease surveillance and control. This study aimed to determine the prevalence and associated factors of SARS-CoV-2 infection among individuals tested at the Laboratoire des Grandes Épidémies Tropicales (LAGET) in N’Djamena, Chad. A retrospective cross-sectional study was conducted from January 2021 to June 2022. Nasopharyngeal swabs were collected from symptomatic and asymptomatic individuals and tested for SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR). Associations between test positivity and demographic/clinical factors were assessed using odds ratios (OR) and chi-square tests. Among 625 participants (mean age 37±14 years; 29.3% female), the overall SARS-CoV-2 positivity rate was 31.5% (197/625). The viral load distribution among positive cases was as follows: 20.3% high (cycle threshold [Ct] <20), 51.3% moderate (Ct 21-30), and 21.3% low (Ct 31-36). Being symptomatic (OR=1.68, 95% confidence interval [CI]: 1.18-2.38, p=0.003) and having a sample collected at an external health facility (OR=0.28, 95% CI: 0.19-0.40, p<0.0001) were significantly associated with a higher likelihood of testing positive. No significant associations were found with age or sex. The high prevalence of SARS-CoV-2 detected at LAGET, far exceeding national figures, indicates substantial community transmission and underreporting in Chad. These findings underscore the critical need for strengthened molecular diagnostic capacity and decentralized testing services. Implementing an integrated One Health surveillance approach is essential for managing the current pandemic and preparing for future epidemic threats.