Viral dynamics and factors associated with duration of COVID-19 positivity: evidence from the first-three epidemiological waves in Cameroon

Background: Coronavirus 2019 (COVID-19) disease progression evidence and viral clearance time remain limited in tropical settings. Understanding this is crucial for public health control measures at community-level. We evaluated the viral dynamics of SARS-CoV-2 infection and factors associated with positivity duration in COVID-19 cases in Cameroon. Material and Methods: We conducted a retrospective cohort-study of SARS-CoV-2 positive cases from the first to third wave (March 2020-October 2021) in Yaounde-Cameroon. RT-PCR was carried out on the participants using nasopharyngeal swabs after every 7 days. SARS-CoV-2 positivity duration was evaluated from the first to last positive PCR-test before a negative result. Epi-info V.7.0 was used for data analyses with p < 0.05 considered statistically significant. Results: A total of 282 participants were enrolled. The mean age was 41 ± 14 years, with male predominant (62.1%). We had 15.6% symptomatic participants of which 59% had cough. The overall median positivity duration was 15[IQR: 9–23] days with 15[IQR: 13–22] in the first, 17[IQR: 12–26] in the second and 9[IQR: 6–12] in the third wave (p < 0.0001). Positivity duration was significantly higher in males (16 versus 14 days, p = 0.03) those aged [35–45] years (16 days) followed by those ≥ 46 years(15 days); p = 0.008). Positivity duration was not affected by presence or absence of symptoms (p = 0.80). No significant correlation was found with viral load (r = 0.03; p = 0.61). Considering baseline (24.7 ± 7.2Ct) and last viral load (29.3 ± 5.9 Ct), the ΔCt (4.6 ± 1.3) and positivity duration (15 days) revealed a kinetic in viral decay of 0.3 ± 0.087 Ct/day. Conclusions: A median positivity duration of 15 days is in accordance with viral clearance around 2 weeks for optimal confinement at community-level. Men and/or the elderly stand at higher risk of prolonged infection. Given the viral decay (0.3 Ct daily), we suggest personalized confinement periods. The variability of positivity duration according to waves could be function of strains which could be a factor influencing positivity duration.