Duration and determinants of SARS-CoV-2 RNA positivity in hospitalized patients in Guinea: a prospective cohort study

Abstract Background This study aimed to determine the duration of SARS-CoV-2 RNA positivity and identify factors associated with delayed RNA clearance among hospitalized COVID-19 patients in Conakry, Guinea. Methods We conducted a prospective cohort study of patients with RT-qPCR-confirmed SARS-CoV-2 infection hospitalized in Conakry between January 2021 and January 2022. Patients were followed longitudinally until documented RNA clearance or censoring due to early outcome or loss to follow-up. Whole-genome sequencing was performed on eligible positive samples using the COVID-19Seq protocol, followed by mutation analysis with Nextclade. Factors associated with RNA clearance were assessed using multivariable generalized Gamma parametric survival regression within an accelerated failure time framework, with time ratios (Exp[β]) and two-sided P values < 0.05. Results Among 330 patients (median age, 39 years; IQR, 27–58; 56.7% male), 311 (94.2%) were followed to complete RNA clearance, whereas 19 (5.8%), primarily older ICU patients, had incomplete follow-up. Clinical presentations were mild (33.3%), moderate (30.6%), or asymptomatic (28.2%). Median RNA positivity duration was 9.0 days (IQR, 8.0–12.0; range, 3–91). Older age (≥ 60 years; Exp[β] = 1.16, P = 0.003), unemployment/farming/manual labor (Exp[β] = 1.14, P = 0.012), and ICU admission (Exp[β] = 1.32, P = 0.007) were independently associated with prolonged RNA positivity. Mild disease was associated with faster clearance than asymptomatic infection (Exp[β] = 0.83, P = 0.001). Among 14 sequenced samples, Omicron (35.7%), Alpha (28.6%), Eta (7.1%), and other lineages were identified. Conclusion Older age, occupational characteristics, and ICU admission were associated with prolonged SARS-CoV-2 RNA positivity, whereas mild disease was associated with faster RNA clearance. These findings support risk-stratified monitoring of hospitalized COVID-19 patients in resource-limited settings.