Genomic and clinical epidemiology of SARS-CoV-2 in Lebanon: a prospective multicenter study 2020–2024

BACKGROUND: Globally, the trajectory of COVID-19 has been shaped by viral evolution, widespread vaccination and immunity from prior infections. We assessed the epidemiological and clinical patterns of COVID-19 in Lebanon between 2020 and 2024, identified the predominant SARS-CoV-2 clades and evaluated risk factors for COVID-19 associated mortality. METHODS: This multicenter prospective study enrolled 1302 patients hospitalized with COVID-19 in Lebanon between November 2020 and October 2024. Multivariate logistic regression was used to determine predictors of COVID-19 associated mortality. Whole genome sequencing (WGS) was utilized to investigate the genomic epidemiology of SARS-CoV-2 and infer viral interactions between Lebanon and other countries. Multiple sequence alignment and phylogenetic analysis were conducted using the augur pipeline. RESULTS: A progressive and significant reduction in severe outcomes, including pneumonia and mortality was observed throughout the study period. Pneumonia (AOR, 6.714; CI, 4.140-10.888; p < 0.0001) and age ≥ 60 years (AOR, 6.051; CI, 2.190-16.723; p = 0.001) were identified as independent predictors of COVID-19 mortality. Moreover, receiving 3 doses of a COVID-19 vaccine significantly reduced the odds of mortality (AOR, 0.229; CI, 0.108-0.486; p < 0.0001). Genomic analysis revealed multiple introductions of the same SARS-CoV-2 clades into Lebanon, which seeded local transmission chains. CONCLUSIONS: The transition of COVID-19 from pandemic to endemic in Lebanon was associated with reduced disease severity. Vaccination remains essential, particularly in older adult patients who are at high risk of mortality. Moreover, early diagnosis and management of pneumonia are crucial, given its association with COVID-19 mortality. Furthermore, WGS has proven valuable in tracking the local evolution of SARS-CoV-2 and its impact on clinical outcomes.