Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore

The evolution and spread of SARS-CoV-2 variants have driven successive waves of global COVID-19 outbreaks, yet the longitudinal dynamics of intrahost variation within the same patient remain less clear. We conducted a longitudinal cohort study by deep sequencing 198 swab samples collected from COVID-19 patients with varying infection durations. Our analysis showed that prolonged infections enhanced viral genomic diversity, leading to emergence of co-occurring variants that maintained high (>20%) frequency and became dominant in virus populations. We observed heterogeneous intrahost dynamics among individual patients, 2 of whom exhibited a minor variant of the spike D614G substitution over the course of infection. The increase in intrahost variants strongly correlated with prolonged infections, highlighting the complex interplay between viral diversity and host factors. This study revealed the intricate evolutionary mechanisms driving the emergence of de novo variants and lineage dominance, which could inform development of effective vaccine candidates and strategies to protect public health.