Clinical SARS-CoV-2 Kinetic Profiles Are Dependent on the Viral Strain and Host Vaccination Status

The SARS-CoV-2 infection kinetics in a real-world, clinical setting represent a knowledge gap in understanding the underlying COVID-19 pathogenesis. There are scant reports on the dynamics describing the two principal components of the viral life cycle, namely the rapid proliferation and slower clearance phases. Here, we present results from an ongoing workplace clinical surveillance study where two vaccinated participants became infected with SARS-CoV-2 Omicron variant (BA.1. lineage). The subjects were followed longitudinally at high temporal resolution allowing the kinetics of both viral phases to be characterized. The viral doubling times in the proliferation phase (3.3-3.5 h) and maximum measured viral loads were similar to those observed for unvaccinated individuals infected with an earlier SARS-CoV-2 strain. However, the clearance phase was much shorter in the current study and unexpectedly displayed a multimodal profile. Longitudinal whole genome SARS-CoV-2 sequencing identified a stable mutation that arose in one of the participants over the 2-week period of positivity. Our small study provides a rare insight into the clinical SARS-CoV-2 dynamics holding significance to public health measures and the biology underlying COVID-19.