Duration of viable virus shedding in SARS-CoV-2 omicron variant infection

Abstract

Clinical features of SARS-CoV-2 Omicron variant infection, including incubation period and transmission rates, distinguish this variant from preceding variants. However, whether the duration of shedding of viable virus differs between omicron and previous variants is not well understood. To characterize how variant and vaccination status impact shedding of viable virus, we serially sampled symptomatic outpatients newly diagnosed with COVID-19. Anterior nasal swabs were tested for viral load, sequencing, and viral culture. Time to PCR conversion was similar between individuals infected with the Delta and the Omicron variant. Time to culture conversion was also similar, with a median time to culture conversion of 6 days (interquartile range 4-8 days) in both groups. There were also no differences in time to PCR or culture conversion by vaccination status.

Figure 1.

Virologic decay from time of first positive PCR or symptom onset. Observations indicate viral loads from nasal swabs from individual patient samples. Fit indicates the median viral load at each time point by variant. Shaded areas represent 95% confidence intervals. 1B-1E. Kaplan-Meier survival curves demonstrating time to negative PCR by viral variant (B) and vaccination status (D) and time to negative viral culture by viral variant (C) and vaccination status (E). Shaded areas indicate 95% confidence intervals from the survival curves. P-values represent log-rank testing comparing the sub-groups on each plot.

Figure 2.

Antigen testing on samples in viral transport media simultaneously cultured. Samples (11 participants with delta infection and 11 participants with omicron infection) subjected to whole genome sequencing, viral load testing, and viral culture were simultaneously tested for antigen using the BinaxNow kit. (A) Viral load per swab for samples tested by laboratory-based antigen test results for delta and omicron infections. (B) Proportion of samples, delta and omicron infections combined, that were antigen test positive, culture positive and PCR positive (Ag+ Cx+), antigen test negative culture positive and PCR positive (Ag− Cx+), antigen test positive, culture negative and PCR positive (Ag+ Cx−), antigen test negative, culture negative and PCR positive (Ag− Cx− PCR+) or antigen negative, culture negative and PCR negative organized by days from first positive PCR or symptoms onset (0–5 or 6–10 days).