Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant

ABSTRACT

BackgroundThe combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. MethodsWe characterized 2,875 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of variant, symptom status, age, infection history, vaccination and antibody titer to founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics. The frequency of viral rebounds was quantified under multiple cycle threshold (Ct) value-based definitions. ResultsAmong individuals detected partway through their infection, 51.0% (95% credible interval [CrI] 48.2-53.6%) remained potentially infectious (Ct<30) five days post detection, with small differences across variants and vaccination history. Only seven viral rebounds (0.7%; N=999) were observed, with rebound defined as 3+ days with Ct<30 following an initial clearance of 3+ days with Ct[≥]30. High antibody titers against the founder SARS-CoV-2 strain predicted lower peak viral loads and shorter durations of infection. Among Omicron BA.1 infections, boosted individuals had lower pre-booster antibody titers and longer clearance times than non-boosted individuals. ConclusionsSARS-CoV-2 viral kinetics are partly determined by immunity and variant but dominated by individual-level variation. Since booster vaccination protects against infection, longer clearance times for BA.1-infected, boosted individuals may reflect a less effective immune response, more common in older individuals, that increases infection risk and reduces viral RNA clearance rate. The shifting landscape of viral kinetics underscores the need for continued monitoring to optimize isolation policies and to contextualize the health impacts of therapeutics and vaccines. FundingSupported in part by CDC contract 200-2016-91779, Emergent Ventures at the Mercatus Center, the Huffman Family Donor Advised Fund, the MorrisSinger Fund, the National Basketball Association, and the National Basketball Players Association.