Personal characteristics and transmission dynamics associated with SARS-CoV-2 semi-quantitative PCR test results: an observational study from Belgium, 2021-2022

Introduction: Following harmonization efforts by the Belgian National Reference Center for SARS-CoV-2, semi-quantitative PCR test (SQ-PCR) results, used as a proxy for viral load, were routinely collected after performing RT-qPCR tests.

Methods: We investigated both the personal characteristics associated with SQ-PCR results and the transmission dynamics involving these results. We used person-level laboratory test data and contact tracing data collected in Belgium from March 2021 to February 2022. Personal characteristics (age, sex, vaccination, and laboratory-confirmed prior infection) and disease stage by date of symptom onset were analyzed in relation to SQ-PCR results using logistic regression. Vaccine effectiveness (VE) against a high viral load (≥10⁷ copies/mL) was estimated from the adjusted probabilities. Contact tracing involves the mandatory testing of high-risk exposure contacts (HREC) after contact with an index case. Odds ratios for test positivity and high viral load in HREC were calculated based on the SQ-PCR result of the index case using logistic regression models adjusted for age, sex, immunity status (vaccination, laboratory-confirmed prior infection), variant (Alpha, Delta, Omicron), calendar time, and contact tracing covariates.

Results: We included 909,157 SQ-PCR results of COVID-19 cases, 379,640 PCR results from index cases, and 72,052 SQ-PCR results of HREC. High viral load was observed more frequently among recent cases, symptomatic cases, cases over 25 years of age, and those not recently vaccinated (>90 days). The vaccine effectiveness (VE) of the primary schedule in the first 30 days after vaccination was estimated at 47.3% (95%CI 40.8-53.2) during the Delta variant period. A high viral load in index cases was associated with an increased test positivity in HREC (OR 2.7, 95%CI 2.62-2.79) and, among those testing positive, an increased likelihood of a high viral load (OR 2.84, 95%CI 2.53-3.19).