Inferring transmission risk of respiratory viral infection from the viral load kinetics of SARS-CoV-2, England, 2020 to 2021 and influenza A virus, Hong Kong, 2008 to 2012

Background: Infectiousness of respiratory viral infections is quantified as plaque forming units (PFU), requiring resource-intensive viral culture that is not routinely performed. We hypothesised that RNA viral load (VL) decline time (e-folding time) in people might serve as an alternative marker of infectiousness. Aim: This study’s objective was to evaluate the association of RNAVL decline time with RNA and PFUVL area under the curve (AUC) and transmission risk for SARS-CoV-2 and influenza A virus. Methods: In SARS-CoV-2 and influenza A virus community cohorts, viral RNA was quantified by reverse transcription quantitative PCR in serial upper respiratory tract (URT)-samples collected within households after an initial household-member tested positive for one virus. We evaluated correlations between RNAVL decline time and RNA and PFU-VL AUC. Associations between VL decline time and transmission risk in index-contact pairs were assessed. Results: In SARS-CoV-2 cases, we observed positive correlations between RNAVL decline time and RNA and PFUVL AUC with posterior probabilities 1 and 0.96 respectively. In influenza A cases a positive correlation between RNAVL decline time and RNAVL AUC was observed, with posterior probability of 0.87. Index case VL decline times one standard deviation above the cohort-mean showed a relative increase in secondary attack rates of 39% (95%credible interval (CrI):−6.9to95%) for SARS-CoV-2 and 25% (95% CrI:−11to71%) for influenza A virus. Conclusion: We identify VL decline time as a potential marker of infectiousness and transmission risk for SARS-CoV-2 and influenza A virus. Early ascertainment of VL kinetics as part of surveillance of new viruses or variants could inform public health decision making.