Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data

Abstract

Abstract Quantitative information on epidemiological quantities such as the incubation period and generation time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is scarce. We analysed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of the incubation period for the Alpha and Delta variants using information on negative polymerase chain reaction tests and the date of last exposure from 282 symptomatic cases. We estimated the distributions of the intrinsic generation time using a Bayesian inference approach applied to 9724 SARS-CoV-2 cases clustered in 3545 households where at least one secondary case was recorded. We estimated a mean incubation period of 4.9 days (95% credible intervals, CrI, 4.4–5.4) for Alpha and 4.5 days (95% CrI 4.0–5.0) for Delta. The intrinsic generation time was estimated to have a mean of 7.12 days (95% CrI 6.27–8.44) for Alpha and of 6.52 days (95% CrI 5.54–8.43) for Delta. The household serial interval was 2.43 days (95% CrI 2.29–2.58) for Alpha and 2.74 days (95% CrI 2.62–2.88) for Delta, and the estimated proportion of pre-symptomatic transmission was 48–51% for both variants. These results indicate limited differences in the incubation period and intrinsic generation time of SARS-CoV-2 variants Alpha and Delta compared to ancestral lineages.