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

Abstract

Quantitative information on epidemiological quantities such as the incubation period and generation time of SARS-CoV-2 variants is scarce. We analyzed 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 PCR 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.

Intrinsic Generation Time of the SARS-CoV-2 Omicron Variant: An Observational Study of Household Transmission

“…Our estimate of the mean generation time (mean: 6.8 days) is compatible with previous estimates for ancestral lineages 18 (including a previous estimate for Italy of 6.7 days 19 ). Existing estimates for Alpha and Delta were in the same range in a study similar to the present one on the same study population in Italy (6.0 and 6.6 days respectively 15 ). We also found a mean household serial interval of 2.38 days, shorter than previous estimates for Delta of 2.56 on a similar study population.…”

“…We also found a mean household serial interval of 2.38 days, shorter than previous estimates for Delta of 2.56 on a similar study population. 15 Available studies have suggested a shorter generation time of Omicron (between 50% and 80% the one of Delta) using population-level data on the growth rate of Omicron relative to Delta in Denmark 20 and United Kingdom. 21 An analysis of 43 infectorinfectee pairs from contact tracing data in Hong Kong 22 estimated a mean realized generation time of 2.38 days (95% confidence interval 2.01−2.80) under very strict control measures (population-wide screenings and quarantine imposed to both contacts and contacts of contacts) that are known to reduce the realized generation time.…”

“…We extended a Bayesian inference model for the reconstruction of transmission links in households. 14,15 The model exploits the temporal information on SARS-CoV-2 infections recorded in the dataset to probabilistically identify, for every infection, the likely source of infection (from outside the household or from a specific household member). Parameters for the generation time, which we assume to be gamma-distributed, are simultaneously calibrated via a Markov Chain Monte Carlo approach where the likelihood of the observed data is defined mechanistically through the computation of the force of infection to which all individuals are subject over time.…”

“…To test the robustness of our results, we conducted an extensive set of sensitivity analyses where we considered: a) the subset of 380 households (1,127 cases in total) for which a case was genotyped as Omicron; b) the subset of 1,148 households (2,770 cases in total) for which all individuals were unvaccinated; c) the estimated incubation period of the Delta variant (mean: 4.5 days; standard deviation: 2.1 days) 15 to reassign the imputed infectious dates (baseline: Omicron variant with mean 3.5 days and standard deviation: 1.2 days); d) a diagnostic delay for asymptomatic cases that was 50% longer than that for symptomatic cases, implemented by increasing the shape of the gamma distribution by 50% (mean: 7.58 days; standard deviation: 1.61 days); e) similar to d), but implemented by changing the scale of the gamma distribution by 50% (mean: 7.58 days; standard deviation: 1.97 days); f) the possibility of false negatives for negative test results when imputing infection dates; g) a halved transmissibility for asymptomatic individuals (baseline: equal to symptomatic individuals); h) a halved transmissibility for vaccinated individuals (baseline: equal to unvaccinated individuals); i) a scenario in which any effort to quarantine positive cases would not impact the force of infection from outside the household, which corresponds to the extreme case where there is 0% compliance to the policy (baseline: 100% compliance); j) that previous infection from other variants provides no cross-protection against Omicron (baseline: 56% cross-protection 16 ).…”

Transmission Dynamics and Epidemiological Characteristics of the SARS-CoV-2 Delta Variant ― Hunan Province, China, 2021

“…To date, only a few studies have provided estimates of the incubation period, serial interval, and generation time of Delta variant infection. These studies suggest that the mean (or median) incubation period of Delta ranges from 3.0 to 6.0 days (3-4), which contains the mean estimate obtained in our study (5.3 days); also, our estimate of the serial interval (4.3 days) falls inside the range reported in previous studies (range 2.6-5.4 days) (5)(6). Regarding the generation time, we found only two studies providing estimates for Delta variant; the first one was conducted in the UK and found a mean value of 4.7 days (7), while the second one was † Contacts who were aged at or over 65 years or whose infectors were aged at or over 65 years were excluded from this analysis due to the small sample size.…”