Background:Estimating key infectious disease parameters from the coronavirus disease (COVID-19) outbreak is essential for modelling studies and guiding intervention strategies. Aim: We estimate the generation interval, serial interval, proportion of presymptomatic transmission and effective reproduction number of COVID-19. We illustrate that reproduction numbers calculated based on serial interval estimates can be biased. Methods: We used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates, we obtained the serial interval, proportions of pre-symptomatic transmission and reproduction numbers. Results: The mean generation interval was 5.20 days (95% credible interval (CrI): 3.78-6.78) for Singapore and 3.95 days (95% CrI: 3.01-4.91) for Tianjin. The proportion of pre-symptomatic transmission was 48% (95% CrI: 32-67) for Singapore and 62% (95% CrI: 50-76) for Tianjin. Reproduction number estimates based on the generation interval distribution were slightly higher than those based on the serial interval distribution. Sensitivity analyses showed that estimating these quantities from outbreak data requires detailed contact tracing information. Conclusion: High estimates of the proportion of pre-symptomatic transmission imply that case finding and contact tracing need to be supplemented by physical distancing measures in order to control the COVID-19 outbreak. Notably, quarantine and other containment measures were already in place at the time of data collection, which may inflate the proportion of infections from pre-symptomatic individuals.

We collated contact tracing data from COVID-19 clusters in Singapore and Tianjin, China and estimated the extent of pre-symptomatic transmission by estimating incubation periods and serial intervals. The mean incubation periods accounting for intermediate cases were 4.91 days (95%CI 4.35, 5.69) and 7.54 (95%CI 6.76, 8.56) days for Singapore and Tianjin, respectively. The mean serial interval was 4.17 (95%CI 2.44, 5.89) and 4.31 (95%CI 2.91, 5.72) days (Singapore, Tianjin). The serial intervals are shorter than incubation periods, suggesting that pre-symptomatic transmission may occur in a large proportion of transmission events (0.4-0.5 in Singapore and 0.6-0.8 in Tianjin, in our analysis with intermediate cases, and more without intermediates). Given the evidence for pre-symptomatic transmission it is vital that even individuals who appear healthy abide by public health measures to control COVID-19.

Background: As the COVID-19 epidemic is spreading, incoming data allows us to quantify values of key variables that determine the transmission and the effort required to control the epidemic. We determine the incubation period and serial interval distribution for transmission clusters in Singapore and in Tianjin. We infer the basic reproduction number and identify the extent of pre-symptomatic transmission.Methods: We collected outbreak information from Singapore and Tianjin, China, reported from Jan.19-Feb.26 and Jan.21-Feb.27, respectively. We estimated incubation periods and serial intervals in both populations.Results: The mean incubation period was 7.1 (6.13, 8.25) days for Singapore and 9 (7.92, 10.2) days for Tianjin. Both datasets had shorter incubation periods for earlier-occurring cases. The mean serial interval was 4.56 (2.69, 6.42) days for Singapore and 4.22 (3.43, 5.01) for Tianjin. We inferred that early in the outbreaks, infection was transmitted on average 2.55 and 2.89 days before symptom onset (Singapore, Tianjin). The estimated basic reproduction number for Singapore was 1.97 (1.45, 2.48) secondary cases per infective; for Tianjin it was 1.87 (1.65, 2.09) secondary cases per infective.Conclusions: Estimated serial intervals are shorter than incubation periods in both Singapore and Tianjin, suggesting that pre-symptomatic transmission is occurring. Shorter serial intervals lead to lower estimates of R0, which suggest that half of all secondary infections should be prevented to control spread.

Background:Estimating key infectious disease parameters from the COVID-19 outbreak is quintessential for modelling studies and guiding intervention strategies.Whereas different estimates for the incubation period distribution and the serial interval distribution have been reported, estimates of the generation interval for COVID-19 have not been provided.Methods: We used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates we obtained the proportions pre-symptomatic transmission and reproduction numbers.Results: The mean generation interval was 5.20 (95%CI 3.78-6.78) days for Singapore and 3.95 (95%CI 3.01-4.91) days for Tianjin, China when relying on a previously reported incubation period with mean 5.2 and SD 2.8 days. The proportion of pre-symptomatic transmission was 48% (95%CI 32-67%) for Singapore and 62% (95%CI 50-76%) for Tianjin, China. Estimates of the reproduction number based on the generation interval distribution were slightly higher than those based on the serial interval distribution.Conclusions: Estimating generation and serial interval distributions from outbreak 1 . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) The copyright holder for this preprint .

Our analysis of data collected from multiple epidemics in Hong Kong indicated a shorter serial interval and generation time of infections with the SARS-CoV-2 Omicron variant. The age-specific case-fatality risk for Omicron BA.2.2 case-patients without complete primary vaccination was comparable to that of persons infected with ancestral strains in earlier waves.

Hong Kong reported 12,631 confirmed COVID-19 cases and 213 deaths in the first two years of the pandemic but experienced a major wave predominantly of Omicron BA.2.2 in early 2022 with over 1.1 million reported SARS-CoV-2 infections and more than 7900 deaths. Our data indicated a shorter incubation period, serial interval, and generation time of infections with Omicron than other SARS-CoV-2 variants. Omicron BA.2.2 cases without a complete primary vaccination series appeared to face a similar fatality risk to those infected in earlier waves with the ancestral strain.

To the editor: We are grateful for the comments provided by S. Bacallado, Q. Zhao and N. Ju [1]. With this reply we wish to clarify the concerns that were raised and provide some more insights.