BACKGROUND: Coronavirus disease 2019 (COVID-19) has caused a heavy disease 
burden globally. The impact of process and timing of data collection on the 
accuracy of estimation of key epidemiological distributions are unclear. Because 
infection times are typically unobserved, there are relatively few estimates of 
generation time distribution.
METHODS: We developed a statistical framework to jointly estimate generation 
time and incubation period from human-to-human transmission pairs, accounting 
for sampling biases. We applied the framework on 80 laboratory-confirmed 
human-to-human transmission pairs in China. We further inferred the 
infectiousness profile, serial interval distribution, proportions of 
presymptomatic transmission, and basic reproduction number (R0) for COVID-19.
RESULTS: The estimated mean incubation period was 4.8 days (95% confidence 
interval [CI], 4.1-5.6), and mean generation time was 5.7 days (95% CI, 
4.8-6.5). The estimated R0 based on the estimated generation time was 2.2 (95% 
CI, 1.9-2.4). A simulation study suggested that our approach could provide 
unbiased estimates, insensitive to the width of exposure windows.
CONCLUSIONS: Properly accounting for the timing and process of data collection 
is critical to have correct estimates of generation time and incubation period. 
R0 can be biased when it is derived based on serial interval as the proxy of 
generation time.