Fig 1.
Transmission dynamics of infectious diseases.
(A) Definitions of epidemiological time intervals and illustration of transmission events on calendar timescales; (B) Modelled (lines) median serial intervals for varying peak infectiousness and hence overall probability of infection for the duration of infectiousness of respective diseases. Range of observed serial interval and attack rate (a proxy for infection probability) for respective diseases in Table 1 (points) for comparison; (C) Modelled serial interval for varying delay in case onset-to-isolation in SARS-CoV-2 wild type and Delta variant with median (lines) and interquartile range (shaded regions). Observed serial intervals from published studies [12,14] as shown in points (mean) with lines (95% CI).
Table 1.
Parameters to model the infectiousness profile of different diseases.
References in parenthesis.
Fig 2.
Power to detect differences in the generation intervals (GI), serial intervals (SI) between reference and alternative pathogen.
(A-C) Different incubation period between reference and alternative pathogen under the same symptoms onset-to-isolation status of either no isolation, mean symptoms onset-to-isolation of 8 days, or 4 days; (D-F) Different incubation period and longer duration of infectiousness post-peak viral load in reference pathogen under the same mean symptoms onset-to-isolation of 4 days. Peak viral load in reference pathogen is varied resulting in a probability of infection, p, of either 20%, 50% or 80% when the mean incubation of the reference pathogen was 4 days; (G-I) Different incubation period and longer duration of infectiousness post-peak viral load in reference pathogen under respective onset-to-isolation. (A,D,G) Theoretical power to detect differences in GI, (B,E,H) power to detect differences in observed SI—lower limit estimates of the theoretical power, (C,F,I) upper limit estimates of the theoretical power.
Fig 3.
Power to detect differences in the theoretical generation intervals (GI), observed serial intervals (SI) and derived GI between reference and alternative pathogen.
(A-C) Different contact patterns of either non-household or household contact but same incubation period under respective peak infectiousness and isolation status. Due to the differences in contact frequency, probabilities of infections (p1 for reference pathogen and p2 alternative pathogen) are different for both types of contact for the same peak infectiousness; (D-F) Different contact patterns of either daily or weekly household contact but same incubation period under respective peak infectiousness and isolation status. (A,D) Theoretical power to detect differences in GI, (B,E) power to detect differences in observed SI—lower limit estimates of the theoretical power, (C,F) upper limit estimates of the theoretical power.
Fig 4.
Generation intervals, GI, under varying outbreak dynamics.
(A) Differences in the generation interval between the reference and alternative pathogen without adjusting for exponential growth or decline outbreak dynamics. Exponential growth of 0.2/day (red), constant outbreak (blue) and exponential decline of 0.2/day (yellow) in alternative pathogen, (B) corresponding power to detect the biased differences in the generation intervals, (C) power to detect differences in the generation intervals after correctly adjusting for exponential outbreak dynamics.
Fig 5.
Differences in mean generation (GI) and serial (SI) intervals for transmission between pairs (i.e. no competing infector) and triples (i.e. competing infectors) with mean incubation period of (A) 2 days, (B) 4 days and (C) 6 days.
Table 2.
Simulated scenarios and how they relate to observations in the SARS-CoV-2 pandemic.