Outbreak Reproduction Number Estimates

CDC is using a model to estimate the effective reproduction number (Rt) for the mpox outbreak in the US. Rt is used to understand the trajectory of an epidemic up to the current time (where we are now). CDC is using a model to estimate the effective reproduction number (Rt) for the mpox outbreak in the US. Rt is used to understand the trajectory of an epidemic up to the current time (where we are now).

As of December 19, 2022, this page was no longer updated due to low case numbers, which can cause wide variations in the estimates.

The graph shows the effective reproduction number (Rt) estimation over time based on complete data (green) or partial data (orange). The most recent data are considered incomplete due to delays in reporting mpox cases. As a result, there is more uncertainty associated with the most recent Rt estimates.

Rt > 1 means the epidemic is growing
Rt < 1 means the epidemic is shrinking
Shading represents the 50% and 90% credible intervals (uncertainty in the estimates)

This plot uses the EpiNow2 package (https://cran.r-project.org/web/packages/EpiNow2/index.html) to estimate the time-varying reproduction number on cases by date of report. The time-varying reproduction number is the average number of secondary cases infected by a single primary case in a large population.

The package requires three distributions:

Generation time: the time between infection of a primary and secondary case
Incubation period: the time between infection and symptom onset in a case
Any other delays: for example, delays from symptom onset to reporting

We approximated the generation time using an estimate of the serial interval (rash onset to rash onset) with mean of 7.0 days (95% CrI 5.8 – 8.4) and standard deviation of 4.2 (95% CrI: 3.2 – 5.6) from 40 case pairs (primary-secondary) across 12 U.S. jurisdictions. Determining case pairs (primary-secondary) has been a challenge in the current outbreak, as information on specific contacts is missing for many cases; in addition, many cases report multiple anonymous sex partners or attendance at large events, such as festivals, in the three weeks prior to symptom onset. We only included cases if there was a high degree of certainty that the secondary case was infected by the primary case. Days between onset of any mpox symptom and days between rash onset in the primary and secondary cases were calculated for each case pair. The EpiEstim package in R software was used to estimate the distribution of the serial interval for known primary and secondary cases in case pairs using Bayesian methods for both symptom and rash onset.

For the incubation period, we used estimates for rash onset from this preprint: Estimating the incubation period of mpox virus during the 2022 multi-national outbreak | medRxiv and updated the analysis to include data from the case pairs for which exposure information was available (14 cases). The updated estimate for 35 cases had mean 7.5 (95% CrI: 6.0 – 9.8) and standard deviation 4.9 (95% CrI: 3.2 – 8.8).

The model assumes that testing procedures and surveillance effort remain constant over the estimation period. The method does not distinguish between imported vs. locally acquired infections and does not account for under-ascertainment.

More information about this analysis can be found in the Mpox Technical Reports.