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РН
SpaceX
Роскосмос
NASA
СпутникиРНSpaceXРоскосмосNASA Hi Erik,
Thank you so much for a great suggestion of how to improve this analysis. Just to clarify, in the original analysis we used only a central estimate of the generation time for Bundibugyo because there was no generation time estimate available.
Below, we extended this original work by using the method you suggested. We use the daily growth rate as estimated by converting the number of doublings per year which are direct outputs from the Delphy analysis. There are currently no published estimates of generation time for BVD and therefore we used the generation time estimates from the WHO Ebola Response Team, with a mean of 15.3 days and standard deviation of 9.3 days. This estimate was based on the first 9 months of the outbreak in West Africa and is assumed to be representative of a non-isolating cohort.
We convert the growth rate r to an estimate of R_0 using the below renewal equation, as described in Green, Ferguson and Cori, 2022:
R_0 = \frac{(r+b)^a}{b^a}
where r is the epidemic growth rate, and a and b are the shape and rate of the Gamma distribution of the generation time, respectively.
Below is an updated version of Table 1 to reflect this new analytic equation for the reproduction number (only the reproduction numbers have changed). Note that this increases the uncertainty of the reproduction number estimates. In particular the upper interval value increases, and the central estimate also increases.
Substitution rate
tMRCA
Doublings/year
R_0
Source
Species
0.84 \times 10^{-3} [fixed]
2026-01-31 [2025-12-22, 2026-03-21]
14.9 [-2.4, 32.2]
1.49 [0.93, 2.23]
Hulseberg et al., Cell Rep Med, 2021
Bundibugyo
0.91 \times 10^{-3} [fixed]
2026-02-06 [2025-12-15, 2026-03-15]
14.9 [-2.4, 32.2]
1.54 [0.82, 2.56]
Ghafari et al., [In preparation] Median of Zaire substitution rates
Zaire
1.2 \times 10^{-3} [fixed]
2026-02-26 [2026-01-25, 2026-03-31]
19 [-7, 51]
1.65 [0.81, 3.26]
Holmes et al., Nature, 2016 (mean of rates for 2013-2016 EBOV outbreak)
Zaire
1.9 \times 10^{-3} [fixed]
2026-03-23 [2026-03-01, 2026-04-12]
24.0 [-10, 67]
1.85 [0.74, 4.33]
Gire et al., Science, 2014 (early outbreak estimate)
Zaire
1.99 \times 10^{-3} [0.06, 4.15]
2026-02-17 [2025-09-10, 2026-04-27]
21.0 [-17, 64]
1.73 [0.60, 4.11]
Fitted to the 10 sequences from this outbreak
Bundibugyo
The number of sequences available to analyse has increased substantially following an updated analysis available here: Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo.
Here we simply extend the previous analysis based on the sequences that were available at the time, although this approach would be applicable to an expanded set of genomic sequences to estimate the reproduction number from the genomic data available and would increase the reliability of these estimates as discussed earlier in this discussion thread.
References:
WHO Ebola Response Team et al., 2014 https://www.nejm.org/doi/full/10.1056/NEJMoa1411100
Green, Ferguson and Cori et al. 2022 https://doi.org/10.1098/rsif.2021.0429
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