2026-05-21 Update - Temporal Tree Estimate
See the top post for authors, collaborators and acknowledgments.
A)
Show in PearTreeB)
Show in PearTreeFigure 1 | Temporal phylogenetic reconstruction of the first 10 genomes using BEAST v10.5.0 and summarised as a HIPSTR tree. Posterior probabilities >= 0.5 are shown in red. 95% highest posterior density (HPD) intervals for node dates shown with blue bars. HKY substitution model, strict molecular clock and exponential coalescent prior used for analysis. A) Rate of evolution fixed to 1.9x10-3 substitutions per site per year based on prior estimates for EBOV. B) Rate of evolution fixed to 1.2x10-3 substitutions per site per year.
Table 1 | Sampled cases
| ID | Pathoplexus accession | Collection date | Country | Location |
|---|---|---|---|---|
| 26FHV061 | PP_006Y8NC | 2026-05-06 | DRC | Bunia |
| 26FHV062 | PP_006Y8PA | 2026-05-06 | DRC | Bunia |
| 26FHV063 | PP_006Y8Q8 | 2026-05-06 | DRC | Bunia |
| 26FHV058 | PP_006Y8ME | 2026-05-06 | DRC | Katwa |
| 26FHV064 | PP_006Y8R6 | 2026-05-16 | DRC | Bunia |
| 26FHV065 | PP_006Y8S4 | 2026-05-16 | DRC | Bunia |
| n/a | PP_006XCJJ | 2026-05-14 | Uganda | ex-Bunia |
| 26FHV045 | PP_006XHKB | 2026-05-03 | DRC | Bunia |
| 26FHV054 | PP_006XHL9 | 2026-05-07 | DRC | Bunia |
| n/a | PP_006XXY51 | 2026-05-20 | Ex-DRC | n/a |
1 Genome submitted to Pathoplexus by Till D. Best, Julia Melchert, Tiina Mauno, Nikolai W. Zaki, Talitha Veith, Tobias Bleicker, Terry C. Jones, Christian Drosten & Victor M. Corman, Charité - Universitätsmedizin, Institute of Virology, Germany.
Genome sequenced used listed in Table 1. Unless otherwise note, the authors of these genomes are listed in the first post in this topic.
Estimates
Table 2 | Time to most recent common ancestor (tMRCA) estimates
| Coalescent model | Assumed Rate substs/site/year |
Mean tMRCA | Lower 95% HPD | Upper 95% HPD |
|---|---|---|---|---|
| Exponential | 1.9 x 10-3 | 2026-04-11 | 2026-03-23 | 2026-04-28 |
| Exponential | 1.2 x 10-3 | 2026-03-25 | 2026-02-20 | 2026-04-20 |
Notes and caveats
To perform this analysis we required a fixed rate of evolution due to the limited temporal range of sampling. A comprehensive review [3] compiled estimates from the literature for the 2014-2016 EBOV epidemic with values between ~1.9 × 10-3 for an early period of the epidemic [4] to ~1.2 × 10-3 across all public data.
Given the uncertainty in the rate of evolution it would probably be most appropriate to consider the estimate for this analysis to be the extent of estimates for both rates. I.e., the date of the MRCA for the cases in this analysis most likely lies between late March and late April.
All but one of the genomes are from Bunia so this estimate should be consider to be specific to the outbreak in that location. Genomes from other locations may change the tMRCA estimate considerably if the Bunia genomes are not representative of the wider epidemic.
The exponential growth coalescent prior was used to allow for a more flexible prior on the tree. The growth rate 95% HPD is very close to zero at its lower range so estimates of this are not informative at this time.
References
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Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020 May 1;37(5):1530-4.
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Baele G, Ji X, Hassler GW, McCrone JT, Shao Y, Zhang Z, et al. BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference. Nat Methods. 2025;22: 1653–1656.
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Holmes EC, Dudas G, Rambaut A, Andersen KG. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature. 2016;538: 193–200.
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Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345: 1369–1372.