2026-05-28 Update
Note: 2026-06-05 This post has been updated to reflect some changes to the geographical location of the new genomes in light of updated information. Other than the labelling of the genomes and the tips in the tree, there are no substantial changes.
Five additional genomes including 4 sampled in Rwampara and 1 in Nyankunnde have been released to Pathoplexus. This update includes a phylogenetic tree of available genomes from the outbreak and a new estimate of the TMRCA
See the top post for authors, collaborators and acknowledgments.
Show in PearTreeFigure 1 | A maximum likelihood phylogeny constructed using the HKY+gamma model in IQTree2. Ultrafast Bootstrap values are shown for each branch. The scale is given in units of substitutions per site. Tree was rooted using the BDBV reference genome, NC_014373.
2026-05-28 Update - Temporal Tree Estimate
This analysis has been updated on the 2026-05-29 after quality control of data (see notes below).
A)
Show in PearTreeB)
Show in PearTreeFigure 2 | Temporal phylogenetic reconstruction of the 14 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 | F |
|---|---|---|---|---|---|
| 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 | ex-Bunia | |
| 26FHV046 | PP_00711R7 | 2026-05-03 | DRC | Rwampara | |
| 26FHV047 | PP_00711S5 | 2026-05-03 | DRC | Rwampara | |
| 26FHV051 | PP_00711T3 | 2026-05-03 | DRC | Rwampara | |
| 26FHV053 | PP_00711U1 | 2026-05-03 | DRC | Rwampara | |
| 26FHV056 | PP_00711VZ | 2026-05-03 | DRC | Nyankunnde |
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 | 2026-04-10 | 2026-03-24 | 2026-04-23 |
| Exponential | 1.2 x 10-3 | 2026-03-26 | 2026-02-27 | 2026-04-16 |
Notes and caveats
Genomes PP_006Y8R6 (26FHV064) and PP_006Y8S4 (26FHV065) are samples from the same patient so the latter one has been removed.
Genome PP_006XCJJ has a tract of 4 T->C mutations within a short span (4165 to 4191) indicative of an ADAR editing event. They are in an intergenic region between the VP35 CDS and the VP40 CDS. All but the first mutation has been masked out. See Phylogenetic analysis of initial genomes from Kasai EBOV outbreak, 8 September 2025 for an example of this in a previous ebolavirus outbreak.
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 February and late April.
The exponential growth coalescent prior was used to allow for a more flexible prior on the tree. The growth rate estimate’s 95% HPD interval overlaps with zero at its lower range so we believe the 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.