https://github.com/epiforecasts/bvdoutbreaksize
Joint Bayesian generative Turing model for the 2026 DRC BVD outbreak. Combines exports, deaths and reported suspected cases (with ascertainment) in a single posterior. Includes a no-onward-transmission deaths lower bound.
https://github.com/epiforecasts/bvdoutbreaksize
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Joint Bayesian generative Turing model for the 2026 DRC BVD outbreak. Combines exports, deaths and reported suspected cases (with ascertainment) in a single posterior. Includes a no-onward-transmission deaths lower bound.
- Host: GitHub
- URL: https://github.com/epiforecasts/bvdoutbreaksize
- Owner: epiforecasts
- License: mit
- Created: 2026-05-19T16:50:45.000Z (24 days ago)
- Default Branch: main
- Last Pushed: 2026-06-07T23:33:08.000Z (5 days ago)
- Last Synced: 2026-06-08T00:23:20.496Z (5 days ago)
- Language: Julia
- Homepage: https://epiforecasts.io/BVDOutbreakSize/stable/
- Size: 1.31 GB
- Stars: 10
- Watchers: 1
- Forks: 2
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
- Codeowners: .github/CODEOWNERS
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README
# Estimating the current size of the 2026 DRC Bundibugyo virus outbreak
**Authors:** Sam Abbott, Kath Sherratt, Samuel Brand and Sebastian Funk.
[](https://epiforecasts.io/BVDOutbreakSize/stable) [](https://epiforecasts.io/BVDOutbreakSize/dev) [](https://github.com/epiforecasts/BVDOutbreakSize/actions/workflows/test.yml) [](https://codecov.io/gh/epiforecasts/BVDOutbreakSize) [](https://github.com/JuliaTesting/Aqua.jl) [](https://github.com/SciML/SciMLStyle) [](https://doi.org/10.5281/zenodo.20312758)
**Last updated:** on each rebuild. This is a live report, re-run as new
data arrive, so the estimates change between updates.
**Data as of:** the most recent situation report. DRC counts come from the
situation reports of the Institut National de Santé Publique (INSP); Uganda
imports come from WHO. The rendered report fills in the build date and the
exact data cut-off automatically; the suspected-case and suspected-death
streams, which carry most of the signal, were last published earlier than
the laboratory-confirmed streams.
**See:**
[current outbreak size](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Summary) ·
[one-week-ahead forecast](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#One-week-ahead-forecast-results) ·
[estimate evolution across releases](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Estimate-evolution-across-releases) ·
[comparison with McCabe et al.](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Comparison-with-McCabe-et-al.) ·
[how the data streams compare](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Outbreak-size-estimated-by-each-data-stream) ·
[limitations](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Limitations) ·
[full joint results](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Results).
**Abstract.** An outbreak of Ebola disease caused by Bundibugyo virus
(BVD) is ongoing in the Democratic Republic of the Congo (DRC), with
cases also detected across the border in Uganda.
This is a real-time joint Bayesian estimate of the current size of that
outbreak, refreshed as new data arrive.
Most infections are not yet reported, so the current size has to be
inferred from the surveillance data that are available.
The model is a discrete-time renewal process on a daily grid that fits the
surveillance streams jointly in a single posterior: the DRC suspected
cases, suspected deaths, laboratory-confirmed cases and confirmed deaths,
and the cases and deaths exported to Uganda.
It estimates the latent infections, symptom onsets and deaths over time,
the reported and confirmed cases, and the time-varying reproduction number
with its growth rate and doubling time, alongside the case-fatality ratio,
the ascertainment of each surveillance system, and a short-term forecast of
each stream over the coming week.
The DRC data come from the INSP situation reports and the Uganda exports
from the WHO situation reports and Disease Outbreak News, with a genetic
bound on the time to the most recent common ancestor and priors taken from
the McCabe et al. report.
**Scope.** This work is motivated by adding an external view of the
current situation, based on our understanding of real-time infectious
disease dynamics and the infection process that gives rise to observed
epidemic surveillance counts.
We are actively developing it and encourage feedback, so please get in
touch.
We fully support reuse and adaptation.
Find out more in the
[contributing guide](https://epiforecasts.io/BVDOutbreakSize/stable/contributing).
**Use of AI.** The model code and analysis were drafted by a language
model and reviewed and revised under human oversight; the named authors
are responsible for that oversight.
## Installing the package
To use the model and the bundled outbreak data from your own Julia
environment, add the package from the repository:
```julia
using Pkg
Pkg.add(url = "https://github.com/epiforecasts/BVDOutbreakSize")
```
You can then load the model machinery and the data the report is
fitted to:
```julia
using BVDOutbreakSize
obs = load_observations()
```
This gives you the exported model components, constants and data
loaders, enough to build your own analysis on top of the package.
Reproducing the full report (fitting the models and writing the
result tables and plots) can be done in a few ways, described next.
## Running
There are a couple of ways to re-fit the model.
### Re-fit from a clone
```bash
git clone --recurse-submodules https://github.com/epiforecasts/BVDOutbreakSize
cd BVDOutbreakSize
julia --project=. -e 'using Pkg; Pkg.instantiate()'
julia --project=. scripts/run.jl
```
`scripts/run.jl` fits the models and writes the output CSVs (the
analysis literate is also run as part of the docs build). Running
`docs/examples/analysis.jl` directly instead steps through the full
narrative.
### Re-fit without cloning
`scripts/reproduce.jl` fetches the package, instantiates its
environment, and runs the fit:
```bash
curl -fsSL https://raw.githubusercontent.com/epiforecasts/BVDOutbreakSize/main/scripts/reproduce.jl | julia
```
Outputs land in `./bvd-output`; set `BVD_OUTPUT_DIR` to write them
elsewhere, or `BVD_REF` to a release tag to reproduce a specific
version. The script clones into a temporary directory and runs from
there, so it leaves your own Julia environments untouched.
### Render the docs page
Executes the literate and produces HTML at `docs/build/`:
```bash
julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
julia --project=docs docs/make.jl
```
Updating the observation counts for a new sitrep is a single-file
edit of `data/observations.toml`; the literate picks the new numbers
up automatically.
## Outputs and releases
Each push to `main` regenerates the model outputs as part of the
documentation build and publishes them as a GitHub Release. The
[latest release](https://github.com/epiforecasts/BVDOutbreakSize/releases/latest)
bundles the saved result tables and plots, thinned posterior draws, a
copy of the input `observations.toml` that produced them, a
`site.zip` snapshot of the rendered report site, and `analysis.html`,
a self-contained single-file copy of the report that opens offline
([download the latest](https://github.com/epiforecasts/BVDOutbreakSize/releases/latest/download/analysis.html));
the same artifacts are
written to the repository's `output/` directory on each build. Browse
[all releases](https://github.com/epiforecasts/BVDOutbreakSize/releases)
for earlier output bundles.
Major versions of the report are kept as GitHub Releases.
The rendered report is published from the
[`gh-pages` branch](https://github.com/epiforecasts/BVDOutbreakSize/tree/gh-pages),
where past and development versions of the analysis page can be found.
## Submodules
- `external/bdbv-linelist-analysis` — Bayesian reanalysis of the 2012
Isiro BDBV line list (Rosello et al. 2015). Source of the
informative onset-to-death gamma shape and scale priors.
## Citation
If you use or build on this project, please cite the works this
repository depends on:
- **This project** — Abbott, S., Brand, S., Funk, S. (2026).
*BVDOutbreakSize: joint forward-generative Turing model for the
2026 DRC Bundibugyo outbreak.*
.
DOI: [10.5281/zenodo.20312758](https://doi.org/10.5281/zenodo.20312758).
- **INSP situation reports** that supply the DRC suspected-case and
suspected-death counts and the sitrep cumulative trajectory —
Institut National de Santé Publique, Démocratique du Congo (2026).
*Situation reports on the 17th Ebola epidemic.*
. Transcribed across health
zones by INRB-UMIE/Ebola_DRC_2026,
.
- **WHO situation reports and Disease Outbreak News** that supply
the Uganda import-case counts and the dated detection and death
events for the first Uganda import —
World Health Organization Regional Office for Africa (2026).
*Ebola disease caused by Bundibugyo virus outbreak, Democratic
Republic of the Congo and Uganda — Weekly External Situation
Report 01.* Data as of 18 May 2026.
World Health Organization (2026). *Disease Outbreak News:
Ebola disease caused by Bundibugyo virus — Democratic Republic
of the Congo and Uganda (DON602, DON603).* Source of the first
Uganda import hospital-admission date (11 May 2026) and the fatal
import death date (14 May 2026).
- **Imperial reports** that this work re-implements and compares
against, in both released versions —
McCabe, R., Ebbarnezh, L., Okware, S., Fotsing, R., Koua, E.,
Mbaka, P., Lofungola, A., van Elsland, S. L., McMenamin, M.,
Ferguson, N., le Polain de Waroux, O., Cori, A. (2026).
*Estimation of the size of the outbreak of Ebola disease caused
by Bundibugyo virus in DRC.* Imperial College London, 18 May 2026.
DOI: [10.25560/130007](https://doi.org/10.25560/130007).
[Report page](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/research-themes/preparedness-and-response-to-emerging-threats/report-ebola-18-05-2026/).
McCabe, R. and others (2026).
*Estimation of the size of the Ebola outbreak caused by Bundibugyo
virus in DRC: May 20, 2026 update.* Imperial College London,
20 May 2026.
DOI: [10.25560/13005307](https://doi.org/10.25560/13005307).
[Report PDF](https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/Report-ebola-update-20-05-2026.pdf).
- **Onset-to-death delay reanalysis** that this work uses for
delay priors — Funk, S. (2026). *bdbv-linelist-analysis:
Bayesian reanalysis of the 2012 Isiro Bundibugyo line list.*
.
## Funding
This work was funded by the National Institute for Health and Care
Research (NIHR) Health Protection Research Unit in Health Analytics &
Modelling, a partnership between the UK Health Security Agency, Imperial
College London and the London School of Hygiene & Tropical Medicine
(grant code NIHR207404).
The views expressed are those of the author(s) and not necessarily those
of the NIHR, UK Health Security Agency or the Department of Health and
Social Care.
## Further references
- Rosello et al., *Ebola virus disease in DRC, 1976–2014*, eLife 2015.
Original Isiro 2012 onset-to-death gamma point estimate.
- Imai et al., *Estimating the potential total number of novel
coronavirus cases in Wuhan City*, Imperial COVID-19 Response Team
Report 1, 17 January 2020. Methodological template for Method 1.
- Charniga et al., *Best practices for estimating and reporting
epidemiological delay distributions*, PLOS Computational Biology 2024.
Followed for the delay-distribution reporting here.