BVDOutbreakSize

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  • Abbott, S.; Hellewell, J.; Sherratt, K.; Gostic, K.; Hickson, J.; Badr, H. S.; DeWitt, M.; Thompson, R.; EpiForecasts and Funk, S. (2020). EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters. R package version 1.3.5.

  • Abbott, S.; Park, S. W.; Charniga, K.; Howes, A.; Funk, S. and epidist contributors (2024), epidist: Estimate Epidemiological Delay Distributions for Infectious Diseases, https://github.com/epiforecasts/epidist. R package. Marginal delay-distribution estimation correcting for double interval censoring and right truncation.

  • Akilimali, P.; Ebengo, D. M.; Scarpino, S. V.; Amuri-Aziza, A.; Wawina-Bokalanga, T.; Matondo-Mbundu, P.; Kanku, B.; Kinganda-Lusamaki, E.; Makangara, J.-C.; Mukadi-Bamuleka, D.; Rojek, A.; Kraemer, M. U.; Ngandu, C.; Mwamba, D. and Mbala-Kingebeni, P. (2026). Clinical Characteristics of Patients Infected with Bundibugyo Virus, DRC 2026. New England Journal of Medicine. Correspondence. Onset-to-sample delays (Table S3) fitted with epidist correcting for double interval censoring and right truncation.

  • Amuri-Aziza, A.; Adroba Tandele, P.; Luakanda-Ndelemo, G.; Kinganda-Lusamaki, E.; Lola-Loway, M.; Djemba-Fundji, B.; Ola-Mpumbe, R.; Cikaya-Kankolongo, F.; Paku-Tshambu, P.; Muswamba-Kayembe, P.-C.; Lumembe, R.; Kashali, N.; Makangara-Cigolo, J.-C.; Akil-Bandali, P.; Kimbonza, S.; Mabika-Bope, E.; Citenga, A.; Mukadi, P.; Mukadi-Bamuleka, D.; Pukuta, E.; Loman, N.; Wilkinson, S.; Quick, J.; Kent, C.; Hodcroft, E.; Ayouba, A.; Peeters, M.; Delaporte, E.; Nsio, J.; Ntumba-Tshitenge, O.; Otshudiema, J. O.; Keita, M.; Kuppalli, K.; Maes, P.; Ariën, K. K.; Liesenborghs, L.; Vercauteren, K.; O'Toole, Á.; Rambaut, A.; Kebede, Y.; Ahuka-Mundeke, S.; Ngandu, C.; Muyembe-Tamfum, J.-J.; Mwamba, D.; Wawina-Bokalanga, T.; Mbala-Kingebeni, P.; Nabadda, S.; Sewanyana, I.; Kyobe Bosa, H.; Wayengera, M.; Tessema, S. K.; Ssemwanga, D.; Balinandi, S.; Onywera, H.; Tanui, C. K.; Mwangi, S. W.; Andrew, T.; Nakintu, V.; Oundo, H. R.; Tenywa, W.; Wenka, G. T.; Murungi, M.; Kabahita, J. M.; Makoha, C.; Ssemaganda, A.; Mbambu, A.; Namakula, S.; Kanyerezi, S. and Ayitewala, A. (2026). Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event, https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032. Virological.org post. Maximum-likelihood phylogeny of the initial BDBV genomes; the 2026-05-21 update adds a BEAST v10.5.0 temporal tree of the first ten genomes (HKY, strict clock fixed to literature EBOV rates, exponential coalescent) reporting the TMRCA. Superseded for rate estimates by the 139-genome BEAST X analysis (mbalaplacide2026).

  • Chamla, D.; Belizaire, M. R.; Co, I. F.; Jinadu, A.; Mamadu, I. and Atagbaza, A. O. (2026). Size of the 2026 Ebola outbreak and risk of cross-border spillover from Bundibugyo virus in Ituri Province, DR Congo, and its implications for preparedness: a recalibrated stochastic modelling study. The Lancet Infectious Diseases. WHO Regional Office for Africa; online first 25 June 2026. A discrete-time stochastic SEIRD ensemble recalibrated by simulation filtering (not formal Bayesian inference) to 598 cumulative laboratory-confirmed cases on 8 June 2026, with the reporting fraction fixed at 1.0, so it projects cumulative confirmed cases and deaths forward over a 24-week horizon under three transmissibility scenarios (R0 1.42/1.71/2.08). Its outbreak-size metric is the confirmed-case count, not the ascertainment-corrected total cases that McCabe et al. and this analysis estimate.

  • Charniga, K.; Park, S. W.; Akhmetzhanov, A. R.; Cori, A.; Dushoff, J.; Funk, S.; Gostic, K. M.; Linton, N. M.; Lison, A.; Overton, C. E.; Pulliam, J. R.; Ward, T.; Cauchemez, S. and Abbott, S. (2024). Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. PLOS Computational Biology 20, e1012520.

  • Cuomo-Dannenburg, G. and Ghafari, M. (2026). Molecular evolutionary analysis of the current Bundibugyo virus disease outbreak in DRC and Uganda, https://virological.org/t/molecular-evolutionary-analysis-of-the-current-bundibugyo-virus-disease-outbreak-in-drc-and-uganda/1042. Virological.org post, 4 June 2026. Phylodynamic reanalysis of the first ten BDBV genomes under six substitution-rate assumptions, reporting a mean epidemic doubling time of 15.2-24.5 days (wide intervals that include zero), basic reproduction number 1.31-1.55, a 9.6-day generation time, and a TMRCA between 01 and 15 March 2026. The outbreak-specific rate (mbalaplacide2026, 139 genomes) now supersedes the substitution-rate assumptions used here.

  • Danisch, S. and Krumbiegel, J. (2021). Makie.jl: Flexible high-performance data visualization for Julia. Journal of Open Source Software 6, 3349.

  • Ferguson, N. M. (2026). Genetic seeding-time estimate for the 2026 Bundibugyo virus disease outbreak. Personal communication. Source of the idea to combine the genetic TMRCA with the other data streams as a lower bound on the seeding time, originally via the root-to-tip distance of the first BDBV genomes (virological2026) and the holmes2016 clock rate, now grounded on the outbreak-specific estimates of mbalaplacide2026.

  • Funk, S. and Abbott, S. (2026). Bundibugyo Ebola virus — Bayesian delay-distribution and stratified CFR estimation from the 2012 Isiro outbreak, https://github.com/sbfnk/bdbv-linelist-analysis. Source of the informative onset-to-death gamma prior.

  • Ge, H.; Xu, K. and Ghahramani, Z. (2018). Turing: A Language for Flexible Probabilistic Inference. In: Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics, Vol. 84; pp. 1682–1690.

  • Hoffman, M. D. and Gelman, A. (2014). The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research 15, 1593–1623.

  • Holmes, E. C.; Dudas, G.; Rambaut, A. and Andersen, K. G. (2016). The evolution of Ebola virus: Insights from the 2013–2016 epidemic. Nature 538, 193–200.

  • Kupferschmidt, K. (2026). Exclusive: Congo's Ebola epidemic started at least 4 months before it was detected, https://www.science.org/content/article/exclusive-congo-s-ebola-epidemic-started-least-4-months-it-was-detected. Science news article, 18 May 2026. Field epidemiology in Mongbwalu (Ituri, DRC) traced a sustained transmission chain back to a death on 25 January 2026 and identified more than 500 suspected cases between mid-January and mid-May 2026, indicating the outbreak was widespread months before it was confirmed in May 2026.

  • MacNeil, A.; Farnon, E. C.; Wamala, J.; Okware, S.; Cannon, D. L.; Reed, Z.; Towner, J. S.; Tappero, J. W.; Lutwama, J.; Downing, R.; Nichol, S. T.; Ksiazek, T. G. and Rollin, P. E. (2010). Proportion of Deaths and Clinical Features in Bundibugyo Ebola Virus Infection, Uganda. Emerging Infectious Diseases 16, 1969–1972. Mean incubation period 6.3 days (n = 24), 2007 Bundibugyo outbreak; recommended incubation prior in the BDBV line-list reanalysis.

  • Mbala-Kingebeni, P. and others (2026). Genomic epidemiology of the ongoing 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo, https://virological.org/t/genomic-epidemiology-of-the-ongoing-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo/1045. Virological.org post, July 2026. BEAST X v10.6.0 analysis of 139 BDBV genomes; evolutionary rate  1.1E-3 subs/site/year with Skygrid and Exponential growth tree priors; tMRCA estimates 15 Mar (Skygrid, baseline) and 08 Mar (ExpGrowth, sensitivity); Exponential growth doubling time 11.7 d (95 HPD 6.8–17.5).

  • McCabe, R.; Ebbarnezh, L.; Okware, S.; Fotsing, R.; Koua, E.; Mbaka, P.; Lofungola, A.; Ebengo, D. M.; Mbala, P. K.; Bishola, T. T.; Ibolobolo, C. M.; Matondo, H. M.; Sibo, J.-C. M.; van Elsland, S. L.; McMenamin, M.; Ferguson, N. M.; le Polain de Waroux, O. and Cori, A. (2026). Estimation of the Ebola outbreak size in the Democratic Republic of the Congo. The Lancet Infectious Diseases. Correspondence, online first 9 June 2026. Peer-reviewed publication of the McCabe et al. outbreak-size estimates, with inputs advanced to 27 May 2026 (1031 DRC suspected or confirmed cases, 240 deaths, three Uganda imports). Both methods vary the epidemic doubling time (7/10/14 days); the back-calculation assumes 30% of deaths are attributable to Ebola. The method numbers are swapped relative to the Imperial reports (its method 1 is the back-calculation, its method 2 the geographic spread).

  • McCabe, R. and others (May 2026). Estimation of the size of the Ebola outbreak caused by Bundibugyo virus in the Democratic Republic of the Congo: May 20, 2026 update, https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/Report-ebola-update-20-05-2026.pdf.

  • McCabe, R. and others (May 2026). Estimation of the size of the outbreak of Ebola disease caused by Bundibugyo virus in the Democratic Republic of the Congo, https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/research-themes/preparedness-and-response-to-emerging-threats/report-ebola-18-05-2026/.

  • Nishiura, H.; Klinkenberg, D.; Roberts, M. and Heesterbeek, J. A. (2009). Early epidemiological assessment of the virulence of emerging infectious diseases: a case study of an influenza pandemic. PLOS ONE 4, e6852.

  • Pinsky, B. A.; Sahoo, M. K.; Sandlund, J.; Kleman, M.; Kulkarni, M.; Grufman, P.; Nygren, M.; Kwiatkowski, R.; Baron, E. J.; Tenover, F.; Denison, B.; Higuchi, R.; Van Atta, R.; Beer, N. R.; Carrillo, A. C.; Naraghi-Arani, P.; Mire, C. E.; Ranadheera, C.; Grolla, A.; Lagerqvist, N. and Persing, D. H. (2015). Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus. PLOS ONE 10, e0142216.

  • Rieger, T.; Kerber, R.; El Halas, H.; Pallasch, E.; Duraffour, S.; Günther, S. and Ölschläger, S. (2016). Evaluation of RealStar Reverse Transcription–Polymerase Chain Reaction Kits for Filovirus Detection in the Laboratory and Field. The Journal of Infectious Diseases 214, S243–S249.

  • Rosello, A. and others (2015). Ebola virus disease in the Democratic Republic of the Congo, 1976-2014, eLife 4, e09015.

  • Semper, A. E.; Broadhurst, M. J.; Richards, J.; Foster, G. M.; Simpson, A. J.; Logue, C. H.; Kelly, J. D.; Miller, A.; Brooks, T. J.; Murray, M. and Pollock, N. R. (2016). Performance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Study. PLOS Medicine 13, e1001980.

  • Tebbutt, W. and Ge, H. (2024). Mooncake: Towards a Differentiable General-Purpose Language, https://github.com/chalk-lab/Mooncake.jl.

  • Thompson, W. (2024). PairPlots.jl — Beautiful and flexible pair plots for Julia, https://github.com/sefffal/PairPlots.jl.

  • Wilson, E. B. and Hilferty, M. M. (1931). The distribution of chi-square. Proceedings of the National Academy of Sciences 17, 684–688.

  • Cepheid (2020). Xpert Ebola Assay Instructions for Use, https://www.fda.gov/media/91944/download. Zaire-ebolavirus GP/NP targets; reactivity with Bundibugyo and Sudan ebolaviruses not established and predicted unlikely by in-silico analysis.

  • INRB-UMIE (2026). Ebola DRC 2026: situation-report archive and processed surveillance data, https://github.com/INRB-UMIE/Ebola_DRC_2026. Archive of the INSP situation-report PDFs and their per-health-zone transcriptions. We take values from the report PDFs rather than the per-zone CSVs, whose zone-level sums are inconsistent with the national totals (they omit cases not yet attributed to a zone).

  • Institut National de Santé Publique and Centre des Opérations d'Urgence de Santé Publique (COUSP-RDC) (May 2026). Rapport de situation de la 17ème épidémie de la maladie à virus Ebola en RDC (SitRep MVE, N°009–012). Daily situation reports of the Democratic Republic of the Congo Ministry of Health. Primary source of the national cumulative suspected-case, suspected-death, confirmed-case and laboratory totals used here, read from the report PDFs.

  • Stan Development Team (2024). Prior Choice Recommendations, https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations. Stan wiki.

  • World Health Organization (May 2026). Disease Outbreak News: Ebola disease caused by Bundibugyo virus — Uganda (DON602). Source of the first Uganda export hospital-admission date (11 May 2026) and the dated export death (14 May 2026) used as timing bounds on the seeding time in this analysis.