{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T14:35:59Z","timestamp":1790174159197,"version":"4.1.0"},"reference-count":27,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T00:00:00Z","timestamp":1776124800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["BMGFINV-044865"],"award-info":[{"award-number":["BMGFINV-044865"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-009125"],"award-info":[{"award-number":["INV-009125"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023693","name":"Vaccine Impact Modelling Consortium","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023693","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["gatesopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Gates Open Res"],"abstract":"<ns5:p>Background Cholera remains a significant public health challenge in Africa, where outbreaks routinely strain public health and healthcare systems. Cholera surveillance time series data could be used to inform the efficient distribution of resources like oral cholera vaccine (OCV) and emergency response personnel, spur research on the impacts of different cholera control activities, and investigate longer-term epidemiologic patterns in cholera dynamics in this region. However, public reporting of cholera surveillance data historically has been sporadic and often limited to outbreak periods, thus limiting the availability of these useful time series datasets. We sought to fill this gap by preparing, cleaning, and processing weekly consecutive time series and outbreak-specific time series from 2010 to 2023 for African countries from heterogeneous data contributed to a global cholera surveillance database. Methods Cholera incidence data in Africa from 2010 to 2023 on suspected cases, confirmed cases, and deaths were compiled from public and non-public cholera surveillance from multiple sources, including ministries of health, World Health Organization, M\u00e9decins Sans Fronti\u00e8res, UNICEF, and other sources. Data were processed by aggregating daily records to weekly levels, averaging duplicate entries, filling gaps and surrounding weeks with zero cases, aligning epidemic weeks, adjusting population data, and removing identifying geographic information to preserve confidentiality as appropriate. Outbreaks were subsequently extracted using a systematic definition and summary statistics were produced by spatial scale and population density. Summary outbreak metrics were compared to previously published cholera outbreak datasets for data validation. Conclusions The unified surveillance and outbreak datasets provide an extensive compilation of reported cholera activity in Africa from 2010 to 2023, serving as a valuable resource for long-term control planning and early warning systems. Public health researchers can also leverage these datasets to analyze outbreak dynamics, anticipate resource needs, and assess the theoretical impact of control strategies.<\/ns5:p>","DOI":"10.12688\/gatesopenres.16378.1","type":"journal-article","created":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T10:49:08Z","timestamp":1783594148000},"page":"16","update-policy":"https:\/\/doi.org\/10.12688\/gatesopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Cholera surveillance time series in Africa between 2010 and 2023"],"prefix":"10.12688","volume":"10","author":[{"given":"Qulu","family":"Zheng","sequence":"first","affiliation":[{"name":"Baltimore Maryland Johns Hopkins University Bloomberg School of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"DePencier","sequence":"additional","affiliation":[{"name":"Baltimore Maryland Johns Hopkins University Bloomberg School of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maya  N.","family":"Demby","sequence":"additional","affiliation":[{"name":"Baltimore Maryland Johns Hopkins University Bloomberg School of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew S.","family":"Azman","sequence":"additional","affiliation":[{"name":"Geneva Geneva University of Geneva"},{"name":"Baltimore Maryland Johns Hopkins University Bloomberg School of Public Health"},{"name":"Geneva Geneva Geneva University Hospitals"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth C.","family":"Lee","sequence":"additional","affiliation":[{"name":"Baltimore Maryland Johns Hopkins University Bloomberg School of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,4,14]]},"reference":[{"key":"ref5","doi-asserted-by":"publisher","first-page":"2024.09.23.24314072","DOI":"10.1101\/2024.09.23.24314072v1.abstract","article-title":"A decade of shifting cholera burden in Africa and its implications for control: A statistical mapping analysis.","author":"J Perez-Saez","year":"2024 cited 2025 Feb 12","journal-title":"medRxiv."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"891-892","DOI":"10.1016\/S0140-6736(24)00467-7","article-title":"The great cholera vaccine shortage.","volume":"403","year":"2024 Mar 9","journal-title":"Lancet."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e831-e839","DOI":"10.1016\/S2214-109X(22)00007-9","article-title":"The seasonality of cholera in sub-Saharan Africa: A statistical modelling study.","volume":"10","author":"J Perez-Saez","year":"2022 Apr 21","journal-title":"Lancet Glob. Health."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"S701-S709","DOI":"10.1093\/infdis\/jiab440","article-title":"Contrasting Epidemiology of Cholera in Bangladesh and Africa.","volume":"224","author":"D Sack","year":"2021 Sep 22","journal-title":"J. Infect. Dis."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1186\/s12916-020-01865-7","article-title":"Early detection of cholera epidemics to support control in fragile states: Estimation of delays and potential epidemic sizes.","volume":"18","author":"R Ratnayake","year":"2020 Dec 15","journal-title":"BMC Med."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"215-221","DOI":"10.1016\/j.ijid.2022.05.039","article-title":"Cholera outbreaks in sub-Saharan Africa during 2010-2019: A descriptive analysis.","volume":"122","author":"Q Zheng","year":"2022 Sep cited 2024 Nov 25","journal-title":"International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"109210","DOI":"10.1016\/j.mbs.2024.109210","article-title":"Modelling techniques in cholera epidemiology: A systematic and critical review.","volume":"373","author":"L Anteneh","year":"2024 Jul cited 2025 Feb 12","journal-title":"Math. Biosci."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"S738-S741","DOI":"10.1093\/infdis\/jiab472","article-title":"Mathematical Modeling of Endemic Cholera Transmission.","volume":"224","author":"D Chao","year":"2021 Dec 20","journal-title":"J. Infect. Dis."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e0006257","DOI":"10.1371\/journal.pntd.0006257","article-title":"Prolonging herd immunity to cholera via vaccination: Accounting for human mobility and waning vaccine effects.","volume":"12","author":"C Peak","year":"2018 Feb 28","journal-title":"PLoS Negl. Trop. Dis."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"2025.02.04.25321698","DOI":"10.1101\/2025.02.04.25321698v1.abstract","article-title":"Estimating the impact of decreasing vaccination response times for outbreaks in low- and middle-income countries.","author":"D Delport","year":"2025 cited 2025 Feb 25","journal-title":"medRxiv."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"2024.06.02.24308241","DOI":"10.1101\/2024.06.02.24308241v1.abstract","article-title":"Estimating the historical impact of outbreak response immunization programs across 210 outbreaks in LMICs.","author":"D Delport","year":"2024 cited 2025 Feb 25","journal-title":"medRxiv."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"S50-S52","DOI":"10.1038\/nature16038","article-title":"Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings.","volume":"528","author":"A Ghani","year":"2015 Dec 2","journal-title":"Nature."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e0004679","DOI":"10.1371\/journal.pntd.0004679","article-title":"Cholera Incidence and Mortality in Sub-Saharan African Sites during Multi-country Surveillance.","volume":"10","author":"D Sauvageot","year":"2016 May 17","journal-title":"PLOS Negl. Trop. Dis."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"222","DOI":"10.11604\/pamj.2016.24.222.8045","article-title":"Cholera public health surveillance in the Republic of Cameroon-opportunities and challenges.","volume":"24","author":"M Ngwa","year":"2016 Jul 12","journal-title":"Pan Afr. Med. J."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1186\/s12889-020-08707-4","article-title":"A rapid assessment of the implementation of integrated disease surveillance and response system in Northeast Nigeria, 2017.","volume":"20","author":"L Ibrahim","year":"2020 May 1 cited 2025 Mar 28","journal-title":"BMC Public Health."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"888-895","DOI":"10.1038\/s41591-024-02810-4","article-title":"Clinical surveillance systems obscure the true cholera infection burden in an endemic region.","volume":"30","author":"S Hegde","year":"2024 Feb 20","journal-title":"Nat. Med."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"A28-A30","DOI":"10.1016\/j.vaccine.2019.06.037","article-title":"Surveillance and the global fight against cholera: Setting priorities and tracking progress.","volume":"38","author":"A Azman","year":"2020 Feb 29","journal-title":"Vaccine."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"A13-A17","DOI":"10.1016\/j.vaccine.2019.07.036","article-title":"Cholera surveillance and estimation of burden of cholera.","volume":"38","year":"2020 Feb 29","journal-title":"Vaccine."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e202","DOI":"10.1016\/S1473-3099(25)00143-4","article-title":"Electronic address: gtfccsecretariat@who.int. Beyond acute watery diarrhoea: New cholera surveillance guidance.","volume":"25","year":"2025 Feb 26","journal-title":"Lancet Infect. Dis."},{"key":"ref24","article-title":"Cholera in the WHO African Region.","year":"cited 2025 Feb 25"},{"key":"ref25","article-title":"Cholera Taxonomy. Middle Distance.","year":"cited 2024 Jun 12"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e0231866","DOI":"10.1371\/journal.pone.0231866","article-title":"geoBoundaries: A global database of political administrative boundaries.","volume":"15","author":"D Runfola","year":"2020 Apr 24","journal-title":"PLOS ONE."},{"key":"ref32","article-title":"Open Spatial Demographic Data and Research.","year":"2020 cited 2025 Mar 13"},{"key":"ref33","article-title":"GitHub - wpgp\/wpgpDownloadR: A toolset for finding and downloading WorldPop (Global Project) products.","year":"cited 2025 Mar 13"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e1004286","DOI":"10.1371\/journal.pmed.1004743","article-title":"Estimating the Proportion of Clinically Suspected Cholera Cases That Are True Vibrio Cholerae Infections: A Systematic Review and Meta-Analysis.","volume":"20","author":"K Wiens","year":"2023","journal-title":"PLoS Med."},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1136\/bmjgh-2024-016491","article-title":"Exploring the burden of cholera in the WHO African region: Patterns and trends from 2000 to 2023 cholera outbreak data.","volume":"10","author":"E Koua","year":"2025 Jan 22 cited 2025 Mar 25","journal-title":"BMJ Glob. Health."},{"key":"ref36","article-title":"Cholera surveillance time series in Africa from 2010 to 2023.","author":"E Lee","year":"2025","journal-title":"OSF."}],"container-title":["Gates Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-16\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-16\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-16\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T10:49:16Z","timestamp":1783594156000},"score":1,"resource":{"primary":{"URL":"https:\/\/gatesopenresearch.org\/articles\/10-16\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,14]]},"references-count":27,"URL":"https:\/\/doi.org\/10.12688\/gatesopenres.16378.1","relation":{"has-preprint":[{"id-type":"doi","id":"10.12688\/verixiv.1061.2","asserted-by":"subject"}]},"ISSN":["2572-4754"],"issn-type":[{"value":"2572-4754","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,14]]},"assertion":[{"value":"Awaiting Peer Review","URL":"https:\/\/gatesopenresearch.org\/articles\/10-16\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"We received funding support from the Vaccine Impact Modelling Consortium (Gates Foundation INV-009125) and Gates Foundation (BMGF INV-044865). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":0,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}