{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T09:14:36Z","timestamp":1787908476417,"version":"build-2784847793"},"update-to":[{"DOI":"10.12688\/aasopenres.12872.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000}}],"reference-count":35,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["110330\/Z\/15\/Z"],"award-info":[{"award-number":["110330\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["207569\/Z\/17\/Z"],"award-info":[{"award-number":["207569\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["aasopenresearch.org"],"crossmark-restriction":false},"short-container-title":["AAS Open Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background<\/ns4:bold>\n                    : Rabies causes an estimated 59,000 human deaths annually. In Kenya, rabies was first reported in a dog in 1912, with the first human case reported in 1928. Here we examine retrospective rabies data in Kenya for the period 1912 \u2013 2017 and describe the spatial and temporal patterns of rabies occurrence in the country. Additionally, we detail Kenya\u2019s strategy for the elimination of dog-mediated human rabies by 2030.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods<\/ns4:bold>\n                    : Data on submitted samples and confirmed cases in humans, domestic animals and wildlife were obtained from Kenya\u2019s Directorate of Veterinary Services. These data were associated with the geographical regions where the samples originated, and temporal and spatial trends examined.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results<\/ns4:bold>\n                    : Between 1912 and the mid 1970\u2019s, rabies spread across Kenya gradually, with fewer than 50 cases reported per year and less than half of the 47 counties affected. Following an outbreak in the mid 1970\u2019s, rabies spread rapidly to more than 85% of counties, with a 4 fold increase in the percent positivity of samples submitted and number of confirmed rabies cases. Since 1958, 7,584 samples from domestic animals (93%), wildlife (5%), and humans (2%) were tested. Over two-thirds of all rabies cases came from six counties, all in close proximity to veterinary diagnostic laboratories, highlighting a limitation of passive surveillance.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions<\/ns4:bold>\n                    : Compulsory annual dog vaccinations between 1950\u2019s and the early 1970\u2019s slowed rabies spread. The rapid spread with peak rabies cases in the 1980\u2019s coincided with implementation of structural adjustment programs privatizing the veterinary sector leading to breakdown of rabies control programs. To eliminate human deaths from rabies by 2030, Kenya is implementing a 15-year step-wise strategy based on three pillars: a) mass dog vaccination, b) provision of post-exposure prophylaxis and public awareness and c) improved surveillance for rabies in dogs and humans with prompt responses to rabies outbreaks.\n                  <\/ns4:p>","DOI":"10.12688\/aasopenres.12872.2","type":"journal-article","created":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T10:10:21Z","timestamp":1550225421000},"page":"23","update-policy":"https:\/\/doi.org\/10.12688\/aasopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":27,"title":["A hundred years of rabies in Kenya and the strategy for eliminating dog-mediated rabies by 2030"],"prefix":"10.12688","volume":"1","author":[{"given":"Austine O","family":"Bitek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Osoro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peninah M","family":"Munyua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7485-6416","authenticated-orcid":false,"given":"Mark","family":"Nanyingi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0720-7747","authenticated-orcid":false,"given":"Yvonne","family":"Muthiani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6605-988X","authenticated-orcid":false,"given":"Stella","family":"Kiambi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathew","family":"Muturi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Athman","family":"Mwatondo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3386-3430","authenticated-orcid":false,"given":"Rees","family":"Muriithi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Cleaveland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katie","family":"Hampson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Kariuki","family":"Njenga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"PM","family":"Kitala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5754-0556","authenticated-orcid":false,"given":"SM","family":"Thumbi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2019,2,15]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"e0003709","DOI":"10.1371\/journal.pntd.0003709","article-title":"Estimating the global burden of endemic canine rabies.","volume":"9","author":"K Hampson","year":"2015","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-2","article-title":"WHO fact sheet on rabies 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The spatiotemporal&nbsp;part lacks detail&nbsp;on the method of data collection, analysis, and results. For example: The objective&nbsp;was to examine the pattern&nbsp;of rabies spread in the country from 1912-2017 but the data in Fig 1-3 shows only for 1958-2017. Thus I advise to clearly state that in the method section.  \n<i>We have provided a clarification for this correct observation under the data collection section (Methods).<\/i> \n<i>For the period prior 1958, data on the number of samples submitted for testing and the species of animals they were obtained from were not available and only aggregate numbers of positive cases of rabies per year per county were available for analyses.<\/i>  The Kenyan strategy aspect of the paper is not mentioned in the methods as well as&nbsp;results section. Was it based on personal opinion or systematic review\/ literature search?  \n<i>We have included a statement in the methods section on how the strategy was developed and provided a reference linking to the detailed strategy.<\/i>  \n<i>\u201cThis manuscript discusses the strategies put in place for the elimination of human rabies in Kenya by the year 2030. This strategic plan was developed through and elaborate consultative process that involved government departments in health and livestock, research and academic institutions, non-governmental organizations and international partners in Kenya working on public and animal health. The detailed strategy is available online<u><sup>13<\/sup><\/u>.\u201d<\/i>  One of the evaluations guidelines of this manuscript asks if the authors provided the necessary data for others to replicate the study. I would recommend the authors to provide the data and R codes used&nbsp;in a usable format.&nbsp;  \n<i>We have provided the datasets and the R codes used for this manuscript under the \u201cData availability\u201d section<\/i> \n<i>\u201c<\/i>\n<i>The data underlying this study is available from Open Science Framework&nbsp;<u>http:\/\/doi.org\/10.17605\/OSF.IO\/B6WKR<\/u><u><sup>35<\/sup><\/u>. It contains two datasets - dataset 1: \u201cKenyaRabiesData1958to2017.csv\u201d that produces Figure 1, 2, 3 and 5 and dataset 2: \u201c100YearsRabiesData.csv\u201d that produces Figure 4. The R codes used are provided in a file named \u201cRcodes_100yearsRabiesinKenya.R\u201d. These datasets are available under a CC0 1.0 Universal license. No records of samples submitted were available for the years 1995, 1996 or 1997.\u201d<\/i> &nbsp; The fact that diagnostic labs were established at different times, comparing the number of samples submitted\/tested positive could be tricky as the distance of countries forms labs, public awareness, lab capacities could have influenced it. For instance Figure 2 tells that the percent positive increased over time. Does it mean that the labs used improved methods over time? As one of the objectives was to see the trend of rabies overtime, the method section does not explicitly show the method applied. The authors may consider statistical methods to explore the trend. However, a higher number of submitted\/reported samples doesn\u2019t mean a high incidence of rabies. Thus, using mixed models where proximity to a lab, the age of the lab (which might have contributed to public awareness) should be included in the analysis to account for the clustering effect.  \n<i>We have carried out the analysis using mixed effect models to account for proximity to the testing laboratories. We did not have any data on the changes in the sensitivities of the testing methods or when the exact time when laboratories would have diagnostic methods. This is however unlikely to have caused a major difference since rabies diagnostic methods using brain samples have been known to have be fairly reliable. We tested models with and without the random effect and the results were consistent \u2013 an increase in the proportion of samples submitted that were positive for rabies.<\/i> \n<i>We have provided details of the data analysis as below \u2013 within the methods section.&nbsp;<\/i> \n<i>\u201cWe determined the proportion of samples submitted that were positive for rabies by year and for each county. Linear mixed-effect models with year as the fixed effect, and the county as a random effect (to account for proximity to testing laboratories) were used to test if the proportion of submitted samples that were positive for rabies changed over time.\u201d<\/i>   The statement \u2018\u2019the first reported case in a dog in the outskirts of Nairobi in 1912, and in a woman from the Lake Victoria basin in 1928\u2019\u2019 was mentioned twice in the MS, one in the second paragraph of the introduction and second, under \u2018\u2019spatial distribution of rabies in Kenya\u2019\u2019. \n<i>The statement under the \u201cspatial distribution of rabies in Kenya\u201d has been rephrased.<\/i>   The last sentence of under the \u2019spatial distribution of rabies in Kenya\u2019\u2019 could move to discussions section.&nbsp; \n<i>We have moved the statement to the discussion section.<\/i>  &nbsp;I think it would be more explicit if table 1 contains info on the region from which the samples came and year.&nbsp;  \n<i>We have 47 regions in the country and including information on region, species and proportion of submitted samples would result in a long difficult to read table. We have however provided all the data as part of the supplementary files (see data availability section).<\/i>  Please make the distinction if numbers given on fig 1-3 are for dogs or all species? As dogs are major sources of rabies for human and others, a line graph or bar graph for all animal spp involved would show the contributions of each over time.  \n<i>We have amended the legend of Figures 1 and 2 to indicate these are from all human and animal samples available in our dataset.<\/i>","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v2#referee-comment-3095","order":1,"name":"referee-comment-3095","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/aasopenres.13938.r26557, Darryn L Knobel, Center\u00a0for\u00a0Conservation Medicine\u00a0and\u00a0Ecosystem Health, Ross University School of Veterinary Medicine\u00a0(RUSVM), Basseterre, Saint Kitts and Nevis, 14 Aug 2018, version 1, indexed","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v1#referee-response-26557","order":2,"name":"referee-response-26557","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Thumbi Mwangi<\/b>; \n<i>Posted: 27 Nov 2018<\/i>; \n<i>We have provided the two datasets:<\/i> \n<i>-&nbsp;&nbsp;&quot;KenyaRabiesData1958to2017.csv&quot; that is used to produce Figure 1, 2, 3 and 5, and<\/i> \n<i>- \u201c100YearsRabiesData.csv\u201d that is used to produce Figure 4.<\/i> \n<i>The R codes for the analysis are also provided named \u201cRcodes_100yearsRabiesInKenya.R\u201d.<\/i> \n<i>These datasets and R codes are available under the \u201cData availability\u201d section of the manuscript through the Open Science Framework -&nbsp;<\/i>http:\/\/doi.org\/10.17605\/OSF.IO\/B6WKR  More detail, either in the article or as metadata to the source files,&nbsp;is also necessary to describe how the dataset was compiled. For example, I know the administrative units in Kenya have not remained constant&nbsp;over the period of the study. How was this handled in attributing location to specimens? &nbsp; \n<i>We have included the statement below under the \u201cData Collection\u201d section to clarify how we attributed location to the specimens submitted.<\/i> &nbsp; \n<i>\u201cWe obtained records for the years 1912 \u2013 2017 from the Kenya Directorate of Veterinary Services and extracted data on the number of samples submitted for rabies testing, dates of sample submission, animal species and humans, administrative units (counties\/districts) where the samples came from, and test results. As the administrative units in Kenya have changed over time, each unit reported in the raw data was matched a current county. The analyses were conducted per existing counties to allow for consistency in reporting.\u201d<\/i>  There is a lack of detail&nbsp;in the paper regarding the distribution of rabies diagnostic laboratories which should be addressed, given the authors' assertion that this affects surveillance effort and creates bias. The county locations of the CVL and RVIL should be given, to allow the reader to relate this information to Figure 5 and the results presented in the section on spatial distribution of rabies. (For example,&nbsp;the Central Veterinary Laboratory is described as 'in Kabete' but in which county is it [relating to Figure 5]? The second paragraph of the Methods section states that specimens should be submitted to only two other regional laboratories that carry out the&nbsp;FAT [n addition to the CVL], namely Kericho and Mariakani, but in what county are these?) Other regional laboratories are mentioned in the second paragraph of the discussion, implying that these have strengthened the surveillance system, but do these laboratories conduct the FAT? Or are they only mentioned as an indicator of the improvements in the general surveillance system (not specific to rabies)? Why is there no evidence of submission bias around the Mariakani RVIL? &nbsp; \n<i>We have included the location of the CVL and RVILs within Figure 5. Under the section \u201cData collection\u201d, we have clarified on the locations of the central and regional veterinary laboratories and how they operate in regard to rabies diagnosis.<\/i> &nbsp; \n<i>\u201cThe samples can be sent to the Central Veterinary Laboratory (CVL) located in Nairobi County or to any of six Regional Veterinary Investigation Laboratories (RVIL). The RVILs are across the country in Nakuru, Eldoret, Kericho, Garissa, Nyeri and Kilifi Counties. After initial testing, all samples were further submitted to one of three laboratories: the Central Veterinary Laboratory (CVL), the Regional Veterinary Investigation Laboratories (RVIL) in Kericho in Western Kenya, or RVIL in Kilifi on the Coast. These three laboratories carry out the Fluorescent Antibody Test (FAT), which is the confirmatory rabies diagnostic test recommended by the World Organisation for Animal Health (OIE)<sup>15<\/sup>. The test results were reported against the sample\u2019s source species and county of origin.\u201d<\/i> &nbsp; \n<i>The Mariakani RVIL is located at the Coast, a region with less cultural practice of keeping dogs associated with the predominant religion and could possibly explain the observation.<\/i>  Although the paper is generally very well written, it would benefit from a further editorial review with a critical eye. For example:&nbsp;the use of a comma separator for 1,000s is inconsistent between the first and second paragraph of the Results; apostrophes should not be used to form plurals of numbers such as &quot;the 1950's&quot; etc. (at least not according to the APA Style); the second and third sentences of the first paragraph of the Discussion should be combined; &quot;US&quot; should be written as &quot;U.S.A.&quot; or in full in the 6th paragraph of the Discussion, and the writing in the 7th paragraph of the Discussion needs to be reviewed (e.g. &quot;there is evidence&nbsp;\n<i>that<\/i>&nbsp;rabies can be eliminated&quot;; &quot;&quot;may be may be contributing&quot;; These misconceptions&nbsp;\n<u>that<\/u>&nbsp;include that rabies&quot;). &nbsp; \n<i>Many thanks for highlighting these errors \u2013 these have been rectified.<\/i>","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v2#referee-comment-3094","order":3,"name":"referee-comment-3094","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/aasopenres.13938.r26554, Deborah J Briggs, College of Veterinary Medicine\u00a0, Kansas State University, Manhattan, KS, USA, 16 Aug 2018, version 1, indexed","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v1#referee-response-26554","order":4,"name":"referee-response-26554","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Thumbi Mwangi<\/b>; \n<i>Posted: 27 Nov 2018<\/i>; Many thanks for taking time to review the work we present in this manuscript and for the encouraging comments.","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v2#referee-comment-3093","order":5,"name":"referee-comment-3093","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/aasopenres.13938.r26556, Bassirou Bonfoh, Centre Suisse de Recherches Scientifiques en C\u00f4te d'Ivoire (CSRS), Abidjan, Cote d'Ivoire, 04 Sep 2018, version 1, indexed","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v1#referee-response-26556","order":6,"name":"referee-response-26556","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Thumbi Mwangi<\/b>; \n<i>Posted: 27 Nov 2018<\/i>; Many thanks for the very useful review comments and suggestions. We have addressed them and please find below some specific responses. &nbsp; Data used in the study came from national records maintained at the central veterinary laboratory and were obtained as a compiled dataset with information on the geographic location and species the samples were obtained from, and the test results. Individual annual reports were not accessed or used.&nbsp;  We have provided details (Methods - Data collection \u2013 Paragraph 2) of how the data were obtained, reviewed, cleaned and used to create the dataset analysed in this manuscript. &nbsp; Paragraph 4 of the discussion section has addressed the structural adjustment programs and their consequence on the provision of veterinary services and disease control including for rabies. &nbsp; \n<i>\u201cThe rapid increase in the number of rabies cases detected and regions affected (from the mid 1970s to the mid 1980s) coincided with the implementation of the Structural Adjustment Policies (SAPs) that privatized veterinary services in Kenya&nbsp;<sup>19<\/sup>. The SAPs resulted in marked reduction in the provision of crucial public goods including decreased public funding for veterinary services. The veterinary sector was privatized with government employing fewer veterinary officers and providing reduced public financing for disease control and animal production.&nbsp;&nbsp;The result was a collapse of veterinary services including of the mass dog vaccination campaigns, which may have contributed to the spread of rabies across the country and resulting endemic status.\u201d<\/i> &nbsp; We have included a statement in the conclusion on the importance of vet services in achieving rabies elimination. &nbsp; \n<i>\u201cA functioning veterinary health care system is critical towards achieving rabies elimination. Countries endemic with the disease require to invest in the adequate provision of veterinary services to have effective mass dog vaccination and rabies surveillance system.&quot;<\/i>","URL":"https:\/\/aasopenresearch.org\/articles\/1-23\/v2#referee-comment-3092","order":7,"name":"referee-comment-3092","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"SMT is an affiliate of the African Academy of Sciences.\nThis work was supported by the Wellcome Trust [110330\/Z\/15\/Z to SMT, 207569\/Z\/17\/Z to KH]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":8,"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"}]}}