Kenya: Integrated Vector Borne Diseases Outbreak - Emergency Plan of Action (EPoA) DREF n° MDRKE050


A. Situation analysis

Description of the disaster Kenya has been affected by numerous health crises and natural disasters in the past two years. Currently, more than 4 million people are affected by drought coupled with the negative effects of COVID 19 on the economy, the situation is very dire among the poor and those in the hard-to-reach areas of the country (mostly in the arid and semi-arid areas) which, as a result, are the localities most affected by health crises.

The recent emergence and re-emergence of viral infections transmitted by vectors in the country namely Chikungunya, Dengue, Yellow Fever (YF), and others is a cause for international concern. In 2021 an outbreak of Dengue Fever affected 3 counties of the coastal region - Mombasa, Kilifi, and Lamu. This was supported by a DREF allocation. The first two months of 2022 have now also recorded two outbreaks that are currently under national response; Yellow Fever and Chikungunya.

The current vector-borne outbreaks are confirmed in two counties of Wajir and Isiolo. The Yellow Fever virus being more lethal has already led to a swift response from the ministry of health that has put the whole country under alert and vaccination is scheduled to start in around two weeks.

Yellow Fever

The risk of Yellow Fever re-emergence is increasing due to the effects of climate change, drought, and globalization. Informed by the 67th session of the WHO regional committee for Africa, and by the PAHO1 Regional Immunization Technical Advisory Group in 2017, all African Member States including Kenya endorsed the global strategy to Eliminate Yellow Fever Epidemics (EYE).

Before the ongoing outbreak, there was a reported yellow fever outbreak thirty years ago in 1992-1993 in the Kerio Valley. There were 55 persons with hemorrhagic fever (HF) from the affected 3 districts (Baringo, Keiyo South, and Marakwet West) in the period of September 10, 1992, through March 11, 1993 (attack rate = 27.4/100,000 population). Twenty-six (47%) of the 55 persons had serologic evidence of recent yellow fever infection, and three of these persons were also confirmed by yellow fever virus isolation. There was a total of 34 fatalities from this outbreak.
This disease which manifests itself between 3 to 6 days after a mosquito bite (Aedes) is characterized by fever, muscle pain, headache, shivers, loss of appetite, and nausea or vomiting. These symptoms disappear after 3 to 4 days among the majority of the patients. However, about 15% of patients enter a second, more toxic phase and within 24 hours of the initial remission are reported to have a high fever and with several body systems, including the kidneys being affected. Half of the patients who enter this toxic phase die within 10 to 14 days, while the rest recover without significant organ damage.

The current outbreak was first reported in January 2022. Its confirmation took 3 weeks due to limited capacity in the remote areas affected and the fact that that region has not traditionally been affected by yellow fever in the past. The cases were first reported in Merti Sub County of Isiolo County. Kenya Medical Research Institute (KEMRI) has since confirmed 3 positive cases out of 6 samples from the sub-county. As of 23rd Jan 2022, a total of 15 patients presenting fever, jaundice, muscle pain and fever pain (13 males and 02 females) were line-listed; and 03 deaths were recorded. A total of 3 cases turned out positive out of 6 samples analyzed. The majority of the cases are between 11 years-40 years (82.41 and are reported to come from Merti (bordering Wajir) and Garba Tulla (bordering Garissa) sub-counties. Unconfirmed reports later this week have indicated a possibility of new cases in Baringo and Elgeyo Marakwet. The Ministry of Health reported an outbreak and issued an Alert on 3 March 2022 received to all the 47 counties and initiated a response both at the County and national levels on 4 March 2022.

As a response, the Ministry of Health is initiating a national vaccination campaign starting with Wajir, Garissa, Marsabit, Meru, Samburu, Elgeyo Marakwet, Baringo, West Pokot, Turkana, Mandera, and Tana River. Yellow fever vaccine is an effective public health prevention intervention and is offered as a scheduled routine vaccine for children aged 09 months in 4 counties in Kenya (Elgeyo Marakwet, West Pokot, Turkana, and Baringo). However, the yellow fever vaccine can be given to 09 months-60 years during supplementary immunization activities.

Merti Sub County is located in the northern part of Isiolo bordering Wajir, Marsabit, and Samburu counties and Garbatulla Sub County to the south. Both sub-counties (Merti and Garbatulla) are inhibited by people of Cushitic origin whose livelihood is dependent on pastoralism. Cherrab ward often has erratic rainfall patterns and dry season. The area has received average rainfall in December 2021 which brought about an increase in mosquito population which may have been contributed to rising cases of fever.

In Isiolo County, the county disease surveillance team faces challenges in early case detection and management due to a shortage of testing capacity (both PCR and Rapid test kits). Currently PCR, samples must be taken from the sub-counties to the KEMRI-Well Trust laboratory in Nairobi County about 500km away.


The first cases were reported in mid-February 2022 in Kotulo within Wajir County. Between February 10th and 24th, 23 samples from the suspected cases were collected and analyzed at KEMRI Nairobi laboratory, out of these, 5 samples tested positive for the Chikungunya virus, this is from the Ministry of health rapid assessment report. A rapid assessment team by MoH and County Government was deployed to the affected area by the Wajir county department of health. The team visited 50 households from different villages that were suspected to be having patients suffering from Chikungunya. The team identified 16 patients with symptoms of Chikungunya disease. The patients were complaining of severe joint pains, headache, joint swelling, headache, nausea, fatigue. Patients were advised to visit the nearest health facility for supportive treatment. The 15 samples were sent to the KEMRI laboratory for investigation.

The team also conducted a data review in the two facilities in the affected area (Kutulo Health Centre and Somaan Nursing Home). With most of the patients presenting fevers and headaches in December 2021 and based on available data, this could mean the outbreak started in December 2021. The nursing home (Private Facility) had reported 12 suspected Chikungunya Cases starting 2nd January 2022 to 14th February 2022. The team has since line-listed a total of 67 cases in which 5 are confirmed and 53 are probable cases in which most of the cases are epidemiologically linked to the confirmed cases from MoH/KEMRI above. Wargadud Ward in Tarbaj Sub-County is the ward affected by those potential cases.

From historical analysis, the last outbreak reported cases in mid-2016 first occurred in Mandera and later spread to other counties including Mombasa between late 2017 and mid-2018, and a Chikungunya fever outbreak occurred in Mombasa. Wajir’s county is neighboring the county of Mandera, and the actual outbreak remains a risk fo the same Mandera and Mombassa even if cases are not declared for the moment in those counties. Also, from previous outbreaks, the female gender is usually the most affected at 58% and the majority of the case is within age 2-33 years.

Vector-borne epidemics:

Previous outbreak data and monthly trends show that annual upsurges are experienced after the short and long rainfall seasons. The next peak would be June after the long rains, however, in this case, the virus is surging at the beginning of the long rains in March. Therefore, the onset of long rains it will likely make the situation worse as the conditions become more conducive for the larger spread of the disease vector. Hence, with the Mach, April, and May (MAM) rains expected, preventive measures need to be accelerated to reduce the impact of the two diseases.

The affected counties are subject to other vector-borne diseases and rains in the coming months in March, April will increase vectors' development hence the spread of the above diseases in addition to others like Malaria, Rift valley Fever among others. This response will hence tackle this problem by preparing communities to ensure that they have adequate information on vector-borne diseases. In addition, Merti has been noted to have other disease challenges that include frequent cases of Kala-azar reported within the expansive areas of Cherrab ward during dry spells, and cases of Rift Valley fever have also been reported in this area in 2020 with some fatalities.

To summarize the outbreak situation, current yellow fever and Chikungunya outbreaks are both vectors borne diseases and for which emergency actions need to be taken aligned with MoH preventive response and vaccination for yellow fever.