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World of Genomics: Kenya

Article originally written by Aaron Khemchandani, November 2022. Updated by Charlotte Taylor, January 2024.

For the latest edition in our World of Genomics series, we head over to Kenya. Famous for its scenic landscapes and vast wildlife preserves, the country’s treasured national parks are well known for their rich biodiversity. This makes Kenya one of the world’s best safari destinations and as a result, millions of tourists visit every year to catch a glimpse of nature in its purest form. While visitors gawk at the wide variety of living things that populate the nation’s parks and reserves, scientists are busy understanding these living things on a genetic level. In fact, Kenya has made large strides in the field of genetics and genomics and its future in this sector has shown significant promise. 

The population of Kenya 

Located in east Africa, Kenya borders the Indian Ocean as well as five countries: Ethiopia, South Sudan, Tanzania, Somalia and Uganda. It is a region with a rich and extensive history that has long been used by archaeologists to understand the evolution of man, as it was inhabited by our early hominin ancestors some 6 million years ago! The earliest records of humans in Kenya date back to around 1.2 million years ago. However, the first modern settlers emerged in 50,000 BC. 

The country remained independent until 1895, when it was colonized and subsequently governed by the British Empire. Kenya remained a colony until 1963, and the near 70-year period of British rule would have long-lasting effects on the country and its people. 

Since gaining independence, Kenya has embarked on the path to stability, making important progress in a range of major economic sectors leading to improvements in overall quality of life. Life expectancy has increased by almost 20 years since 1963, and this aligns with a similarly significant decline in infant mortality in the same period. Furthermore, the country has also showcased notable technological advancements, with mobile phone subscriptions per 100 people among the highest in the continent. It has also been cited as a hub for scientific progress in East Africa, with genetics research being a major focus. 

Geographic and demographic information 

Summary statistics 

  • Total: 113.42 billion USD 
  • Per capita: 2,081 USD 

Population statistics 

  • Population size: 2022 estimate: 55,171,364 (2019 Census: 47,564,296) 
  • Birth rate:2021 estimate: 28 per 1000 people  
  • Death rate:2021 estimate: 8 per 1000 people 
  • Infant mortality rate:2021 estimate: 28 per 1000 people 
  • Life expectancy:2021 estimate: 61 
  • Ethnicities: Kenya has a very diverse population and is home to at least 42 ethnic groups. Nilotes (30%) and Bantus (67%) make up the overwhelming majority of people, with the remaining 3% mainly accounted for by Arabs, Indians and Europeans. 

Healthcare system 

The Kenyan healthcare system is comprised of both public and (both profit and non-profit) private healthcare, with the latter contributing to over 40% of the country’s health services. The government provides coverage through contributory health insurance, subsidies financed by general taxation and out-of-pocket payments by healthcare consumers. 

Policy reforms within the last decade have demonstrated the intent to extend healthcare coverage for the poorest and most vulnerable of Kenya’s population, including the provision of free maternity services in all public health facilities, which has contributed to a reduction in maternal mortality rates. In addition, a health insurance subsidy program (HISP) was introduced in 2014 that fully subsidises insurance premiums for the lowest income households, aimed at improving access to public and low-cost private healthcare services. 

Five years ago, the government announced an ambitious plan to provide universal healthcare (UHC) for all citizens and, although healthcare spending initially increased to finance this agenda, the combination of COVID-19 and significant private sector growth has led to what many describe as underfunding of the public sector. As a result, the quality of public healthcare has declined in many areas of the country and, while the strategies mentioned above have aided the removal of access barriers for those in poverty to both public and private healthcare, because direct costs only account for a small proportion of total healthcare costs, the poor remain vulnerable to catastrophic healthcare expenditure (CHE). Recent data highlights that while those in the richest quintile have a CHE incidence of 2%, the same figure for the poorest quintile is approximately 10%, highlighting the continued lack of financial protection for this population group.  

In conclusion, Kenya’s healthcare system has made significant progress in the past decade, leading to improvements in quality of life and life expectancy. However, the system faces challenges in achieving UHC, and the poorest households remain exposed to financial risk and declining healthcare services. 

Health priorities 

Communicable, maternal, neonatal and nutritional diseases account for the top 4 leading causes of death in Kenya. Of these diseases, HIV/AIDS is by far the most prevalent source of mortality and morbidity, despite being well below the continental average. It accounted for 103 deaths per 100,000 people as of 2019, while lower respiratory tract infections represent the second-highest cause of mortality in the region. Despite these challenges, the general improvement of Kenya’s healthcare capacities as well as the emergence of novel prevention and control strategies have led to a decline in the burden of communicable diseases on mortality, and this trend is expected to continue. 

One such strategy was developed in 2016, when the United States Centres for Disease Control and Prevention (CDC) partnered with the Kenyan government to introduce the Detection and Response to Respiratory Events (DaRRE) strategy to better control respiratory disease outbreaks, mainly by increasing surveillance and improving detection training for healthcare professionals. This strategy was a success, helping to reduce the burden of lower respiratory tract infections throughout its implementation. 

Another CDC partnership involved the development of targeted strategies to reduce the transmission of HIV in the country. This took the form of providing antiretroviral therapy for the disease as well as creating information campaigns, supporting male circumcision and improving laboratory training. Among other things, this initiative resulted in significant declines in perinatal HIV transmission as well as increased accessibility of care for patients. 

Non-communicable diseases (NCDs), meanwhile, also contribute considerably to morbidity and mortality, as they are responsible for 50% of inpatient hospital admissions and 39% of all annual deaths. However, due to screening levels varying widely throughout the country, the prevalence of NCDs is thought to be underestimated. The burden of NCDs continues to pose significant challenges to the Kenyan healthcare system, as a 2015 survey revealed that just one-third of chronic disease patients have access to their medicines at home, owing in part to a lack of access to treatments in the public sector and a lack of affordability in the private sector. 

Genomic medicine capabilities 

The scope of genomics infrastructure in Kenya has grown rapidly in recent years. Newly loosened restrictions surrounding genetically modified crops have enabled the country to establish itself as a market leader in agricultural biotechnology on the African subcontinent, as since 2011, strict biosafety regulations had been in place that did not adapt to or account for the constant emergence of new and revolutionary technologies. Now, though, Kenya has taken the initiative to redraft these laws as it seeks to harness the power of gene editing to help expand its agricultural economy. Further to this, universities in Kenya have begun partnering with science and technology centres to generate several genomics-related education programs, aiming to ensure the next generation of scientists carries on with the quest for genetic innovation. 

However, the most notable aspect of Kenya’s recent genomics research relates to viral sequencing. Laboratories throughout the country were among the first to sample the SARS-CoV-2 virus and have been integral to supporting continent-wide sequencing networks. New variants were collected and sequenced quickly, with some labs able to sequence up to 700 samples daily. Kenyan labs have also worked extensively with the World Health Organisation (WHO) to support neighbouring countries with less extensive diagnostic capabilities, collecting samples and returning sequences at a fast rate. The COVID-19 pandemic, while devastating, enabled Kenya to progress in its gene sequencing capabilities and the nation’s scientific infrastructure has been invaluable to surrounding countries.  

Despite this progress, some challenges remain. As previously mentioned, almost 4 in 10 people in Kenya die from NCDs and a large part of this burden arises from genetic blood disorders. Therefore, widespread access to genetic screening is crucial in reducing disease mortality. However, availability is limited – particularly in the public sector. Instead, patients are most often consulted by general physicians with varying levels of experience and training in genetic diagnoses. Although the screening industry has gradually grown in the private sector, affordability as well as a lack of insurance coverage present major barriers to access. 

In addition, as of last year, genetic counselling was not a licensed profession in Kenya and as such, the number of people providing this service remains low.  A 2021 study surveying the sentiments of a sample of 15 genetic counsellors revealed that a majority felt they had not received enough practical experience and that opportunities for in-person training within Kenya were severely limited. Most counsellors reported sourcing most of their information online due to a lack of local availability, highlighting deficits in the training infrastructure set up for this field. 

Notable projects 

  • Striga resistance in Sorghum: Sorghum is an important local crop that is in high demand not only for food, but for the near billion-dollar brewery industry in the country. However, the parasitic striga weed poses strict constraints to the production of sorghum and other cereal grains, and Prof. Steven Runo is working on a project that aims to evaluate the knockout of particular sorghum genes in conferring striga resistance. If successful, this research has the potential to drastically increase sorghum growth, thus propelling multiple sectors of Kenya’s economy. 
  • Developing transgenic animal resistance to animal trypanosomiasis: Animal trypanosomiasis is a disease that brings about huge losses for livestock-dependent communities throughout sub-saharan Africa, and eradication efforts have long been unsuccessful. However, Wilkister Nakami Nabulindo of the International Livestock Research Institute (ILRI) is working on a project to introduce a transgene into groups of indigenous goats that may confer resistance when goats carrying this gene are bred. If this novel strategy is successful, it has the potential to significantly boost livestock growth and greatly reduce the prevalence of animal trypanosomiasis. 
  • Machine learning in the provision of treatment insights: The Sydney Brenner Institute for Molecular Bioscience is working on a project that involves analysing genomic data collected in South Africa and Kenya over the past two decades using curated AI and machine learning algorithms. The goal of this project to provide health planning and treatment insights into multi-morbidity within those regions. 
  • The Bioinformatics Mentorship and Incubation Program: The Bioinformatics Mentorship and Incubation Program was established as a solution to the rising demand for skilled bioinformaticians in genomics research. This mentorship program bridges the gap after undergraduate programs, producing competent bioinformaticians with the hope of advancing genomics research in Kenya. 
  • The Bovine Pangenome Consortium (BPC): This project focuses on assembling cattle genomes to achieve a more complete understanding of cattle genomic diversity. The BPC was established with the goal of providing genome assemblies and a shared pangenome reference that will be accessible to the research community. This resource will serve as a foundation for future advancements in cattle genomic selection. 

Notable organisations and companies 

  • Kenya Medical Research Institute (KEMRI): A national department responsible for carrying out the majority of health and genetics research in the country. It was established in 1979, and has since grown to be one of the leading research centres across the continent. During the height of the COVID-19 pandemic, KEMRI partnered with the Wellcome Trust to provide diagnostic testing for the country’s coastal region, vastly improving viral detection. 
  • Genetic Resources Research Institute (GeRRI): A subsidiary of the Kenya Agricultural and Livestock Research Organisation, the GeRRI aims to document and disseminate plant, microbial and animal genetic data in order to inform policy as well as biotechnology innovation. 
  • International Livestock Research Institute (ILRI): Co-hosted by Kenya and Ethiopia, the ILRI is a research partnership that focuses on, among other things, extensive research on understanding the genetics of livestock in order to expand the scope of agricultural genetic technologies. Recent research centres around poultry stem cells and how they can be used to safeguard against loss of diversity. 
  • Bioinformatics Institute of Kenya (KIBS): KIBS is a leading provider of DNA testing and sequencing in the country, run by teams of geneticists who are at the vanguard of Kenya’s genomics research. KIBS also runs FreeLab, a service delivering wide varieties of genetic tests free of charge. As such, the organisation has had an important role to play in increasing the accessibility and affordability of diagnostic tests throughout the region. 

Notable individuals 

  • Prof. Anne Muigai: Muigai is a molecular population geneticist at the Jomo Kenyatta University of Agriculture and Technology in Kenya and chair of the African Biogenome Project. This initiative aims to dramatically increase non-human genome sequencing efforts with the end goal of informing policy and maintaining biodiversity across the continent. 
  • Dr. Ruth Wanyera: Wanyera is the National Wheat Research Program Coordinator at the Kenya Agricultural and Livestock Research Organisation (KARLO), and has won numerous awards over the span of her career dedicated to understanding the genetics of plant protection and growth. She made significant breakthroughs in the phenotyping of stem rust, a fungal disease that devastates cereal crops. Her efforts have contributed to increased crop growth and food security throughout the country, and she has laid the groundwork for Kenya’s encouraging future in plant genetics. 
  • Dr. Hussein Abkallo: As one of Kenya’s leading scientists in the field of CRISPR/Cas9 gene editing, Akballo has published novel research outlining the pathogenic mechanisms of Plasmodium falciparum, a protozoa that causes severe malaria. He has spearheaded Kenya’s increasingly promising foray into gene editing research, and continues to conduct important work on prominent diseases in the region. 
  • Dr. Godwin Macharia: Macharia is the Centre Director of KARLO and another scientist internationally recognised for his work understanding the genetics of cereal crops and their reaction to certain diseases, most notably stem rust. He helped characterise the genetics of disease resistance in wheat and barley, thus contributing to better and more robust crop production. 
  • Dr. Michele Ramsay:Ramsay led the Africa Wits-INDEPTH Partnership for Genomics Research (AWI-Gen), a transcontinental study across five African countries including Kenya, that aimed to understand the genetic and environmental contributions to cardiometabolic diseases in these regions. The data collected by Ramsay’s team has shed a light on population sub-structures across the continent as well as expanded the extent to which African people and environmental contexts are taken into account within the overall research field. 

The future genomics landscape 

As previously mentioned, cutting-edge gene editing is leading Kenya’s steep ascent into the world of genomics and genetics, as a number of ongoing projects involving CRISPR/Cas9 technology aim to increase the robustness of agricultural sectors by conferring disease resistance and growth efficiency. In addition, recent stem cell research conducted by national genetic institutions has shown how biodiversity can be protected in nature as well as livestock, and this research is poised to continue. 

Whilst Kenya has more developed sequencing infrastructure than some other African countries, there are still many barriers to conducting independent projects. Although sequencing can be carried out within the country, developments in analysing and interpreting the data centrally are required. This would enable Kenyan public health organisations to address a variety of issues, improving patient outcomes and mortality rates. The continuation of projects such as the aforementioned Bioinformatics Mentorship Program will continue to bridge this gap. 

The integral role of Kenyan laboratories in quickly screening and sequencing new COVID-19 variants allowed for better viral control throughout the continent, showcasing just how promising the country’s future in this field is. Furthermore, increased prevalence of genetic programs in early and higher education sets up the next generation of Kenyan geneticists to continue this research and usher in a new era of scientific success.