Could a Kikuyu and a Luhya child need different vaccines?

Prof Zaza Ndhlovu, an associate Professor of Medicine at Harvard Medical School. He explained that a vaccine designed for populations in Europe or North America may not trigger optimal antibody responses in Kenyan populations.

Imagine two children, one in Nyeri and another in Bungoma. They are both vaccinated on the same day with the same vaccine. But what if their bodies react in completely different ways?

That is the possibility raised by a new study that reveals Kenya’s biggest tribes, the Kikuyu and Luhya, are genetically farther apart from each other than many other African communities, at least when it comes to the genes that control how the body fights infections.

The researchers examined genetic data from more than 2,700 people in Kenya, Uganda, Rwanda, Zambia, South Africa, and comparison groups in the United States. Most of the African data came from existing HIV research cohorts that already had genetic information available. The team calculated how diverse each population was and how genetically similar or different they were to one another.

Their findings, published in Nature’s Scientific Reports last month, particularly focus on similarities of the Human Leukocyte Antigen(HLA) genes, which are central to how the body identifies and fights off infections.

“The genetic distances between the Kenyan tribes (Kikuyu and Luhya) are farther apart from each other at all loci (any of the three locations of a gene in a chromosome),” the researchers wrote. They added: “Despite belonging to the same African country, Kikuyu and Luhya tribes had low similarity of 47 per cent and 38 per cent at loci A and B, respectively.”

The study also reported that the Kikuyu have relatively low similarity with almost every other African tribe examined. “The Kikuyu tribe showed relatively low similarity to other African tribes at all loci,” the paper noted.

The findings show the Kikuyu are only between about one-third and two-thirds similar to other groups, which is considered unusually low.

The Star spoke with the study’s lead author, Zaza Ndhlovu, an associate Professor of Medicine at Harvard Medical School, and faculty at the Africa Health Research Institute (AHRI) in South Africa.

He linked this genetic gap, especially between the Kikuyu and Luhya, who are all Bantu in one country, to deep-rooted historical, geographical, linguistic, and evolutionary factors. These differences have important implications for immunological responses, including vaccine efficacy and treatment outcomes, he said.

“While the Kikuyu are part of the Bantu-speaking Eastern Highland groups, the Luhya belong to a Western Bantu cluster but have strong links to Great Lakes Nilotic neighbours. Their divergence likely reflects different ancestral migrations, gene flow, and admixture histories,” he explained.

The Kikuyu live in the central highlands, while the Luhya settled in western Kenya. The two groups had limited intermarriage for centuries, reducing gene flow. Over time, differences were amplified by random genetic drift and by exposure to different disease environments, he said. “Since HLA loci are among the most polymorphic (extremely diverse) in the human genome, they are shaped by local infectious disease landscapes. Kikuyu and Luhya tribes might have been exposed to different pathogen spectra, promoting selection of different HLA alleles and haplotypes,” Prof Ndhlovu said.

Kenya is home to more than 40 tribes, so why did the researchers analyse only Kikuyu and Luhya? The researchers explained that although 109 Kenyans were included, only the Kikuyu (25 individuals) and Luhya (21) had enough individuals to be analysed reliably.

The other Kenyan tribes had too few participants and were excluded to avoid compromising the statistical validity. Prof Ndhlovu said that more communities could be studied in future. “If the needed funding is provided, we may expand this research to include other communities in Kenya,” he told The Star.

The real-world importance of these findings lies in how HLA gene differences influence health. HLA genes determine how the body responds to vaccines, infections and even medicines. Prof Ndhlovu explained: “Divergence in HLA types means each population may present different vaccine-derived epitopes to T cells. A vaccine optimised for alleles common in Luhya may be less immunogenic in Kikuyu, and vice versa.”

 A recent typhoid vaccination at Nyalenda Health Awareness Centre, in Kisumu County. In future, scientists can tailor vaccines to an individual’s needs, reducing potential side effects and predicting in advance how many doses a person might need before they take a shot.

He noted that certain HLA alleles (types) are associated with better outcomes. For example, HLA-B57 has been linked to slower HIV disease progression. If one group carries such gene variants in high numbers and another does not, the course of the disease may differ sharply. This could extend to how well people respond to new vaccines. “Immune-related adverse events or vaccine failure can occur when the immune response is misdirected or insufficient due to poor MHC-peptide compatibility,” Prof Ndhlovu said.

However, the researchers of the study noted that the diversity between the Kikuyu and Luhya is not unusual. Most African tribes have low (less than 70 per cent) similarity between them, even when those tribes are from the same country.

Their paper is titled, “High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations.”

“While there isn’t a universal quantitative cutoff, thresholds of at least 70 per cent are usually considered in practical applications and scientific goals such as large-scale vaccine design or HLA-based matching,” they said.

Prof Ndhlovu said this diversity has direct implications for medical research. “The study’s warning that African countries should not rely on US or European HLA data when designing vaccines for African populations is a scientifically grounded call to action,” he explained. “Most vaccine antigens are optimised for HLA alleles common in Western populations, potentially reducing efficacy in Africa.”

He argued that detailed maps of African HLA diversity are needed to ensure future vaccines work effectively. “Kenya and other African nations must move from data consumers to data producers and decision-makers in vaccine development,” he said.

Prof Ndhlovu said the risks of ignoring these findings are serious. “A vaccine designed for populations in Europe or North America may not trigger optimal T-cell or antibody responses in Kenyan populations. This can lead to suboptimal vaccine efficacy,” he said, explaining that this could result in more breakthrough infections and less protection, undermining herd immunity.

 “If vaccines are perceived as ineffective or harmful for certain communities, vaccine hesitancy and resistance can rise,” he said.

Continued reliance on foreign-designed vaccines also discourages local research and manufacturing and risks leaving Kenya vulnerable in future pandemics.

The study confirmed that Africa is the most genetically diverse region in the world, but remains underrepresented in global genetic datasets. “Africa, being one of the most genetically diverse regions in the world, remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data,” the researchers wrote. This underrepresentation makes it harder to design vaccines that work well in Africa.