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.