High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations
Abstract Africa, being one of the most genetically diverse regions in the world, remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data. The extensive genetic variation in HLA alleles across the region underscores the need for population-specific immunogenetic d...
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Nature Portfolio
2025-07-01
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| author | Alabi W. Banjoko Tiza Ng’uni Nitalia Naidoo Veron Ramsuran Ollivier Hyrien Zaza M. Ndhlovu |
| author_facet | Alabi W. Banjoko Tiza Ng’uni Nitalia Naidoo Veron Ramsuran Ollivier Hyrien Zaza M. Ndhlovu |
| author_sort | Alabi W. Banjoko |
| collection | DOAJ |
| description | Abstract Africa, being one of the most genetically diverse regions in the world, remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data. The extensive genetic variation in HLA alleles across the region underscores the need for population-specific immunogenetic data to guide T-cell vaccine development. This study analysed Class I HLA data from Eastern and Southern African populations to assess regional genetic diversity. Analyses included allele and haplotype frequency distributions, deviations from Hardy–Weinberg equilibrium, linkage disequilibrium, and homozygosity test of neutrality across various populations. To further contextualise African HLA diversity, comparisons were made among African populations and also with African American and European American populations using the Hellinger diversity index and multidimensional scaling methods. The results revealed that South African populations exhibited an estimated average of 34.1% genetic diversity with respect to other African populations. Rwanda demonstrated an estimated 26.9% genetic diversity, Kenya (26.5%), Zambia (26.5%), and Uganda (24.7%). Additionally, in-country analyses revealed variations in HLA diversity among different tribes within each country. The estimated average in-country diversity was 51% in Kenya, 35.8% in Uganda, and 33.2% in Zambia. These results reveal various levels of genetic diversity among African populations. The highlighted differences in HLA Class I allele frequencies between Eastern and Southern African populations compared to US populations, demonstrate that it is inappropriate to extrapolate HLA data from US populations including that of African Americans when designing T-cell-inducing vaccines tailored to African populations. Our findings underscore the urgent need to generate high-resolution HLA data to guide vaccine development tailored to African populations. |
| format | Article |
| id | doaj-art-dab125061cbc4f42978e2ebac8bc2532 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-dab125061cbc4f42978e2ebac8bc25322025-08-20T03:37:31ZengNature PortfolioScientific Reports2045-23222025-07-0115111810.1038/s41598-025-06704-4High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populationsAlabi W. Banjoko0Tiza Ng’uni1Nitalia Naidoo2Veron Ramsuran3Ollivier Hyrien4Zaza M. Ndhlovu5Africa Health Research Institute (AHRI), Nelson R. Mandela School of MedicineAfrica Health Research Institute (AHRI), Nelson R. Mandela School of MedicineAfrica Health Research Institute (AHRI), Nelson R. Mandela School of MedicineSchool of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-NatalBiostatistics, Bioinformatics and Epidemiology Program, Fred Hutchinson Cancer Center, Vaccine and Infectious Disease DivisionAfrica Health Research Institute (AHRI), Nelson R. Mandela School of MedicineAbstract Africa, being one of the most genetically diverse regions in the world, remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data. The extensive genetic variation in HLA alleles across the region underscores the need for population-specific immunogenetic data to guide T-cell vaccine development. This study analysed Class I HLA data from Eastern and Southern African populations to assess regional genetic diversity. Analyses included allele and haplotype frequency distributions, deviations from Hardy–Weinberg equilibrium, linkage disequilibrium, and homozygosity test of neutrality across various populations. To further contextualise African HLA diversity, comparisons were made among African populations and also with African American and European American populations using the Hellinger diversity index and multidimensional scaling methods. The results revealed that South African populations exhibited an estimated average of 34.1% genetic diversity with respect to other African populations. Rwanda demonstrated an estimated 26.9% genetic diversity, Kenya (26.5%), Zambia (26.5%), and Uganda (24.7%). Additionally, in-country analyses revealed variations in HLA diversity among different tribes within each country. The estimated average in-country diversity was 51% in Kenya, 35.8% in Uganda, and 33.2% in Zambia. These results reveal various levels of genetic diversity among African populations. The highlighted differences in HLA Class I allele frequencies between Eastern and Southern African populations compared to US populations, demonstrate that it is inappropriate to extrapolate HLA data from US populations including that of African Americans when designing T-cell-inducing vaccines tailored to African populations. Our findings underscore the urgent need to generate high-resolution HLA data to guide vaccine development tailored to African populations.https://doi.org/10.1038/s41598-025-06704-4AfricaHLAAllelesHaplotypesDiversity indices |
| spellingShingle | Alabi W. Banjoko Tiza Ng’uni Nitalia Naidoo Veron Ramsuran Ollivier Hyrien Zaza M. Ndhlovu High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations Scientific Reports Africa HLA Alleles Haplotypes Diversity indices |
| title | High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations |
| title_full | High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations |
| title_fullStr | High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations |
| title_full_unstemmed | High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations |
| title_short | High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations |
| title_sort | high resolution class i hla a b and c diversity in eastern and southern african populations |
| topic | Africa HLA Alleles Haplotypes Diversity indices |
| url | https://doi.org/10.1038/s41598-025-06704-4 |
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