Banjoko Alabi W, Ng'uni Tiza, Naidoo Nitalia, Ramsuran Veron, Hyrien Ollivier, Ndhlovu Zaza M
Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, Durban, South Africa.
Department of Statistics, University of Ilorin, Ilorin, Kwara State, Nigeria.
Sci Rep. 2025 Jul 2;15(1):23667. doi: 10.1038/s41598-025-06704-4.
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.
非洲作为世界上基因多样性最高的地区之一，在高分辨率人类白细胞抗原（HLA）数据中所占比例仍然极低。该地区HLA等位基因广泛的遗传变异突出表明，需要有针对特定人群的免疫遗传学数据来指导T细胞疫苗的研发。本研究分析了来自东非和南非人群的I类HLA数据，以评估区域遗传多样性。分析内容包括等位基因和单倍型频率分布、与哈迪-温伯格平衡的偏差、连锁不平衡以及各人群中性纯合性检验。为了进一步说明非洲HLA的多样性，使用海林格多样性指数和多维标度法，对非洲人群之间以及与非裔美国人和欧裔美国人进行了比较。结果显示，南非人群相对于其他非洲人群的遗传多样性估计平均为34.1%。卢旺达的遗传多样性估计为26.9%，肯尼亚为26.5%，赞比亚为26.5%，乌干达为24.7%。此外，国内分析揭示了每个国家不同部落之间HLA多样性的差异。肯尼亚国内多样性估计平均为51%，乌干达为35.8%，赞比亚为33.2%。这些结果揭示了非洲人群之间不同程度的遗传多样性。与美国人群相比，东非和南非人群在I类HLA等位基因频率上的显著差异表明，在设计针对非洲人群的T细胞诱导疫苗时，外推包括非裔美国人在内的美国人群的HLA数据是不合适的。我们的研究结果强调了迫切需要生成高分辨率HLA数据，以指导针对非洲人群的疫苗研发。
