Genomic characterization of HLA class I and class II genes in ethnically diverse sub‐Saharan African populations: A report on novel HLA alleles

Abstract

HLA allelic variation has been well studied and documented in many parts of the world. However, African populations have been relatively under‐represented in studies of HLA variation. We have characterized HLA variation from 489 individuals belonging to 13 ethnically diverse populations from rural communities from the African countries of Botswana, Cameroon, Ethiopia, and Tanzania, known to practice traditional subsistence lifestyles using next generation sequencing (Illumina) and long‐reads from Oxford Nanopore Technologies. We identified 342 distinct alleles among the 11 HLA targeted genes: HLA‐A, ‐B, ‐C, ‐DRB1, ‐DRB3, ‐DRB4, ‐DRB5, ‐DQA1, ‐DQB1, ‐DPA1, and ‐DPB1, with 140 of those alleles containing novel sequences that were submitted to the IPD‐IMGT/HLA database. Sixteen of the 140 alleles contained novel content within the exonic regions of the genes, while 110 alleles contained novel intronic variants. Four alleles were found to be recombinants of already described HLA alleles and 10 alleles extended the sequence content of already described alleles. All 140 alleles include complete allelic sequence from the 5′ UTR to the 3′ UTR that are inclusive of all exons and introns. This report characterizes the HLA allelic variation from these individuals and describes the novel allelic variation present within these specific African populations.

The subdued post-boost spike-directed secondary IgG antibody response in Ugandan recipients of the Pfizer-BioNTech BNT162b2 vaccine has implications for local vaccination policies

“…This study offers valuable insights but is limited by its small sample size (n=48), which may not fully represent the diverse SSA demographic ( 37 – 39 ). In line with this, our study’s limited sample size precluded an extensive stratification by gender.…”

Nomenclature for factors of the HLA system, update July, August and September 2023

“…Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. An additional 140 alleles were recently published but have not been included in Table 3 due to space considerations 3,4 …”

“…An additional 140 alleles were recently published but have not been included in Table 3 due to space considerations. 3,4 All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IPD-IMGT/ HLA Database using the sequence submission tool provided. 5 The IPD-IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/ ipd/imgt/hla…”