Genotypic and serotypic characterization of HIV in Ethiopia

Abstract

The human immunodeficiency virus type I (HIV-1) is characterized by a high genomic heterogeneity. Different subtypes and inter-subtype recombinants have been identified in the HIV pandemic. The most precise and widely used method for subtype classification is based on molecular biology techniques; nucleotide sequencing of partial genomic fragments. However, since these methods are expensive, and demands high sample quality, it is not applicable for large epidemiological studies of subtype distributions.

The aim of the present study was, to serologically and genotypically characterize HIV- 1 strains in Ethiopian patient materials. The pattern of serological reactivities of anti-HIV-1 antibodies to synthetic peptides of the five most prevalent subtypes, A-E, was studied by enzyme immunoassay (EIA). The peptides were 15 amino acids long and covered the middle part of the V3 region. The vast majority of the tested Ethiopian sera recognized the V3 peptide produced based on the local subtype C strain. Using substitution analogue peptides of the Ethiopian subtype C V3 sequence, it was found that the most essential amino acid residue for subtype C specific reactivity, was the glutamine (Q) within the GPGQ motif. Whereas, the GPG motif was responsible for the cross-reactivities with subtype B (MN) strain.

Based on these observations, a method was developed in order to group HIV-1 infection into the major subtypes, A-E. The method was evaluated with a total of 106 sera obtained from Ethiopians, Swedes and Africans residing in Sweden. Swedish patients were mainly infected by subtype B and Ethiopian patients were mainly infected by subtype C. The serotyping results were compared with sequences of the V3 region. Using this method, 83 % of the sera were singly serotyped, and a 100 % concordance was found with V3 genotyping.

To further evaluate the serotyping method, V3 and pl7 DNA sequences were obtained. The serotyping was done using a large sample size. The serotyping and genotyping were 74 % concordant. Discrepancy was found between V3 and pl7 DNA genotypes in some strains, suggesting possible recombinant strains. One of the putatively recombinant strains was from an Ethiopian patient. The presence of putative recombinant strains may partially explain the discordance between serotyping and genotyping.

The putative recombinant strain identified from the Ethiopian patient was further investigated. To identify the pattern of recombination, and to indicate the recombination break points, a full length sequence was obtained. Using Recombination Identification Program (RIP), the recombination break point was suggested to be in the envelope region. The genetic organization of the Ethiopian HIV-1 subtype C strains was further investigated, by sequencing parts of the long terminal repeat (LTR), enhancer motif. The sequences were compared with Swedish and published sequence data. A sequence which appeared to be a third NF-kB binding site was identified in all Ethiopian sequences. This third NF-kB binding site was the first to be reported. However, the biological consequences of the additional site need to be investigated. Serotyping with short synthetic peptides and anti-HIV-1 antibodies could be valuable for seroepidemiological studies. Due to the dominance of the subtype C in Ethiopian HIV-1 epidemic, the existence of other subtypes and inter-subtype recombinant strains is still limited compared to some other African countries.