Investigation of the molecular epidemiology of HIV-1 in Khayelitsha, Cape Town, using serotyping and genotyping techniques

[摘要] There are currently an estimated 5.3 million people infected with humanimmunodeficiency virus / acquired immunodeficiency syndrome (HIV/AIDS) inSouth Africa. HIV-1 group M Subtype C is currently responsible for the majority ofHIV infections in sub-Saharan Africa (56% worldwide). The Khayelitsha informalsettlement, located 30 km outside Cape Town, has one of the highest HIV prevalencerates in the Western Cape. The objective of this study was to investigate themolecular epidemiology of HIV-1 in Khayelitsha using serotyping and genotypingtechniques.Patient samples were received from the Matthew Goniwe general health clinic locatedat site C in Khayelitsha. Serotyping was performed through a competitive enzymelinkedimmunosorbent assay (cPEIA). RNA was isolated from patient plasma and atwo step RT-PCR amplification of the gag p24, env gp41 IDR, env gp120 V3 and polgenome regions performed. Sequences obtained were used for detailed sequence andphylogenetic analysis. Neighbour-joining and maximum likelihood phylogenetictrees were drawn to assess the relationship between the Khayelitsha sequencesobtained and a set of reference sequences obtained from the Los Alamos NationalLibrary (LANL) HIV database (http://www.hiv.lanl.gov/).Through serotyping and genotyping the majority of HIV strains were characterised asHIV-1 group M subtype C. One sample (1154) was characterised as a possible C / Drecombinant strain. In 9 other samples HIV-1 recombination cannot be excluded, asonly one of the gene regions investigated could be amplified and characterised inthese samples. The gag p24 genome region was found to be more conserved than theenv gp41 IDR, with the env gp41 IDR more conserved than the env gp120 V3. Thevariability of the env gp120 V3 region indicates that patients might be dually infectedwith variant HIV-1 subtype C strains or quasispecies. Conserved regions identified inthe Khayelitsha sequences can induce CD4+ T-cell responses and are importantantibody recognition target sites. These conserved regions can play a key role in thedevelopment of an effective HIV-1 immunogen reactive against all HIV-1 subtypes.The majority of subtype C viruses were predicted to use CCR5 as their major chemokine co-receptor. The pol sequences analysed indicate that mutationsassociated with minor resistance to Protease Inhibitors (PIs) might be present in theKhayelitsha community. The identification of resistant mutations is vital for peoplereceiving antiretroviral treatment (ART). It can influence the success of theirtreatment and delay the onset of AIDS.Serotyping is a quick characterisation method, but not always accurate. Withgenotyping detailed molecular analysis can be performed. However, with genotypingthe success of amplification often depends on viral load. In Southern Africa a subtypeC candidate vaccine appears to be the best option for future vaccine considerations.The sporadic detection of non-subtype C and recombinant subtype C viruses remainsa concern and will thus have to be closely monitored. Phylogenetic analysis can helpto classify and monitor the spread and evolution of these viruses.

[发布机构] Stellenbosch University