Hepatitis C Virus Genotype 5 Variability in Treatment-Naïve Patients in South Africa.

INTRODUCTION: Hepatitis C virus (HCV) genotype 5 was originally identified in South Africa, where it represents 35-60% of all HCV infections. There are limited data on resistance-associated variants (RAVs) in South Africa. Thus, we investigated variability within the NS3/NS4A, NS5A, and NS5B genes of treatment-naïve individuals with HCV genotype 5 infection at the Dr. George Mukhari Academic Hospital (DGMAH) in Pretoria, South Africa. METHODS: Nested PCR was performed to amplify the NS3/4A, NS5A, and NS5B genes. RAVs were evaluated using the Geno2pheno tool. RESULTS: In the NS3/4A gene, F56S and T122A were detected in one sample each. The D168E mutation was detected in 7 samples. Within the NS5A gene, the T62M mutation was detected in 2 individuals. In the NS5B gene, 8 of 12 individuals (67%) had the A421V mutation, while all 12 individuals (100%) had the S486A mutation. DISCUSSION: RAVs were detected frequently among treatment-naïve individuals with HCV genotype 5 infection in South Africa. Thus, resistance testing may be prudent when initiating treatment of patients with genotype 5 infection. Additional population-based studies are needed to understand the prevalence of these RAVs during HCV genotype 5 infection.

Phylogenetic studies of larval digenean trematodes from freshwater snails and fish species in the proximity of Tshwane metropolitan, South Africa.

The classification and description of digenean trematodes are commonly accomplished by using morphological features, especially in adult stages. The aim of this study was to provide an analysis of the genetic composition of larval digenean trematodes using polymerase chain reaction (PCR) and sequence analysis. Deoxyribonucleic acid (DNA) was extracted from clinostomatid metacercaria, 27-spined echinostomatid redia, avian schistosome cercaria and strigeid metacercaria from various dams in the proximity of Tshwane metropolitan, South Africa. Polymerase chain reaction was performed using the extracted DNA with primers targeting various regions within the larval digenean trematodes' genomes. Agarose gel electrophoresis technique was used to visualise the PCR products. The PCR products were sequenced on an Applied Bioinformatics (ABI) genetic analyser platform. Genetic information obtained from this study had a higher degree of discrimination than the morphological characteristics of seemingly similar organisms.

Identification and genetic characterization of unique HIV-1 A1/C recombinant strain in South Africa.

HIV isolates from South Africa are predominantly subtype C. Sporadic isolation of non-C strains has been reported mainly in cosmopolitan cities. HIV isolate j51 was recovered from a rural South African heterosexual female aged 51 years. Near full length amplification of the genome was attempted using PCR with primers targeting overlapping segments of the HIV genome. Analysis of 5593 bp (gag to vpu) at a bootstrap value greater than 70% found that all but the vpu gene was HIV-1 subtype A1. The vpu gene was assigned HIV-1 subtype C. The recombination breaking point was estimated at position 6035+/- 15 bp with reference to the beginning of the HXB2 reference strain. Isolate j51 revealed a unique genome constellation to previously reported recombinant strains with parental A/C backbones from South Africa though a common recombination with subtype C within the vpu gene. Identification of recombinant strains supports continued surveillance of HIV genetic diversity.

Descriptions of diplostomid metacercariae (Digenea: Diplostomidae) from freshwater fishes in the Tshwane area.

The metacercarial (larval) stages of diplostomid digeneans are known to inhabit freshwater fish, causing tissue damage in the process. Due to their widespread diversity, little is known about their life cycle. The classification of these parasitic stages to the species level using only the morphology is very challenging due to the lack of genitalia; they are regarded to be the most important structures in the identification of these organisms. In this study, additional morphological information through light and scanning electron microscopy is given for two different diplostomids found in the cranial cavity of Clarias gariepinus and the vitreous chambers of Tilapia sparrmanii and Pseudocrenilabrus philander. The diplostomid metacercaria inhabiting the cranial cavity of Clarias gariepinus was morphologically identified as Diplostomulum (Tylodelphys) mashonense and an unknown metacercaria of the genus Diplostomum was found in the vitreous chambers of Pseudocrenilabrus philander and Tilapia sparrmanii. Both parasitic species' 28S recombinant deoxyribonucleic acid genomic regions were successfully amplified using Dig 125/1500R primer pairs. The assay yielded a product of approximately 1300 base pairs as seen on the gel images. There were 14 nucleotide differences over the entire analysed sequences resulting in a 1.1% (14/1273) nucleotide difference. In line with the morphological characteristics of these parasites, there seemed to be a slight difference in their genetic make-up. The application of molecular techniques on digenetic trematodes seems very promising and may yield great potential in future descriptions of morphologically similar parasitic species.

Genetic characterization of HIV before widespread testing of HIV vaccine candidates at a clinical trial site in Pretoria, South Africa.

We studied 123 samples from adult chronic HIV patients initiating HAART from various centers around a newly established clinical trial site in Pretoria. Each sample was sequenced in at least one structural gene (pol, gag, and env) or functional gene (vif, vpr, and vpu). A subset of 25 samples was subjected to near full-genome analysis. All samples were HIV-1 subtype C. Highly conserved regions within the gene sequences were observed. Overall, the gag and vif sequences showed closer similarity followed by the env, vpr, pol, and vpu. The env gene was the most difficult to sequence, resulting in only 31 sequences from 40 samples; of these, 25 were predicted to be R5 coreceptor tropic, while 6 were X4 tropic. The study asserted the predominance of HIV-1 subtype C within the catchment population.