Background Acyclovir (ACV) is the first-line treatment for symptomatic primary and recurrent genital herpes in South Africa. Resistance to ACV is mainly due to mutations in the HSV-2 viral UL23gene that codes for thymidine kinase (TK), resulting in an inability for the drug to inhibit viral replication. The objectives of this study were to obtain genotypic data on the frequency of HSV-2 TK resistance mutations and natural polymorphism as well as to assess the prevalence of ACV-resistant HSV-2 among participants in the genital ulcer aetiological studies conducted between 2007 and 2011.

Methods We amplified and fully sequenced the UL23gene of 254 HSV-2 positive specimens obtained from participants in genital ulcer aetiological studies conducted between 2007 and 2011 in Gauteng Province, South Africa. Additionally, intratypic differences between the HSV-2 were determined based on the number of reiterated sequences located in the non-coding regions of the US1and US12genes of HSV-2.

Results We identified 63 single and/or double nucleotide mutations in the UL23genes analysed, that resulted in 30 silent mutations and 32 amino acid changes. 41% of these amino acid changes were due to natural polymorphism. In addition, we identified 19 unknown amino acid changes in 30 samples that have not been described before. All unknown mutations detected were outside the TK resistance “hotspots”, which are renowned sites for ACV resistance mutations to occur. No frameshift mutations or mutations causing stop codons were identified in the UL23genes of the samples analysed.

Conclusions No evidence was found of known ACV resistance mutations in HSV-2 following the addition of ACV as first-line therapy for genital ulceration in South Africa. Genotyping of HSV-2, based on the length of reiterated sequences in the US1and US12 genes of HSV-2, revealed a high degree of HSV-2 heterogeneity in this population.