a b s t r a c tBackground: Noroviruses (NoVs) are important enteric pathogens that cause gastroenteritis worldwide. The first documented NoV outbreaks in South Africa (SA) were described in 1993. The current NoV prevalence and circulating genotypes are unknown. SA lacks NoV outbreak reporting systems and therefore the number and impact of NoV infections is underestimated. Objectives: This study aimed to determine the prevalence and genetic diversity of NoV infections in hospitalised paediatric patients with gastroenteritis in SA during 2008. Study design: Stool specimens referred for virological analysis from hospitalised children ≤13 years, with gastroenteritis, were screened for rotavirus, human adenovirus and human astrovirus by enzyme immunoassay and for NoV genogroup I (GI), II (GII) and sapovirus by real-time RT-PCR. NoV strains were genotyped, and variants identified, based on sequence and phylogenetic analyses of the 5 end or the full length of the capsid gene, respectively. Results: Rotavirus was the most prevalent virus detected in 24.2% (61/252) of specimens, followed by NoV in 14.3% (35/245) and adenovirus, astrovirus and sapovirus in 9.6%, 6.7% and 4% of specimens, respectively. NoVs were only detected in children ≤2 years. The GII NoVs (89%) predominated and eight types were identified with GII.4 (43%) detected most frequently. The emerging 2008 GII.4 variant represented 80% of the GII.4 strains. Conclusions: A diverse range of NoV genotypes were identified in hospitalised children with gastroenteritis. The 2008 GII.4 variant was the most frequently detected strain in the study. This is the first report of NoV GII.4 viruses in SA.

Drinking water supplies which meet international recommendations for source, treatment and disinfection were analysed. Viruses recovered from 100 L-1,000 L volumes by in-line glass wool filters were inoculated in parallel into four cell culture systems. Cell culture inoculation was used to isolate cytopathogenic viruses, amplify the nucleic acid of non-cytopathogenic viruses and confirm viability of viruses. Over a period of two years, viruses were detected in 23% of 413 drinking water samples and 73% of 224 raw water samples. Cytopathogenic viruses were detected in 6% raw water samples but not in any treated drinking water supplies. Enteroviruses were detected in 17% drinking water samples, adenoviruses in 4% and hepatitis A virus in 3%. In addition to these viruses, astro- and rotaviruses were detected in raw water. All drinking water supplies had heterotrophic plate counts of < 100/mL, total and faecal coliform counts of 0/100 mL and negative results in qualitative presence-absence tests for somatic and F-RNA coliphages (500 mL samples). These results call for a revision of water quality guidelines based on indicator organisms and vague reference to the absence of viruses.

The value of selected indicators for assessment of faecal pollution, as well as the distinction of faecal pollution of human or animal origin, has been investigated. The following indicators were included: faecal coliform bacteria, faecal streptococci, sorbitol-fermenting bifidobacteria, Rhodococcus coprophilus, somatic and male-specific coliphages, phages of Bacteroides fragilis, and cytopathogenic viruses. Comparative tests were carried out on samples collected from a stream and river exposed to predominantly faecal pollution of domestic animal origin, and the same stream and river after downstream exposure to run-off from a low socio-economic informal settlement with restricted sanitation. Samples were collected from perennial flow during the dry season and from stormwater run-off after thundershowers. Stormwater run-off from the settlement reached faecal coliform counts of up to 4 400 000 per 100 ml, which is equivalent to that of many raw sewage effluents. Faecal pollution was less during the dry season. Sorbitol-fermenting bidifobacteria were identifiable with faecal pollution of human origin, and R coprophilus bacteria with that of animal origin. The ratio of faecal coliforms to faecal streptococci was in the order of 3.5 to 4.7 immediately after exposure to sewage pollution of human origin. In water exposed to faecal pollution predominantly of animal origin, and downstream from pollution of human origin, this ratio varied from 0.8 to 1.7, which indicates that under circumstances the ratio may also distinguish between faecal pollution of human and animal origin. Phages of B fragilis and cytopathogenic viruses were not detected by direct titration in any of the samples, which implies that their application in this situation would require more sensitive techniques. The results show that the run-off from the informal settlement constituted a major source of pollution for a river catchment which downstream is used as a source of water for human consumption, and that faecal pollution of human and animal origin can reliably be distinguished by means of combinations of appropriate indicators.

Assays that detect p24 antigen reduce the diagnostic window period of HIV testing. Most point-of-care HIV assays have poor sensitivity to diagnose acute HIV infection as they only detect antibodies against HIV-1 and HIV-2 (HIV-1/2). This was a cross-sectional laboratorybased study that evaluated the performance of the Determine TM HIV-1/2 Ag/Ab Combo fourth generation rapid strip -currently the only rapid assay that detects both HIV-1/2 antibodies and p24 antigen. A total of 79 serum specimens (29 positive for HIV antibodies only, 14 positive for HIV antibodies and p24 antigen, 20 HIV-negative, and 16 positive for p24 antigen only) were used for the evaluation. Results were compared with those from validated fourth generation HIV ELISAs. The Determine TM Combo rapid strips had a sensitivity of 90.7% and a specificity of 100% for the detection of HIV-1/2 antibodies. Its sensitivity for the detection of p24 antigen was only 10% (3 out of 30 p24 antigen positive specimens). This implies that most acute HIV infections will be missed with this assay. The need for a point-of-care assay which can detect acute HIV infection reliably still remains, particularly for use in a high prevalence setting such as South Africa.