Real-time PCR quantitative assessment of hepatitis A virus, rotaviruses and enteroviruses in the Tyume River located in the Eastern Cape Province, South Africa

We applied real-time RT-PCR (reverse transcription-polymerase chain reaction) to assess the incidence of hepatitis A virus, rotaviruses and enteroviruses in the Tyume River, an important water resource in the impoverished Eastern Cape Province of South Africa. Detection of noroviruses was done using conventional semi-nested RT-PCR. Water samples were collected once monthly from 6 sampling sites over a 12-month period starting in August 2010 and ending in July 2011. Hepatitis A virus was detected in 13% of the samples in concentrations ranging between 1.67×103 genome copies/ℓ and 1.64×104 genome copies/ℓ while rotaviruses were detected in 4% of the samples with concentrations ranging from 9×101 genome copies/ℓ to 5.64×103 genome copies/ℓ. Enteroviruses were not detected in any of the samples, while noroviruses were detected in 4% of the samples. All hepatitis A and rotaviruses positive samples were from the upstream sections of Tyume River while noroviruses were detected in samples from downstream sections only. Statistical analysis showed that occurrence of the viruses in Tyume River was sporadic. Risk analysis showed that hepatitis A virus posed greater risk than rotaviruses for both recreational and domestic water uses. Because of the low infectious dose of enteric viruses, the detection of even low concentrations of hepatitis A virus, rotaviruses and noroviruses in surface water poses a significant risk to public health.