RT-PCR amplification detects inactivated viruses in water and wastewater

Nucleic acid (NA) amplification techniques are useful to detect viruses in water and other environmental samples because they are highly sensitive, specific and can detect fastidious enteric viruses that do not grow well or not at all in cell cultures. However, RT-PCR was found to detect inactivated viruses. In terms of risks to public health this constitutes a false positive result, as inactivated viruses are no longer infectious. When poliovirus type 1 and coliphage MS2 were studied for (a) persistence in water and sewage and (b) inactivation in water by free chlorine, chlorine dioxide and UV radiation, RT-PCR assays underestimated virus inactivation. The use of multiple RT-PCR amplification sites, larger RT-PCR genomic targets and immunocapture RT-PCR sometimes reduced, but did not eliminate, the discrepancy between loss of infectivity and loss of RT-PCR titre. Virus presence based on RT-PCR detection must be interpreted with caution when predicting human health risks.