Comparison of common methods for the detection of enteric viruses from environmental sources

Cell cultureInfectivity can be determined; provides quantitative dataLong processing time (takes days to weeks); relatively more expensive than conventional PCR; not all viruses can grow on cultured cells101, 149
PCR (RT-PCR)Rapid; increased sensitivity and specificity compared to cell culturePresence or absence only (nonquantitative); inhibitors present in environmental samples may interfere with PCR amplification; infectivity cannot be determined61, 99
Nested PCR (semi/heminested)Increased sensitivity compared to conventional PCR; can replace PCR confirmation steps, such as hybridizationPotential risk of carryover contamination when transferring PCR products79, 127, 161
Multiplex PCRSeveral types, groups or species of viruses can be detected in a single reaction; saves time and costDifficult to achieve equal sensitivity for all targeted virus species, groups, or types; may produce nonspecific amplification in environmental samples49, 57
Real-time PCRProvides quantitative data; confirmation of PCR products is not required (saves time); can be done in a closed system, which reduces risk of contamination compared to nested PCRExpensive equipment; occasionally less sensitive than conventional PCR and nested PCR7, 40, 120
ICC-PCRImproves detection of infectious viral pathogens compared to conventional cell culture; detects viruses that do not produce CPE in cell culture; provides results in half the time required for conventional cell cultureLess time-efficient and more costly than direct PCR detection; carryover detection of DNA of inactivated viruses inoculated onto cultured cells is possible26, 59, 89