TABLE 2.

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

Method	Advantages	Disadvantages	References
Cell culture	Infectivity can be determined; provides quantitative data	Long processing time (takes days to weeks); relatively more expensive than conventional PCR; not all viruses can grow on cultured cells	101, 149
PCR (RT-PCR)	Rapid; increased sensitivity and specificity compared to cell culture	Presence or absence only (nonquantitative); inhibitors present in environmental samples may interfere with PCR amplification; infectivity cannot be determined	61, 99
Nested PCR (semi/heminested)	Increased sensitivity compared to conventional PCR; can replace PCR confirmation steps, such as hybridization	Potential risk of carryover contamination when transferring PCR products	79, 127, 161
Multiplex PCR	Several types, groups or species of viruses can be detected in a single reaction; saves time and cost	Difficult to achieve equal sensitivity for all targeted virus species, groups, or types; may produce nonspecific amplification in environmental samples	49, 57
Real-time PCR	Provides 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 PCR	Expensive equipment; occasionally less sensitive than conventional PCR and nested PCR	7, 40, 120
ICC-PCR	Improves 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 culture	Less time-efficient and more costly than direct PCR detection; carryover detection of DNA of inactivated viruses inoculated onto cultured cells is possible	26, 59, 89