Table 3.

Pros and cons of some approaches to assess virus infectivity in water.

Approach	Pros	Cons	References
Long target region-PCR	Easy; may reveal the presence of damaged viral genome	Each targeted fragment may have different sensitivity to the disinfectant; sole use of genome integrity as the criterion for the infectivity; PCR of LTR may have low sensitivity.	Allain et al., 2006, Li et al., 2002a, Simonet and Gantzer, 2006a, Simonet and Gantzer, 2006b, Wolf et al., 2009
Integrated cell culture-PCR	More sensitive and faster than cell culture alone; less susceptible to PCR inhibitors	Costly; carryover detection of nucleic acid of inactivated viruses; non-appropriate for non-culturable viruses	Reynolds et al. (1996)
Detection of virus specific mRNA and negative strand RNA of positive RNA viruses	Faster than conventional cell culture; less susceptible to PCR inhibitors	Costly; carryover detection of nucleic acid of inactivated viruses; non-appropriate for non-culturable viruses, specific to certain type of viruses	Ko et al., 2003, Ko et al., 2005
Nuclease and proteinase treatment before PCR	Rapid; may confirm damaged viral capsid; no need for cell culture	Unable to assess the thermal inactivation that may occur at 37 °C; use capsid integrity as the criterion for the infectivity	Nuanualsuwan and Cliver, 2002, Nuanualsuwan and Cliver, 2003
Dye treatment of water samples before PCR	Rapid; may confirm damaged viral capsid; no need for cell culture	Use capsid integrity as the criterion for the infectivity; possible PCR inhibition by the residue of the dye; was unable to detect thermal inactivation of enterovirus at 19 °C	Graiver et al., 2010, Kim et al., 2011, Parshionikar et al., 2010
The use of flow cytometry	Rapid; sensitive; high-throughput detection; automated	Expensive, non-appropriate for non-culturable viruses	Abad et al., 1998, Barardi et al., 1998
The use of fluorescence microscopy	Rapid, sensitive; may study the real-time monitoring of viral replication	Expensive antibodies may be needed, false positive results may be obtained owing to short life time of the MB probe.	Calgua et al., 2011, Hwang et al., 2006, Ridinger et al., 1982, Smith and Gerba, 1982, Yeh et al., 2008a, Yeh et al., 2008b
Immunomagnetic separation of viral particles	Selective detection of virus particles; the effect of PCR inhibitor is minimal	Depends on the antigenic properties of the virus, antibody may be not able to target all possible strains of virus; may be costly	Casas and Sunen, 2002, Gilpatrick et al., 2000, Grinde et al., 1995, Haramoto et al., 2010, Jothikumar et al., 1998, Monceyron and Grinde, 1994, Myrmel et al., 2000
Measurement of the capsid carbonyl content	Sensitive, may demonstrate the decrease in infectivity of non-culturable viruses	Insufficient to reveal the presence of the infectious viruses; costly	Sano et al. (2010)