Table 9.2.

Summary of pre-treatment approaches prior to PCR to distinguish between infectious and non-infectious viruses

Pre-treatment prior to PCR	Rationale	Advantages	Disadvantages	References
Proteinase and RNase treatment	The capsid of infectious particles is resistant to proteinase digestion and thus protects the genome against RNases.	Usable for non-cultivable viruses Practical and easy pre-treatment	Works only in defined conditions (inactivation at 72 °C or by hypochlorite)	Nuanualsuwan and Clivei; 2002; Nuanualsuwan and Cliver, 2003
Antibody capture of the virus	The capsid of inactivated virus might alter its antigenic properties (changes in protein conformation) thus resulting in the virus losing the ability of being recognised by specific antibodies.	Isolation of infectious viruses from large volume samples (e.g., water)	Detection depends on antigenic properties of viral capsid	Gilpatrick et al., 2000, Schwab et al., 1996
		Usable for non-cultivable viruses	Effective only if the antigenic properties of the viral capsid are defined
Attachment of virus to cell monolayer	The capsid of inactivated viruses changes its antigenic properties (changes in protein conformation) and thus the virus is unable to attach to receptors of the monolayer.	Able to distinguish between infectious and non-infectious viruses (in defined conditions)	Applicable only for cell-cultivable viruses	Li et al., 2011, Nuanualsuwan and Cliver, 2003
Intercalating dyes treatment (Propidium monoazid; PMA)	The PMA penetrates the damaged or compromised capsid of the inactivated virus and binds covalently to the genome upon exposure to visible light, which prevents detection of the genome using PCR.	Usable for non-cultivable viruses	Works only in defined conditions (inactivation at 72 and 37 °C or by hypochlorite)	Fittipaldi et al., 2010, Parshionikar et al., 2010