EFFECT OF VIRAL GENOME PROPERTY ON THE EFFICIENCY OF VIABILITY (RT-)qPCR

Abstract

 It is important to determine the infectivity of viruses in waters and foodstuffs so that the risk of viral infection can be assessed. The use of viability markers such as propidium monoazide (PMA), ethidium monoazide (EMA) and more recently cis-dichlorodiammineplatinum (CDDP) has been applied to discriminate between infectious and inactivated viruses by (RT-)qPCR (viability (RT-)qPCR). However, the efficiency of viability (RT-)qPCR in eliminating inactivated viruses can be influenced by viral genome property. The main objective of this study is to evaluate the effects of viral genome types and amplicon lengths on the efficiency of viability (RT-)qPCR. Naked viral genomes extracted from RNA or DNA viruses were treated with PMA (100 µM), EMA (100 µM) or CDDP (1, 000 µM) markers and analyzed by (RT-)qPCR. Among viability markers tested, CDDP was the most effective to remove the detection of the naked viral genomes by (RT)-qPCR. All viability markers tested generally eliminated (RT-)qPCR detections of RNA viral genomes more effectively than those of DNA viral genomes. PMA/EMA/CDDP-(RT-)qPCR was likely to remove the naked viral genomes more efficiently when targeted the longer amplicon lengths than the shorter ones. Thus, the property of viral genomes should be considered as one of the governing factors on the efficiency of viability (RT-)qPCR in exclusion of inactivated viruses.