20Capsid-integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses 21 combining azo-dye pretreatment with qPCR, has been widely used in recent years; however, 22 variations in pretreatment conditions for various virus types can limit the efficacy of specific 23 protocols. By identifying and critically synthesizing forty-two recent peer-reviewed studies 24 employing capsid-integrity qPCR for viruses in the last decade (2009 to 2019) in the fields of food 25 safety and environmental virology, we aimed to establish recommendations for the detection of 26 infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided 27 the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of 28 attachment or genomic damage, are less well detected using this approach. Although optimizing 29 specific protocols for each virus is recommended, we identify a framework for general assay 30 conditions. These include concentrations of ethidium monoazide, propidium monoazide or its 31 derivates between 10 and 200 µM; incubation on ice or at room temperature (20 -25ºC) for 5 to 32 120 min; and dye activation using LED or high light (500 -800 Watts) exposure for periods 33 ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus 34 transmission in routine (water) monitoring settings and during viral outbreaks such as the current 35 COVID-19 pandemic or endemic diseases like dengue fever. 36 37 Graphical abstract 38 39 Keywords: (6) azo dye, EMA, PMA, microbial contamination, viability, water quality 40 41