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Like other atomic strategies, qPCR has additionally a few downsides. This methodology can't observe among irresistible and non-irresistible viral particles and, thus, the outcomes might be misjudged as far as individual danger of contamination (Girones et al., 2010; Hamza and Bibby, 2019). Natural and inorganic toxins are broadly found in ecological examples; accordingly, these inhibitors might influence the affectability of qPCR bringing about bogus negatives (Girones et al., 2010; Hamza and Bibby, 2019; Hamza et al., 2011). qPCR requires a standard bend with known measurement of the objective quality to contrast and obscure examples and, in outcome, this standard requires cautious alignment and reliable source material to stay away from mistaken outcomes (Monteiro and Santos, 2017; Pinheiro et al., 2012). 

As to the viral infectivity issues, many investigations have portrayed various methodologies that are consolidated and applied before qPCR to diminish or block the likelihood to recognize harmed capsid therefore diminishing the recognition of non-irresistible viral particles. These strategies can be joined with cell culture as Integrated cell culture – PCR (ICC-PCR), insusceptible based strategy as IMS-qPCR, enzymatic medicines as nuclease and proteinase, and color medicines as ethidium monoazide (EMA) and propidium monoazide (PMA) (Graiver, Saunders, Topliff, Kelling, and Bartelt-Hunt, 2010; Hamza and Bibby, 2019; Haramoto et al., 2010; Rigotto, Sincero, Simões, and Barardi, 2005).Even with these inconveniences, the advantages of this technique have been adding to spreading its utilization in ecological investigation. Accordingly, qPCR is broadly utilized in examinations to research intestinal infections in various water sources like mineral water (Rodrigues dos Santos et al., 2015), waterway (Vecchia et al., 2015), stream (Girardi et al., 2019), wetlands (Gularte et al., 2017), seawater (Gularte et al., 2019; Staggemeier et al., 2017) and different sorts of natural lattices (Gularte et al., 2019).