Novel Approach Improves Understanding of Virus Occurrence in Drinking Water

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Waterborne viruses, one of the leading causes of gastrointestinal illnesses, were measured in United States drinking water sources and finished water. Scientists used a combination of measurement and statistical techniques to overcome limitations to quantifying these viruses, thus offering an enhanced method for virus monitoring.

Bacterial and viral pathogens in drinking water have historically posed significant health risk to humans.  Drinking water treatment, including filtration and disinfection, in the United States in the early 20th century is credited with dramatically reducing the incidence pathogens from incoming water to provide communities with safe drinking water. However, pathogens are still reported as one of the leading causes of gastrointestinal illnesses from drinking water ingestion.

Pathogens, including viruses, can enter drinking water sources (rivers, lakes, groundwater, and reservoirs) through runoff from urban and agricultural areas; leakage from sewers and septic systems, storm water, and sewer overflows; and treated wastewater.  If the pathogens persist through treatment, they can contribute viruses to drinking water and result in human exposure.

Enteric viruses, those that can replicate in the human digestive track, are one of many pathogens that are monitored in the Nation’s drinking water. Typically, drinking water facilities estimate the removal efficiency of enteric viruses based on the presence of fecal indicator bacteria. However, fecal indicator bacteria presence is not always indicative of viral presence, given the different survival rates and transport mechanisms of bacteria and viruses.

Showing equipment used to collect water for analyses of viruses

Picture showing equipment used to collect water for analyses of viruses (Varughese and others 2019).
​​​​​​​(Credit: Eunice Varughese, U.S. Enviromental Protection Agency.)

When viruses are measured in water, a technique called polymerase chain reaction (PCR) or quantitative PCR (qPCR) is used. One advantage of the qPCR method is that it can quickly generate a sufficient amount of genetic material for analysis. However, virus occurrence and concentration may be underestimated owing to its multistep viral concentration process or to PCR inhibition, where chemicals in the water sample prevent generation of sufficient amounts of genetic material for analyses. These limitations present a challenge to accurate estimation of virus concentration in public drinking water supplies.

As a result, U.S. Environmental Protection Agency (EPA) and U.S. Geological Survey (USGS) scientists collaborated and developed a unique approach to better quantify virus occurrence and concentration in drinking water as part of a larger study on contaminants in drinking water in the United States. First, they measured the occurrence of five waterborne virus groups (adenovirus, norovirus GI, norovirus GII, entero-virus, and polyomavirus) from 25 drinking water treatment facilities across the United States using qPCR methods. Measurements included paired source (rivers, lakes, reservoirs, and groundwater) and treated water samples.

The results showed that treated drinking water had fewer viruses than source waters, indicating that treatment methods used at the facilities in this study were helpful in reducing the viruses measured. However, samples from all 25 water treatment plants had false negatives (determinization that there were no viruses present when viruses were present) due to inhibition, indicating that a method accounting for inhibition is important for better estimation of virus occurrence and concentrations in environmental waters.

The scientists applied a statistical model to account for factors affecting viral detection, including the measured sample inhibition and recovery efficiency. The qPCR data were converted to count data and input into the statistical model to calculate virus concentrations. By using a statistical framework that accounted for factors affecting viral detection, this study offers an alternative approach to estimate the occurrence and concentration of viral pathogens in environmental waters used as sources of drinking water.

This research is part of a long-term approach by the USGS Environmental Health Mission Area Infrastructure Team to understand microbial and chemical contaminants in drinking water and potential human exposure. It was supported by the USGS Environmental Health Mission Area Toxic Substances Hydrology and Contaminant Biology Programs and the EPA.


Varughese, E.A., Brinkman, N.E., Anneken, E.M., Cashdollar, J.L., Shay Fout, G., Furlong, E.T., Kolpin, D.W., Glassmeyer, S.T., Keely, S.P. 2018. Estimating virus occurrence using Bayesian modeling in multiple drinking water systems of the United States. Sci. Total Environ. v. 619-620, p. 1330-1339. 

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