"The intention is that the covid alert system, in time, will be sufficiently sensitive and flexible to detect local flare-ups, so that, for instance, if the covid is detected in the water supply of a certain town or in a school in an area, steps can be taken..." 

Claim 

Boris Johnson said that an alert system for Covid-19 could involve detecting the infection in the water supply. 

There is no evidence that Covid-19 can be found in treated water 

During a statement on the government's Covid-19 strategy, Prime Minister Boris Johnson spoke about an alert system that would allow for the detection and management of "flare ups" in local cases. As part of this he said Covid-19 -the infection casued by the new coronavirus- could be detected in the water supply. 
 
A spokesperson for Number 10 has said that Boris Johnson misspoke: he meant to say wastewater, not water supply. The spokesperson said that this alert scheme, which would involve monitoring levels of Covid-19 infection in the population through sewage, is something the government is looking into (but is not something that is in place currently). 
 
There is some evidence showing that genetic material from the new coronavirus can be detected in wastewater and researchers in several countries have begun to assess whether this could be used as an early-warning tool. 
The Drinking Water Inspectorate, which independently assesses the public water supply in England and Wales, says that the UK public should continue to use tap water as normal. They explain that routine disinfection of drinking water in the UK "removes all harmful pathogens including viruses". 

Cryptosporidium 

 
 
Cryptosporidium which causes cryptosporidiosis, an infection that may present as a diarrhoeal with or without a persistent cough in immunocompetent hosts is an example of a pathogen that is mostly removed from the water supply by disinfection, but outbreaks do occur. 
 
In January 2018 residents of the Clevedon area (BS21 and BS49) were advised by Bristol Water to boil their water before drinking it after cryptosporidium was found in the system. 
 
An example that whilst the water supply is disinfected some pathogens can and do sometimes survive the process and find their way into the domestic supply.  
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