Our poo – the best early warning system against future waves of Covid-19

Amongst the unsung research heroes for tackling this pandemic have been waste water engineers and geographers.  Examining sewage for traces of the virus has been a truly worldwide effort that is now a key component for managing the pandemic. In this post I address the background and the questions raised by this development. 

How is sewage testing used?

  • Sewage testing looks for evidence that there are cases of Covid-19 infection amongst a community of people 
  • There is a statistically close relationship between the amount of viral fragments found in a sample of sewage and the number of cases in that area
  • In the study below from Canada, the orange bars represent the amount of virus traces in sewage and the blue line the average number of cases
  • Sewage testing can then reveal which areas or communities have high, low  or even absent levels of infection 
  • The street diagram below from Boston in USA shows a map of the sewage pipelines, where the cases occurred and which manholes (the blue circles) should be entered for testing
  • Similarly, sewage testing can also reveal how infection rates in an area change over time
  • In this series of diagrams from Spain, the maps show the changing sewage patterns over the early months of the pandemic and hence where the most cases then emerged

What are the pros and cons of using sewage compared to looking at data from the number of positive swab tests in an area?

  • Sewage testing of course cannot be used for diagnosing individuals or for individual tracing of cases
  • It is however probably superior for  charting infection rates in different areas and communities than local swab test results
  • This is for a number of reasons:
    • The number of people with a positive swab test depends on how many people turn up for testing
    • Thus unless everyone is swabbed there are biases
    • Sewage testing by its nature covers the whole  of that area
    • It is also far cheaper 

What size of population can be tested?

  • The simple answer depends on where in the sewage system the samples are collected
  • Thus, sample collection close  or ‘high up’ in the system has been used in schools and university campuses
  • By contrast sample collection further away can be used in streets/districts and whole towns

If the sewage in my area/community tests negative does that mean there is no infection?

  • There are no guarantees and not every individual, with a current or recent infection, who has provided samples for the laboratory, will pass viral fragments in their stool
  • It is reasonable though to conclude where no viral traces are found in a sewage sample from your area that the likelihood of a significantly risky rate of infection in the community contributing  that sewage is very low
  • More importantly, given the uncertainties in interpreting the swab test data from any small area, I would be more reassured by the absence of virus in the sewage than there were no swab positive cases in my area 

Are the data of the level of viral traces from sewage publicly available?

  • They should and could easily be made as available to the public , in the same way as the number of people with a positive swab test
  • In some countries, such as Netherlands and Australia, these data are on publicly accessible websites
  • This is not yet true for the UK

Will testing sewage be capable of picking up on new variants?

  • Absolutely, the technique is focused on a detailed genetic analysis of the material
  • It is thus probably the most efficient strategy for identifying and then monitoring the spread of new variants
  • Indeed, in one sample of sewage tested in Bristol, they identified 118 different genetic variants

Can you catch Covid-19 from handling sewage?

  • That’s the interesting thing – this appears very unlikely – not that anyone is recommending handling sewage!
  • The viral content in sewage is genetic traces, in the form of RNA and not whole viruses, ie unlikely to be capable of infecting people
  • For the record there have been some laboratory studies which have cultured the virus from sewage but most have been unable to do this

Could this technique provide ‘early warning’ of other serious viral infections?

  • Yes, now the sample gathering processes and testing techniques have been upscaled, it is easy
  • This is now being done in some countries – alooking for early evidence of other viruses such as norovirus (which causes major outbreaks of gastro-enteritis on cruises)

How sensitive is the testing?

  • Difficult to be completely certain, but sewage can show viral traces even if only a tiny proportion of people were infected 
  • One expert suggested that viral RNA could be detected in a sewage system even if there was only one person affected in a system that was ‘served’ by 10,000 people

How quickly would sewage show traces of infection from someone who is infected?

  • This is the interesting result!
  • It seems that sewage is likely to be positive some days before any symptoms develop
  • There are many examples suggesting that the delay between sewage in an area being positive and there being a report of a clinical case is around  5 days
  • Even more fascinating are the data from Italy suggesting that viral RNA was detected in the waste from Milan 64 days before the first clinical case was detected in that city

How long after people had been infected would traces of the virus still be present in sewage?

  • People who had been infected could continue to shed bits of virus material in their stool possibly be for weeks
  • This is not surprising, as we know from PCR tests that viral RNA can still be cultured from swabs long after the infection is passed and the person is neither ill nor infectious

Is there a place not just for testing sewage but testing stool samples from individuals (to replace swab testing)? 

  • In theory stool testing from individuals would pick up that they had viral fragments
  • But the test would not distinguish between active or old infection
  • At an individual level, stools could also be falsely negative when an infection was present so not appropriate for diagnosis or contact tracing for example 
  • There are also considerable and obvious logistic issues in the individual collection, processing and analysis


Worldwide there is now the technology, at an affordable cost, that by the simple act of regular testing of sewage, we now have an early warning system that can monitor how the virus is, and is not, spreading, and with that have the data to help in advising communities about the success of all their policies they’ve introduced to limit the spread of infection

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