Pipe probe
The science behind testing wastewater for Covid-19
Health officials have turned to testing sewage as part of the country’s wider fight against Covid-19. Hannah Martin looks at how it works.
Wastewater testing in South Auckland continues to come back negative for Covid-19, despite a flurry of new community cases.
A new case announced over the weekend – which saw Auckland return to level 3 lockdown – was in the community while infectious for a week before testing positive for the virus on Saturday.
However, there had been no positive wastewater samplings in the area that week, the Institute of Environmental Science and Research (ESR) told Stuff on Monday.
So how does wastewater testing actually work, and how sensitive is it?
How is wastewater sampled?
Every day, about 400 million litres of wastewater are collected and treated in Auckland, across 7999 kilometres of wastewater pipes, 518 wastewater stations, 18 treatment plants and 167,264 manholes.
Wastewater testing is not new – ESR routinely tests wastewater for viruses and illicit drugs, such as MDMA and cocaine.
There are two ways to take wastewater samples, says Dr Joanne Hewitt, head of ESR’s environmental virology laboratory: automatic composite samples, and grab samples.
Automatic composite sampling – where a pump automatically collects a small volume of wastewater every 15 minutes over 24 hours – is the preferred method.
Pumps are set up at most wastewater treatment plants, and most of the samples are taken this way.
This method means scientists get a sample reflective of multiple points in time over the day.
While many treatment plants have these samplers, some don’t. If scientists are looking to investigate a smaller area, such as from a particular manhole, they have to use grab sampling.
Grab sampling is as it sounds – sampling directly from wastewater at one point in time.
Grab sampling essentially provides a ‘‘snapshot’’ in time which is dependent on diffusions and flows, so it is less reflective of the overall virus in the sewage at that time.
How does testing work?
One-litre samples are collected in Auckland and sent to ESR in Wellington to be processed.
Laboratory staff first take up to 500ml from the samples and store the rest.
‘‘As viruses can be attached to the solids (poo) and be in the water, we use methods that will recover viruses from both parts, so we don’t lose any virus,’’ Hewitt says.
This is important if they don’t expect a high level of virus in the sample.
The sample is then concentrated to about half a teaspoon – basically removing all the water, leaving the virus behind.
From there, the testing process is the same as for regular testing for the virus from a nasal swab.
Scientists extract the viruses, turn the RNA into DNA and run it on a PCR (polymerase chain reaction), which will tell them if the sample is positive or negative for Sars-CoV-2.
As if wading through wastewater samples wasn’t enough, the team at ESR takes things one step further (and weirder).
They also add a cat coronavirus and a mouse norovirus to every sample they test as a control, to see how good their methods are.
The cat coronavirus is a good control for Sars-CoV-2, and the mouse norovirus is similar to enteric viruses (transmitted when people ingest faeces particles, often through contaminated food or water) that ESR typically looks for in wastewater, Hewitt says.
The other 500ml is stored to confirm any unexpected results. Any remaining nucleic acid and concentrated samples are also stored for future work.
While the Sars-CoV-2 virus is detectable in wastewater, it is not infectious. This means it is ‘‘extremely unlikely’’ anyone would get infected with the virus from wastewater.
However, as sewage contains other infectious viruses such as norovirus, all wastewater samples are processed in a biological safety cabinet – an enclosed, ventilated workspace specifically for working safely with contaminated materials.
If scientists find something they weren’t expecting, they immediately analyse a second sample taken at the time, and then a repeat sample from a day or two after.
How long can the virus live in wastewater?
Lab studies have shown Sars-CoV-2 can persist in wastewater for days, if not weeks, Hewitt says.
As the number of people shedding the virus into wastewater increases, the probability of detection also increases.
However, what scientists detect in sewage only reflects ‘‘relatively recent inputs’’ as the millions of litres of new wastewater each day dilute and wash out any input from previous days, Hewitt says.
This means it isn’t likely the testing could pick up any virus shed days or weeks ago, as people continue to flush their toilets and have showers.
‘‘While our methods are sensitive, they aren’t sensitive enough to detect a few stray viruses stuck to the side of a pipe.’’
How sensitive is it exactly?
While it’s theoretically possible to detect a single person shedding the
virus, this is ‘‘unlikely in practice’’, Hewitt says.
Based on what scientists have observed so far, ESR’s test is sensitive enough to discover about 10 positive cases in an area of 100,000 people. However, this is not a ‘‘hard and fast’’ rule, as some people shed at different rates based on time of infection.
‘‘Generally, we would need more cases in large catchments to increase the likelihood of detection because as more people contribute to a sewerage stream there will be dilution in the wastewater which will alter the level of sensitivity,’’ Hewitt says.
She likens it to sharks detecting blood in water – if the blood is the virus and the sharks are sampling.
‘‘The more drops of blood in the water, the more likely they detect it.
‘‘On the same line, the more sharks in the water in the right area, the more likely they detect it.’’
How long do people shed the virus in their faeces?
How long shedding in faeces occurs in most Covid-19 cases in New Zealand is largely unknown, ESR science leader Dr Brent Gilpin says.
Evidence shows people who have been infected may continue to shed virus after they are no longer infectious – with some published data suggesting this can continue for weeks after the initial illness.
However, most of this data comes from people who are very unwell in hospital, which is not the situation we have in New Zealand.
Infectious diseases expert Professor David Murdoch, of Otago University, says it is not unusual for respiratory vaccines to be detectable in faeces.
Given the virus lived in the upper respiratory tract – the nose and throat – it could be swallowed into the gut and end up in faeces, particularly if the person had a high viral load and was more symptomatic.
But wastewater testing is not without its limits. It can show someone in the network shedding virus, but not specifically who or where, or the exact number of people who have contributed to a positive detection, Gilpin says.
Shedding levels could vary significantly between individuals and at different stages in an infection, and not every infected person may shed the virus.
Why aren’t we seeing positive samples despite having community cases?
By ESR’s calculations, the number of cases shedding virus into the wastewater tested at Papatoetoe and at the Eastern Interceptor did not reach the 10 in 100,000 people threshold last week, Gilpin says.
This is because people are quickly moved into quarantine as they test positive, moving them out of the wastewater detection area.
He reiterates that the threshold is not a concrete rule as some people shed at different rates based on the time of infection, and says ‘‘many other factors’’ affect detection.
Essentially, wastewater testing is an ‘‘extra layer’’ of detection in case there are lots of Covid-19 cases in the community going undetected, rather than a tool to catch individual cases.
Murdoch says wastewater testing negative provides ‘‘reassurance’’ isn’t a large number of active case in the community ‘‘that we don’t know about’’.
‘‘While our methods are sensitive, they aren’t sensitive enough to detect a few stray viruses stuck to the side of a pipe.’’
Where is wastewater being tested?
ESR has been undertaking daily sampling of wastewater outside the quarantine facility Jet Park Hotel since July, and from the South Western Interceptor where the Jet Park wastewater mixes with that from 130,000 other Aucklanders.
The Jet Park wastewater is ‘‘almost always’’ positive for SarsCoV-2.
ESR also routinely undertakes sampling of municipal wastewater from Auckland’s Western and Eastern Interceptors, North Shore (Rosedale), Hamilton, Rotorua, Wellington and Christchurch.
These are almost always negative.