Covid 19 coronavirus: Inside the fascinating world of wastewater testing

How quickly we get tested and how often we scan QR codes can all help health officials quickly get on top of Covid-19 outbreaks. But what we flush can also be critical too. Science reporter
Jamie Morton looks at how wastewater sampling has evolved to play a star role in New Zealand’s elimination strategy.

What is wastewater testing?

What’s formally known as wastewater-based epidemiology isn’t new, and has already been used in New Zealand to study other viruses – and even the use of illegal drugs like cocaine.

But it’s become all the more important during the Covid-19 pandemic, as collecting and analysing samples from wastewater stations can give us a surprisingly good picture of how the Sars-Cov-2 is spreading at a community scale.

Soon after the virus emerged, scientists overseas found that live virus could be isolated from the faeces and urine of infected people – and sometimes survive for up to several days after leaving the body.

ESR has been carrying out increasing levels of wastewater testing over the past few months, and last week ramped up surveillance in Auckland – including the Papatoetoe area – and New Plymouth and Hamilton.

With the exception of Auckland’s South Western Interceptor, which is regularly positive due to sewage input from the Jet Park Hotel quarantine facility, all the samples tested negative.

That gave authorities some reassurance that the latest community cases weren’t the tip of a Covid-19 iceberg.

« If we had found positives in the wastewater that may well have influenced the decisions made in another direction, but this is just one piece of health intelligence used to inform the response, » said ESR’s science leader, Dr Brent Gilpin.

As clever as it was, wastewater testing couldn’t replace nasal swabs – of which 67,000 were collected in the last week alone – but Gilpin said it might support and guide it.

« It also can do this on a population scale that isn’t otherwise possible, » he said.

« In the last week wastewater testing provided screening surveillance of 2.3 million people, and for 1.5 million of those, repeat daily testing.

« It is non-invasive, captures symptomatic and asymptomatic and while we can’t do 10,000 tests a day, each test we do, can provide information on hundreds of thousands of people. »

So how does it work, exactly?

« The methods that we are using are similar to ones we have used for other viruses in wastewater, polio for example, » said Dr Joanne Hewitt, head of ESR’s Environmental Virology Laboratory.

In many cases, the « auto-samplers » used for collection were the same as those used in earlier testing that have revealed some interesting insights into community drug use.

« ESR has been able to rapidly request samples from wastewater treatment plants because of the long-standing relationships we have built with many of them through our drug surveillance programme, » Hewitt said.

« The testing procedure, however, is quite different with Covid-19 surveillance looking for specific viral RNA using PCR, versus looking for drugs and metabolites of drugs by chemical analysis. »

ESR scientists prefer to use what’s called an automatic composite sample, where a pump collects a small volume of wastewater every 15 minutes over 24 hours.

« These are already set up at most wastewater treatment plants and most of the samples are taken this way, » Hewitt said.

« It means you get a sample which is reflective of multiple points in time over the day. »

While many treatment plants have these samplers, some don’t – and if you are looking to investigate a smaller area, sampling from a manhole for instance, you have to use grab sampling, which is exactly as it sounds.

« You are taking a sample directly from the wastewater at one point in time. »

This essentially offered a snapshot dependent on different diffusions and flows, and thus was less reflective of the overall virus in the sewage for that time.

However, ESR is looking at different approaches, such as using passive samplers that can capture viruses from wastewater as it passes through it.

These could be rapidly deployed at locations across the sewerage network when composite samplers weren’t available – and this was precisely what happened with the extra sites sampled in the latest investigation.

Hewitt said scientists at ESR’s Wellington laboratory had become deft at quickly processing the one-litre samples as soon as they receive them.

First, they took up to 500ml from the samples, and stored 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, » she said.

« This is important if we don’t expect a high level of virus in the sample. »

Next, the scientists concentrated it all down to about half a teaspoon, basically removing all the water and leaving the virus behind.

« From there it’s the same process as you go through for regular testing for the virus of someone’s swab – we extract the viruses, turn the RNA into DNA and run it on a PCR to tell us if the sample is positive or negative for the virus. »

Fascinatingly, they could also add a « cat » coronavirus and a « mouse » norovirus to every sample they test as a control to see how good the methods were.

« The cat coronavirus is a good control for SARS CoV-2, while the murine norovirus is more like the enteric viruses we usually look for in wastewater, » Hewitt said.

« We store the other 500ml to confirm an unexpected result. »

How long does the coronavirus hang around in sewage?

Long enough to be detected, in most cases.

Lab studies have shown SARS-CoV-2 can persist in wastewater for days – if not weeks.

And while it was detectable, it wasn’t infectious.

« In other words, it is extremely unlikely that anyone would get infected with SARS-CoV-2 from wastewater, » Hewitt said.

« However, sewage contains other viruses such as norovirus that will be infectious, so all wastewater samples are processed in a biological safety cabinet and with care. »

Could a positive detection be possible from a virus shed days or weeks ago?

Hewitt said this wasn’t a practical concern, as long as people kept flushing their toilets and having showers.

« What we detect in sewage only reflects relatively recent inputs as the millions of litres of new wastewater each day dilutes and washes out any inputs from previous days, » she said.

« While our methods are sensitive, they aren’t sensitive enough to detect a few stray viruses stuck to the side of a pipe. »

So how sensitive, exactly?

While it was theoretically possible to detect a single person shedding virus, that was unlikely in practice – at least in a reproducible manner.

« Based on what we have observed so far, our test is sensitive enough to discover approximately 10 cases in an area of 100,000 people, » Hewitt said.

« That’s not a hard and fast rule as some people shed at different rates based on time of infection, and there are many other factors that affect detection. »

Generally, scientists would need more cases in large catchments to increase the likelihood of detection.

That was because, as more people contributed to a sewerage stream, there’d be dilution in the wastewater, which would alter the level of sensitivity.

« It’s kind of like sharks detecting blood in the water, » she said.

« If we think of the blood as the virus and the sharks as our sampling. People say that sharks can detect a single drop of blood from hundreds of metres away.

« 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 higher likelihood they detect it. »

But just as important was specificity – or how precise the tests themselves were.

« When we detect viral RNA in a sample, we are very confident that it is actually from SARS-CoV-2. »

Before reporting a positive, particularly a very low level unexpected positive, scientists typically always repeated the PCR – and then carried out the whole extraction on a stored replicate sample.

« It’s tough on the lab as this would invariably require working late into the night, but we are committed to results that we are completely confident in, and which can inform decisions made by Government. »

Are there any other major limitations?

Wastewater testing still couldn’t tell us from whom, or from where, the virus was being shed.

Nor could it tell us the exact number of people involved in a positive detection.

« Shedding levels can vary significantly between individuals and at different stages in an infection and not every infected person may shed the virus, » Gilpin explained.

It was possible for people to continue shedding the virus after they were no longer infectious, he noted, and there was evidence to suggest this could carry on for weeks after the initial illness.

« However, most of the data we have in this space comes from hospitalised individuals, most of whom are very sick and some with ongoing immune issues, » Gilpin said.

« That’s not really the situation we have in New Zealand with those in managed isolation, where a third of cases are asymptomatic. »

Also most cases here were younger, and had milder symptoms.

« Therefore, how long shedding in faeces occurs in most of the Covid-19 cases in New Zealand is an unknown, » he said.

« What we do know is that this post infectious shedding by people will produce much lower levels of virus in faeces, which is good for New Zealand’s unique situation with the small number of cases we currently have. »

ESR had now tested several hundred wastewater samples, many of which will have had people who previously had Covid-19 contributing to them.

« What we see when an outbreak occurs is a consistent detection of virus at relatively high levels, » Gilpin said.

« That’s one of the reasons we like to collect a series of samples. Historical cases could produce the occasional sporadic low-level result, but they are not going to produce ongoing detectable levels. »

The protocol ESR has developed with the Ministry of Health meant that, if a very low-level unexpected detection ever occurred, scientists would immediately analysis a second sample taken at the same time – and then a repeat sample taken a day or two after.

« It is also important to remember that not everyone’s home is connected to a municipal wastewater system, » Gilpin said.

« Many of these people may however work or socialise in places that are connected to sewer and therefore still get captured by wastewater testing

« And those in most isolated places are less likely to get infected, and less likely to spread the virus to others, than those living in higher populated centres.

« There are always complicating factors, but we continue to learn and build upon our findings. »

And ESR scientists have learnt a lot just by undertaking daily sampling of wastewater from the Jet Park Hotel since July 2020, and from the South Western Interceptor, where the Jet Park wastewater mixes with 130,000 other Aucklanders.

Gilpin said the Jet Park wastewater was « almost always » positive for SARS-CoV-2, and this allowed his colleagues to better understand detections in municipal wastewater.

« It’s a controlled place to study detection because we know how many positives are inside Jet Park, » he said.

« So, when we see the positive detection right outside Jet Park, we can match it with the number of positive guests.

« Then we check whether we get that positive further down the line at the South Western Interceptor where it mixes with more wastewater. »

They’ve now found that this municipal treatment plant was positive for SARS-CoV-2 approximately half of the time, although that varied when there were numbers of cases at Jet Park.

« We have also had detections in wastewater from Christchurch and Rotorua which we could match with known cases in quarantine facilities, » he said.

« We use this knowledge and apply it to the other sites not showing any positives. »

How much further can we take it?

In a pilot study, ESR recently rolled out wastewater testing across centres with MIQ facilities, such as East Auckland, Christchurch, Hamilton, Rotorua and Wellington.

It also targeted some other cities and suburbs, including West Auckland and Rosedale, Dunedin, Gisborne, Invercargill, Napier, central and north Nelson, New Plymouth, Palmerston North, Queenstown, Taupō and Whangārei.

Gilpin said ESR was working with the Ministry of Health on where and how it could be deployed further.

« While we will continue to have some core sites and areas where we collect wastewater from, in other situations we will be quite dynamic and responsive to the epidemiological needs, » he said.

« As we saw for this investigation, we instigated daily testing of wastewater from New Plymouth because the cases had visited there, and additional sites across the Auckland region.

« We also took additional samples from areas around Northland for the cases associated with that investigation area earlier this year.

« This level of intensive sampling and testing isn’t sustainable, so we will be reverting to twice weekly sampling at most sites. »

At the same time, ESR was honing its response capability.

« How do we deploy samplers across a network to really gauge the size and extent of any outbreak? » he said.

« As we start to vaccinate people, and even more so when we open up our borders, this wastewater testing is potentially going to be of even greater value. »

« Wastewater testing may allow us to identify areas of increasing prevalence, provide warnings to those at risk, and allow targeting of public health responses. »

He thought it was also important to look beyond the pandemic – and to a future where the technology could take us to some fascinating places.

« Illicit drugs and infectious viruses are just two of the possible areas that wastewater analysis may allow us to understand. »

The smart toilet of the future may analyse what we deposit in our toilet to help with our personal wellbeing.

At a wider scale, wastewater analysis might allow researchers to better understand the behaviours and health of Kiwis, across a vast range of areas.

« You might say there really is ‘information gold’ in wastewater – and wastewater epidemiology is something you are only going to see more of in the coming years. »