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Wastewater samples that arrive at ESR are condensed into these test tubes for further tests. (Photo: ESR)
Wastewater samples that arrive at ESR are condensed into these test tubes for further tests. (Photo: ESR)

ScienceJune 13, 2022

As Covid case counts become less accurate, wastewater testing is riding to the rescue

Wastewater samples that arrive at ESR are condensed into these test tubes for further tests. (Photo: ESR)
Wastewater samples that arrive at ESR are condensed into these test tubes for further tests. (Photo: ESR)

New Zealand’s move to self-reporting has made our official case numbers less reliable than ever before – and that’s where wastewater testing comes in, explain microbiologist Siouxsie Wiles and ESR geneticist Mike Bunce.

As Aotearoa New Zealand grapples with widespread Covid-19 in the community, our current approach to the pandemic is that everyone needs to take personal responsibility for their safety. It’s an approach that requires far more physical and mental resources than many would like to admit, and one where the burden can fall disproportionately on New Zealanders who might be most at risk of serious disease from Covid-19.

It’s also an approach that requires data so that people know how risky or safe it is for them to go to certain places or do certain things. Given our individual threshold for risk differs, it is important we don’t project our risk appetite onto others. Siouxsie and Dr Jin Russell have written about how the global data on Covid is becoming more and more unreliable and harder to interpret as countries stop testing and mothball their surveillance systems. But putting that aside, what data do we have access to here in Aotearoa to assist with personal decision-making?

Well, we still don’t have a robust prevalence survey running that would help us accurately calculate how many people are infected (and with what variant). The Ministry of Health does still issue a press release most days that includes a long list of Covid stats. Like the total number of daily cases from PCR tests and rapid antigen tests (RATs), the case numbers by region, the rolling seven-day average of case numbers, the number of people vaccinated, the number of people in hospital, and the number of people in a high dependency or intensive care unit.

Now that we are almost entirely relying on the self-reporting of RAT results, we know that the number of daily cases is an underestimate because there are a sizable number of people who are asymptomatic, don’t test, or fail to report their results. The Ministry of Health currently estimates under-reporting at ~50% (of reported cases) as a ballpark figure. Regardless, reported cases are still a useful number to know, as they are a lower bound on the true number of cases. Also important is the number of hospitalisations. Is the Covid curve “flat enough” not to overwhelm the hospital system, and thus deal with all the ripple effects that come with an overloaded health system, like postponed surgeries and procedures?

The important question, as omicron (including all the subvariants) sweeps through Aotearoa, is whether case numbers and hospital metrics still the best barometer for where we are at with regard to the pandemic. Are they the data you need to help with your decision-making, or are there other ways to forecast the pandemic trends in your neighbourhood? The answer is definitely yes, there are other ways. And the good news is that we’ve been doing one of them for a while now: tracking the Covid virus in our wastewater. This technique could be a game-changer for us moving forward. Let’s unpack why.

Testing wastewater in Christchurch (Photo: ESR)

Using wastewater to track Covid-19

Technically referred to as wastewater-based epidemiology, this technique describes a way to go “fishing” for the small bits of viral RNA that we excrete out of our bodies as we (hopefully) clear the virus. While some people continue to shed low levels of the virus for a few weeks after they’ve recovered, the bulk of it comes out when we have an active infection.

Tracking infectious diseases using wastewater isn’t a new idea, it’s actually been around for decades. The most cited example of wastewater testing in action is the detection of the polio virus which the world has been trying to eradicate. For example, using data gathered from wastewater triggered Israel to rapidly and effectively respond to a polio outbreak in 2013.

But like so many things, it’s taken a pandemic to show just how useful this technique can be. In 2020, using wastewater to track the Covid-19 virus quickly gained traction across the globe. Across the US, university academics started using their laboratories and ninja-like skills with a PCR machine for early detection on their campuses. This was before vaccines were available, and the aim was to protect staff and students. Ultimately this “niche” way of detecting and tracking Covid-19 expanded and morphed into a Centres for Disease Control (CDC) programme for the whole country, complete with dashboards and multi-year funding.

Like the field of real-time genomic sequencing, the profile of wastewater-based epidemiology has risen in this pandemic and the technique is now interwoven into the international pandemic response. There seems to be a dashboard for everything in this pandemic and wastewater is no exception; the ‘CovidPoops19’ dashboard currently records 67 countries with wastewater programmes.

ESR’s Dr Joanne Hewitt with a wastewater sample that needs testing. (Photo: ESR)

Tracking Covid-19 in Aotearoa’s wastewater 

Here in Aotearoa, our Covid wastewater journey has been a little different to other places. When we were pursuing elimination, wastewater detections of Covid would be rare outside of catchments that had MIQ facilities. That meant wastewater testing had the potential to be used as an early warning system of undetected community transmission – if it was sensitive enough. The beauty of wastewater-based epidemiology is that it doesn’t rely on people stepping up to get tested if they have symptoms, or reporting their results if they are testing at home. All they have to do is take a trip to the bathroom.

Wastewater testing might sound simple. Just scoop up some sewage, isolate the RNA present, and then do some PCR testing to determine if the Covid virus is present, and if so, how much. In fact, in the early days of the pandemic, the wastewater team at ESR were: (i) racing around building relationships with all the wastewater plant operators across the country, (ii) figuring out how to deploy autosamplers that would “sip” samples of sewage over the course of a day, (iii) developing and testing ultra-sensitive methods for isolating viral DNA, and (iv) working out how best to PCR the viral RNA and determine how much is in a sample. Oh, and they also had the small task of convincing decision-makers that wastewater testing was a tool worth paying for and deploying.

Fortunately, it was funded and early detections in towns like Stratford in Taranaki were able to contain local outbreaks. Indeed, the July 2021 Stratford case study was highlighted in the World Health Organisation’s 2022 guidance on environmental surveillance for Covid-19.

Wastewater sampling post-elimination

Now we are no longer following an elimination strategy, wastewater-based epidemiology is arguably even more important. The gross underreporting of Covid cases is an issue that the US has been grappling with for some time, and continues to. They are not alone. An apathy towards testing is also developing here in Aotearoa. Many of you reading this will probably know of someone who just hasn’t gotten tested. They may have already contracted Covid-19, can’t afford to isolate, or are just “over” the whole pandemic and can’t be bothered. As we said earlier, all those are reasons why case counts are becoming an increasingly poor indication of what is happening in a given area. Enter wastewater.

Each week, ESR produces a wastewater report. It’s full of graphs showing the wastewater detections for different areas of the country. Below is the graph for Moa Point in Wellington, a catchment with ~168,000 people. The grey shaded area is the rolling seven-day average of cases in the wastewater catchment, plotted on the right-hand axis. The thick greeny-blue line is the rolling 14-day trend of Covid viral RNA in the wastewater, plotted on a log scale on the left axis. The wastewater levels are the number of viral copies per person, per day – a sum that takes into account how much “flow” goes through a given wastewater plant and the number of people that contribute.

Image: ESR wastewater report 2022.

What can wastewater tell us that case numbers can’t?

So what can monitoring the levels of viral RNA in wastewater tell us that case numbers aren’t able to? If we look at the Wellington data, we can see that wastewater testing picked up the February/March omicron surge before the daily case reports did. In other words, wastewater was a lead indicator, a pattern seen in most sites across the country. After the initial surge, both case numbers and wastewater viral RNA levels plateaued, reflecting steady ongoing transmission in the catchment area. Interestingly, wastewater levels started to trend upwards again in May around the time the school term started. In contrast, case numbers stayed steady.

So which result do we believe? Is relying too heavily on counting cases using self-reported RATs giving us – as our cousins across the ditch would say – a bum steer? Researchers at Massey University are taking wastewater and case data and trying to build models. For example, if we see a more than 50% increase in viral RNA in wastewater two weeks in a row, how certain can we be that a bump in cases will follow? If we could be fairly certain, then we could use the wastewater data to give us a heads-up that transmission is on the rise in a particular area. That means we could target public health messages to let people know they are at a heightened risk of infection. Of course, the same is also true when wastewater viral RNA levels are low. Then the data could be used to provide some reassurance to people that the risk of infection is lower in a particular area.

Tracking Covid variants

The other big advantage of wastewater testing is the ability to sequence the viral RNA to get an idea of which Covid variants are circulating. This is the data we are missing by relying so heavily on RATs – you simply can’t sequence the sample from a rapid antigen test. At the moment, only a limited number of people are getting PCR tests and a smaller number of them are being sequenced.

But each week, ESR is extracting wastewater RNA from around 20 sentinel sites and sending it to a company called Wilderlab which specialises in sequencing trace bits of genetic material from water. Below is a snapshot of some recent data. It shows that the majority of cases across the country are the BA.2 omicron variant – that’s the sea of orange – though some BA.1 is still being detected in Dunedin, shown in green. But it also shows that the new variants, BA.4 and BA.5 in red, and BA.2.12.1 in yellow, are now being detected. These are the omicron variants that are currently driving new waves of the pandemic overseas. It’s highly probable we will see these new variants, particularly BA.4/5, overtake BA.2 in the coming weeks. In combination with sequencing swabs from people in hospital, wastewater monitoring will help us to keep a close watch on how these new variants are adapting and spreading across Aotearoa.

Image: ESR wastewater report 2022. Sites denoted with * indicate that variants were only detected in some replicates.

If there is one thing that this pandemic has taught us, it’s that good data underpins good decisions. We could also add that good communication is needed to translate good decisions into action. While we will always count infectious diseases such as Covid-19 from cases detected in the community, we have to be aware that data can become less reliable.

While wastewater testing has its limitations – not all people are on mains wastewater, different catchments have different flow rates, and different Covid variants may well have different viral loads making it a straight conversion of viral RNA to “cases” tricky – when used in combination with our existing metrics, it provides a new, if a little murky, lens on how Covid is playing out around the country. If you knew cases were rising in your area and that soon your local hospital was going to have to postpone elective surgeries, wouldn’t you want to know so you could do what you could to help prevent a surge?

The good news is that the utility of wastewater testing reaches far beyond the Covid-19 pandemic. It provides the ability to detect a whole range of important microbes, work out how much of them are present in a particular area, and by sequencing their genetic material, track individual strains and variants. We should be learning the lesson from Covid, and support the infrastructure and people needed for this technique to be utilised to its full potential. That’ll help generate robust data to underpin our decision-making in relation not only to the pandemic and other emerging infectious diseases, but also to the endemic diseases that have impacted the health, well-being and productivity of New Zealanders for years.

ESR is currently working on a web-based tool that will enable you to easily visualise wastewater trends in your neck of the woods. Watch this space. Maybe one day soon, checking the wastewater reports will be like checking the weather! Because against the backdrop of infectious disease – and if we have to take responsibility for our own safety – then forewarned is forearmed.

Disclosure statement: Professor Mike Bunce was formerly employed at the New Zealand Ministry of Health where he wrote science advice on wastewater-based epidemiology. He is currently employed at ESR which is contracted to run the wastewater surveillance programme across Aotearoa.


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