Tracking Coronavirus Via The Sewer System

Wastewater samples are being used to track the spread of SARS-CoV-2

An employee of a sewage treatment plant takes a sample of the sewage water, on July 22, 2020 in ... [+]

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It’s sometimes called ‘wastewater-based epidemiology’ (WBE) – a scientific and public health field that involves detecting and monitoring specific molecules in untreated wastewater, to determine how prevalent they are. First proposed more than 70 years ago as a way to track the spread of the deadly poliovirus, WBE has since been used to measure human population exposure to pollutants, and even to estimate the level of drug consumption in major cities. In 2020, it hit global news headlines when it was first proposed as a way to track SARS-CoV-2, the virus that causes COVID-19.

SARS-CoV-2 is a respiratory virus, so it is mainly shed into the environment through an infected person coughing, sneezing, speaking and breathing. But it can also be found in their urine and feces – hence the interest in all things sewage (or wastewater, to give it its official name).* To date, 58 countries have established a wastewater testing process, with many of them sharing the data they collect publicly, via the aptly named COVIDPoops19 dashboard.

Here in Aotearoa New Zealand, the COVID wastewater project is managed by ESR, a major research lab on the outskirts of Wellington. And leading the effort is the head of ESR's Environmental Virology Laboratory, Dr Joanne Hewitt. Dr Hewitt has been looking for viruses in wastewater for 25 years – everything from polio to norovirus – but acknowledges that before the pandemic, “…it was seen as quite a niche topic.” Back then, Hewitt and her small team of scientists typically processed 200 wastewater samples a month, but the recent arrival of Delta to NZ’s shores changed that. “I checked our totals yesterday. We processed 825 samples in September, and 750 in October.”

The technique used to test wastewater for the presence of SARS-CoV-2 varies a bit from lab to lab, but it all starts with getting samples. As Hewitt explains, most of ESR’s come from wastewater treatment plants or nominated locations on the wastewater network. “We take what are called ‘composite samples’ and they are either time-weighted or flow-weighted. The wastewater has been primary screened at this stage, but it hasn’t yet been treated.” Composite samples are typically collected automatically, via pumps already installed within the sewer system, but ‘grab sampling’ – which is exactly what it sounds like – is also very common in more remote areas. “In some parts of New Zealand, towns within one council can be spread out over a huge area,” says Hewitt. “So because of the amount of driving involved, it sometimes takes all day to get eight samples. Sample collection can be as time consuming as sample detection!”

These wastewater samples, which I’ve been told look like “very murky, dirty river water”, get packed into cool-boxes filled with ice, and sent to ESR. When I spoke to Hewitt, she’d just finished a busy weekend of lab work. “On Friday, we had 70 samples come in. Unpacking and sorting through those takes quite a bit of time, and that’s before we start doing the analysis.” From start to finish, she says, a single sample can be processed in seven hours.

The first step is to compress the wastewater into a much smaller volume. “Our method allows us to recover virus from both the liquid and the solid bits of the wastewater. But we know that the virus attaches very well to solids, so we centrifuge it a lot.” Centrifuging involves spinning the sample rapidly so that the solids are forced together. It also removes much of the liquid, concentrating the sample into something much thicker and denser. In ESR’s case, what started off as a 250 ml sample of wastewater becomes a 1 ml sample of sludge. Hewitt says that this step is especially important when dealing with small quantities of virus, “We don’t have huge numbers of cases in each catchment. So when you’re looking for not very much, it’s a good idea to concentrate your sample.”

A researcher processes wastewater samples from dorm sewage lines while testing for Covid-19 at the ... [+]

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Next, the team start looking for any sign of the viral RNA – the part of a SARS-CoV-2 virus that contains its genetic material. There are lots of commercially-available kits to extract RNA, and Hewitt says “every lab has their favorite….the key thing is that they all do the same job.” As well as recovering RNA, this extraction step also removes any other chemicals that might interfere with the next stage of the process – what’s called PCR, or Polymerase Chain Reaction. PCR’s job is to rapidly copy (or amplify) DNA molecules, making it easier to detect and study. “But because we’re looking at an RNA virus, we first have to convert the RNA into its complementary DNA,” Hewitt explains. Once that’s done, they can start on the PCR. “In PCR, you use sets of what we call ‘primers and probes’ that are specific to the target that you're looking for. So you’ll have different ones for norovirus, Influenza A, SARS-CoV-2, etc. That’s how we determine whether the virus is present or not.” ESR scientists also add control molecules to the process, measuring them throughout, to ensure that everything works reliably.

The technique seems to be remarkably sensitive. While a figure of “10 cases in a catchment of 100,000” is often used to describe its effectiveness, Hewitt tells me that last month they detected SARS-CoV-2 from a single individual – a truck driver – in a sample taken from a catchment that serves 90,000 people.

For the moment, New Zealand is using COVID-focused wastewater-based epidemiology solely as an early warning system, “Mainly for new detections in areas where there's no cases. We’re asking ‘Is the virus detected or is it not detected?’”, says Hewitt. “Which is why we want to make sure it's as sensitive as we can get it.” Despite facing some criticism in recent months, it it looks set to stick around, “It’s just one tool, of course, but I think it’s been really useful.”

* It’s very unlikely that SARS-CoV-2 is still infectious when it reaches the sewers. According to the WHO, “there has been no reports of faecal−oral transmission of the COVID-19 virus to date.”

Source: https://www.forbes.com/sites/lauriewinkless/2021/11/08/tracking-coronavirus-via-the-sewer-system/?sh=1e0e86444298