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How sewage can warn us about the next pandemic

The ins and outs of wastewater surveillance.

Christina Animashaun/Vox

Part of Pandemic-Proof, Future Perfect’s series on the upgrades we can make to prepare for the next pandemic.

Your poop doesn’t lie. Feces and urine are useful barometers of an individual’s health because what goes into the body inevitably comes out. And thanks to advances in genomic sequencing that allow researchers to decode whatever is present in waste, researchers today can examine sewage to ascertain in real time the presence of drugs like opioids, as well as diseases like salmonella and, increasingly over the past two years, Covid-19.

The process is called wastewater surveillance, also known as wastewater-based epidemiology. What makes it such an effective method of detecting the prevalence of Covid-19 in an area is that while it can be difficult to get every person in a community to take a polymerase chain reaction (PCR) test or rapid antigen test, everyone, after all, poops. By examining the genetic sequences found in sewage, public health policymakers can passively detect whether a virus like Covid-19 is surging in an area, regardless of testing levels or hospital capacity.

In fact, because Covid-19 has been shown to appear in wastewater in advance of a disease outbreak (a study last year found that Covid-19 was already present in northern Italy in December 2019, before the first recorded cases of Covid-19 in Wuhan, China), wastewater surveillance could be used as part of a localized early warning system for emerging pathogens. The omicron variant was first discovered to be spreading inside the United States because it was detected in sewage.

With Covid-19 serving as the ultimate test case, wastewater surveillance has transformed from a niche approach to epidemiology to one widely adopted by scientists, universities, firms, and public health agencies around the United States, including the Centers for Disease Control and Prevention (CDC). It is also being rolled out in at least 63 other countries, according to the COVIDPoops19 dashboard maintained by researchers at the University of California Merced.

If wastewater surveillance can become a basic part of global public health infrastructure, not only will we be able to more quickly detect and forecast outbreaks of disease, we’ll also be able to deploy whatever public health measures are necessary to control and stem off community spread, ideally before it takes off.

Biobot Analytics, a public health research, data, and analytics firm based in Cambridge, Massachusetts, that is the brainchild of researchers at the Massachusetts Institute of Technology (MIT), has been at the forefront of using, developing, and promoting wastewater surveillance technology. To learn more about the promise and potential of wastewater surveillance, I contacted Newsha Ghaeli, Biobot’s president and co-founder, to speak about their work and how wastewater surveillance needs to be upgraded to head off future pandemics.

The conversation, edited for length and clarity, is below:

Muizz Akhtar

What is wastewater surveillance? And is it different from wastewater epidemiology?

Newsha Ghaeli

Wastewater epidemiology essentially refers to this field of study where we can understand the health of a large group of people by analyzing the sewage that they’re all connected to. Some refer to it now as wastewater monitoring or wastewater surveillance, but that’s all effectively the same thing as wastewater epidemiology. And it works because almost everything that you eat — the viruses, bacteria, all these things in your body — are excreted in your urine and stool.

Every time you use the toilet, you’re actually flushing this information on the diseases in your body down the toilet, where it’s collected in our city sewers and aggregated at a community’s wastewater treatment plant. So wastewater epidemiology means tapping into that resource to then be able to understand and map the health of a very large group of people.

Muizz Akhtar

What is the history of wastewater epidemiology and how did Biobot come to specialize in it?

Newsha Ghaeli

Some of its early and most well-known uses were to detect and monitor poliovirus. There’s an example from 2013 where researchers in Israel were actually successful in detecting and isolating the poliovirus in sewage in Israel.

At Biobot, our work is actually based on quite a bit of research that my co-founder, Dr. Mariana Matus, and I have been doing at MIT while she was a PhD student in computational biology and I was a graduate researcher in the Department of Urban Studies and Planning. My work was focused on looking at the future of our cities and how we can leverage technology to address some of our fundamental urban challenges. And when I met her in 2014, she had started to work on this project to essentially expand on the science of the microbiome into looking at our sewer systems as being the microbiome of an entire community. The concept just completely blew my mind, and we ended up working together for a few years on the research, and then started the company in 2017 to bring this technology to market.

Muizz Akhtar

What can wastewater surveillance see and predict? What is gleaned from it that can’t be otherwise found in standard mass Covid-19 testing?

Newsha Ghaeli

It’s less about seeing things that we can’t see in clinical data or other forms of surveillance, and it’s more about the fact that wastewater provides an opportunity for us to be more comprehensive in what we’re looking at. If there is an infectious disease like Covid-19, if we’re analyzing sewage, we’re actually looking at data that’s representative of everybody who lives in that community as opposed to just the folks who are interacting with our health care services who might have health insurance and are getting tested — and therefore get counted in the official numbers.

What we like to say in the company is everybody has a voice in our sewer systems, it’s not just biased toward those who have access to clinical care. And so when we think about things like Covid-19 or other infectious diseases, wastewater becomes tremendously complementary to other forms of epidemiological surveillance because we’re able to fill the gaps of where other forms of data may fall short.

And beyond Covid-19 and its variants, at Biobot we’ve already been analyzing data for influenza virus. We can also look at the consumption of high-risk substances that range anywhere from fentanyl, which is one of the leading causes of overdoses, all the way to nicotine. We imagine expanding very quickly into other forms of infectious disease — antimicrobial resistance is another one that is being talked about a lot, but the possibilities are endless.

Muizz Akhtar

How does wastewater surveillance work in tandem with public health measures to control disease, like quarantines, masking, testing, and contact tracing, especially now that many of these policies are being lifted once again?

Newsha Ghaeli

Fast-forward to December 2021, when we were just starting to see the omicron wave take off. People in the Greater Boston area had seen the wastewater data track clinical cases and, if anything, precede clinical cases time and time again. And so in December, we actually saw people make very legal, operational, and high-stakes decisions based on just the wastewater data because that trust had been built into this information.

My favorite example of this is in a New York Times article from January 2022, where they interviewed the chief medical officer of Boston Children’s Hospital, where he said that the wastewater data related to omicron led to them canceling a lot of their non-emergency procedures for Q1 of 2022, and then later in late January of 2022, when the wastewater data started to decline, they were starting to reschedule some of those appointments again.

Muizz Akhtar

How can wastewater surveillance be scaled up and maximized in the future for later pandemic and disease outbreaks? Where do you see wastewater surveillance and epidemiology in three to five years?

Newsha Ghaeli

Our vision is that this is a permanent infrastructure layer on our sewer systems, so that it becomes one of the core kinds of pandemic preparedness in this country and disease surveillance globally. It just absolutely makes sense for us to have some base case level of monitoring for, let’s say, a variety of pathogens of concern around the world.

And there needs to be a connected global network that is communicating what we’re seeing around the world because we’ve learned from Covid that the virus and also the variants spread to different corners of the world very, very quickly. That’s not going to happen without very strong leadership from governments globally, and here in the US, both federal and state-level leadership.

In addition to that leadership and coordination, something else that’s really needed is transparency of outcomes. And I think this feeds into this point of having people actually use the data. I think that we need to be — as a community and then also individuals, [essentially] public health departments and agencies — we need to be very transparent around the actions that are taken with this data and the outcomes that are facilitated, because that’ll just further build and reinforce trust in the fact that this data is making a difference in how we respond to and mitigate this pandemic.

Muizz Akhtar

If you had a magic wand and could design a fully effective wastewater program for the future, what would it look like, how much would it cost, and what would it achieve?

Newsha Ghaeli

I don’t know the numbers off the top of my head, but [it would be] a fraction of the cost of testing every single person. Biobot had a short contract with [the CDC and Department of Health and Human Services] last summer and we tested 300 locations that represented just under 100 million people, or about 30 percent of the US population. Just imagine the cost of clinically testing 30 percent or even 10 percent of the US population. It’s not even comparable.

But how do we turn this into one of the core tenets of pandemic preparedness in the US? Number one, make sure that there is funding allocated toward our national wastewater infrastructure — not just for two years or three years, but for 10 years. Then everyone can just focus on building the best version of this network and of this platform. Wastewater has the potential to transform how we understand public health and how we respond to a lot of our public health priorities. Let’s actually design the system to do that as opposed to just staying focused on Covid.

Muizz Akhtar

What would you say are the holes or gaps in wastewater epidemiology that need to be filled?

Newsha Ghaeli

We see a tremendous amount of work still to do, and some of the challenges have been that this endeavor brings together communities that don’t traditionally work very closely together. This data is consumed by public health agencies. But in order for them to get the data, you need the full buy-in of the wastewater treatment folks. And sometimes we hear from a wastewater treatment plant that we work with that they just can’t get their public health department to engage.

I would say that that component of building bridges between these communities has come a very, very long way. But I think that can still continue to strengthen.

Muizz Akhtar

What do you do in a place that doesn’t have much of a sewage or public wastewater system to begin with? There are plenty of communities, including in the Global South, where you just have pit toilets.

Newsha Ghaeli

We don’t work in communities [that use] septic tanks, which is about one-third of the US. The current version of our technology relies on sewer infrastructure, so in regions where you are either relying on septic tanks or pits or port-a-potties, the approach would have to change.

We have just done some research work at MIT, where we had done an analysis of samples in Nepal where samples were actually collected from open channel sewers, which obviously collect not only sewage but also street runoff, rainwater, everything. [Different] systems will need a different approach, but I think it’s definitely a challenge that can be overcome.