Coronavirus Traces Found in Massachusetts Wastewater at Levels Far Higher Than Expected

Researchers have detected traces of the novel coronavirus in wastewater treated by a facility in Massachusetts, and based on the quantities found, they estimate that the true number of COVID-19 cases in the area served by the plant could be significantly higher than the official figures suggest.

Wastewater analysis of this kind has previously been used by scientists to track other infectious diseases, as well as substance abuse in a given population. Now, several research groups around the world have started using this method to look for the novel coronavirus in a bid to estimate how many people are infected in a community.

Researchers hope that these kinds of techniques could complement traditional testing, which has been severely lacking in many parts of the world.

For the latest study, published on the pre-print server medRxiv, a team involving scientists from startup Biobot Analytics, the Massachusetts Institute of Technology (MIT,) Harvard University, and Brigham and Women's Hospital tested water at a major urban treatment facility serving a large area of Massachusetts in the period March 18-25, in order to detect the novel coronavirus—known as SARS-CoV-2.

"At Biobot, we have been using wastewater based epidemiology to generate data on the opioid crisis in the U.S.," Eric Alm, one of the authors of the study, told Newsweek. "At my academic laboratory at MIT and also in Singapore, we have been developing wastewater based epidemiology to estimate disease prevalence of typhoid in Nepal, and dengue in Singapore."

"We realized that by working together, we could combine Biobot's scale of operations with MIT's expertise in molecular biology to help supplement the limited capacity for individualized testing," he said.

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It is possible to detect the SARS-CoV-2 virus in wastewater by looking for its genetic fingerprint—a molecule known as RNA. These traces that are detectable in wastewater are no longer able to cause disease.

"Even if those viral particles are no longer active or capable of infecting humans, they may still carry genetic material that can be detected using an approach called PCR (polymerase chain reaction,) which amplifies the genetic signal many orders of magnitude creating billions of copies of the genome for each starting virus. We use a technique called qPCR or quantitative PCR to estimate how many copies of SARS-COV-2 specific genomes are present in a given sample," he said.

Viral particles in wastewater are greatly diluted, so the researchers enriched them using a special chemical process and a high-speed centrifuge, before extracting the genetic materials. They then used quantitative PCR to determine the quantity of virus traces in the wastewater, enabling them to come up with a preliminary prediction for the number of people who could be infected in a community.

coronavirus
Stock photo: Illustration of the novel coronavirus. iStock

"If we find the genetic name tag of the virus, it implies that there must be an infected human excreting it," Rolf Halden, a researcher at Arizona State University who was not involved in the study, told Newsweek.

"But looking for the viral name tag is like searching for a needle in the haystack. Virus particles are few, interferences are many, and the virus is notoriously unstable, falling apart rather quickly in wastewater. In our laboratories, we work to concentrate virus particles from wastewater and then detect them in a purified concentrate using a genetic copy machine called quantitative PCR," he said.

"You can compare it to looking at a busy highway from the distance through binoculars: spotting that one license plate of interest is hard when the traffic is heavy and the visibility limited. If and when the genetic copy machine latches on and gives us a positive result, we then count the copy number produced to estimate the quantity of viruses present. This can be fuzzy math, where dangerous potholes abound. That's why it is so important to have multiple research teams demonstrate independently that the technique works. The scientific community is making progress but we are not quite there yet."

During the study period, the authors of the pre-print say there were nearly 450 confirmed cases of COVID-19 in the area served by the water treatment facility, but the latest results suggest that this figure could be an underestimate, although more research is needed to verify this. While the team currently lack the data to provide an accurate figure for the number of people infected in the area, they estimate that it could be anywhere between 2,300 and 115,000—far higher than the official figure in both cases.

"The amount of virus we found in wastewater was higher than we expected given the number of clinically confirmed cases in the area that we sampled," Alm said. "We still have additional follow up experiments to perform before we can say exactly how many undiagnosed cases there might be, but we believe it could be significantly higher than the number of confirmed cases."

Halden, who is currently conducting similar research of his own, said that the pre-print adds to earlier, preliminary findings from Europe indicating that SARS-CoV-2 can be detected successfully in municipal sewage.

"But more work is needed to validate the methods used. So we are cautiously optimistic," he told Newsweek. "Community wastewater is a proven source of information that otherwise is difficult to obtain. It's simple math: how do you get the most information on the largest number of people with the least amount of resources? Answer: Perform a population-wide assessments; and if a problem is identified, mobilize an emergency response in areas of need. In the healthcare setting, screening is slow because we examine one individual at a time."

"The same test applied to wastewater, provides information on thousands or hundreds of thousands of people. While wastewater analysis does not replace testing of individuals, it provides useful data very economically, rapidly and at scale," he said.

"It would be foolish, not to harness wastewater analytics for managing the COVID-19 outbreak; and it represents a promising tool for informing us on where, when and for how long we need to intervene to protect both the people and the economy. More work is needed to fully demonstrate the robustness of this method for monitoring of the new coronavirus. However, early evidence is encouraging."

According to Alm, wastewater testing could help to provide a more accurate picture when modelling the spread of COVID-19, as well as future pandemics.

Spread of COVID-19 in the U.S.
The spread of the COVID-19 virus in the U.S. Statista

"For example, if the number of actual cases is much higher than the number of known cases, then the reported case fatality rates may be lower than they currently appear," he said. "Having accurate estimates of disease prevalence will help cities plan for what kind of resources they will need when disease prevalence hits its peak."

"In addition, testing of small communities might alert city officials to when outbreaks are happening, so that they can respond more quickly by implementing social distancing measures. Testing over time can give a good idea of when the peak number of infections is trending downward, and could help policymakers decide when to relax quarantine measures," he said.

Another author of the study, Fuqing Wu from MIT, adds that this kind of data could alert people and governments about an epidemic several days, or even weeks, before confirmed cases appear since clinical infection symptoms of COVID-19 usually come later than the virus's replication in the human body and its excretion into the wastewater.

Despite the promise of analyzing wastewater to monitor the spread of COVID-19, Halden stresses that there is still some way to go before such methods can be put into widespread use.

"There's still a big if. The studies available thus far do not rise to the scientific rigor that instills complete confidence," he said. "The international research community is working hard to fill those gaps quickly, however. The technology for testing is common to thousands of laboratories around the country and the world. So, once the assays are validated and up and running, monitoring can spread quickly, as long as the necessary supplies are in place."

"If we succeed, our data will help to save not only lives but also livelihoods, by isolating areas that show infections and by getting people back to school, work and normalcy when it's safe to do so," he said.

Encouragingly, there are already systems in place for monitoring wastewater that could help to see us through the COVID-19 pandemic, according to Halden.

"Here at Arizona State University, we have created the Human Health Observatory (HHO,) a wastewater monitoring network that stretches across the U.S. and around the world to reach a quarter-of-a-billion people. We started building the HHO some 10 years ago, when few people knew what wastewater-based epidemiology is," he said.

Furthermore, Biobot recently launched a campaign to provide its wastewater sampling services for free in several locations across the country, enrolling around 100 treatment plants to date, with the aim of signing up a further 10,000 by the end of next month, Mariana Matus, CEO and co-founder of the company told Stat.

"The beauty of wastewater analysis is that it cannot only inform on infectious diseases but also on many other dimensions of human wellbeing, such as substance abuse," Halden said. "In Tempe, Arizona, we have been monitoring the use of opioids, including heroin and fentanyl, for years now, with our data directly informing the city's decisions on how to address the opioid epidemic. That's why we built the first U.S. wastewater monitoring network in the first place, to obtain information that otherwise is difficult or impossible to obtain."

"Today, wastewater analysis already has paid huge dividends for managing the U.S. opioid epidemic, and we and other teams globally are working furiously to duplicate this success when monitoring new coronavirus," he said. "For the sake of the people around the world, we ought to get this right. And when a validated method is in place, we have to get it to those people at greatest risk."

This article was updated to include additional comments from Eric Alm, Fuqing Wu and Rolf Halden.

Centers for Disease Control and Prevention Advice on Using Face Coverings to Slow Spread of COVID-19

  • CDC recommends wearing a cloth face covering in public where social distancing measures are difficult to maintain.
  • A simple cloth face covering can help slow the spread of the virus by those infected and by those who do not exhibit symptoms.
  • Cloth face coverings can be fashioned from household items. Guides are offered by the CDC. (https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/diy-cloth-face-coverings.html)
  • Cloth face coverings should be washed regularly. A washing machine will suffice.
  • Practice safe removal of face coverings by not touching eyes, nose, and mouth, and wash hands immediately after removing the covering.

World Health Organization advice for avoiding spread of coronavirus disease (COVID-19)

Hygiene advice

  • Clean hands frequently with soap and water, or alcohol-based hand rub.
  • Wash hands after coughing or sneezing; when caring for the sick; before, during and after food preparation; before eating; after using the toilet; when hands are visibly dirty; and after handling animals or waste.
  • Maintain at least 1 meter (3 feet) distance from anyone who is coughing or sneezing.
  • Avoid touching your hands, nose and mouth. Do not spit in public.
  • Cover your mouth and nose with a tissue or bent elbow when coughing or sneezing. Discard the tissue immediately and clean your hands.

Medical advice

  • Avoid close contact with others if you have any symptoms.
  • Stay at home if you feel unwell, even with mild symptoms such as headache and runny nose, to avoid potential spread of the disease to medical facilities and other people.
  • If you develop serious symptoms (fever, cough, difficulty breathing) seek medical care early and contact local health authorities in advance.
  • Note any recent contact with others and travel details to provide to authorities who can trace and prevent spread of the disease.
  • Stay up to date on COVID-19 developments issued by health authorities and follow their guidance.

Mask and glove usage

  • Healthy individuals only need to wear a mask if taking care of a sick person.
  • Wear a mask if you are coughing or sneezing.
  • Masks are effective when used in combination with frequent hand cleaning.
  • Do not touch the mask while wearing it. Clean hands if you touch the mask.
  • Learn how to properly put on, remove and dispose of masks. Clean hands after disposing of the mask.
  • Do not reuse single-use masks.
  • Regularly washing bare hands is more effective against catching COVID-19 than wearing rubber gloves.
  • The COVID-19 virus can still be picked up on rubber gloves and transmitted by touching your face.
Coronavirus Traces Found in Massachusetts Wastewater at Levels Far Higher Than Expected | Tech & Science