Using wastewater to track the pandemic

Scientists around the world are studying the new coronavirus (SARS-CoV-2) from many different perspectives in an effort to better understand how it infects the body and spreads from person to person. The goal is to find therapies to neutralize and eliminate it. One approach taken by EPFL and Eawag researchers, until drug and vaccine treatments are developed, is to test wastewater samples so that health officials can detect the virus before the disease is clinically diagnosed. “Our study looks at how we can detect the virus in wastewater and measure its concentration before people begin to develop clinical symptoms, and determine how long before,” says Tamar Kohn, head of the EPFL Laboratory of Environmental Chemistry (LCE). .

In collaboration with Christoph Ort in the Eawag Urban Water Management Department and Tim Julian in the Eawag Department of Environmental Microbiology, the researchers accomplished a great feat by demonstrating that the new coronavirus can be detected and measured in wastewater in a matter of weeks. The researchers analyzed samples from Lausanne, Zurich and Lugano, including samples from Zurich and Lugano that were collected in late February when the first cases were recorded in Switzerland. “As an environmental virology specialist, I was ready to work on the pandemic when it first came to Italy,” says Xavier Fernández Cassi at the LCE. “It was clear to me that the virus would spread to Switzerland. Given how interconnected countries are today, I would have been surprised if it did not.”

The researchers found traces of the virus in all the samples they collected. While the concentrations in the most recent samples were so high that it was easy enough to measure them, this was not true for the February samples. “We were pleasantly surprised to find a signal in the wastewater of Lugano, where only one case had been identified at the time, and Zurich, where only six had been identified,” says Kohn. Working with colleagues from Eawag, they collected samples from nine wastewater treatment plants in Ticino, two in Zurich and one in Lausanne, corresponding to a total of around 800,000 city residents.

The possible ramifications of this study are so important that Cassi and Marie-Hélène Corre, another LCE biologist, received special authorization to work in their EPFL laboratory during closure. They were particularly efficient in conducting their experiments, as almost no one else was using the test equipment, since the campus was nearly deserted. But the researchers had to be very careful because the new coronavirus, despite coming from a known viral family, is a zoonotic virus. “The main feature of this virus is that it has an envelope, its viral capsid is wrapped in a biological membrane,” says Corre. “Seasonal influenza virus and HIV also have envelopes.”

Objective: early warning system

Samples collected since the first cases of COVID-19 were reported in Switzerland are valuable archives. However, the main objective of this study is not to go back in time, but to develop an early warning system. Ort says: “With samples from 20 large treatment plants distributed in Switzerland, we could monitor the wastewater of around 2.5 million people.” If samples are analyzed quickly, we could probably detect a resurgence of infections earlier than with diagnostic tests, approximately a week earlier, especially during the period when the block is lifted. Ort has been concerned with wastewater-based epidemiology, previously focusing on comparisons of drug use in Europe. “The wastewater does not lie, it reflects what has been excreted by a population in a few hours,” he says. The research team has built on its established contacts with local government agencies and wastewater treatment plants.

Tracking infection trends, not absolute case numbers

Since the researchers were able to successfully detect low viral concentrations in the early stage of the COVID-19 outbreak in Switzerland, they should be able to reconstruct the infection curve. But it will still take a few weeks to analyze the more than 300 currently stored samples frozen at Eawag and EPFL. They will not be able to calculate the exact number of infections using this data, as there is too much variation in the amount of virus each patient sheds. However, what will be important to follow is the trend. For example, using samples collected in Lausanne in March and April, researchers were able to roughly track the increase in SARS-CoV-2 wastewater concentration. Kohn estimates that the concentration increased by a factor of between ten and one hundred.

Complex method

Despite the initial success of the researchers, they still need to further improve their method. For example, they still don’t know what percentage of the viral load in wastewater is captured when RNA is extracted after a series of other steps (filtration and centrifugation). There is also a lot of uncertainty in the subsequent selective amplification process for the target sequence. Only when uncertainty is reduced will they be able to draw solid conclusions about viral concentrations in the original samples.

Coronavirus unlikely to spread through water or sewage

While the genetic material of the new coronavirus can be detected in wastewater, there is currently no evidence to suggest that the pathogen spreads through water or wastewater. Drinking water in Switzerland is of excellent microbiological quality and remains suitable for consumption even during the pandemic.