From the Berlin sewer system to the laboratory spotlight
The moment has arrived. After hours of winding its way through Berlin’s centuries-old sewer system – picking up solids, fungi, and even the occasional creature – one sample of wastewater is nearing the treatment plant. But before it gets there, it will serve one final purpose as a subject of molecular biology research. The 500-milliliter sample, yellow and murky, is about to be filtered by Emanuel Wyler. A molecular biologist at the Max Delbrück Center (MDC) on Hannoversche Straße in Mitte, Wyler isn’t interested in the cocaine or ketamine residues left behind by the city’s ravers. He’s focused solely on the viruses—because these tiny pathogens might soon help scientists predict entire pandemics.
In January 2021, at the height of the coronavirus pandemic, the “RNA Biology and Posttranscriptional Regulation” research group launched a study of Berlin’s wastewater. Their method: metagenomic sequencing – analyzing the genetic material of all organisms present in a sample. The sequencing took place over 17 months, with support from Berliner Wasserbetriebe (Berlin Waterworks) and the Berlin State Office for Health and Social Affairs (Lageso).
Thousands of new viruses discovered in Berlin’s wastewater
Researching wastewater is nothing new. For decades, scientists have used sewage to track the spread of pathogens. Techniques like PCR testing are standard, allowing them to detect individual molecules – and with them, specific viruses like SARS-CoV-2, which rose to prominence during the pandemic. The advantage? Wastewater testing offers a more accurate picture of actual infection rates than official case numbers, which only ever reflect a fraction of the true total. Still, comprehensive RNA and DNA sequencing of wastewater remains rare. Such studies could not only identify all known viruses but also uncover entirely new ones.
Using metagenomic sequencing, the Max Delbrück Center has uncovered thousands of previously unknown viruses – by scanning for a genetic pattern shared by all viruses. This approach led the team to identify members of the Bunyavirus family, a group of pathogens that primarily infect insects and amoebas. The more we learn about the viral world, the better our chances of preventing zoonotic diseases – those that jump from animals to humans. Many researchers now believe the coronavirus pandemic originated from the wildlife trade and a resulting zoonosis.
Back in the research lab in Mitte, Wyler holds up the results of the wastewater filtration. The murky color has vanished, replaced by a clear liquid – just 50 microliters, about the size of a thimble. It contains ten to twenty thousand different organisms. To give us a closer look at his work, Wyler runs through a simulation of the experiment. It’s this kind of scientific sleuthing that gives his team their virological insights.
The metagenomes are sequenced using a device called the “FlowCell,” roughly the size of a shoebox. Wyler holds it up and points to the front panel, where a display contains a billion tiny dots. Each dot is linked to a molecule from the wastewater sample, allowing the device to read the genetic information of up to 100 million molecules. It’s a feat of cutting-edge nanotechnology – and the sequencing process takes around 24 hours.
Tracking how viruses spread can help predict future pandemics.
Using this sequencing method, the team was able to track how strains within virus families evolve over time and across different regions. One of the most common viruses they observed was the astrovirus—a leading cause of gastrointestinal illness. Initially, the emergence of various astrovirus strains appeared to mirror the timing of pandemic infection waves. To put their findings in context, the Max Delbrück Center compared its data with wastewater samples from Los Angeles and Nagpur, India, collected in 2021. Despite strict global contact and travel restrictions at the time, the virus still managed to spread across continents, even between places like Los Angeles and Nagpur – where direct transmission seemed highly unlikely.
If you can follow the global movement of astroviruses, you can start to map out an entire network of how viruses spread worldwide.
Wyler sees enormous potential in this kind of virus tracking. “If you can follow the global movement of astroviruses, for example,” he explains, “you can start to map out an entire network of how viruses spread worldwide.” Because viruses, unlike bacteria, can only reproduce through host organisms – such as humans or animals – their movement also reflects human mobility patterns.
This kind of information could make targeted outbreak interventions possible. High-traffic hubs like airports play a crucial role. “If a virus emerges somewhere in the world, we could test people specifically along likely transmission routes,” Wyler says. But to build an effective epidemiological network, more sampling locations and more data are needed. In this context, wastewater has already become a vital source of insight.
- This article was adapted from German. See the original here.
