Queensborough Community College: What Lies Beneath: Scientists Discover A New Coronavirus Variant

Press release from Queensborough Community College:

February 14, 2022

It all started when Covid hit.

“I quickly switched gears and revised the curriculum,” said Dr. Monica Trujillo, microbiologist and Associate Professor, Biological Sciences and Biology at Queensborough.

“In one day, students went from the lab to their living room. Luckily, science requires many distinct types of research and my students swiftly adapted to studying all relevant articles on Covid,” said Trujillo, who has been teaching science majors at Queensborough since 2007.

“We regularly discussed their findings when one day my curiosity was piqued by a group of researchers, we looked at a paper from a group in the Netherlands, they t had tested wastewater at an airport and detected the virus before any clinical cases had taken place. It occurred to me that this research should be done in New York. I reached out to my friend and colleague Dr. John Dennehy, a virologist at Queens College, and proposed we look into it.”

Since then, a lot has happened.

Trujillo and Dennehy—with funding from the city’s Department of Environment Protection (DEP), developed a protocol for measuring the concentration of SARS-CoV-2 in the 14 New York’s deep-well influx wastewater. She and colleagues from Queens College and The New School began testing samples and sequencing.

“I didn’t know anything about the wastewater system until I started working with the DEP.

The preliminary results of their collaborative research allowed the team of scientists to detect the presence of the virus in most samples obtained from the NYC DEP.

“Everyone with the virus sheds it in their fecal matter,” said Trujillo. “If we see an increase of the virus in our samples that means in ten days to two weeks, we will see an increase of Covid cases emerging. That’s because most people are asymptomatic,” Trujillo said.

In the months that followed the team began to detect increasing numbers of covid lineages not recognized before, so called cryptic sequences. These samples contained mutations that had been rarely observed in clinical samples. The results were published in Nature Communications on February 3, 2022. The published paper was written by Trujillo, Dennehy and a handful of scientists from across the country. The discovery of the variant has led to differing theories on its origin and the implications this may have on the origin for other Covid variants such as Omicron.

“This is a crucial discovery,” said Trujillo. “Though we don’t know its origin we do know that it is not expanding to the general population. So, while we do not fully understand why the virus changes, we must understand how it changes. That is the purpose of our work.”

The team looked at small pieces of the genome of the whole virus, the receptor binding domain (RBD). The RBD determines which host will have a compatible receptor. To answer questions about where the cryptic sequences are coming from, the team looked at what organisms can be detected in wastewater using ribosomal RNA sequencing. In their paper they find predominantly human signal as expected at lower concentrations they detected signals from human food, additionally at even lower concentrations then they found signals from rats, dogs, and cats. In particular the number of rats and rat feces in wastewater has led to varying theories about the diversity of the virus’s strains, but many questions remain.

“That is why it is so important to keep searching,” she said. “These results highlight the importance of wastewater surveillance. Access to wastewater during a pandemic has proved to be critically important.”

She continued, “The variants will always be with us. The key is to stop the transmission. If we stop the transmission the chances of a new variant appearing are diminished.”

Trujillo, who was born and raised in Uruguay, moved to the U.S. when she was 33 years of age and had three children ages 9-5 by the time she completed her PhD experimental work at the University of California in San Francisco. She then worked in the biotech industry in California until she and the family moved to New York in 2001 where her husband, also a scientist, was offered a job.

“Finally, the kids were off to college, and I thought; what can I do to fill my life? Then Queensborough started a search for a biology teacher. I applied and here I am.”

Now, Trujillo is ‘thrilled’ to be back in the lab with students. She has presented her microbiology students with a project related to her work in wastewater, they will safely identify the bacteria present in the different wastewater samples using molecular biology tools. She believes it is crucial for science students to have their independent research experience.

“Our conversations spark questions and critical thinking. It is a process so important to share with students and bring it back into the classroom.”

The work that the CUNY team has performed was done with little funding. Trujillo laughed when thinking about her work outside the classroom at QCC and the research lab at Queens College where she analyzes experiments results, drafts papers and trains students.

“You should see me in my tiny car driving between rows of garbage trucks and sky-high metal scraps to reach my water collection destination.”

Then she became serious.

“This is a pandemic, and we must look at it with a global vision. Unfortunately, there have been factors working against progress in fighting this disease. Travel can’t be controlled. People are covid exhausted and mandates for masks and vaccines continue to fluctuate across the country and around the world. The population is tired of this for sure, but the virus is not. This is what we must accept. We must be consistent in order to protect ourselves and each other.”

This press release was produced by Queensborough Community College. The views expressed here are the author’s own.