KEYS Intern Discovers Hundreds of New Viruses Through Data Science Project

July 28, 2020

Esha Mathur harnessed the powers of multiple computer software programs to advance the field of terrestrial viruses.

Due to the remote nature of this year’s Keeping Youth Engaged in Science (KEYS) program, many students were skeptical about the quality of personal connections they would form and the professional support their would receive from their mentors while isolated at home amid the COVID-19 pandemic.  

Now able to reflect on her KEYS experience, incoming University High School senior Esha Mathur is immensely grateful for the daily guidance her mentors provided the past seven weeks as she sought to understand the relationship between viruses, bacteria and the environment. Esha met remotely with her mentor, Dr. Bonnie Hurwitz, and her fellow lab members every morning to ensure that Esha had the tools she needed to succeed. 

“I truly felt like I had the support I needed throughout this entire internship,” Esha said.

In addition to the support she received while interrogating bacteria genetic material for viral invaders, the intern is grateful for the personal connections she made with her lab members. Esha fondly remembers meeting her graduate mentor’s cats and talking to Dr. Hurwitz about her daughter’s progress learning multiplication times tables. 

“We weren’t ‘business’ all the time. We built friendships, too,” Esha said. 

Discovering new viruses and their functions
Curious about understanding the complex interactions between organisms, Esha’s summer research project was a perfect fit. 

Little is known about the phages, or viruses, that inhabit terrestrial environments. Through her work in Dr. Hurwitz’s lab, Esha explored the diversity and biological functions of prophages integrated into the genetic material of Nostoc, a photosynthetic cyanobacteria found free-living in soil and freshwater or in a symbiotic relationship with mosses and lichens. 

Esha’s colorful teal and sunset orange poster, entitled “Exploring the Diversity of Prophages Associated to the Cyanobacteria Nostoc,” featured a visual depiction of her workflow over the past six weeks. Esha explained that she used two programs, VirSorter and Vibrant, to retrieve viral sequences from Nostoc genomes. Across 48 samples, Esha identified more than 500 prophages, the majority of which were entirely new.

With HMMER, a software used to study sequences of genetic material, Esha determined the biological functions of the prophage genes. Since she found that many viral genes were involved in cellular functions like amino acid synthesis, Esha speculates the prophages may be in a symbiotic relationship with the bacteria they inhabit. She also found that many of the known prophages originated from marine ecosystems. 

Esha is interested in further examining the relationship between Nostoc and the hundreds of novel prophages living among the cyanobacteria. In the future, Esha aims to understand the precise impact of the viral genes on prophage-host interactions.  

Finding significance through data science
Prior to KEYS, Esha assumed statistically significant results could only be found through research conducted in the field or at the laboratory bench. Since she wouldn’t be able to get her hands dirty this summer due to the virtual nature of the program, Esha presumed her research wouldn’t hold a great deal of scientific value.

After discovering hundreds of new viruses with novel functions, Esha’s perspective on the importance of data science has been entirely transformed. 

“My project really proved my original stereotype wrong because we found so many significant results,” Esha said. “In my lab alone, we discovered new viruses and a virus-host symbiosis, so it shows that data science is really important.”

Esha Mathur, an intern in the lab of Dr. Bonnie Hurwitz, virtually presented her findings on the diversity of viruses among a species of cyanobacteria on July 20, 2020.