UBC Postdocs use the power of cloud computing to identify over 100,000 new RNA viruses

Map of global RNA sequencing data analyzed by Dr. Babaian and his team to identify new RNA viruses [Source: Serratus Project]

An international team led by a former postdoctoral fellow in medical genetics has discovered nearly 10 times more RNA virus than previously known, including several new species of coronavirus.

The team discovered it by reanalyzing all published RNA sequencing data. The planetary-scale database of RNA viruses they have developed may help to quickly identify viruses that affect humans, livestock, crops, and endangered species.

Dr. Artem Babaian is behind the collaboration of the Serratus Project, which published amazing results in leading scientific journals. Nature this week.

Dr. Babaian said the Serratus Project was able to work with the Cloud Innovation Center (CIC), a public-private collaboration between UBC and Amazon Web Services (AWS), to build a “tremendously powerful” supercomputer equivalent to 22,500 CPUs. I am.

Dr. Artem Babaian

Supercomputers analyzed 20 million gigabytes of published gene sequence data from 5.7 million biological samples worldwide to search for specific genes that indicate the presence of RNA virus. Samples have been collected and freely shared within the global research community for over 13 years, including everything from ice core samples to animal dung.

Researchers at the Serratus Project have discovered 132,000 RNA viruses, but previously only 15,000 were known. The discovery included nine new species of coronavirus.

Without the Cloud Innovation Center, Dr. Babaian estimates that a traditional supercomputer would take more than a year and hundreds of thousands of dollars to run the 2,000 years of CPU time required for this analysis. Saw muscle achieved that for $ 24,000 in 11 days.

“We are entering a new era of understanding the genetic and spatial diversity of viruses in nature and how a wide variety of animals interact with these viruses. Cause COVID-19. We hope that we will not be surprised if something like the new corona virus SARS-CoV-2 reappears. These viruses are easier to recognize and their nature. The real goal is to be recognized so early that these infectious diseases do not become pandemic, “said UBC, with a PhD in Genetic Medicine. Dr. Babaian, now a Banting Fellow at the University of Cambridge, said.

“If a patient shows an unexplained fever, once the blood is sequenced, an unknown human virus can be connected to a much larger database of existing viruses, for example, in St. Louis. If you indicate an unexplained virus infection, you can search the database in about two minutes and connect the virus to, for example, a camel in sub-Saharan Africa sampled in 2012. “

Dr. Babaian, 32, was conducting genetic research on cancer with a BC Cancer when the COVID-19 pandemic occurred and he switched gears.

The work, which the modest Dr. Babaian says began as a “fun side project,” was “behind the napkin” by Jeff Taylor, a UBC engineering student who is a friend of him and his climbing partner, on March 3, 2020. It started when I sketched an idea. “Dr. Babaian said.

“I should have kept the napkin,” he said.

Dr. Babaian immediately turned to UBC’s Cloud Innovation Center for help and the Serratus project was born. Named after the Serratus Mountain in British Columbia, it was seen by him and Taylor during the 2020 climb.

Dr. Babaian remembered sitting in his wife’s nursing chair when the first result began to flash on his laptop. This shows that Seratas is not only working, but it is also generating data so fast that it is almost incomprehensible.

“The real goal is that these infections are recognized very quickly and never become a pandemic.”
Dr. Artem Babaian

“It was probably the most exciting scientific period of my life,” he said. “There are two types of fun. Type 1 is smiley and fun. Type 2 is miserable while you do it, but when your memory is shining like rock climbing. Many In terms of points, sawing is a type 2 fun. You have to believe it works. “

Dr. Babaian said this task could not have been done without the support of the UBC Cloud Innovation Center.

“The Cloud Innovation Center was really there to open our doors,” he said. “We came up with the idea and they invited experts from the network to make it happen. Now the global community can benefit from all this previously untapped research. . “

“Artem approached us with an innovative vision. The power of the Cloud Innovation Center is to pair UBC’s internal innovation and technology teams with the Amazon Web Services team,” said UBC Cloud Innovation Center Director. Marianne Schroeder says. “It was our great privilege to support the realization of this vision. It is our job to help find technology solutions for complex problems.”

Launched shortly before the January 2020 pandemic, the center supports issues focused on community health and well-being. To date, the team has published more than 20 projects, including reference architectures and deployment guides, in all available open source.

Coral Kennett, head of the Amazon Web Center, said: service. “We were able to give Artem access to Penny’s computing power in the query. We strongly encourage the research community to submit projects and ideas to the Cloud Innovation Center. Doing so will benefit the community. The innovations we bring will become even clearer. “

Find out more about other Cloud Innovation Center projects here..