SIU researchers receive grant to study COVID-19 genome

SIU researchers receive grant to study COVID-19 genome
Koushik Sinha assistant professor of computer science in SIU Carbondale’s School of Computing, left, and Keith Gagnon, associate professor of chemistry and biochemistry in the College of Agricultural, Life and Physical Sciences, have received a one-year grant from the Walder Foundation aimed at better understanding and tracking the COVID-19 virus as it moves through populations. SIU will receive about $360,000 of the $500,000 grant, which involves sequencing the virus genomes and using analytic tools to track it. (Source: Yenitza Melgoza)

CARBONDALE, Ill. (KFVS) - Keith Gagnon, associate professor of chemistry and biochemistry at SIU, and Koushik Sinha, assistant professor of computer science, have received a grant from the Walder Foundation.

The SIU researchers will work with other scientists from the Open Commons Consortium in Chicago on the one-year, $500,000 project aimed at improving our understanding of the virus, with SIU receiving about $360,000 of the money.

Under the grant, the Illinois Department of Public Health will supply Gagnon’s lab with COVID-19 samples from patients mostly located in the Chicago area.

Gagnon’s team will then sequence the virus genomes, and perform evolutionary and phylogenetic analyses on the genome sequences.

Gagnon said his lab will sequence the genome of SARS-CoV-2 viruses, which cause COVID-19, from positive patient samples. The study will sequence 5,000 virus genomes over the course of the project.

“The genomic and analytic tools we will use should help us understand how the virus is moving and changing over time in the Chicago area by identifying variants of the virus,” Gagnon said. “We expect to identify the original founder outbreaks of the virus, such as geographic location in the world, and predict when different variants were introduced into the Chicago area.”

The lab will sequence and analyze the genomes within two weeks of a positive case, Gagnon said. Combing that information with Google mobility data – as practiced by Sinha and his team – will reveal the demographics to understand how the virus is affecting certain populations, allowing authorities to make rapid decisions about public health policies.

Sinha’s team will combine the mutation signatures of each virus, as well as where and when the sample was taken, with powerful analytical tools and map-view visualizations, rapidly sharing results with IDPH and other researchers and making them publicly available for viewing and downloading.

“Mapping the diversity of mutations that the virus acquires will provide critical insight into better vaccine development,” Gagnon said. “And our tools can be used to evaluate the success of future vaccines as they are deployed.”

Sinha said the goal is to create a “one-stop-shop” data and analytics infrastructure for storing, integrating, analyzing, and visualizing multiple types of epidemiological data. His group will create a custom visualization and data-analytics platform called COVID-19 Data Map (CoVD-Map). The platform will be an offshoot of the platform that he began developing in spring during some of the early, uncertain months of the pandemic.

The team’s CoVD-Map will be integrated with the Chicago CAN Commons and designed to work with other public-health surveillance systems, such as Illinois’s National Electronic Disease Surveillance System and the National Notifiable Diseases Surveillance System.

The advances the teams hope to make might eventually be applied to other theaters and populations

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