Clarkson University Assistant Professors Andrew David and Susan Bailey were recently awarded an institutional grant to study the COVID-19 genome from various countries with the goal of unraveling their connectivity patterns.
With the help of undergraduate and graduate students, the researchers will mine thousands of COVID-19 genomes that have been archived in various governmental databases, including the United States’ GenBank repository and Germany’s GISAID database, since December 2019. The team plans to dive into the virus’ genome and carry out a series of analyses to determine the number of genetically distinct regional clusters present, and how connected these regional clusters are to each other using statistical analyses.
Such information has far-reaching epidemiological consequences because it will provide valuable data on the long term viability of the virus and its transmission patterns, according to David.
“The motivation to write this proposal occurred in early March as the virus was spreading throughout the United States,” David said. “We noticed that COVID-19 genome samples were being archived on a daily basis and each sample had well-curated metadata such as the city and country of where the sample came from, date collected, etc.”
The study will be funded by the Clarkson Innovation Fund Project. The results from this research will add to a growing number of similar studies that are leveraging the same dataset to better understand the evolution of this virus.
“We are certainly not the only labs in the race to understand the genetic origins and continued spread of this virus,” David said. “There are numerous teams from around the world that have taken different routes to explore the same issue. Our approach is to use the tools of phylogeography – a field that traditionally caters to the study of multi-cellular animals and plants. We hope to modify these tools so they can be scaled down to investigate the virus”