Researchers have created lightning-fast computer software that can help nations track and analyze pandemics, like the one caused by COVID-19, before they spread like wildfire around the globe.
The group of computer science and mathematics researchers says its new software is several orders of magnitude faster than existing computer programs and can process more than 200,000 novel virus genomes in less than two hours. The software then builds a clear visual tree of the strains and where they are spreading. This provides information that can be invaluable for countries making early decisions about lockdowns, quarantines, social distancing and testing during infectious disease outbreaks.
«The future of infectious outbreaks will no doubt be heavily data driven,» said Alexander Zelikovsky, a Georgia State computer science professor who worked on the project.
The new software was co-created with Pavel Skums, assistant professor of computer science, Mark Grinshpon, principal senior lecturer of mathematics and statistics, Daniel Novikov, a computer science Ph.D. student, and two former Georgia State Ph.D. students — Sergey Knyazev (now a postdoctoral scholar at the University of California at Los Angeles) and Pelin Icer (now a postdoctoral scholar at Swiss Federal Institute of Technology, ETH Zurich).
Their paper describing the new approach, «Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations,» was published in the Journal of Computational Biology.
«The COVID-19 pandemic has been an unprecedented challenge and opportunity for scientists,» said Skums, who noted that never before have researchers around the world sequenced so many complete genomes of any virus. The strains of SARS-CoV-2 are uploaded onto the free global GISAID database (), where they can be data-mined and studied by any scientist. Zelikovsky, Skums and their colleagues analyzed more than 300,000 different GISAID strains for their new work.
Story Source: Materials provided by Georgia State University. Note: Content may be edited for style and length.