via Georgia State University
Researchers at Georgia State University 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 Zürich).
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.
“There are over 5 million genomes in the GISAID database now,” said Zelikovsky. “Scientists around the globe are probably sequencing a new variant almost every hour.”
Zelikovsky said that this astounding amount of data allows scientists to see the evolution of the virus in action in real time — if we have software capable of rapidly analyzing it.
In the early days of the pandemic, in March 2020, scientists were working much more slowly. Scientists thought the virus had first arrived on our shores in the state of Washington in February. However, later sequencing presented in a paper by Skums and his colleagues showed the arcs of viral variants traveling across countries and oceans. With new studies, scientists learned that the virus had also likely arrived quietly in New York City in February, from strains originating in Europe.
Back then, scientists were sequencing data too slowly to capture the true migration of this global virus and its mutations in real time.
“The programs were not fast enough, not scalable enough,” said Skums. “The algorithms were not equipped to handle huge amounts of data.” It could take hours or days to process even a small subset of viral genomes, he said.
Zelikovsky, Skums and their colleagues created a novel algorithm for viral sequencing called SPHERE (Scalable PHylogEny with Recurrent mutations.) SPHERE can rapidly handle huge amounts of real-time data and create evolutionary trees of the virus and its mutations. These visualizations can be easily grasped at a glance. The computer program itself is freely available for download to any researcher in the world.
When the researchers applied their algorithm to genomes from the GISAID database, they found their SPHERE approach to be highly reliable in tracking the way the virus was spreading. SPHERE can help scientists explore how a virus is evolving in real time.
“We can see how the mutations spread from country to country and region to region,” said Zelikovsky. “We can determine how lockdowns and closures impact spread. This has consequences for government policy.”
The SPHERE algorithm could prove invaluable in future pandemics.
“You could track down chains of transmission very quickly,” said Zelikovsky. Seeing those chains will help governments to make sound decisions about social policies such as distancing or lockdowns during times of high transmission.
SPHERE can also show the impact of different approaches to outbreaks. For instance, said Skums, Sweden took a more relaxed approach to the COVID-19 pandemic than other Nordic countries. An analysis of the sequencing data shows that Swedes have longer “transmission chains.” This means that in Sweden, one strain is able to infect many more people, one by one.
“The danger of long chains is that a new strain may appear,” said Zelikovsky. “And one of those strains may be a variant that is very good at infecting people.”
These kinds of insights will help us should we face another global pandemic.
“The tools we and others have developed can be used anywhere for any outbreak,” said Zelikovsky. “That is the beauty of computer science.”
The Latest on: Pandemic tracking software
- Post pandemic, BMC to keep track of students’ health tooon May 26, 2022 at 8:00 am
A software is being developed which will ensure that each student’s health-related data is available on one click. The idea is to keep all health-related information of students ready for better ...
- Flexjet Adds GE Digital Maintenance Insight Software to Fleeton May 26, 2022 at 7:13 am
Company becomes first in the fractional jet space to incorporate this data-driven software, but how will it help them?
- Session Replay Software Market to Register a CAGR Of 14% through 2032on May 25, 2022 at 2:06 pm
The session replay software market is expected to develop at a CAGR of 14.0% through 2032, from USD 313 Million in 2022 to USD 1.2 billion by 2032. The primary reasons driving the ...
- Remote Learning Software Tracked Kids’ Data to Sell to Advertisers and Brokers: Reporton May 25, 2022 at 12:35 pm
A new report says California, Texas and countries across the world endorsed technology that took advantage of kids’ data.
- Asure Software’s (NASDAQ: ASUR) Innovation Has Positioned Them for Post-Pandemic Successon May 23, 2022 at 12:24 pm
The remote workforces employed during the height of Covid-19 are proving to be cost-effective and efficient in a post-pandemic world. Asure, a payroll and HR service for over 80,000 businesses, has ...
- Opera Streaming Software Unveiled At Opera America Conferenceon May 20, 2022 at 3:12 pm
May 20, Cerise Jacobs and her activist opera company, White Snake Projects (WSP), roll out a Special Access Early Release of their Tutti Remote software in a spotlight presentation at OPERA America's ...
- Military commands spent pandemic money on space analytics, IT upgradeson May 20, 2022 at 11:53 am
The U.S. military command responsible for North America misused at least $19 million in COVID-19 relief money on space-related data analytics connected to the Pentagon’s JADC2 endeavor, as well as ...
- Multifamily rents still haven't reached pre-pandemic levels in the Bay Area's two biggest cities. That could soon changeon May 20, 2022 at 8:13 am
Many other markets nationwide have seen rents not just recover to pre-pandemic levels, but surpass them. What's behind the lag in San Jose and San Francisco?
- Understanding... PMI New Export Orders Index: Tracking Worldwide Trade Flows And Changing Demand, By Country And Sectoron May 20, 2022 at 8:00 am
The new export orders index from S&P Global's PMI business surveys tracks foreign demand for both goods and services. Click here to know ...
- How Students Can Catch Up on Learning Lost During the Pandemic - Albert Parkon May 19, 2022 at 9:11 pm
Across Asia and the Pacific, students and parents are breathing a sigh of relief as schools reopen and in-person classes gradually resume.
via Bing News
The Latest on: Pandemic tracking software
via Google News