
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.”
Original Article: Georgia State Researchers Develop Rapid Computer Software To Track Pandemics As They Happen
More from: Georgia State University | University of California Los Angeles | ETH Zürich
The Latest Updates from Bing News & Google News
Go deeper with Bing News on:
Tracking pandemics
- DocuSign Is on Track for Its First Profitable Year in Its History. Is It Time to Buy DocuSign Stock?
Now, DocuSign is three quarters into fiscal 2024, and it has delivered net income of $47 million so far. That places it on track to deliver its first ever full-year profit, assuming there are no ...
- The one pandemic-era trend that has stuck
Shippers are bucking history and giving carriers more time to pick up their freight in a relatively soft market. What could be causing this and will it stick? The post The one pandemic-era trend that ...
- International tourism sector to finish close to 90% of pre-pandemic levels
International tourism is on track to recover almost 90% of pre-pandemic levels by the end of this year. According to the latest data from the ...
- Private, charter, homeschooling grew after pandemic, but most kids attend public schools
The pandemic has remade the American school landscape with enrollment in charter schools and homeschooling surging.
- The pandemic remade the US school landscape. Private, charter, and homeschooling all grew.
The pandemic has remade the American school landscape with enrollment in charter schools and homeschooling surging.
Go deeper with Google Headlines on:
Tracking pandemics
[google_news title=”” keyword=”tracking pandemics” num_posts=”5″ blurb_length=”0″ show_thumb=”left”]
Go deeper with Bing News on:
Pandemic tracking software
- The one pandemic-era trend that has stuck
Shippers are bucking history and giving carriers more time to pick up their freight in a relatively soft market. What could be causing this and will it stick? The post The one pandemic-era trend that ...
- The pandemic remade the US school landscape. Private, charter, and homeschooling all grew.
The pandemic has remade the American school landscape with enrollment in charter schools and homeschooling surging.
- How to choose the best project management software
Zoho Projects: An excellent option for small teams, Zoho offers easy visualizations, document storage options, and nice integration options. Pricing is dependant on how many users there are within an ...
- Bursting of Pandemic-Stock Bubble Fuels Big Wave of ETF Closures
The notoriously saturated $7.7 trillion ETF industry is this year poised for the second-highest number of closures, as the pandemic-era day trading boom fizzles out.Most Read from BloombergElon Musk's ...
- Is Tipping Broken in America? A Post-Pandemic Primer
During the pandemic, tipping seemed to have changed for good. In America overnight, it seemed, tipping became a way to virtue signal—to support local businesses, to show gratitude for those working on ...
Go deeper with Google Headlines on:
Pandemic tracking software
[google_news title=”” keyword=”pandemic tracking software” num_posts=”5″ blurb_length=”0″ show_thumb=”left”]