Newswise Drexel University researchers have reported a method to quickly identify and label mutated versions of the virus that causes COVID-19. Their analysis, using information from a global database of genetic information gleaned from coronavirus testing, suggests that there are at least 8 to 14 slightly different versions of the virus infecting people in America, some of which are either the same as, or have subsequently evolved from, strains directly from Asia, while others are the same as those found in Europe.
First developed as a way of parsing genetic samples to get a snapshot of the mix of bacteria, the genetic analysis tool teases out patterns from volumes of genetic information and can identify whether a virus has genetically changed. They can then use the pattern to categorize viruses with small genetic differences using tags called Informative Subtype Markers (ISM).
Applying the same method to process viral genetic data can quickly detect and categorize slight genetic variations in the SARS-CoV-2, the novel coronavirus that causes COVID-19, the group reported in a paper recently published in the journal,PLoS Computational Biology.The genetic analysis tool, designed by Drexel graduate researcher Zhengqiao Zhao, that generates these labels is publicly available forCOVID-19 researchers on GitHub.
"The types of SARS-CoV-2 viruses that we see in tests from Asia and Europe is different than the types we're seeing in America," saidGail Rosen, PhD,a professor inDrexel's College of Engineering, who led the development of the tool. "Identifying the variations allows us to see how the virus has changed as it has traveled from population to population. It can also show us the areas where social distancing has been successful at isolating COVID-19."
The ISM tool is particularly useful because it does not require analysis of the full genetic sequence of the virus to identify its mutations. In the case of SARS-CoV-2, this means reducing the 30,000-base-long genetic code of the virus to a subtype label 20 bases long.
The ISM tool also identified certain positions in the virus's genetic sequence that changed together as the virus spread. The researchers found that from early April to the end of the summer, three positions in the SARS-CoV-2 sequence mutated at the same time. Those positions are in different parts of the genetic sequence. One part is thought to be associated with cellular signaling and replication. Another portion is associated with formation of the protein spike - the part of the virus that enables its entry into healthy cells - changed in tandem with a third portion of code, which doesn't translate to protein.
While more investigation is needed on how these simultaneous mutations impact the transmission and severity of the virus, sites that change together can be used to consolidate the subtype label into 11 bases, which could make downstream analysis more efficient, according to the researchers.
"It's the equivalent of scanning a barcode instead of typing in the full product code number," Rosen said. "And right now, we're all trying to get through the grocery store a bit faster. For scientists this means being able to move to higher-level analysis much faster. For example, it can be a faster process in studying which virus versions could be affecting health outcomes. Or, public health officials can track whether new cases are the result of local transmission or coming from other regions of the United States or parts of the world."
While these genetic differences might not be enough to delineate a new strain of virus, Rosen's group suggests understanding these genetically significant "subtypes," where they're being found and how prevalent they are in these areas is data granular enough to be useful.
"This allows us to see the very specific fingerprint of COVID-19 from each region around the world, and to look closely at smaller regions to see how it is different," Rosen said. "Our preliminary analysis, using publicly available data from across the world, is showing that the combination of subtypes of virus found in New York is most similar to those found in Austria, France and Central Europe, but not Italy. And the subtype from Asia, that was detected here early in the pandemic has not spread very much, instead we are seeing a new subtype that only exists in America as the one most prevalent in Washington state and on the west coast."
In addition to helping scientists understand how the virus is changing and spreading, this method can also reveal the portion of its genetic code that appears to remain resistant to mutations - a discovery that could be exploited by treatments to combat the virus.
"We're seeing that the spike protein and the part of the virus responsible for packaging its genetic material have developed a few major mutations, but otherwise they are changing at a slower rate," said Bahrad Sokhansanj, PhD, a visiting scholar at Drexel. "Importantly, both are key targets for understanding the body's immune response, identifying antiviral therapeutics, and designing vaccines.
Rosen's Ecological and Evolutionary Signal-Processing and Informatics Laboratory will continue to analyze COVID-19 data as it is collected and to support public health researchers using the ISM process.
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Original post:
Genetic tracing 'barcode' is rapidly revealing COVID-19's journey and evolution - Newswise
- History of Evolution | Internet Encyclopedia of Philosophy - December 9th, 2016 [December 9th, 2016]
- Evolution - Bulbapedia, the community-driven Pokmon encyclopedia - December 12th, 2016 [December 12th, 2016]
- What is Evolution - explanation and definitions - December 21st, 2016 [December 21st, 2016]
- Evolution (2001 film) - Wikipedia - January 28th, 2017 [January 28th, 2017]
- EvolutionM.net - Mitsubishi Lancer Evolution | Reviews, News ... - February 1st, 2017 [February 1st, 2017]
- YMCA evolution continues at lake - Gaston Gazette - February 7th, 2017 [February 7th, 2017]
- Ivanka Trump's Beauty Evolution, From 1998 to Today Watch - Us Weekly - February 7th, 2017 [February 7th, 2017]
- Lumpy, hairy, toe-like fossil could reveal the evolution of molluscs - The Guardian - February 7th, 2017 [February 7th, 2017]
- How Evolution Alters Biological Invasions - ScienceBlog.com (blog) - February 7th, 2017 [February 7th, 2017]
- Cultural evolution and the mutilation of women - The Economist - February 7th, 2017 [February 7th, 2017]
- Late-night hosts on the evolution of Trump: 'Dickish to dictatorish' - The Guardian - February 7th, 2017 [February 7th, 2017]
- Gold's Gym Regina rebrands to become Evolution Fitness - Regina Leader-Post - February 7th, 2017 [February 7th, 2017]
- Incremental Versus Radical Innovation: A Response to Josh Swamidass on Evolution and Cancer - Discovery Institute - February 7th, 2017 [February 7th, 2017]
- Blockchain: Investment (R)Evolution For Developing Markets - Forbes - February 7th, 2017 [February 7th, 2017]
- See the Evolution of the Famed Porsche 911 in 7 Photos - WIRED - February 7th, 2017 [February 7th, 2017]
- Exhibition charts 500 years of evolution of robots - Phys.Org - February 7th, 2017 [February 7th, 2017]
- How evolution turned ordinary plants into ravenous meat-eaters - Wired.co.uk - February 7th, 2017 [February 7th, 2017]
- Are Evolution Fresh Drinks 'Poison'? - snopes.com - February 7th, 2017 [February 7th, 2017]
- Non-Chromosomal DNA Drives Tumor Evolution - The Scientist - February 8th, 2017 [February 8th, 2017]
- Chimpanzee feet allow scientists a new grasp on human foot evolution - Phys.Org - February 8th, 2017 [February 8th, 2017]
- 'Goldilocks' genes that tell the tale of human evolution hold clues to variety of diseases - Science Daily - February 8th, 2017 [February 8th, 2017]
- Pac-Man is Coming to 'The Sandbox Evolution' Next Week - Touch Arcade - February 9th, 2017 [February 9th, 2017]
- Chimpanzee feet allow scientists a new grasp on human foot ... - Science Daily - February 9th, 2017 [February 9th, 2017]
- Bacteria sleep, then rapidly evolve, to survive antibiotic treatments - Phys.Org - February 9th, 2017 [February 9th, 2017]
- Orangutan squeaks reveal language evolution, says study - BBC ... - BBC News - February 9th, 2017 [February 9th, 2017]
- Evolution gives rhyme its reason - Aurora News Register - February 9th, 2017 [February 9th, 2017]
- Deeper origin of gill evolution suggests 'active lifestyle' link in early vertebrates - Science Daily - February 9th, 2017 [February 9th, 2017]
- From Tara Palmer-Tomkinson to Cara Delevingne: the evolution of the It girl - The Guardian - February 10th, 2017 [February 10th, 2017]
- Banned TED Talk: Rupert Sheldrake The Science Delusion - Collective Evolution - February 10th, 2017 [February 10th, 2017]
- VOTD: Watch the Evolution of Keanu Reeves' Acting Career - /FILM - February 10th, 2017 [February 10th, 2017]
- Pokmon Go Eevee evolution: How to evolve Eevee into Vaporeon, Jolteon and Flareon with new names - Eurogamer.net - February 10th, 2017 [February 10th, 2017]
- Horse evolution bucks evolutionary theory - Science News - February 10th, 2017 [February 10th, 2017]
- Samsung's Chromebook Pro highlights the category's continued evolution - TechCrunch - February 10th, 2017 [February 10th, 2017]
- Scientists solve fish evolution mystery - Phys.Org - February 10th, 2017 [February 10th, 2017]
- Wildfire evolution forces Forest Service into new thinking - The Daily Progress - February 11th, 2017 [February 11th, 2017]
- How the horse can help us answer one of evolution's biggest questions - Raw Story - February 11th, 2017 [February 11th, 2017]
- A primer on Darwin Day: Some religious groups embrace 'Theistic evolution' - LancasterOnline - February 11th, 2017 [February 11th, 2017]
- Apple: Evolution of in-car audio tech moving at 'speed of sound ... - Times of India - February 11th, 2017 [February 11th, 2017]
- Mariska Hargitay's Evolution from '80s Glam to Law & Order: Special Victims Unit - TVOvermind - February 12th, 2017 [February 12th, 2017]
- Evolution of baseball from power to speed has left SBs behind ... - Chicago Sun-Times - February 12th, 2017 [February 12th, 2017]
- More order with less judgment: An optimal theory of the evolution of cooperation - Science Daily - February 12th, 2017 [February 12th, 2017]
- J. Albert C. Uy speaks on evolution, biodiversity in bellied flycatcher population - The College Reporter - February 12th, 2017 [February 12th, 2017]
- See the Evolution of Movie Magic With Every Oscar Winner for Visual Effects in History - Gizmodo - February 12th, 2017 [February 12th, 2017]
- Numerology: Here's What Your Name Says About You - Collective Evolution - February 13th, 2017 [February 13th, 2017]
- The Evolution of Valentine's Day - Inside Science News Service - February 13th, 2017 [February 13th, 2017]
- Why evolution may be tech billionaires' biggest enemy - The Week Magazine - February 13th, 2017 [February 13th, 2017]
- Community Viewpoint: Evolution, like gravity, is much more than theory it is a fact - Kdminer - February 13th, 2017 [February 13th, 2017]
- How the horse can help us answer one of evolution's biggest questions - Phys.Org - February 13th, 2017 [February 13th, 2017]
- How evolution alters biological invasions - Science Daily - February 13th, 2017 [February 13th, 2017]
- Cockeyed squid shines light on deep sea evolution - Christian Science Monitor - February 13th, 2017 [February 13th, 2017]
- Eye Evolution: A Closer Look - Discovery Institute - February 14th, 2017 [February 14th, 2017]
- Evolution always wins: University of Idaho video game uses mutating aliens to teach science concepts - The Spokesman-Review - February 14th, 2017 [February 14th, 2017]
- Geneticists track the evolution of parenting - Phys.Org - February 14th, 2017 [February 14th, 2017]
- How this cockeyed squid shines a light on deep sea evolution - Christian Science Monitor - February 14th, 2017 [February 14th, 2017]
- 4 Possible Roadmaps For macOS and iOS Evolution - The Mac Observer (blog) - February 15th, 2017 [February 15th, 2017]
- The Evolution of the Energy Capital of the World - Texas Monthly - February 15th, 2017 [February 15th, 2017]
- Humons presents an atypical dance evolution - Detroit Metro Times - February 15th, 2017 [February 15th, 2017]
- Pokemon Go Adds 80 Generation 2 Pokemon, New Evolution Items This Week - IGN - February 15th, 2017 [February 15th, 2017]
- Fossil discovery rewrites understanding of reproductive evolution ... - Science Daily - February 15th, 2017 [February 15th, 2017]
- 'X-Men: Evolution' Is the Gateway Drug of Comic Book Shows - Geek - February 16th, 2017 [February 16th, 2017]
- A cultural catch: Evolution of wooden halibut hooks carved by native ... - Science Daily - February 16th, 2017 [February 16th, 2017]
- Bremerton's Fitness Evolution now Planet Fitness - Kitsap Sun (blog) - February 16th, 2017 [February 16th, 2017]
- Eye Evolution: The Waiting Is the Hardest Part - Discovery Institute - February 16th, 2017 [February 16th, 2017]
- Evolution Of The Yeezy: 2009-2017 - HotNewHipHop - February 16th, 2017 [February 16th, 2017]
- Prebiotic evolution: Hairpins help each other out - Science Daily - February 16th, 2017 [February 16th, 2017]
- This 'Live Birth' Fossil Could Change Humanity's Understanding Of Evolution - Daily Caller - February 16th, 2017 [February 16th, 2017]
- Mysterious Ancient Stonehenge-Like Circles Found in Amazon Rainforest - Collective Evolution - February 16th, 2017 [February 16th, 2017]
- 'Pokemon Go': How to Evolve Poliwhirl Into Politoed - Heavy.com - February 17th, 2017 [February 17th, 2017]
- 'Pokemon Go': How to Evolve Slowpoke Into Slowbro or Slowking - Heavy.com - February 17th, 2017 [February 17th, 2017]
- 'Pokemon Go': How to Evolve Gloom Into Bellossom - Heavy.com - February 17th, 2017 [February 17th, 2017]
- Pokmon Go Dragon Scale - how to evolve Seadra into Kingdra and how to get the Dragon Scale - Eurogamer.net - February 17th, 2017 [February 17th, 2017]
- Pokmon Go Eevee evolution: How to evolve Eevee into Umbreon, Espeon, Vaporeon, Jolteon and Flareon with new ... - Eurogamer.net - February 17th, 2017 [February 17th, 2017]
- University of Pittsburgh guest speaker discloses evolution findings - UTA The Shorthorn - February 17th, 2017 [February 17th, 2017]
- 'Pokemon Go' Special Items: Drop Rates for Evolution Items & Berries at Pokestops - Heavy.com - February 17th, 2017 [February 17th, 2017]
- How Vedic Philosophy Influenced Nikola Tesla's Idea of 'Free Energy' - Collective Evolution - February 18th, 2017 [February 18th, 2017]
- Migration to America took long enough for evolution to happen on the way - Ars Technica - February 18th, 2017 [February 18th, 2017]
- How To Choose Your Eevee Evolution In 'Pokmon GO:' Umbreon And Espeon Edition - Forbes - February 18th, 2017 [February 18th, 2017]
- Evolution Items - IGN - February 18th, 2017 [February 18th, 2017]
- Congo River fish evolution shaped by intense rapids: Genomic study ... - Science Daily - February 18th, 2017 [February 18th, 2017]
- Pokmon Go - How to evolve, use Special Items, when to evolve or Power Up your Pokmon - Eurogamer.net - February 18th, 2017 [February 18th, 2017]