As the coronavirus pandemic has swept across the U.S., in addition to tracking the number of COVID daily cases, there is a worldwide scientific community engaged in tracking the SARS-CoV-2 virus itself.
Efrem Lim leads a team at ASU that looks at how the virus may be spreading, mutating and adapting over time.
To trace the trail of the virus worldwide, Lim's team is using a new technology called next-generation sequencing at ASU's Genomics Facility, to rapidly read through all 30,000 chemical letters of the SARS-CoV-2 genetic code, called a genome.
Each sequence is deposited into a worldwide gene bank, run by a nonprofit scientific organization called GISAID. To date, over 16,000 SARS-CoV-2 sequences have been deposited GISAID's EpiCoVTM Database. The sequence data shows that SARS-CoV-2 originated a single source from Wuhan, China, while many of the first Arizona cases analyzed showed travel from Europe as the most likely source.
Now, using a pool of 382 nasal swab samples obtained from possible COVID-19 cases in Arizona, Lim's team has identified a SARS-CoV-2 mutation that had never been found before----where 81 of the letters have vanished, permanently deleted from the genome.
The study was published in the online version of the Journal of Virology .
Lim says as soon as he made the manuscript data available on a preprint server medRxiv, it has attracted worldwide interest from the scientific community, including the World Health Organization.
One of the reasons why this mutation is of interest is because it mirrors a large deletion that arose in the 2003 SARS outbreak." Efrem Lim, Assistant Professor, ASU's Biodesign Institute
During the middle and late phases of the SARS epidemic, SARS-CoV accumulated mutations that attenuated the virus. Scientists believe that a weakened virus that causes less severe disease may have a selective advantage if it is able to spread efficiently through populations by people who are infected unknowingly.
Teasing apart what exactly this means is of profound interest to Lim and his colleagues. The ASU research team includes LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda G. Hogue and Matthew Scotch.
The ASU virology team had been setup to perform research on seasonal flu viruses, but when the 3rd case of COVID-19 was found in an Arizona individual on January 26, 2020, they knew they had all technical and scientific prowess to rapidly pivot to examining the spread of SARS-CoV-2. Related Stories
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