Source For COVID-19 Coronavirus Revealed By Genetic Tracing ‘Barcode’

Part of the challenge of the COVID-19 coronavirus has been the difficulty in locating the origins of each genetic variation, or strain, of the virus. Without understanding which strains are active, it’s harder to know for sure if the worst has passed and how best to combat the virus.

Major SARS-CoV-2 genetic subtypes in countries/regions with the most sequences (indicating date subtype was first sequenced in that country/region). Subtypes with less than 5% abundance are plotted as “OTHER.” Credit: Drexel University

Quickly identifying which strains of the COVID-19 virus were active in each region or country has been a challenge. Now, scientists at Drexel University report that they have developed a method of rapidly identifying and labeling mutated versions of the virus.

They have identified six to ten different variations of the SARS-CoV-2, the underlying virus that causes COVID-19, currently infecting people in America. Their preliminary analysis was performed using material and information from a global database of data acquired during coronavirus testing. Their research indicates that these strains are the same as, or have evolved from, strains affecting both Asia and Europe.

The technique they used was originally designed to scrutinize genetic samples in order to get a snapshot of the pathogen or cell being tested. The analysis method draws out patterns from within huge amounts of genetic information and can determine whether the virus has changed genetically. Those patterns are then used to categorize the viruses which have small genetic variables, using tags known as Informative Subtype Markers (ISM.)

Applying this process to the genetic material of SARS-CoV-2 can quickly find and classify even slight genetic changes in the virus. The research group published their early findings on the preliminary research archive bioRxiv.

“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,” said Gail Rosen, Ph.D., a professor in Drexel’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.”

Relative abundance of ISMs in DNA sequences from Canada as sampled over time.
Credit: Drexel University

The ISM tool, which was developed by Rosen and several other researchers, can identify mutations without having to analyze the entire genetic sequence of the virus to find the mutations. That’s good, because reading the entire genetic code of SARS-CoV-2 would mean reducing its 30,000-base-long code and delving into a myriad of subtypes.

“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 individual genetic variances may not be enough to delineate a new strain of COVID-19, the team suggests that understanding the “subtypes” that are genetically significant, knowing where to find them and gleaning how prevalent they are is enough data to be meaningful and 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.”

Using this technique not only helps scientists understand how the virus is mutating and spreading. It will also expose that portion of its genetic code which remains resistant to mutation. That knowledge can be critical in the development of treatments for COVID-19.

“We’re seeing that the two parts of the virus that seem not to be mutating are the ones responsible for its entry into healthy cells and packaging its RNA,” Rosen said. “Both of these are important targets for understanding the body’s immune response, identifying antiviral therapeutics and designing vaccines.”

Once again, science reveals that often, by digging in deeply on the smallest of details, big things can happen. Hopefully, this genetic discovery will help the world get a handle on this virus and we can all go back to some version of our lives that doesn’t involve hiding out at home.

In the meantime, stay safe and as always…keep the faith and keep after it!

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Journal Reference – Zhengqiao Zhao et al. Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers, bioRxiv (2020). DOI: 10.1101/2020.04.07.030759

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