What Strain of COVID-19 Is in a Sample? Scientists Use Next Generation Sequencing to Learn Details Amidst the Global Pandemic

The world has been dealing with the COVID-19 pandemic since March 2020, and our response is becoming more sophisticated as scientists have new tools to check the virus. We’ve come a long way since the initial methods to protect populations were social distancing and wearing masks as we awaited for scientists to develop vaccines and therapies.

One challenge of addressing the novel coronavirus pandemic is the fact that variants have been appearing in different populations and then spreading across the globe. Routine air travel between continents makes it difficult for any nation or population to hide from emerging coronavirus strains.

As the COVID-19 virus mutates, it may exhibit changes in how virulent it is or how severe its infections are. Accordingly, public health researchers and other scientists have a vested interest in identifying strains. They are using a powerful tool in the form of next generation sequencing to check what strain they are dealing with in a sample from a patient.

How the World Health Organization Views Variants of COVID-19

The World Health Organization, which helps gather information and coordinate research, breaks the novel coronavirus into two types of variants. “Variants of Concern” are variants that present with a reduced efficacy in vaccination or treatments, or cause disease that’s more severe or that is easier for people to transfer to one another.

“Variants of Interest,” by contrast, are virus mutations that can spread more easily and whose changes might result in our vaccines and treatments to be less useful, but are not as problematic yet as those variants that are “of concern.”

Why do we need to sequence and identify COVID-19 mutations? As New York State’s COVID-19 Variants page reports, “tracking a variant with high transmissibility, like the currently circulating Delta variant, can help hospitals prepare for a surge in cases.”

Using NGS for COVID Strain Research and Identification

Scientists have identified more than 12 strains of the novel coronavirus, as noted by a recent report from KENS5, which examines research efforts at UT Health San Antonio in Texas. At UT Health, researchers are employing next generation sequencing to get a detailed look at the genetic makeup of many thousands of genes obtained from a wide range of samples.

They are harnessing large Panther instruments capable of testing as many as 2,000 samples in a day. (Prior to automation during the early days of the pandemic, the researchers at UT Health could only do a few tests at a time, all by hand).

The scientists extract nucleic acid from the samples and measure how big the viral load is with the help of a PCR device. Then, it’s time to sequence the sample.

KENS5 explains that “Next-generation sequencing is needed to figure out the strain of the virus, to track transmission routes of the virus globally and detect mutations to prevent the spread of new strains.” It NGS is also invaluable for helping researchers discover viral mutations that might make a difference in how potent our existing vaccines are. They will be useful in developing new therapeutics for coronavirus too.

NGS Is Crucial for Determining What Mutated Version of COVID-19 Has Infected a Population

Tools like next generation sequencing are proving to be invaluable in the global war against the novel coronavirus.

Patients will appreciate it when their doctors can quickly determine what mutation they’ve been infected with, and public health researchers are able to better identify and keep track of COVID-19 mutations as they move through populations. NGS tools can help us find a light at the end of the tunnel for all people suffering from the novel coronavirus.

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