Using NGS to Study the Epidemiology of 2019 Novel Coronavirus

The global COVID-19 pandemic caused by the coronavirus SARS-CoV-2 is anticipated to continue, even as countries put strict measures in place to flatten the curve in an attempt to avoid overwhelming healthcare systems. Labs are implementing high-throughput nucleic acid testing to detect viral sequences in suspected patients and are ramping up to meet the demands of population testing.

Though not at the immediate forefront in the fight to contain this viral crisis, investigators around the world are working diligently to understand the epidemiology of the virus since the publication of the SARS-CoV-2 genetic sequence on February 28. Next-generation sequencing (NGS) is the method of choice for sequencing the virus. As described by Dr. Rambaunt, researchers have noticed that this virus and its 30,000 bp genome acquires only about one or two mutations per month, making its mutation rate twice to four times slower than the flu (Kupferschmidt, 2020). Analyzing these mutations helps researchers connect and recreate the path the virus has taken from city-to-city or nation-to-nation. As of March 31th, 2,447 genomes have been sequenced and openly shared on GISAID. As the global number of confirmed cases grow, investigators try to piece together the viral path of transmission through mutational diversity studies. This may help us develop better protocols for future viral outbreaks.


Kupferschmidt, K. (2020). Mutations can reveal how the coronavirus moves—but they’re easy to overinterpret. Science. doi: 10.1126/science.abb6526

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