UK variant hunters lead global race to stay ahead of COVID

by Joseph K. Clark

LONDON — On March 4, 2020, when there were just 84 confirmed cases of COVID-19 in the U.K., professor Sharon Peacock recognized that the country needed to expand its capacity to analyze the genetic makeup of the virus.

hunters lead global

“They’ve shown the world how you do this,” said Dr. Eric Topol, chair of innovative medicine at Scripps Research in San Diego, California.

Genomic sequencing is essentially the process of mapping the unique genetic makeup of individual organisms — in this case, the virus that causes COVID-19. While the technique is used by researchers to study everything from cancer to outbreaks of food poisoning and the flu virus, this is the first time authorities are using it to provide real-time surveillance of a global pandemic.

Peacock, 62, heads Britain’s sequencing effort as executive director and chair of the COVID-19 UK Genomics Consortium, known as COG-UK, the group she helped create a year ago.

During the first week of this month, COG-UK sequenced 13,171 viruses, up from 260 during its first 12 days of operation in March last year, according to weekly reports on the group’s website.

Behind that growth is a system that links the science of genomic sequencing with the resources of Britain’s national health care system.

Positive COVID-19 tests from hospitals and community testing programs around the country are sent to a network of 17 laboratories where scientists spend their days extracting the genetic material from each swab and analyzing it to identify that virus’ unique genetic code. The sequences are then cross-referenced with public health data to better understand how, where, and why COVID-19 spreads.

When mutations in the virus correspond with an otherwise unexplained increase in cases, that’s a clue that a new variant of concern is circulating in the area.

The importance of genomic sequencing became obvious late last year as the number of new infections began to spike in southeastern England. When cases continued to rise despite harsh local restrictions, public health officials went to work to find out why.

Through genome sequencing data, scientists identified a new variant that included several mutations that made it easier for the virus to hop from one person to another.

Armed with this information, Prime Minister Boris Johnson imposed a national lockdown, scrapping a strategy of local restrictions that had failed to contain the new variant.

The scientific sleuthing is crucial, but it’s like looking for a needle in a haystack because researchers must sift through the genetic sequences from thousands of benign variants to find the rare, dangerous ones, Peacock said.

The effort is a worldwide collaboration, with more than 120 countries submitting sequences to GISAID, a data-sharing hub created initially to track influenza viruses.

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