The US sequences 0.01% of its coronavirus cases – a glaring Achilles’ heel in the country’s pandemic response

covid testing college students
A college student in Chicago, Illinois gets tested for COVID-19.

Thousands of coronavirus strains circulate all the time.

Each version of the virus is separated by a handful of tiny changes in its genome. To keep tabs on these strains, and identify which ones may be better at infecting humans or evading vaccines, researchers must genetically sequence samples of the virus.

In the last five months, experts in the UK, South Africa, and Brazil have identified more transmissible variants that could exacerbate the pandemic.

But the US has limited capacity to spot variants on its own: The country genetically sequences less than 0.01% of its 26.5 million coronavirus cases – only three out of every 1,000.

According to Dr. Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases, that dismal track record is a “somewhat inexcusable deficiency.”

The UK does “many, many, many fold more sequenced surveillance than we do,” Fauci said during the Precision Medicine World Conference in January. “We really have got to build that up.”

The US is 30th in the world in genetic sequencing 

UK testing antibody
A UK paramedic holds a blood sample for a COVID-19 testing program in June 2020.

The UK sequences 45 out of every 1,000 coronavirus cases – about 15 times the number of cases that are sequenced in the US. These efforts likely helped UK researchers detect the more infectious B.1.1.7 strain outside London in September.

Studies have shown that B.1.1.7 is between 56% and 70% more contagious than its viral predecessors. UK officials said in January that people infected with B.1.1.7 may face a higher risk of death than those who get other strains, though more data is needed to confirm this hypothesis.

But even the UK’s sequencing efforts pale in comparison to those in Iceland, Australia, and New Zealand. These nations have sequenced 64%, 41%, and 35% of their coronavirus cases, respectively – the most of any countries so far, according to data from GISAID, a global database that collects coronavirus genomes.

The US ranks 30th on that list – behind countries like Canada, China, Papua New Guinea, and the Republic of Congo – an improvement from its 43rd ranking in December.

Jeff Zients, coordinator of President Joe Biden’s COVID-19 task force, called the situation “totally unacceptable” during a White House briefing on January 27. More genetic sequencing, he said, “will allow us to spot variants early, which is the best way to deal with any potential variants.”

Indeed, knowing where a more transmissible variant is spreading could inform public health measures and travel bans, among other mitigation measures. A country lacking proper genetic surveillance has no way of knowing if a strain is spreading silently within its borders – and that “comes back to bite us,” Fauci said during the January conference.

Variants were circulating undetected in the US

covid scientist lab coronavirus testing samples
Scientists work in a lab testing COVID-19 samples at New York City’s health department, April 23, 2020.

To identify which coronavirus strain has infected a patient, scientists need to map out roughly 30,000 genetic letters in a sample of the patient’s blood or saliva.

The process is time-consuming. Samples collected from patients aren’t always sent in for sequencing and a limited number of labs can complete the genetic analysis.

“Part of the challenge of recognizing these variants is a lack of public health laboratory infrastructure in order to do the surveillance,” Dr. Rochelle Walensky, director of the Centers for Disease Control and Prevention, recently told JAMA.

Nearly all of the US’s initial cases of B.1.1.7 and B.1.351 – another more infectious variant first found in South Africa – involved patients with no travel history. This suggests the strains have been spreading undetected for some time. 

The US didn’t report its first case involving B.1.1.7 until December 29, at least three weeks after the variant entered the country, according to some disease experts

The US’s first B.1.351 cases, reported last week in South Carolina, were detected by chance. Researchers had been testing random samples “in order to identify any instances of the variant viruses,” the state health department said in press release.

Preliminary research published last month suggests vaccines might not provide as much protection against B.1.351, and people who have already been infected with a different version of the virus could get reinfected with the new strain.

The more you look, the more you’ll find

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Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, speaks during a Senate hearing in June.

According to Fauci, the CDC is working on partnering with the National Institutes of Health to improve the US’s sequencing infrastructure.

The agency launched a consortium in May called SPHERES to coordinate and standardize genomic sequencing in the US. But “poor funding, coordination, and capacity” has resulted in “patchy” data, according to a report from the National Academies of Science.

Fauci said SPHERES is working on consolidating all the sequencing data from independent US labs by “streaming it into one accessible database so that we can do much more than we’re doing.”

Coordinating sequencing efforts is crucial to improving the country’s pandemic response.

The more viral genomes countries sequence, “the more able we are to spot new lineages” like B.1.1.7 and B.1.351, according to Lucy van Dorp, a geneticist at the University of College London Genetics Institute.

This probably won’t be the last time we learn of a new, potentially more infectious strain, she told Insider.

“There may be other similar variants elsewhere which have not been detected in other regions of the world due to less intensive sequencing efforts,” she said. 

los angeles coronavirus testing
A long line for COVID-19 testing at St. John’s Well Child and Family Center in Los Angeles, California on July 29, 2020.

Dr. Peter Hotez, a vaccine scientist at Baylor College of Medicine in Texas, said on Twitter last month that the US likely had its own “homegrown variants” circulating. 

California researchers confirmed Hotez’s prediction in a preliminary study published on January 20: Experts at Cedars-Sinai Medical detected a new variant called CAL.20C, which represented 24% of all coronavirus cases in Southern California in December.

There’s no indication that the variant is more transmissible yet, but the researchers said CAL.20C may have contributed to LA’s record case surge over the last few months.

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