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The United States is expanding its ability to track coronavirus mutations with genomic sequencing as experts have warned new variants could lead to increased cases and hospitalizations.
As the more transmissible B.1.1.7 Covid-19 variant has led to stricter lockdown measures in the UK, the US Centers for Disease Control and Prevention has signed partnerships with the US company Illumina, which develops sequencing technologies, and Helix, which has a Covid -19 testing platform.
It is also working with LabCorp, one of the largest clinical lab networks, in addition to seven university labs, and has released more funding for sequencing to state and local health departments.
Throughout the pandemic, the United States’ genomic sequencing capacity has lagged behind that of the United Kingdom, which has blinded it, experts said, to the emergence of new variants such as B.1.1.7, which the CDC predicts could become the most prevalent strain in the United States by March.
By early December, the UK had tracked viral mutations in around 9% of tests, according to the Covid-19 Genomics UK Consortium. The CDC said in late December that the United States had only sequenced about 0.3% of tests.
Francis deSouza, Managing Director of Illumina, said it was important to “sound the alarm bells” about the need to quickly create better infrastructure. The lack of a central hub to track new variants meant labs often shared footage on open-source platforms, he said.
The identification of two more variants in Ohio last week increased the urgency. “We are now in a running race between these [more] transmissible strains and vaccine deployment, ”warned Mr. deSouza.
The UK has a long tradition of genetic code research, dating back to the original discovery of the double helix structure of DNA by Francis Crick and Jim Watson in the 1950s, followed by the pioneering development of DNA technology. genetic sequencing by Fred Sanger in the 1970s.
Scientists use genomic sequencing to identify each gene in the virus, creating a series of letters. They then look for differences in the sequence and try to understand if these mutations change the behavior of the virus.
The UK government provided £ 20million to fund sequencing capacity at the start of the pandemic in March and provided additional funding in November. Denmark and Australia have also sequenced a high proportion of positive coronavirus cases.
Loyce Pace, executive director of the Global Health Council and a member of President-elect Joe Biden’s Covid-19 advisory committee, said he recommended the new US administration to focus more on genomics surveillance to understand where it is the variants and whether existing vaccines and treatments would be able to combat them.
“We recognize that the United States is not really doing enough to keep up with these variations,” she said at an event hosted by Johns Hopkins University.
In Ohio, Daniel Jones, the researcher who discovered the new variants, said his team had started sequencing 10 samples per week, but planned to increase that number tenfold.
Bill Haseltine, a scientist who has done pioneering work on infectious diseases and the human genome, said the United States has been “very complacent” in not tracking mutations.
“Once we look, we’ll find them, and they could be behind some of the extraordinary infection rates that have intrigued people like those in Southern California,” he said.
The United States is set to hit 400,000 deaths from Covid-19, the highest in the world, while the current third outbreak of infections has seen California overtake New York, the hard-hit state, which has the more deaths in the pandemic.
Bette Korber, a computer biologist at the Los Alamos National Laboratory, said scientists in Los Angeles recently started submitting genomic sequences of Sars-Cov-2 samples online.
“Everyone and their brother that I know who works in a lab right now started on this,” she says. “The UK variant will do a positive thing and wake people up to the importance of continuing to monitor the virus, especially as we roll out vaccines and therapies.”
With confirmed cases in the United States approaching 24m, Dan Barouch, a professor at Harvard Medical School, said the United States must follow the mutation of the virus.
“Unfortunately, the United States has the highest Covid rates in the world. And, therefore, there is also a chance that a variant could emerge here, ”he said. “If we can’t control Covid in our country, it also puts the whole world at risk.”
Additional reporting by Kiran Stacey in Washington
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