The US is expanding its ability to track coronavirus mutations with genomic sequencing as experts warned that new variants could be driving up cases and hospitalisations.
Since the more transmissible B.1.1.7 Covid-19 variant led to stricter lockdown measures in the UK, the US Centers for Disease Control and Prevention has signed partnerships with 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 laboratory networks, in addition to seven university labs, and has released more funding for sequencing to state and local health departments.
Throughout the pandemic, US genomic sequencing capacity has lagged behind that of the UK, blinding it, experts said, to the emergence of new variants such as B.1.1.7, which the CDC forecasts could become the most prevalent strain in the US by March.
By early December, the UK had tracked virus mutations in about 9 per cent of tests, according to the Covid-19 Genomics UK Consortium. The CDC said in late December that the US had sequenced only about 0.3 per cent of tests.
Francis deSouza, chief executive of Illumina, said it was important to “sound the alarm” about the need to rapidly create a better infrastructure. The lack of a central hub for tracking new variants meant labs were often sharing sequences on open-source platforms, he said.
The identification of two further variants in Ohio last week has increased the urgency. “We’re in a foot race now between these emerging [more] transmissible strains and the vaccine rollout,” Mr de Souza warned.
The UK has a long tradition of research into the genetic code, dating back to the original discovery of DNA’s double helix structure by Francis Crick and Jim Watson in the 1950s, followed by Fred Sanger’s pioneering development of gene sequencing technology in the 1970s.
Scientists use genomic sequencing to identify every 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 how the virus behaves.
The UK government provided £20m to fund sequencing capacity early in the pandemic in March and provided further 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 board, said it had recommended that the new US administration put a “greater focus” on genomics surveillance to understand where the variants were and whether existing vaccines and treatments would be able to tackle them.
“We recognise that the US isn’t really doing enough to track these variants,” she said at an event organised by Johns Hopkins University.
In Ohio, Daniel Jones, the researcher who discovered the new variants, said his team had begun sequencing 10 samples a week, but was planning to increase that number tenfold.
Bill Haseltine, a scientist who has done pioneering work on infectious diseases and the human genome, said the US had been “very complacent” in not tracking mutations.
“Once we look, we will find them, and they may be driving some of the extraordinary infection rates that have puzzled people such as those in southern California,” he said.
The US is on the verge of hitting 400,000 deaths from Covid-19, the highest in the world, while the current third surge in infections has seen California overtake hard-hit New York as the state with the most fatalities in the pandemic.
Bette Korber, a computational biologist at the Los Alamos National Laboratory, said scientists in Los Angeles had recently begun submitting genomic sequences from Sars-Cov-2 samples online.
“Everybody and their brother I know who is working in a laboratory right now has started on this,” she said. “The UK variant will do a positive thing and wake up people to the importance of continuing to track the virus, especially as we are rolling out vaccines and therapies.”
With confirmed cases in the US approaching 24m, Dan Barouch, a professor at Harvard Medical School, said the US must track how the virus was mutating.
“Unfortunately, the United States has the highest rates of Covid in the world. And, as a result, there’s also a chance that a variant could emerge here,” he said. “If we can’t control Covid in our country, then it keeps the entire world at risk as well.”
Additional reporting by Kiran Stacey in Washington