The fragmented US healthcare system is hampering the country’s efforts to rapidly sequence Covid-19 cases so it can track the Delta variant and potential future mutations, scientists and laboratory companies have warned.
Genomic sequencing is a vital weapon in the armouries of public health officials as they scramble to keep tabs on variants such as the rapidly-spreading Delta, as well as the effectiveness of vaccines against the new strains.
However, healthcare in the US, which is delivered via a huge patchwork of private and public operators that often struggle to share data, has resulted in the country’s genomic sequencing capabilities lagging behind other nations with high vaccination rates.
“The UK really got in front in this space early on,” said Bronwyn MacInnis, director of pathogen genomic surveillance at the Broad Institute in Massachusetts. “The US didn’t do that, didn’t prioritise genomic sequencing until really the threat of the variants arose early this year.”
In the past 30 days the US has sequenced 2.8 per cent of its positive Covid cases and shared that information with GISAID, the leading global genomic database that helps keep track of new variants.
By comparison, the UK and Israel, countries which have similarly high rates of vaccination, have sequenced cases and shared data at about triple that rate: 9.3 per cent and 8.5 per cent, respectively.
It also took the US more than two weeks to add its data to GISAID, versus nine days for the UK and 12 days for Israel.
In the UK, healthcare is provided by the single-payer National Health Service, while Israelis are mandated to join one of four official health insurance plans known as Kupat Holim.
“It remains a logistical challenge,” said Will Lee, vice-president of science at the genomics company Helix, which has a sequencing contract with the US Centers for Disease Control and Prevention, the main public health agency. “With so many different places and means of getting tested, it can be hard to get the sequences.”
“Because of the disparate nature of how things are run in the US both from a healthcare provider perspective and a public health perspective, getting all the data together is the challenge,” Lee added.
The CDC said it had partnered with clinical laboratory companies and university labs in order to expand the scale and speed of the country’s sequencing abilities.
“As variants began to emerge . . . CDC established a multi-faceted approach to genomic surveillance to monitor the evolution of Sars-Cov-2 and detect variants that are emerging in the United States,” the agency said.
“With our current surveillance strategy, CDC is confident that new and emerging variants will be detected well before they become prominent,” it added.
But scientists say genomic sequencing infrastructure in the US remains slow and bureaucratic, and that the country runs the risk of spotting variants less quickly.
The CDC said it currently sequences about 10 per cent of the positive cases identified in its own labs and its partners’, although that accounts for a fraction of testing capacity, which is predominantly performed by private operators and hospitals.
Arthur Reingold, head of epidemiology at Berkeley Public Health in California, said the scattered nature of testing and sequencing was the “central reason” why the US had been slower at sequencing the virus than the UK.
“If you have an NHS and labs that go with it . . . you can organise people and get them to do things in a coherent manner a lot more easily than you can if you’re trying to organise lots of different providers and labs,” he said. “It’s just a whole lot more difficult to put that together.”
MacInnis from the Broad Institute said: “We certainly had the ability to sequence and had no shortage of positive tests for quite a while throughout the pandemic.” The biggest barrier to “closing the gap” with other countries was the difficulty in getting positive tests to sequencing sites, she added.
Differing rules by US states on data sharing are also hindering attempts to build a coherent picture of how and where new variants are emerging. Some states and health departments are unwilling to share granular location data or detailed information such as whether an individual who tests positive has been vaccinated.
“At each step of the path there are regulations in place that rightly seek to protect individual privacy . . . but [they] can also prevent the kind of rapid sharing of information that we need,” said Thomas Friedrich, professor of pathobiological sciences at the University of Wisconsin-Madison, which has been sequencing Covid cases.
He added: “Each state and locality has its own mix of these regulations and different ways of interpreting federal regulations.”