The race to find the first confirmed case of the Omicron variant in the United States has suffered a setback due to lab closures over the Thanksgiving holiday, according to the chief executive of the world’s largest gene sequencing company.
Francis deSouza, managing director of Illumina, told the Financial Times: “As the labs return after Thanksgiving, we’ll likely see Omicron’s presence in the United States, but ideally there should be a 24/7 sequencing operation. 24 and 7 days a week.
The slowing of vacations is the latest sign that the United States is lagging behind several other developed countries in its ability to use genomic sequencing to identify and track new variants of the disease.
“Everything slowed down over the Thanksgiving vacation,” said William Schaffner, medical director of the National Foundation for Infectious Diseases, a nonprofit group. “If you asked me, ‘Is Omicron already there and we haven’t found it yet? I would say “of course”.
The highly mutated variant of Omicron was first detected in southern Africa and cases have since been identified across the world, including the UK, Spain and Canada.
The United States has yet to record a single case, although President Joe Biden warned on Monday, “Sooner or later we’ll see cases of this new variant here.”
While the United States has overseen a rapid deployment of Covid-19 vaccines, it lags behind many other developed countries in their ability to both test for the disease and sequence positive samples to detect variants.
Figures from the Global Avian Influenza Data Sharing Initiative show that in the past 90 days, the United States has sequenced 5.8% of its samples, up from 11.7% and 13.5% for Canada and the United Kingdom, respectively.
Some American states are doing much better than others. In the past 90 days, Vermont has sequenced more than a third of its samples, while Alabama has only sequenced 2%.
DeSouza said, “The amount of sequencing varies among states in the United States. What would help is a national strategy around sequencing positive cases here in the United States. “
Scientists say capacity has improved in recent months, in part thanks to additional funding of $ 1.7 billion from the Biden administration. But the coverage remains uneven both by area and by type of case analyzed.
Bronwyn MacInnis, director of genomic pathogen surveillance at the Broad Institute, said: “Variant sequencing is much improved, but it is not consistent across the country in terms of coverage or turnaround times.”
Some of the sequencing work is being done by the US Centers for Disease Control and Prevention, which said their labs have been operating throughout the past week.
But a much larger amount is conducted by state health departments and academic institutions, which operate mainly Monday through Friday and are mostly closed on public holidays.
The US Department of Health said, “Currently, the United States is sequencing approximately 80,000 samples per week, more than any other country. We expect any emergence of Omicron in the United States to be identified quickly. “