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Thanksgiving impeded detection of Omicron, warns genomics giant

The race to unearth the first confirmed case of the Omicron variant in the US has been dealt a setback by laboratory closures over the Thanksgiving holiday, according to the chief executive of the world’s largest gene sequencing company.

Francis deSouza, chief executive of Illumina, told the Financial Times: “As labs come back after Thanksgiving we are likely to see the presence of Omicron in the US, but ideally there should be a 24/7 sequencing operation.”

The holiday slowdown is the latest sign that the US lags several other developed nations in its ability to use genomic sequencing to identify and track new variants of the disease.

“Everything slowed down over the Thanksgiving holidays,” said William Schaffner, medical director of the National Foundation for Infectious Diseases, a non-profit group. “If you were to ask me, ‘is Omicron here already and we haven’t found it yet?’ I would say ‘sure’.”

The heavily mutated Omicron variant was first detected in southern Africa and cases have now since been identified across the world, including in the UK, Spain and Canada.

The US has not yet recorded a single case, though president Joe Biden warned on Monday: “Sooner or later we are going to see cases of this new variant here.”

While the US has overseen a rapid rollout of Covid-19 vaccines, it remains behind many other developed countries in its ability both to test for the disease and to sequence positive samples to detect variants.

Figures from the Global Initiative on Sharing Avian Influenza Data show that over the past 90 days the US has sequenced 5.8 per cent of its samples compared with 11.7 per cent and 13.5 per cent for Canada and the UK, respectively.

Some US states fare much better than others. In the past 90 days Vermont has sequenced over a third of its samples, while Alabama has sequenced just 2 per cent.

DeSouza said: “The amount of sequencing varies across the states in the US. What would help is a national strategy around sequencing positive cases here in the US.”

Scientists say that capacity has improved in recent months, in part thanks to an additional $1.7bn of funding from the Biden administration. But coverage is still uneven both by area and the type of cases being analysed.

Bronwyn MacInnis, director of pathogen genomic surveillance at the Broad Institute, said: “Sequencing for variants is much improved, but it is not uniform across the country in terms of either coverage or turnaround times.”

Some of the sequencing work is carried out by the US Centers for Disease Control and Prevention, which said its labs were working throughout last week.

But a far larger amount is conducted by state health departments and academic facilities, which mainly operate Monday to Friday and are mostly closed on public holidays.

The US health department said: “Currently, the US 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.”

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