Thanksgiving thwarts Omicron discovery, giant genome warning

The race to unearth the first confirmed case of the Omicron variant in the US has hit a snag due to lab closures over the Holidays, according to the chief executive of the world’s largest gene-sequencing company. Thanks.

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

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

“Things slow down over the Thanksgiving holiday,” said William Schaffner, medical director of the National Foundation for Infectious Diseases, a nonprofit group. “If you ask me, ‘Omicron is already here and we haven’t found it yet?’ I would say ‘for sure’. “

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

The US has yet to record a single case, despite President Joe Biden warning on monday: “Sooner or later, we will see instances of this new variant here.”

While the US has overseen the rapid rollout of a Covid-19 vaccine, it lags many other developed nations in terms of the ability of both. to check for disease and sequencing positive samples to detect variants.

Figures from the Global Initiative on Sharing Avian Influenza Data show that in the past 90 days, the US processed 5.8% of samples compared with 11.7% and 13.5% for Canada and the UK respectively. Great Britain, respectively.

Some US states have much better fares than others. Over the past 90 days, Vermont has sequenced more than a third of its samples, while Alabama has sequenced only 2%.

“The number of sequences varies from state to state in the US,” says DeSouza. What would help is a national strategy around aligning positive cases in the US. “

The capacity, scientists say, has improved in recent months, thanks in part to an additional $1.7 billion in funding from the Biden administration. However, coverage remains uneven both by region and by case type analysed.

“Sequencing for variants has improved a lot, but it’s not uniform across the country in terms of coverage or timing,” said Bronwyn MacInnis, director of surveillance of pathogen genomes at the Broad Institute. turn around.”

Some of the sequencing work was done by the US Centers for Disease Control and Prevention, which said its labs had been working throughout last week.

But a larger number is carried out by state health authorities and academic institutions, which operate mainly Monday through Friday and are mostly closed for public holidays.

Currently, the US is sequencing about 80,000 samples per week, more than any other country. We expect any occurrence of Omicron in the United States to be identified quickly.”

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