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The use of genomic sequencing in the UK to identify a more infectious strain of SARS-COV-2 has largely served as a wake-up call for the inappropriate use of technology in the US.
As of mid-December, the US had sequenced about 0.3% of its COVID-19 samples, a percentage that is significantly lower than in other developed countries despite having a quarter of the world’s cases. .
By comparison, the UK is sequencing around 10% of its samples, with Australia aiming to sequence the entire relatively limited number of positive COVID-19 tests there in real time.
“The United States has not appeared in the sequencing if you look at the world stage,” said Dr. Eric Topol, director of the Scripps Translational Research Institute. “Sequencing gives us a lot of different things. It tells us how the virus moves from one place to another. It tells us how fast it is changing. We can say that he was here on this day, and he was there another day. You can distinguish a super spreader. “
See also: Here’s what we know so far about the new strain of COVID-19
Growing concern about new “hypertransmittable” strains of SARS-COV-2 has raised awareness about the lack of federal funding and the development of the type of genomic surveillance that helped the UK to identify the B.1.1.7 strain and South Africa identify strain B. 1,351 in December.
“We just don’t have the kind of robust surveillance capabilities we need to track outbreaks and mutations,” President-elect Joe Biden said Thursday, calling for a dramatic push in genomic sequencing and surveillance as part of his $ 1 proposal. 9 trillion US dollars. Rescue plan.
While a good chunk of pandemic federal dollars has so far gone to immediate needs like testing, contact tracing, and helping drug makers expand their vaccine manufacturing capabilities, experts are now putting pressure on the US. To build a stronger genomic surveillance system that can help public health Departments identify new strains while better addressing regional or community outbreaks.
All viruses evolve and SARS-COV-2 is believed to develop one or two variants per month, although it mutates much more slowly than the flu virus. In mid-2020, researchers began talking about the 614G mutation, which is now considered the dominant form of the virus worldwide. Now the concern has shifted to strains B.1.1.7 and B. 1.351, which are believed to be more infectious.
The UK strain B.1.1.7 has been detected in at least 76 people in 12 states, as of Jan. 13, according to the Centers for Disease Control and Prevention. (The B. 1.351 strain from South Africa has not been identified in the US at this time.)
In the US, where infection, hospitalization and death rates continue to rise, less emphasis has been placed on public health initiatives at the population level when testing and care continues to be in such high demand.
Read: Biden plans to distribute COVID-19 vaccine doses immediately
Intermountain Healthcare, a Salt Lake City-based hospital system, sent all positive COVID-19 tests for sequencing in the early days of the pandemic. But when the cases began to increase and the workload increased, the process started too disruptive and time-consuming, and stopped, said Dr. Bert Lopansri, chief of Intermountain’s Division of Infectious Diseases and Epidemiology.
“With the increase in treatment options, the launch of vaccines and the emergence of new variants, scaling up sequencing is critical going forward,” he said in an email.
If the US sequenced at least 5% of positive COVID-19 tests, then it could detect emerging strains or variants when they represent less than 1% of total positive cases, according to a model developed by sequencing company Illumina Inc. ILMN,
(His model will be released this weekend as a preprint, a type of preliminary medical study.)
This would cost less than $ 500 million in 2021, according to Dr. Phil Febbo, the company’s chief medical officer.
Experts say putting money behind a national genome sequencing surveillance network can not only help identify new variants in the future, but it can help overworked public health departments prioritize who should get it. test, trace the contact and isolate it.
It could also be used to inform vaccine manufacturers if there is a “vaccine escape strain,” a strain of the virus that could make currently available vaccines less effective or ineffective.
(A laboratory study conducted in mice by BioNTech SE BNTX,
and Pfizer Inc. PFE,
showed that its vaccine remains effective against the new strains, according to the Jan.7 preprint. Moderna Inc. MRNA,
He has also said that he is confident that his mRNA vaccine will work against the UK strain)
“When they see a small group of a new variant enter a community, they can react quickly,” Febbo said, “and they can raise awareness among those who are infected and make sure they do everything they can to contain it.”
See also: FDA Identifies 3 COVID-19 Tests That May Be Affected by New Variant
Earlier this month, Illumina announced plans with a private testing company called Helix OpCo to develop a CDC-backed national sequencing surveillance system. Helix looks for COVID-19 positive test samples with the “S gene dropout” for Illumina to sequence. So far, they have identified at least 51 cases of B.1.1.7. In the USA
Incorporating genomic sequencing into national surveillance is not the only way to modernize the way the United States can track and take action against the virus. Beyond testing, contact tracing and isolation, this could include genomic sequencing, wastewater monitoring, mobility data collection and use of digital sensors, according to Topol.
“As we get vaccines on full blast, we will start to see containment of the virus,” he said. “And then there will be places that will be like whack-a-mole, where the virus tends to show up again. If you’re sequencing, doing sewage, digital, mobility, you basically have a real-time dashboard in the country, and you see that, ‘Oh wow, Kalamazoo is lighting up.
Illumina shares have gained 18% in the last 12 months, while SPDR S&P Biotech’s XBI ETF,
has gained 59% and the S&P 500 SPX,
has gained 15%.
