The UK’s use of genomic sequencing to identify a more contagious strain of SARS-CoV-2 has largely served as a wake-up call for the inadequate use of the technology in the US.
By mid-December, the U.S. had evaluated about 0.3% of its COVID-19 samples, a percentage significantly lower than other developed countries, despite having a quarter of the world’s cases.
By comparison, the UK monitors about 10% of its samples, and Australia strives to track all the relatively limited number of positive COVID-19 tests there in real time.
“The U.S. was a no-show for sequencing when you look at the world stage,” said Dr. Eric Topol, director of the Scripps Research Translational Institute. ‘Sequence gives us many different things. It tells us how the virus moves from place to place. It tells us how fast it changes. We can say it was here on this day, and it was another day. It can tell a super spreader. ‘
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Growing concerns about “hyperportable” new strains of SARS-COV-2 have raised awareness of the country’s lack of federal funding and the kind of genomic surveillance that has helped the UK to meet the B.1.1.7 tribe and South Africa. determined the B. 1.351 strain in December. The Centers for Disease Control & Prevention said on Friday it was likely that B.1.1.7 would become the most dominant form of the virus in the US by March.
“We simply do not have the kind of robust observation ability we need to detect outbreaks and mutations,” President-elect Joe Biden said on Thursday when asked for a dramatic boost in genomic sequencing and observation as part of his proposed American of $ 1.9 billion Americans. Rescue plan.
Although much of the federal pandemic dollar has gone so far as to address immediate needs, such as testing, contact detection and drug manufacturers to increase their vaccine production capacity, experts are now urging the US to develop a stronger genomic monitoring system public can help. departments identify new tribes, while the outbreak of regions or communities can also be better addressed.
All viruses develop and it is suspected that SARS-CoV-2 develops one to two variants per month, although it mutates much more slowly than the flu virus. By mid-2020, researchers began talking about the 614G mutation, which is now considered the dominant form of the virus worldwide. The concern has now shifted to the B.1.1.7 and B. 1.351 strains, both of which are considered more contagious.
According to the Centers for Disease Control and Prevention, the B.1.1.7 strain from the United Kingdom has been detected in 13 countries in 12 states, as of January 13th. (The B. 1.351 strain from South Africa has not yet been identified in the USA.)
In the US, where the number of infections, hospitalizations and deaths is increasing, there has been less emphasis on public health initiatives at the population level when there is such a huge demand for testing and care.
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Intermountain Healthcare, a hospital system in Salt Lake City, sent all positive COVID-19 tests for sequencing in the early days of the pandemic. But as business began to increase and workload increased, the process began to become disruptive and time-consuming, and it was halted, said Dr Bert Lopansri, head of Intermountain’s infectious diseases and epidemiology division.
“With increasing treatment options, vaccination of vaccines and the emergence of new variants, scaling up sequences is critical going forward,” he said in an email.
If the US sequences at least 5% of the positive COVID-19 tests, it could detect emerging strains or variants if it accounts for less than 1% of the total positive cases, according to a model developed by the company’s sequence Illumina Inc. ILMN,
(Their model is being published this weekend as a pre-print, a kind of preliminary medical study.)
According to Dr. Phil Febbo, the company’s chief medical officer, said it would cost less than $ 500 million in 2021.
Experts believe that putting money behind a national genomic sequence monitoring network can not only help identify new variants in the future, but that it can also help overworked public health departments to give preference to those tested. and must be isolated.
It can also be used to notify vaccine makers if there is a “vaccine escape strain”, a virus strain that may make the currently available vaccines less effective or ineffective.
(A study conducted by BioNTech’s BNTX in a laboratory in mice,
and Pfizer Inc. PFE,
showed that their vaccine is still effective against the new strains, according to the January 7 preview. Moderna Inc. MRNA,
also said he was confident the MRNA vaccine would work against the British strain)
“When they see a small group of a new variant coming into a community, they can react quickly,” Febbo said, “and they can make those affected aware and make sure they do their best to make it happen. to limit. ‘
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Earlier this month, Illumina announced plans with a private testing company called Helix OpCo to develop a national CDC-backed national sequence monitoring system. Helix is looking for samples from positive COVID-19 tests with the “S gene dropout” for Illumina to order. To date, they have identified at least 51 cases of B.1.1.7. in the usa
The integration of genomic sequencing into national surveillance is not the only way to modernize the way the US can detect the virus. In addition to testing, contact detection and isolation, it can include genomic sequencing, monitoring wastewater, collecting mobility data and using digital sensors, according to Topol.
“Since we are getting vaccines at full tilt, we are going to limit the virus,” he said. ‘And then there will be places like a mole, where the virus tends to reappear. If you do sequence, wastewater, digital, mobility, you basically have a real-time dashboard in the country, and you see that ‘Oh, wow, Kalamazoo is on fire.’ ‘
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