The UK’s use of genomic sequencing to identify a more infectious strain of SARS-COV-2 has largely served as a warning for the inappropriate use of technology in the United States.
By mid-December, the United States had sequenced about 0.3% of its COVID-19 samples, a percentage significantly lower than that of other developed countries, despite having a quarter of the world’s cases.
In comparison, the UK is sequencing about 10% of its samples, and Australia plans to sequence in real time all the relatively limited number of positive COVID-19 tests there.
“The United States did not attend the sequencing if you look at the world stage,” said Dr. Eric Topol, director of the Scripps Research Translational Institute. “Sequencing gives us many different things. It tells us how the virus is moving from place to place. This tells us how fast it is changing. We can say that it was here this day and it was there the other day. You can say a super spreader. “
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The growing concern about the new “hyper-transmissible” strains of SARS-COV-2 has raised awareness about the country’s lack of federal funding and the development of the type of genomic surveillance that has helped the United Kingdom to identify strain B.1.1. 7 and South Africa identify the B. 1,351 strain in December.
“We just don’t have the kind of robust surveillance capability we need to track outbreaks and mutations,” said President-elect Joe Biden on Thursday, when he called for a dramatic increase in genomic sequencing and surveillance as part of his $ 5 proposal. 1.9 trillion rescue plan.
While a large portion of the federal pandemic dollars has gone so far for immediate needs, such as testing, contact tracking and helping drug manufacturers to increase their vaccine manufacturing capabilities, experts are now lobbying the United States to build a system of vaccines. stronger genomic surveillance that can help public health departments identify new strains and, at the same time, better deal with regional or community outbreaks.
All viruses evolve, and SARS-COV-2 is believed to develop one to two variants per month, although its mutation is much slower than the flu virus. In mid-2020, researchers started 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 considered more infectious.
The United Kingdom’s B.1.1.7 strain has been detected in at least 76 people in 12 states as of January 13, according to the Centers for Disease Control and Prevention. (South Africa’s B. 1,351 strain has not been identified in the United States at this time.)
In the United States, where rates of infections, hospitalizations and deaths continue to rise, there has been less emphasis on public health initiatives at the population level when testing and care remains in high demand.
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Intermountain Healthcare, a hospital system based in Salt Lake City, sent all positive COVID-19 tests for sequencing in the early days of the pandemic. But when the cases started to escalate and the workload increased, the process started very disturbing and time-consuming, and was stopped, said Dr. Bert Lopansri, head 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, increasing sequencing is essential for the future,” he said by email.
If the US sequenced at least 5% of the positive COVID-19 tests, then they would be able to detect emerging strains or variants when they represented less than 1% of the total positive cases, according to a model developed by the sequencing company Illumina Inc. ILMN,
(Their model is set to be published this weekend as a prepress, a type of preliminary medical study.)
This would cost less than $ 500 million in 2021, according to Dr. Phil Febbo, the company’s medical director.
Experts say that investing money in a national genomic sequencing surveillance network can not only help identify new variants in the future, it can also help overburdened public health departments prioritize those who should be tested, screened and isolated.
It could also be used to inform vaccine manufacturers if there is “an escape vaccine strain”, a strain of the virus that could make the currently available vaccines less effective or ineffective.
(A study conducted in a rat laboratory by BioNTech SE BNTX,
and Pfizer Inc. PFE,
showed that their vaccine is still effective against the new strains, according to the January 7 preprint. Moderna Inc. MRNA,
also said 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,” said Febbo, “and they can raise awareness for those who are infected and make sure they do their best to contain it.”
See too: FDA identifies 3 COVID-19 tests that may be affected by a new variant
Earlier this month, Illumina announced plans with a private testing company called Helix OpCo to develop a national sequencing surveillance system supported by the CDC. Helix looks for samples of positive COVID-19 tests with the “S dropout gene” 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. In addition to testing, contact tracking and isolation, this can include genomic sequencing, wastewater monitoring, mobility data collection and use of digital sensors, according to Topol.
“As we get the vaccines in full swing, we will start to see the virus contained,” he said. “And then there will be places that will be like whack-a-mole, where the virus tends to arise again. If you’re sequencing, doing sewage, digital, mobility, you basically have a real-time panel in the country and you see, ‘Oh, wow, Kalamazoo is lighting up’ ”.
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