The UK’s use of genomic sequencing to identify a more infectious strain of SARS-VOC-2 has largely served as a wake-up call for the inappropriate use of technology in the US
By mid-December, the US had sequenced approximately 0.3% of COVID-19 samples, a percentage that is significantly lower than other developed countries, despite having a quarter of cases worldwide.
In comparison, the United Kingdom sequences approximately 10% of its samples, and Australia aims to sequence in real time all the relatively limited number of positive COVID-19 tests there.
“The United States has been a failure in sequencing if we 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 moves from one place to another. It tells us how fast it changes. We can say that he was here on this day and was there on another day. You can tell a super spreader. ”
See also: Here’s what we know so far about the new strain of COVID-19
Growing concern about the new “hypertransmissible” strains of SARS-VOC-2 has raised awareness of the lack of national federal funding and the development of the type of genomic surveillance that has helped the UK identify strain B.1.1.7 and South Africa identified strain B. 1,351 in December.
“We simply don’t have the kind of solid surveillance capabilities we need to track outbreaks and mutations,” President-elect Joe Biden said Thursday when he called for a dramatic boost in genomic sequencing and surveillance as part of his proposal to 1 , 9 trillion US dollars Rescue plan.
While a good amount of federal dollars for the pandemic have gone so far into immediate needs, such as testing, tracking contacts and helping drug manufacturers increase their vaccine manufacturing capabilities, experts are now pushing the U.S. to build a system of vaccines. Stronger genomic surveillance that can help public health departments identify new strains while better addressing regional or community outbreaks.
All viruses evolve and it is believed that SARS-VOC-2 develops one or two variants per month, although it moves much slower 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, both of which are thought to be more infectious.
Strain B.1.1.7 in the UK has been detected in at least 76 people in 12 states since January 13, according to the Centers for Disease Control and Prevention. (Strain B. 1,351 from South Africa has not been identified in the United States at this time.)
In the US, where rates of infections, hospitalizations and deaths continue to rise, less emphasis has been placed on population-based public health initiatives when testing and care remain in high demand.
Read: Biden intends to distribute COVID-19 vaccine doses immediately
Intermountain Healthcare, a Salt Lake City-based hospital system, sent all positive COVID-19 tests to be sequenced in the early days of the pandemic. But when cases began to increase and workload increased, the process began too disruptive and time-consuming and was halted, said Dr. Bert Lopansri, head of Intermountain’s Infectious Diseases and Epidemiology Division.
“With the increase in treatment options, the launch of the vaccine and the emergence of new variants, expanding sequencing is essential in the future,” he said in an e-mail.
If the US sequenced at least 5% of the positive COVID-19 tests, then it could detect strains or emerging variants when they represent less than 1% of all positive cases, according to a model developed by the sequencing company Illumina Inc. ILMN,
(Their model will be published this weekend as a prepress, a type of preliminary medical study.)
That would cost less than $ 500 million in 2021, according to Dr. Phil Febbo, the company’s chief physician.
Experts say putting money behind a national genomic sequencing surveillance network can not only help identify new variants in the future, but can help overburdened public health departments by prioritizing who should be tested, tracked and isolated .
It could also be used to inform vaccine manufacturers if there is a “vaccine release strain”, a virus strain that could make vaccines currently less effective or ineffective.
(A laboratory study in mice by BioNTech SE BNTX,
and Pfizer Inc. PFE,
showed that their vaccine is still effective against new strains, according to the January 7 prepress. Moderna Inc. MRNA,
also stated that it is confident that its MRNA vaccine will work against the UK strain)
“When I see a small group of new people entering a community, they can react quickly,” Febbo said, “and they can raise awareness among those who are infected and make sure they make every effort to contain it.”
See also: The 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 CDC-supported national sequencing surveillance system. Helix is looking for evidence from positive COVID-19 tests with “abandonment of the S gene” for Illumina to be sequenced. To date, they have identified at least 51 cases of B.1.1.7. in the United States
Incorporating genomic sequencing into national surveillance is not the only way to modernize the way the US can track and act against the virus. Beyond testing, contact tracking and isolation, this could include genomic sequencing, wastewater monitoring, mobility data collection and the use of digital sensors, according to Topol.
“As we receive vaccines there, to the fullest, we will begin to see the confinement of the virus,” he said. “And then there will be places that are like whack-a-mole, where the virus tends to reappear. If you do sequences, do sewage, digital, mobility, you have practically a real-time dashboard in the country and you see that “Oh, wow, Kalamazoo lights up”. ”
Illumina shares have gained 18% in the last 12 months, while SPDR S&P Biotech ETF XBI,
gained 59% and the S&P 500 SPX,
gained 15%.