This interview is part of a series of conversations MarketWatch is having with some of the leading voices in the United States about the COVID-19 pandemic.
Of all the news about the virus that has devastated our lives over the past year, the emergence of several potentially contagious variants in different parts of the world is worrying.
Why? Some of the new variants, including the B.1.1.7 identified by health authorities in the UK, the P.1 in Brazil, and the B.1.351 in South Africa, are considered transmissible, which then raises questions about infection rates, disease severity and hospital burden who are already grappling with an ever-increasing number of cases.
"If they're transferable, they double up every week," said Dr. Eric Topol, founder and director of the Scripps Research Translational Institute, in an interview on January 13th. "You go exponentially."
It is for this reason that Topol, a multi-field digital health expert and longtime advocate of genome sequencing, is advocating wider use of genome sequencing monitoring in the United States. Until recently, not many people have embraced this type of widespread use of the technology, but that is already changing, driven by fear of the new B.1.1.7 strain.
Over the past few weeks, President Joe Biden has said the US "simply does not have the robust surveillance capabilities we need to track outbreaks and mutations," and called for new resources for genomic surveillance. Illumina Inc.
and Helix OpCo announced plans to create a CDC-supported national sequence surveillance system. And Quest Diagnostics Inc.
signed a contract with the CDC to sequence new mutations as part of a longitudinal genomic study of the virus.
Market observation: Has the US paid enough attention to genome sequencing during the pandemic by then?
Dr. Eric Topol: The US was a no-show for sequencing when you look at the world stage. We haven't started up yet. You can see countries sequencing up to half of their infections. You will know at the earliest possible time whether there is a new variant of concern and you can quickly determine whether an "X" mutation can lead to more transmission.
Countries like Australia and New Zealand are up there at over 40 percent, and the UK was the champion of sequencing, not that their percentage is that high, but they have done the most by far. You got through all of this, and it's a country that is only a fifth as many people as the US [Britain had about 66 million people in 2019, while the US had about 328 million people at the time.] We're 0, 2% [by mid-December, the US had sequenced nearly 0.3% of its virus samples] and they're in the high single digits. We need to do at least 5% of the sample sequencing to know what's coming.
Sequencing gives us a lot of different things. It shows us how the virus moves from place to place. It shows us how quickly it changes. We can say it was here that day and it was there another day. It can detect a super spreader. Take the White House Rose Garden [event in late September that saw several White House officials including former President Donald Trump test positive for COVID-19] – these people have never been sequenced. We could have determined if it came from Trump or his source. There are so many drill downs you can drill down to, and most importantly, it can help you see if you have a worrying variant of what may be a five-alert.
Market observation: How common do you think strain B.1.1.7 is in the US?
Topol: It's all over the US. It can be around 1%. These variants … if they are transferable they will double every week. They go exponentially. We're probably only around 1%, and if you're only on the road for six or eight weeks, we're 30% to 40%. And what happens in Ireland and the UK, we will have it here unless we get extremely serious, which obviously isn't happening right now. This is the worst case, because it means more people die, more people in the hospital.[According to the Centers for Disease Control and Prevention, strain B.1.1.7 was detected in at least 293 people in 23 states by January 22nd. The P.1 variant was detected in Minnesota on January 15th The B. 1.351 strain has not yet been identified in the USA.
It is a burden when the properties change significantly. So we can upgrade the B.1.1.7 and the South African B.1.351 to load, as they are transferable. This is not entirely clear with the P.1 from Brazil. What we're likely to say is still a variant unless it becomes clear that it's transferable.
The other thing is, do they have mutations that will disrupt the vaccines? We do not know that, yet. You have to test on animals to be sure, and you have to test it on the entire virus, not just the mutation of interest. There are more than 20 of these mutations and they interact. So if you're only testing one mutation, you won't know. There is great uncertainty about vaccines. I suspect they are unlikely to interfere with the vaccines, but it is possible that they have had a modest impact. [Moderna Inc.
and Pfizer Inc.
The company developed the two COVID-19 vaccines available in the U.S. and believes their vaccines will still protect people from the new strains and variants. BioNTech and Pfizer released a preprint on January 19th detailing their results.] One day we'll likely see another drift where it will interfere, especially if we don't include that fire hose. The more it spreads, the more this can happen.
One more thing: It was quickly dismissed that the virus strain does not cause worse disease. I don't know we still know.
Market observation: Why didn't the US focus more on sequencing? Is it because it was too busy putting out instant fires to think about sequence monitoring?
Topol: Around 400,000 viruses have likely been sequenced in the world, and the US only contributed 50,000. Of the 50,000, number one was made at the University of Washington, and number two is with Scripps. The point is that these are academic labs that have no support for this. There is no scholarship and we just do it. To get to 5%, you have to get support or money from somewhere to get more people, more sequences, more reagents. We had reagent shortages. The virus samples have to come in and don't just come from the air.
Market observation: Has the UK already been a leader in sequencing or has it been focused on in their COVID response?
Topol: [National Health Service of the United Kingdom] is the premier genomic center in the world. We are both hit very hard by this virus, but their answer is: We are growing. They got support straight away because they think that way. It's part of their culture. And even though they don't have Illumina and even though they don't have Thermo Fisher Scientific Inc.
There the academic laboratories have just seized the opportunity and the need. [Although Illumina is based in San Diego, she has been working with Genomics England since January 2020 on a genomics sequencing program in the UK, including COVID-19. Topol is a consultant to Illumina.] This B.1.1.7 goes all over the world. You have put the rest of the world on high alert.
Market observation: With B.1.1.7 is that a burden and no longer a variant?
Topol: I hate to use the term "promoted" or "upgraded" to any sort because that's the real deal. It's not like the original so-called wild type D614G. [This mutation, which likely appeared in Europe from the originally sequenced Wuhan strain, became the dominant strain of the virus in most of the world in mid-2020.] After being nice and calm for a year, she evolved into a monster. And the B.1.351 could be a bit worse. This is the one that disturbs the neutralizing antibody somewhat, while the B.1.1.7 does not seem to have this.
Market observation: If there is more emphasis and funding on sequencing, could it help change the course of the pandemic in the US?
Topol: If you found B.1.1.7 and we looked at it, you would prioritize this for contact tracing, isolation, as it is a super spreader load. They have super spreader venues. This is a super spreader strain and the first one we had. You'd say, okay, well, everyone who has this has a flashing neon sign on their forehead and we have to leave everything behind to keep track of contacts because we have to stop. We need to make this a priority because this is a little bit of wildfire.
The other thing is that you also have your general surveillance: sewage, genomics, mobility, digital sensors. As soon as we get the vaccines in full swing, we will find that the virus is contained. And then there will be places that are like Whack-a-Mole, the Whack-a-Virus, where it reappears. If you sequence and do these other things, you basically have a real-time dashboard in the country. And you see, Oh, wow, Kalamazoo lights up. It's just one of the layers of data we should be streaming in real time that gives us a grip because since that launch the US has flown blind in every way.
These questions and answers have been edited for clarity and length.
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• People of color shouldn't be treated the same way in COVID-19 vaccine studies, the ambulance says: They should be over-represented