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Why New Covid “Super Strain” is a Game-Changer

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Why New Covid “Super Strain” is a Game-Changer


Yves here. We are still in the “fog of war” stage as far as knowing enough about the more infectious strain of Covid that seems to be spreading quickly in the UK and has landed in the US. But the early indications still look to be intact, and they are not good.

By Lynn Parramore, Senior Research Analyst at the Institute for New Economic Thinking. Originally published at the Institute for New Economic Thinking website

According to Phillip Alvelda, a former NASA & DARPA technologist-turned-entrepreneur, the pandemic is about to get even uglier for Americans as the fast-spreading U.K. strain makes its way across the country. He talks to Lynn Parramore of the Institute for New Economic Thinking about what you need to know and how our behavior must change in order to beat the coronavirus.

Lynn Parramore: Let’s start with a little about your background as well as what you’re working on now.

Phillip Alvelda: My career has always been about developing interesting technologies and turning what used to be science fiction into science, and then into working technology.

I had the good fortune to work in interesting places like NASA, and I got some schooling at Cornell University in physics and computer science and later at the artificial intelligence laboratory at MIT. My most recent efforts at DARPA [Defense Advanced Research Projects Agency] were in the biological technologies office that did a lot of work leading to building the pandemic warning systems in China, like pandemic prediction software. It even invested the first money into the company that became Moderna. So, I’ve been tied into the development of all technologies at the boundary of engineering, machines and biology for many years.

When I left DARPA, I began building a company called Brainworksto apply new artificial intelligence techniques and the new technologies out of the biological technologies office to a new generation of health care tools. Then along comes Covid, and the whole medical industry is turned upside down. But we happened to be plugged into all the critical pieces and the community, so we could quickly understand more about the virus and help guide countries and states and so on.

I’m also involved in a biotechnology security group that has the MIT, NASA, and DARPA community involved. This was tremendously helpful at assembling a team to collect data and get it directly from the sources and the hotspots without the intervening politics filtering it. The team is not just medical doctors, but data scientists, economists, polymaths, epidemiologists, and mathematicians who can look at the complexities and figure out what’s going on and what we should be doing.

LP: New, fast-spreading “super strains” are raising a lot of concerns, such as more infection among young people. You’ve been studying the U.K. variant, which has shown up in the United States. What do we need to know?

PA: We saw the U.K. strain coming for some time. All of a sudden there began to be dramatic upticks in infection rates, even without material changes in individual behavior en masse or the abatement measures enacted and observed. England has not been the most Johnny-on-the-spot responder to the coronavirus, and there has been a lot of confusion about what abatement measures should be observed, in which areas, etc. Of the developed nations, the U.S. and the U.K. have struggled the most as societies to communicate, plan and observe reasonable measures that other countries have more successfully applied.

The U.K. variant, which has now spread across Europe and into several U.S. states, has what appear to be a couple of important mutations in the spike protein, which allows the virus to attach to the receptors in the lungs. Apparently, the new variant is stickier – better at binding to the receptors. That means that it takes less of the virus to get you sick, or the same viral load gets you sicker.

A big change is that the U.K. variant appears be somewhere between 40 and 70% more infectious. For a person who has this variant, they’re likely to infect 40% to 70% more people. If you think about what we have done to reduce the effectiveness of transmission, getting people to wear masks has been a successful campaign. But some masks are better at protecting people than others. A well-fitted N95 and KN95 masks will filter 95% of the virus particles from coming into your lungs, but there are also terrible masks that don’t protect people much at all. If you average mask-wearing over the population, it seems that the mask mandates reduce the infectiousness of the virus by about 40 to 50%.

To put the U.K. variant in perspective, with its faster spread, we are effectively put back to where we once were without masks — even when we’re now wearing masks!

LP: The idea of young people under 20 getting infected at high rates is alarming, though there have been conflicting reports as to why those numbers are higher, such as behavior patterns. What’s your take?

PA: There is no doubt that the U.K. strain is infecting more young people than any prior variants. I think the conflicting reports may have more to do with where that variant is prevalent and where it is not. It would not be true to say that all of the hospitals in the U.K. are being overrun by younger patients. But in those regions where the new variant is prevalent, the hospitalization and case data now show that more than ever before, young people are having almost as many cases and hospitalizations as the older people.

That is a substantial change. With older variants, symptoms were usually not bad enough to even bring the kids in to test — and we know there were a lot of asymptomatic carriers that were never tested or acknowledged. With the new variant, symptoms are bad enough that kids need the testing and they’re being hospitalized. It’s probably premature to speculate on the lethality. There is some hope, for example, that the U.K. variant could be more infectious but less lethal. But we just don’t know. It’s likely going to be weeks before the case trend that is now beginning to translate into the hospitalization trend will translate into the mortality trend.

Unfortunately, given what we’ve seen in the past from the virus, it’s our expectation that if the case data is showing more young people infected, and the hospitalization data is showing more of them hospitalized, in a matter of weeks we will see more deaths.

LP: What does this mean for schools?

PA: We’ve already seen tremendous challenges in the schools with older variants. We have the data now and we have learned that there were many states where the moment the schools opened for in-person instruction (as opposed to remote learning), that was the beginning of the exponential growth of the virus. The virus typically reasserted itself in late August and early September, congruent with the public school openings in these states.

Now, it didn’t happen in every state. There were some areas and regions and some individual schools which had adequate abatement measures and adequate testing regimes where they could identify cases, even the asymptomatic ones, very early before they had infected a lot of people. They were able to sequester those folks into separate dormitories or tell them to stay home and continue operations on a relatively safe basis – maybe they’d have a breakout, but it would be only a couple of people infected.

LP: What is the best way to keep schools safe, especially with the more communicable strains?

PA: With the U.K. variant, it’s trickier and we don’t have all the answers. For the older variants, we recommended to minimize indoor time as the number one priority. The virus is airborne and there’s a very high risk of spreading it indoors. We also know that the six-foot social distancing rule is a little bit of a hopeful fiction for indoor activities. Kim Prather of the Scripps Aerosol Chemistry Lab led one of the first groups to demonstrate that the virus was airborne and transmitted via aerosols. Her group did a lot of work figuring out how it traveled in indoor environments and what sort of ventilation was needed to protect people.

Rather than the six-foot rule, it’s better to imagine that everyone around you is smoking. If you can smell the smoke, you can be infected by the virus, because the virus aerosol behaves more or less like cigarette smoke. Now, you’d have to get a good slug of smoke to get an infectious dose, but Kim showed that there are enough examples, like the Diamond Princess cruise ship transmitting the virus through the air conditioning system across the ship; the restaurants in Korea and Wuhan; the restaurant in Madrid; and the buses where people infected others sitting 50 feet away; to tell us that staying six feet away doesn’t really protect you. If you’re engaged in a prolonged period of indoor eating and drinking or singing in church, you could infect people 50 feet away, not six feet away.

You also have to think of the total dose that you can take in to get infected. For the older, less communicable variants, the CDC [Centers for Disease Control] said that a cumulative dose of 15 minutes inside from someone infected over the course of a day is enough to infect you. There are examples in which the flow of air from an air-conditioning system going in the wrong direction got someone infected in five minutes indoors who was 12 feet away.

You get the idea pretty quickly that if you’re going to be inside, you should have all the windows open and the HVAC going full blast. Kim estimated that you need to be exchanging the air within the environment every six minutes if you want to minimize your risk of exposure.

LP: How many schools are able to do all this?

PA: Well, it’s easier where the weather is nicer, for sure. My sense is that very few schools are observing all of these measures. It’s impractical. I think that part of the challenge with teasing apart the different effects is that it’s not completely clear that it’s just the transmission inside the classroom itself that’s the problem. When you say, let’s open the schools, there’s a whole bunch of social activity, transportation and organization, parent events, and sports that kick in at the same time that collectively led to higher transmission.

LP: So, even if you had classrooms perfectly set up, with open windows, etc., the virus could still be spreading?

PA: Yes. There are subtleties that are gotchas. The cafeterias were fairly easy to deal with. Instead of having all the kids coming together in the cafeteria, you have them pick up a box lunch and take it back to their class. Turns out one of the harder things to deal with is the restrooms. If you’re infectious and you use the toilet and flush it, that aerosolizes the virus and it makes the whole bathroom infectious for about 30 to 45 minutes.

LP: How does testing fit in to all this?

PA: This is one of the areas, full disclosure, that our company is working on. We realized about five months ago that it doesn’t matter whether you’re wearing masks if the kids are inside.

With the more infectious variant, even with masks and ventilation, it’s not safe. There are many questions. Do we need to evacuate all the air in three minutes instead of six because it’s twice as infectious? It starts to become really difficult to protect the infected from the non-infected. That means you have to pull infected people out of the community before they can infect others. The critical realization is that 40% of all the coronavirus carriers, at least, are completely asymptomatic and you can’t detect them any other way than a molecular lab test.

LP: How often do people need to be tested?

PA: Someone can become infectious in two-and-a-half to three days. So, even if I tested this morning and came out negative, I might have caught the virus this afternoon and in three days I’ll be infectious.

LP: That means everybody in the school needs to be tested at least twice a week – teachers, students and staff, right?

PA: That’s right, and there are not nearly enough schools where this is taking place. This is where our company came into play, because it’s clear that there are two or three key barriers to getting sufficient testing regimes in place. The first and probably the most important is cost. When you talk about a good, high-precision test coming in at a hundred dollar price point, and you say to schools, ok, test all 700 of your students plus staff twice a week, they just don’t have the money to do it.

LP: Only schools with vast resources could pull it off, like private universities. Do you foresee that economic and social gaps that were already widening in education will be further torn apart because of scenarios like this?

PA: Yes. You have all the social equity issues of advantaged and disadvantaged students and communities.

Part of the goal is to find a high-precision technology that can work at scale and reduce the cost enough to make it affordable. We have succeeded and found a technology and are in the process of rolling that out. The other piece is that it has to be operationally feasible. If you tell a school to line up all the students and staff and test them twice a week, and by the way, you’ll have to place a syringe deep into the noses of kindergartners, well, that’s just not really going to work. One of the other big technology advances that we were able to help bring about is a shift from the nasal swabs to a saliva test. We needed to invent a test that was low-cost, but would also be simple to use and harvest.

The other important feature is quickly available results. In many of the PCR [Polymerase chain reaction] testing labs, whenever you have a surge in the region, the testing backlog climbs and the turnaround slows to over 72 hours, making it completely useless as a surveillance tool. The key is to keep the response time to less than 24 hours. The technology we were trying to develop, along with the processes and the shipping strategies and so on, were all important pieces for a feasible system. We have done all that. The last barrier is the translation of science into policy.

LP: Let’s talk about that policy challenge. How do you view the shortcomings in Covid policy so far?

PA: I think we can point to a series of failures and also the fact that it’s a rapidly-evolving situation that’s difficult to manage. There are so many different parameters and challenges. Probably the most important thing is that the federal government has been absent. We now know from released documents that guidance from the CDC has been diluted and washed-down to minimize the apparent damage from the virus.

Think of any public school district in any of the 50 states — at some level, you are responsible for doing the things that the government tells you to do to protect kids. If the federal government says it’s fine to go ahead and open the schools, there’s not a lot of incentive either monetarily or operationally to do something different.

A couple of states early on were much more aggressive, like New York, where some of the public school districts issued fantastic guidance on what to do with bathrooms, how to upgrade your HVAC, close the windows, turn the fans up, and have everyone masked, and so on. In states that did all that diligently and offered a testing regime, even if it was only once a week or even once a month, they could open, and even so, the incidence of the virus would drop.

Some of the universities did very well, and this tells you the level of resources necessary in the early days when the tests were so expensive. A lot of universities that had strong biochemistry departments could put together very strong abatement measures on campus and twice-a-week molecular testing for the entire campus community. MIT, Harvard, Duke University, Syracuse, Rochester, U.C. Santa Cruz, and UC Berkeley did it. These were schools in areas that took the virus very seriously and had the technical wherewithal and budget.

But the schools in Florida, some districts in California, and even some in Massachusetts had problems. We saw them open, and there would be reports that would say, look, we can show now, based on places like MIT, Harvard, etc., that if a school takes proper measures, it’s safe to open. The policy makers would say, “go ahead and open the schools” without paying attention to the part about taking appropriate measures. They rushed to open but did so without having the measures in place, most notably the testing regime.

LP There’s a lot of pressure on authorities to keep schools open. This argument is strengthened by observing the obvious problems with cyber education in general, and especially with disadvantaged students. What’s your view?

PA: Well, it’s a really difficult situation. I feel it very personally because I have one erstwhile college freshman and one high school sophomore here at home. As parents, we see them suffering social deprivation, showing deficits of learning, and suffering social anxiety and depression. All those things are very real. We’re seeing reports of the general rise in child anxiety and self-harm. That’s the clear and present damage that is ongoing. I take it very seriously and see that damage. On the other hand, I think that’s better than being dead or killing your parents or grandparents or teachers.

The CDC has now confirmed a couple of really important points. They now show that 75% of the transmission of the virus is coming from asymptomatic carriers, and they’ve shown that children are very effective asymptomatic carriers, and in fact have very high likelihood of transmitting the virus to their parents. There have been studies in the U.S. and more recently in the U.K. showing an increase in transmission from students taking the virus home to infect their parents.

LP: Obviously teachers and teachers’ unions, along with other front-line workers, will want to have a say about better safety measures as the more infectious variants spread.

PA: The teachers are on the front-line and at tremendously elevated risk. They should have a say. It’s bizarre how OSHA [Occupational Safety and Health Administration] has been largely absent from the scene. You see all the gyrations in Congress, where they’re trying to strip away protections from workers so that they can’t sue when the workplaces are negligent about protecting the staff. Teachers’ unions have legitimate concerns. In the defense of the school districts, they really haven’t had a cost-manageable and operationally-practical tool to address the problems until what we’re developing for the start of this year.

As for other occupational hazards, we now know that the bars and restaurants are disastrous settings. Conversation and eating and drinking amplify the number of virus particles you exhale. The very moment bars and restaurants were opened for indoor dining and socializing, the virus skyrocketed even more than when just schools were opened.

LP: A lot of people argue that taking more robust measures to control the spread of the virus will cause too much economic damage. What do you say to that?

PA: I think there’s an attribution problem. The damage is not coming because we’re closing things. The damage is coming because the virus is killing people. Yes, we’re closing things to try and manage it. But I think the solution has been demonstrated for us.

There are several nations that have been very successful. In China, Wuhan did an excellent job of eliminating the virus. They were the first ones to have it and they gave everyone a crystal clear example. They had all the data. They made it public. They had all the abatement efforts that they took public. Countries that followed that model were also successful: Taiwan, South Korea, New Zealand, and Australia all did excellent jobs in extreme lockdowns, virtually eliminating the cases and eliminating the deaths. They then put in systems to be very vigilant, like very high-volume surveillance testing so that any time an outbreak happened, they would squash it before it got to more than 20 people.

The solution is that you need a very stringent, tight lockdown quickly. Fast-action. As soon as you detect exponential growth, you lock down. You don’t lock down to suppress or flatten the curve, you lock down until you eliminate the virus.

LP: Do you see places like Los Angeles running out of options to contain the virus?

PA: It’s already happened. You already have triage where they’re no longer taking patients that are too serious. You already have hospitals that are turning away people.

LP: Since the new variants move so fast, how do we prepare quickly enough?

PA: I do think we have a little bit of time before the U.K. variant becomes prevalent in the U.S. It took about two months for it to become the dominant strain in the U.K. and we’re about two months behind the U.K. in that process. But make no mistake, it’s happening. We don’t have the testing regimes to even know where it is. It will happen before the end of the school year, and it wouldn’t surprise me that in some of the areas where we’re seeing the caseloads get really high, they’re already being driven by this new variant.

The key point is that we have to do everything we were doing before, but we have to do twice as much — to just tread water.

LP: In your view, what doesn’t work? Should we just forget about social distancing?

PA: Being indoors with other people outside your household or your pod is really just a bad idea. There are some things that are easy, like mask wearing. Here in California, we have mask compliance over 95% — that’s good. But the quality of masks is not all that great. We now know from data that the mask regimes generally provide about a 50% reduction in transmission. You might think it should be better because we have KN95 and N95 masks, but very few people wear them. The blue surgical masks, for example, don’t fit very tightly over the face, so aerosols can escape from the edges. They only offer 40-50% protection. Other masks and gaiters are even worse.

One thing people should be doing is getting a (K)N95 mask and making sure that it fits tightly over the face with an unbreakable air seal.

LP: Are we talking about young children needing to wear N95 and KN95 masks?

PA: Yes, we are. It’s either that or keep them home.

LP: What do you say to parents with kids returning to school after the holidays who are worried about school safety?

PA: In my house, we’re talking to the schools about their abatement measures and what sort of testing regime they’re having. From our perspective, if those are insufficient, we keep the child home. Testing has to be twice a week, there has to be serious HVAC, more than six feet separation, most classes outside, and high quality mask-wearing – none of those gaiter kinds of things that satisfy the letter of the law but don’t actually protect you. All of those things.

LP: What about pods – small groups for studying or socializing? Do they work?

PA: I think it’s better to have them than not. Any reduction in the number of contacts you have drops your chances of catching and transmitting the virus. But one of the things that I think schools are missing comes through in that recent CDC report, which shows that kids are very effective virus transmitters in the home. The chance of home transmission is very, very high both ways, from and to children. So, when you do your pod calculation, you have to think about how big your community is. It’s not just teachers and students, it’s also the parents and siblings and their respective pods.

LP: Do you see positive changes coming with the new administration?

PA: I really do. We see the policies rapidly evolving and much more federal participation and leadership. We’re already seeing some good effects. California, just a couple of days ago, announced a new $1.2 billion program to finance weekly testing for every K-12 student in the state. And just yesterday, a $22 billion federal program was announced for the same purpose. That’s an absolute improvement. We’d like to see it extended to twice a week. It’s cost-based, of course, and we’re hoping that with the solution we’re developing, we’ll be able to do three or four tests for the price of one. It should be relatively straightforward to increase the same frequency with pretty much the same budget in a month or two.

We expect to see this kind of guidance go nationwide with the Biden administration. Now, how smartly each of the states will follow it, I think, will largely follow the politics of those states.

LP: What’s your perspective on vaccine distribution?

PA: It’s pretty clear now that the pronouncements of the Trump administration were fantastic at best. We’ve administered something like 4.2 million doses– and that’s only the first dose. We haven’t fully immunized anyone. As with other Trump policies, he decided to work from the federal level in kind of a minimalist way and left the end point, the last mile of distribution, to the states, which didn’t have the foggiest clue how to manage distribution at that scale.

We’re seeing a supply chain that doesn’t have sufficient cold storage, that doesn’t have enough people, that isn’t organized, that doesn’t have tracking systems, that is just one tenth of the speed that you’d imagine. They didn’t do any testing or preparation for the last mile at all. I think the sad truth is that at the rate we’re going, it’s going to be mid to late 2022 before we start to see the effects of induced immunity from the vaccine.

But take some heart—-the 2022 estimate is if we keep going the way we’re going. I’m confident that the Biden administration will exercise more centralized control and we’ll have some real experts managing the distribution where it’s been largely a political exercise up until now. It’s odd because I do know many of the experts in the Trump administration and I respect many of them tremendously. But somehow their efforts have been stymied or disintermediated or delayed or diluted and the whole is just not functional. My hope is that as more vaccines get approved and some have more relaxed handling requirements, you’ll start to see the rate of vaccination pick up. But I do think that best-case scenario, we’re going to be in this until the end of 2021 maybe slightly into 2022.


And a final caution, don’t think that just because people are vaccinated means that they don’t get the virus and that they can’t be communicable. A vaccine means that if you get the virus, your system deals with it, but you’re still communicable. You still need testing.

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