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February 16, 2021
America Dissected
The Variants Episode with Dr. Angela Rasmussen

In This Episode

Abdul talks about how our failure to invest in public health is hurting our vaccine effort. He talks to Dr. Angie Rasmussen, America Dissected’s resident virologist to break down the new variants and what they tell us about where we go from here.






Dr. Abdul El-Sayed: My friends, Abdul, here, I just wanted to remind you about my new Substack newsletter, The Incision. We take the topics that we explore here in America Dissected and cut a little bit deeper, particularly on the political side. So if you’re interested, go to And I hope that you’ll subscribe today. Our most recent article is about why the vaccines won’t save us. I hope you’ll check it out. Please subscribe.


Dr. Abdul El-Sayed: The federal government plans to ship vaccine directly to health centers in low income communities across the country to address disparities in vaccine access. Meanwhile, cases, hospitals and deaths are all continuing to decline, for now. In response, governors are opening up dine-in eating, gyms and other facilities that had previously been shut down. This is America Dissected. I’m your host, Dr. Abdul El-Sayed, and it is way too early to declare victory.


Dr. Abdul El-Sayed: When you take an antibiotic for a bacterial infection, you have to take the whole course, even if your symptoms go away well before you’re done. Why? Because any little bit of bacteria left can start replicating again, bringing back the symptoms in full force or worse. And even worse than that, bacteria that survive are often the ones that are most immune to the antibiotic you took and you’ve now selected for antibiotic resistant variants of the bacteria that are a lot harder to treat. This is a pretty good analogy for what’s happening with this pandemic, but instead of bacteria in one body, we’re talking about a virus across the country. Cases, hospitalizations and even deaths are down, and they’re down significantly. Case rates are back down to where they were in November, before Thanksgiving. And that’s a good thing. The fever is starting to break, but only slightly. These “low case rates”, there’s still five times higher than the low point we experienced back in June. But in response to the decline, governors across the country are starting to ease restrictions. They’re doing the pandemic equivalent of skipping doses of their medicine. Make no mistake, it is way too soon. Less coronavirus, doesn’t mean no coronavirus. Oh, and there’s this:


[Voice clip] Scientists say cases of the UK variant now appear to be doubling here in the U.S. about every 10 days.


[Voice clip] And then we have projections that it may be the dominant strain by the end of March.


Dr. Abdul El-Sayed: There are a few things I need you to understand about the new variants of COVID-19 beginning to spread across the United States. The first is obvious. Letting our guard down now risks allowing these variants to spread. And because they’re more resistant to our immunity, that’s a really bad thing. But the second thing I want you to understand is that it’s not just the variants that we have right now, but the variants we could have in the future. Every person coronavirus infects is another opportunity it has to mutate and potentially evolve the ability to acquire resistance to our vaccines entirely. The prevailing wisdom is that the vaccine was going to be the answer. That might be true if we could snap our fingers and vaccinate everyone all at once, there’d be no problem here. But we can’t. And as all of you well know, vaccination has been slow, to say the least. Right now, only about four percent of the population is fully immunized, and only about 10 percent of people have had a single vaccination. We need to get about 70 percent. And at this pace, it’s going to be a while. That means we can’t just give up on basic public health, on mass testing, on masks, on hand hygiene and yes, on physical distancing, which has to include limiting risky things like dine-in restaurants. That’s like deciding not to take the rest of your antibiotic because the symptoms are starting to get better. Instead, we’ve got to finish our course. And don’t get me wrong, this is really hard. Particularly people who work in the restaurant and hospitality industry rely on their livelihoods to be able to go in and take care of customers who are eating. But that’s why we can’t get this next COVID-19 relief bill passed fast enough. If we fail to stop the virus once and for all, it would be much, much worse. Today, we’re talking to Dr. Angela Rasmussen, our resident virologist here in America Dissected. She’ll help us understand more about these variants and what they mean for how we think about the future after the break.


[ad break]


Dr. Abdul El-Sayed: Our guest today is no stranger to our podcast. She’s Dr. Angie. Rasmussen, who is our resident virologist here on America Dissected and God knows we need one! Angie, thank you so much and welcome back to the pod.


Dr. Angie Rasmussen: Oh, thanks for having me back, Abdul.


Dr. Abdul El-Sayed: So we’ve got a lot of different variants at this point. And maybe even more than just the variants themselves, is the astonishing speed with which this virus we now understand can evolve and the convergent evolution that it’s undergone. So stepping all the way back, can you just tell us what variants we’re worried about right now?


Dr. Angie Rasmussen: So there’s really three variants that people have been expressing a lot of concern about. And that’s because unlike all of the other variants that have emerged throughout the course of the pandemic and there have been many, these three—B117 first discovered in the UK, B1351 first discovered in South Africa, and P1 first discovered in Brazil—all appear to be more transmissible than the other variants that are circulating, meaning that they pose a greater risk in terms of spreading through the community. For a couple of them, for B1351 and P1, there is also some indication that they may not be as effectively neutralized by antibodies produced either by vaccines or prior infection with one of the “old variants.” So that’s why people are worried about these three variants in particular. But one thing people should keep in mind is that these didn’t just pop up overnight. They didn’t emerge more rapidly than any other variants. Variants have been emerging throughout the course of the pandemic because they really emerged any time the virus has a lot of opportunities to replicate, it’s just that these have finally emerged to the point where we are actually seeing, based on epidemiological data, that they do have an effect on transmission. So that’s why all of a sudden it seems like these are worrisome, but they’ve actually been evolving throughout the course of the pandemic.


Dr. Abdul El-Sayed: Mmm. And one of the interesting things is that we’re finding that these variants are all starting to pick up very similar evolutionary traits, very similar mutations that suggest to us that there is some sort of force pushing them in that direction. And we call that convergent evolution. Can you break that down and explain why the variants in South America and the southern tip of Africa and the UK all figured out how to change in this very specific way?


Dr. Angie Rasmussen: Yeah, absolutely. So, convergent evolution happens when evolution occurs or mutation occurs at a site in the genome that’s important and it is when that mutation gives the virus some type of advantage. So we call that positive selection or being under positive evolutionary selection. Mutation itself is a random process. Essentially what mutation is, is when the virus is copying its genome while it’s replicating, it makes a mistake sometimes and it makes that mistake at random. If that mistake doesn’t have any effect whatsoever, it won’t be selected for, it doesn’t give the virus a particular advantage. It may be acquired sort of like a fingerprint, but it doesn’t necessarily mean that it’s doing anything to make the virus more effective at virusing, which for a virus is replicating itself. Sometimes those mutations can actually be detrimental to the virus, but we don’t see those emerge because obviously, if a mutation messes up the virus’s ability to replicate, it’s not going to replicate. So then it would be under negative evolutionary selection. These mutations, the ones that they have in common, the one that all three have of these variants have in common is N501Y, which is in the spike protein. It’s the change between an arginine, uh, it codes asparagine, and that’s changed to coding a tyrosine, because proteins are essentially long strings of amino acid. So this is really just a substitution of one amino acid for another at that site. All three of these variants have acquired that mutation and it does appear that that makes the spike protein more effective at binding ACE-2, the receptor. We don’t know if this is the basis for which these are more transmissible, but it may give the virus some type of advantage in that it’s easier for it to bind the receptor. It’s therefore easier for the virus to get into a cell and infect it. That’s an example of a mutation that has an effect that you can understand I think more or less how that gives the virus an advantage in terms of being able to infect a new cell. So what we still have a lot of question marks about, though, are the other mutations that all of these variants have acquired. They do have other mutations in common. There has been reports of these mutations emerging independently of these three variants as well, suggesting that all of these different variants that are emerging independently are an example of convergent evolution, meaning that those sites are particularly important and can give the virus an advantage in terms of its ability to replicate.


Dr. Abdul El-Sayed: So it’s interesting, right, because we don’t really think about the different variants of the virus competing with each other, but they really are. And the ones that figure out how to replicate themselves better are the ones that are going to enrich in the population, outcompete all the others. And what you’re telling us is that we’ve at least identified one of these mutations as, in effect, being a gene for stickiness, that they’ve all sort of converged upon in the evolutionary process. And then it would it seems like, is that there are other advantages that we just don’t understand yet, that they’ve also sort of figured out how to take on. And it seems like that that’s going to be a really important direction for research. But one of the bigger issues here is that now we’re starting to understand just how fast this thing can evolve. And it’s set up a bit of an arms race between the vaccine and the variants. Can you talk us through how this changes the strategy and the way that we think about vaccinations moving forward?


Dr. Angie Rasmussen: Yeah, absolutely. So one thing to keep in mind about all of these variants is that it’s not necessarily because these variants are mutating more quickly, it’s because the virus is replicating a lot. There is so much transmission. SARS Coronavirus-2, is so widespread in all of these communities and all these countries where these variants have emerged, it’s entirely possible we could see some new US variants emerging as well just because there have been so many opportunities for these mutations to be acquired, for these variants to emerge in these populations. With regard to immunity, there’s a very open question right now as to whether prior immunity led to the selection of these variants. And you can imagine how if many people in the population are at least partially immune, that would select for viruses that can evade that immunity. We don’t really know if that’s the case, if that’s what’s happened. And it certainly doesn’t look like these viruses are completely impervious to prior immune responses or to vaccination-induced immune responses. But it does suggest it’s a warning call, to me anyways, that we need to do two things right now. We need to vaccinate as many people as possible as quickly as possible. And simultaneously, we need to take away opportunities for the virus to replicate, which means doubling down on our efforts to reduce transmission in the community. We will see the emergence of new variants beyond these ones if we don’t do that. And right now, it would be nice to say we could do this all with vaccination, but we just don’t have the supplies. We don’t have the capabilities to distribute vaccines to enough people. And many of my colleagues have said, you know, it’s not vaccines that are going to save us, it’s immunization that’s going to save us. It’s using those vaccines. Simply having those vaccines isn’t enough. We need to actually get those vaccines into people’s arms. Right now, we don’t have enough vaccines to actually get into all the arms that, that it needs to be into. So in addition to ramping up vaccination, we need to double down on wearing masks, on physical distancing, on avoiding gatherings, on avoiding enclosed spaces, ventilating if possible, washing hands and disinfecting high touch surfaces. We need to do all of those things. Ideally, we’d also have some policy that could support people’s ability to layer on those, those risk-reduction measures, such as being able to take paid sick leave if they don’t feel well, being able to keep their jobs if they need to quarantine, if they’ve been exposed to somebody with SARS Coronavirus-2. So we really need to think about not only vaccination and vaccinating as many as possible as quickly as possible. We also really need to think for the next couple months until we could get vaccine supplies up about reducing transmission through non-pharmaceutical interventions.


Dr. Abdul El-Sayed: So what you’re telling us is that, frankly, everybody that acquires SARS-CoV-2 is a potential for the next level of evolution to occur. And we have a responsibility to be thinking about not just how we get as many people vaccinated, but also how we can stop the virus from spreading to as many bodies as possible as we do it. Because one of the frustrations I’ve had as you know, as a tried and true public health person is that in a lot of ways we were waiting for our medicine to save us. And we’ve done this incredible medical miracle of devising a safe and effective vaccine, multiple safe and effective vaccines in under a year. But it’s like dropping a V12 engine into a Ford Pinto and the rest of the public health infrastructure that we had forgotten about and decided not to invest in, is hampering our ability to do this too. And meanwhile, it’s not like we’re now only focused on the vaccine, right? We just have the vaccine of people. We still have to do all the other basic blocking and tackling in public health that we failed to do from the very beginning. And this insight, I think is just really important for us. So, you know, there is a potential, I’m not going to say doomsday scenario but we’re pretty close to that, which is that we see the evolution of a new variant that is truly resistant to our vaccines and our acquired immunity. What in your mind is the probability of that happening and what would we do if it did?


Dr. Angie Rasmussen: That’s a really good question. And my short answer is, I don’t know, because I can’t really assign or quantify the probability of that happening. But I will say that if, you know there’s a lot of ifs involved in this calculation here. If the variants that are already here and let’s just talk about the US for now, since your podcast is America Dissected, not The World Dissected, if we’re talking about the world this, this is a much, it’s not a different conversation, but it’s a more complex conversation because there’s obviously major challenges with vaccine distribution globally. But let’s just talk about the U.S. So we know that all three of these variants are in the US. We know that they’re associated with cases not linked to travel. So that means that they’ve been spreading here in the US. If we don’t take measures to reduce transmission of those viruses, which right now policy decisions are going in the opposite direction of that—governors are saying that because transmission has been reduced in case new cases are falling, hospitalizations are down, that we can go ahead and open up indoor dining in some states, that we can open up gyms, things like that—then these variants have a very good shot at spreading again rapidly. We’re going to be right where we were a month ago in terms of new cases, cases being on the rise, hospitalizations being on the rise and deaths being on the rise. It’s going to be that much more difficult if these variants are capable, at least in part, of evading the vaccines or of evading prior immunity. So I think that that is really, I don’t know if I’d call it a doomsday scenario, but it’s a very, very bad scenario in which we would be essentially dealing with widespread transmission, potentially needing to make new boosters very rapidly for a large part of the population for months to come. So that’s why I’ve been trying to encourage people to not do what you just talked about: place all their faith in vaccines. I love vaccines. I think they’re fantastic. I think vaccination is one of the greatest public health triumphs of the modern era. It has saved so many lives worldwide. But, right now, it’s exactly like you said. If you put a V12 engine in a Ford Pinto, especially a Ford Pinto that has four flat tires, it’s not really going to do much. So we really need to think about other ways to stop transmission and get it lower while we upgrade these vaccines. And right now is the perfect time to be doing that, because we know that the vaccines are at least partially protective against these variants. If there’s low enough transmission and we’ve already seen other countries do this successfully, like Australia and New Zealand, they’ve been able to control the pandemic through tried and true epidemiological measures: testing, isolation, contact tracing and quarantine. That, in addition to vaccination, could really get us out of this in a more sustainable way a lot sooner than this cycle of more transmission, more restrictions, less transmission, less restrictions and back and forth. It’s especially important that we think about that now, given that we know that these variants are already here.


Dr. Abdul El-Sayed: Yeah, I mean, like when we drop the V12 into the Ford Pinto that’s been driving for 150,000 miles straight, right? And I agree with you entirely that we need a public health-driven strategy. I want to step back from here, right? Because at the same time that we’re staring down the potential for that really awful scenario, cases are dropping. And I’ll be honest with you, like there’s very little that I can point to that necessarily explains that, right? Is probably some combination of people following basic public health protocols and wearing masks and deciding not to break their physical distancing protocols. And, you know, both acquired immunity and vaccine-meted immunity, but there’s not a silver bullet here. How do you make sense of this consistent dropping in cases? And what do you think we need to do to keep it going in the face of these variants?


Dr. Angie Rasmussen: Well, I think it’s, and I’m not an epidemiologist so I’m just going to preface what I say by saying that this is not an expert epidemiological analysis of this, but just looking at timing, it seems that this may have, cases started to go down a few weeks after the holidays. It seems like any surge that occurred because of the the holiday season might explain this to a certain degree. Also because of the surge that occurred around the holidays, more restrictions were put into place in many states. People following those restrictions will allow case numbers to go down. The problem with that is that governors of many of these states, Governor Cuomo in New York, for example doesn’t seem to realize that when you still have a really high background of tons and tons of people with SARS coronavirus, even though fewer people are getting it every day, there’s still a bunch of people who have it and it’s still out there. It’s not that it’s completely just gone away just because it’s going down. You open indoor dining, if you open gyms, if you open non-essential businesses and lift those restrictions, then you will probably see an increase in cases, especially now that it’s wintertime and it’s more difficult in many states for people to gather outdoors in a safer environment. So that would be my guess. But for a truly expert opinion, I’d suggest asking an epidemiologist.


Dr. Abdul El-Sayed: Hmm. You know, this is a moment where we’re sort of caught a bit in limbo and people are trying to figure out what their lives are going to look like. And, of course, all of us going into the New Year had a lot of faith in a lot of hope in the vaccines. And we still should, right? Everybody should get vaccinated the moment that their number is called. But at the same time, right, there is this sort of question of, well, when do we get there? What, as a virologist, are you looking for in terms of thinking about how to plan your long term, and what kind of thing in this set of variants or in a new set of variants are you looking for to really change the way that you think about how we manage this?


Dr. Angie Rasmussen: In terms of how we manage this, I mean, I’m going to be looking to see if it’s going to take a complete reversal of the declines in cases for, for governors to implement policies that will allow people to not be in danger. And I’m not a policy person either. I’m just a scientist, an academic scientist. But it does seem to me that it’s very difficult to ask people to not go to work or to stay home if they have to put food on the table, if they have to pay their rent or their mortgage, if they can’t even call in sick from work. So I’m really going to be looking for government to make policies that enable people, and more than just a $1,400 check that will enable people to take the precautions that need to be taken until we can get vaccines more widespread and more accepted. I’m also going to be looking very carefully once we do have vaccine supplies at how many people are willing to actually take those vaccines. Right now, it appears that there’s just huge demand for the vaccines because the supplies are so limited that the demand greatly outstrips the supply. In a few months when anybody can get a vaccine when they want one, I’m going to be very interested to see how many people actually do, how large the proportion of people are who are just going to wait and see or maybe won’t want to get a vaccine at all. And I think some of that will depend on how we are talking about this right now. I’m very concerned that all the discussion of like, no worries we have vaccines now, is going to make people more hesitant to take those vaccines because of a perception that the vaccines don’t work if we have another surge. And if we have another surge, it’s not going to be because the vaccines didn’t work. It’s going to be because we had crappy policy overall that forced people to go out and engage in higher risk behavior that’s not avoidable. It’s not a choice of going to work or not for most people. If we are not able to implement maximum exposure risk reduction for maximum people, we will potentially see another surge. And I’m very worried that people are going to say: well, look, the vaccines aren’t doing anything, and now I just heard this news from South Africa that it looks like the vaccines are less effective anyway, so why should I even bother? I’m very concerned about that happening because the really bad thing about this whole situation is that right now, if we all take as many measures as we can to reduce our own exposure risk, to reduce transmission, we’re only going to be doing this for a few more months because then we will have enough vaccines. We will simultaneously get transmission down to a level that it’s manageable. We could open up sooner and in a more sustainable way. If people do not do that, if they’re like: OK, cases are in decline, I’m going to get a vaccine eventually maybe but at least all, all the high risk people will be protected. Then people are going to go right back out. We might see cases go back up and we’re going to be caught in this horrible cycle that we’ve been living in for the last year, you know, year plus. And I think people are really going to lose hope more than they already have. So I keep trying to tell people, to ask people, you know, just to hang in there a little bit longer, because once we get vaccine supplies to the point that everybody can get vaccinated, if we can simultaneously build confidence in vaccines and get transmission down, then that’s going to lead to a sustainable way out of this for all of us. It’s just, you know, we’re all tired. And I think it’s really hard to ask people to just keep on truckin for a little bit longer because it feels like we’ve been doing this forever, unfortunately.


Dr. Abdul El-Sayed: It does. This is the hard part, right? It’s almost like we’ve set up this yo yo between vaccines and the rest of public health, right? And so you’ve got the situation where if cases continue to rise, it may dissuade people, like you said, from getting vaccinated because it creates this perception that the vaccines don’t work. And at the same time, right, I think people are overinvested in the vaccine as if the rest of everything else we were doing doesn’t really matter anymore because, because we have a safe and effective vaccine. And it’s really the combination of these two things that matters most and the point that you make about, about governors, right, and our failure to finally, you know, it’s like the bad guy in one of those horror movies, right, like there’s a moment where the protagonist of the movie almost has a chance to kill the bad guy. Right? But then they let up just, just soon enough. And we’ve done this multiple times now, right? We open up way too early and we think that we’re done with the virus and then, and then there it comes again. We really appreciate you making time to share with us your knowledge and your wisdom and your perspective on what we need to do with public policy. You want to take us out of note of hope if you have one?


Dr. Angie Rasmussen: Yeah, I do have one. And it’s what I kind of hold on to every day because, you know, during the pandemic, time is a flat circle and it feels like January 2020 was yesterday. And it also feels like it was a 1,000 years ago. And I, too, am sick of this. I’m tired of being inside my house like nonstop. I’m tired of, not that I’m tired of my husband, but I’m tired of having him be the only person that I see every day. I’m tired of not being able to go out to dinner and see my friends and see my family and see all the people that I love and have the normal interactions that, that humans like to have with each other. And where I get hope—I realize this is a way downer way to set up a message of hope—but I just think to myself that if we can just tough it out a little bit longer, I try to think of it like running a marathon, even though that’s something I’ve never actually accomplished. I’ve run a 5K at least, and the last part of that is always the hardest. But if you can get that, like last burst of energy to get across the finish line, you’re going to get there. And I think that that’s kind of where we’re at right now. If we can just muster that last bit of energy, if we can do that just for a little bit longer, we have incredible vaccines that have exceeded our expectations. All of them have. Whether it’s Pfizer or Moderna, whether it’s Johnson and Johnson which is overall slightly less efficacious but is efficacious where it counts and has only one dose. We have multiple options that are all performing well above what we expected them to. If we can just stick this out for a couple more months and all get vaccinated, we can be done with this by summer. We can go back to living normal lives. We could go back to eating out in restaurants, seeing our parents and hugging our friends and our family. We just have to stick it out a little bit longer. So my message is one of hope. I want this to end as much as you do. Just tough it out and we’re going to get there.


Dr. Abdul El-Sayed: Inshallah. Really, really appreciate you taking the time as always, Angie. That was Dr. Angie Rasmussen, who is a virologist and a leading voice in helping us to understand what these variants mean vis-a-vis the vaccines and the future. Thank you again.


Dr. Angie Rasmussen: Thank you so much, Abdul. It’s always wonderful to be here.


Dr. Abdul El-Sayed: As usual, here’s what I’m watching right now. The Biden administration announced plans to ship vaccines directly to a network of health centers that provide primary health care in low income communities across the country to address disparities in vaccine access. But even the data we’re using to understand disparities is incomplete. Nearly 48 percent of data collected lacks any information about race or ethnicity. And as they say in management, you can’t manage what you can’t measure. If we’re serious about equity, we’ve got to be serious about equity. So I applaud the administration’s efforts to address inequities and hope we can do a better job moving forward in understanding the disparities we’re observing so we can keep innovating approaches to take them on. That’s it for our show this week. Next week, we’ll talk to John Barry, author of The Great Influenza, about the last global pandemic of this magnitude and about what he predicts about how this all ends. And don’t forget to pick up your America Dissected swag now. Our Science Always Wins hat are sold out, but we still got a few more of our sweatshirts and t-shirts. They’re going quick, so make sure to grab one before they’re gone. Oh, and I hope I get to see you all at my new substack newsletter: The Incision. Subscribe today and tell your friends.


Dr. Abdul El-Sayed: America dissected is a product of Crooked Media. Our producer is Austin Fisher. Veronica Simonetti mixes and masters the show. Production support from Tara Terpstra, Lyra Smith and Alison Falzetta. The theme song is by Taka Yasazawa and Alex Sigiura. Our executive producers are Sandy Girard, Sarah Geismer and me, Dr. Abdul El-Sayed, your host. Thanks for listening.