Uh-Omicron | Crooked Media
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December 07, 2021
America Dissected

In This Episode

Omicron has now made landfall in the US. We are learning more about the variant every day—good, bad, and ugly. We turn to Dr. Angie Rasmussen, America Dissected’s resident virologist to get into the nitty-gritty and help us understand what it means for us and the future of the pandemic.






Dr. Abdul El-Sayed: The Omicron variant’s now been detected in at least 17 states and counting. In response, the Biden administration rolled out a new strategy to contain the variant. The Supreme Court heard arguments in a Mississippi abortion ban case that could spell the end of Roe v. Wade and abortion access in this country. This is America Dissected. I’m your host, Dr. Abdul El-Sayed. Buckle up. It was only a matter of time until this happened:


[news clip] Tonight, the variant spreading across the globe. Confirmed now in at least 28 countries. Eight more in the past 24 hours. Of course, now including the U.S. as well.


[voice clip] Mayor London Breed stood with leaders of San Francisco’s pandemic response to formally confirm the first U.S. case of COVID linked to the Omicron variant.


Dr. Abdul El-Sayed: After all, with a variant as transmissible as early evidence suggests Omicron may be, it was bound to hit our shores. And yet, even as Omicron made landfall, there remain a number of unanswered questions about the threat it poses and what comes next. Though evidence has demonstrated that Omicron may be twice more transmissible than Delta, what does it mean for our ability to prevent transmission via masks and social distancing? We also don’t yet know the answer to the question on everybody’s mind: what is Omicron vaccine escape capability—or, in other words, its ability to render our vaccines less effective? The first cases of Omicron in the U.S., after all, were among fully-vaccinated individuals, though neither were boosted. And then there’s the question of severity. Here’s one of the South African doctors who first treated Omicron cases:.


[clip of South African doctor] The cases that we have seen last week and the week before last week was mild cases. So we are looking for the severe cases, because the severe cases is what’s going to say we are in trouble. I presume that might come later. But not now. Now it’s mild symptoms, easily treated at home.


Dr. Abdul El-Sayed: And yet with only a handful of cases, most of whom are young, it’s unclear whether or not the early perception of lock of severity was a function of the people who are infected or rather Omicron is actually less severe. Meanwhile, the Biden administration has announced a new plan to contain the variant.


[clip of President Biden] Today, I’m back to announce our action plan to battle COVID-19 this winter. And it doesn’t include shutdowns or lockdowns, but widespread vaccinations and boosters, and testing a lot more.


Dr. Abdul El-Sayed: The plan includes a requirement of a negative PCR test within 24 hours of an international flight inbound in the United States, an extension of the mask requirement for domestic airline travel until March, and a requirement that insurance companies fully reimburse for at-home tests. They’re establishing family vaccination clinics to address some of the barriers to vaccinating for working people and their children, and they’re stepping up the COVID-19 strike teams to support states where cases and hospitalizations may surge. We’ll talk more about this in a bit but first, I wanted to dig deeper into the nature of Omicron itself. We’ve heard a lot about the virus’s 50 mutations, most of which sit on its spike protein, its docking station to the body. But we know less about what they are and what they mean for the three key questions we’re asking about Omicron: transmissibility, vaccine escape and severity. And what does the virus’s nature mean for public health efforts to contain it? So I invited our resident virologist here at America Dissected, Dr. Angela Rasmussen, to share the latest on the science of Omicron. More with virologist Dr. Angie Rasmussen after the break.


[ad break]


Dr. Angie Rasmussen: OK, we’re good.


Dr. Abdul El-Sayed: All right. This is, of course, a guest who needs no introduction, but you know, as is usual, can you introduce yourself for the tape?


Dr. Angie Rasmussen: Absolutely. I’m Angela Rasmussen or Angie. I’m a virologist at the Vaccine and Infectious Disease Organization, it’s a Vaccine Research Institute at the University of Saskatchewan. I’m also an adjunct professor in the Department of Biochemistry, Microbiology, and Immunology here at the University of Saskatchewan. And finally, I’m an affiliate of the Georgetown Center for Global Health Science and Security.


Dr. Abdul El-Sayed, narrating: By now, all of you should know Dr. Angie Rasmussen. She’s making her record fourth appearance on our show. She’s a virologist at the Vaccine and Infectious Diseases Organization at the University of Saskatchewan. Last time we had her on, she helped us break down the Delta variant, so I wanted to have her back to help us understand Omicron.


Dr. Abdul El-Sayed: Why did Omicron raise scientists worries, right, as soon as it was discovered? What was it about Omicron in particular that makes it so concerning?


Dr. Angie Rasmussen: So it’s really two things. Omicron was first detected in South Africa, where they have the world’s best genomic surveillance systems, and they also have really fantastic epidemiologists. And from that data, we found out two things. We found out that Omicron had rapidly replaced Delta, specifically in one province in the larger Johannesburg area, in Gauteng province. And also, we found from looking at the sequence that Omicron has a number of mutations. It has more mutations, as the media has been talking about, than any of the other four variants of concern. The number of mutations itself is not the problem, it’s what some of those mutations are. Basically, Omicron has some of the mutations that have been associated with increased transmissibility in Alpha and Delta, and it has a number of the mutations that have been associated with increased escape from neutralizing antibodies that were seen in Beta and Gamma. And it has an additional 9 or 10 or so mutations that are predicted to also confer some level of immune evasion because they are located within the N-terminal domain and the receptor binding domain of the spike protein. Those are both parts of the spike protein that are thought to be really important for antibodies to bind the spike protein and neutralize it, or render the virus noninfectious. So basically, what that means is that we could be looking at a variant that has the increased transmissibility of Alpha or Delta. And we all have seen what’s happened with more transmissible variants as each of those variants essentially took over, along with the immune evasive capacity of Beta and Gamma, which means that potentially there would be more breakthrough infections and the vaccines may not be as protective against severe disease. Now, we don’t know that for sure yet, and these are some of the many uncertainties that I think we’re probably going to be talking about. So I’ll just stop there for the moment, but it’s really those two things that made everybody say, Whoa, hold up, this, this could actually be a problem.


Dr. Abdul El-Sayed: So what you’re describing is a lot of theory about the way that Omicron is going to behave in the population as a function of what we understand about the accumulation of a set of mutations at really, really important proteins. As we learn more, I want to sort of dig in to each of those aspects, right, because it’s really these three pieces that we’re talking about: the transmissibility, the immune escape, and the severity. What is it going to mean for us to actually learn more about its transmissibility? There’s a lot of really good circumstantial evidence: the speed with which it enriched itself in South Africa, the speed with which it’s spreading across the world. When are we going to have really firm evidence regarding the transmissibility of this particular variant? What’s that going to look like and what’s it going to mean for everyday folk?


Dr. Angie Rasmussen: Well, I mean, I think we’re continuing to gather that data. Certainly, we’re getting it from South Africa as more and more cases are identified. You can understand how the spread of a given variant will compare to other variants that have previously spread there. And again, it’s pretty concerning. There’s a graph that shows the trajectory of all of the different waves in South Africa. There have been three, one of which was caused by the Beta variant, which previously was thought to be the most immune-evasive, and basically Omicron is way out in front of all of those. Cases are increasing very, very rapidly, much more quickly after the variant was detected than occurred, for example, with Beta or with Delta. So that in itself is concerning but for me, I think what we’re going to be really closely watching is what’s going to happen in communities where there’s already large Delta surges occurring now. Because there wasn’t a ton, they weren’t having a surge when Omicron displaced Delta in South Africa. So there wasn’t a ton of active Delta cases going on. In Europe right now, there is a huge Delta surge and in some parts of the U.S., including, I believe, in Michigan where you are, Delta is taking off again. So when we see Omicron cases popping up in these communities—and we’ve already seen evidence that there’s community transmission potentially in the U.S., there’s community transmission in multiple countries in Europe—if we see Omicron really start to displace Delta in the face of a large Delta surge, that’s going to be a real problem. That suggests that Omicron really is the real deal. Delta so far has pretty much out-competed everything that’s emerged against it, to the point where I’ve been asked in some interviews about this or that variant, and I’m like, Well, that’s still Delta, it’s the Delta sublineage. So Delta is really dominant everywhere. If Omicron can outcompete Delta in the population in the face of an already-existing large body of Delta cases, that really is going to suggest that Omicron has advantages over Delta and is more transmissible.


Dr. Abdul El-Sayed: So what’s happened sort of is that it had a relatively open lane in South Africa, but as it makes landfall in Europe and in the United States, it’s going to have to run head to head with Delta. And if it can outcompete Delta, that’s going to give us a real head-to-head analysis of exactly how transmissible this is relative to what has been by far the most transmissible variant that we’ve engaged with. I want to ask you about immune escape, right? And just to be clear, what terms for listeners, right, we’re talking about really two kinds of immune escape. One is escape from the immunity that you get from having had COVID, which is acquired immunity. And the other is escape from the immunity that you get from having gotten vaccinated, which is vaccine escape. And you know, it is concerning that the first two cases that were diagnosed here in the United States were both among fully-vaccinated individuals. How are we, what are we looking at when we think about the specifically the vaccine escape? What is gold standard evidence that you’re watching and that folks ought to be paying attention to, to really get the signal from the noise?


Dr. Angie Rasmussen: Well, I think, you know, in some ways, vaccine escape in this case and escape from an infection-acquired immunity isn’t really that different because you, in many cases, you’re going to be making neutralizing antibodies to the same parts of the spike protein that are in question here. The reason why vaccine escape is a bigger deal than reinfection after an infection is that we know that vaccines reliably induce these protective immune responses, whereas the response to an infection is going to be a lot more variable. Some people will mount responses that are similar to a vaccine, some people will not. And so that, I think, gets really confusing for people because they think, Well, I’ve already been infected, I don’t need to be vaccinated. The reason that you do is because you may be on the lower end of that spectrum in terms of your response. But either way, escaping that type of immunity—and there are many parts of your immune system, and the part that we’re talking about specifically here is the neutralizing antibodies. These are proteins that are made by your B cells, and their job basically is to float around in your bloodstream or in your mucosa—that’s the part that lines your nose—and binds to viruses, bind to a specific part of a virus. If that changes, then they won’t be able to bind to that anymore. And a virus, especially if it’s a very fit virus that can replicate very easily and that can cause an infection very easily, isn’t stopped by those antibodies, it can get past that barrier and establish a breakthrough infection. Now we know that Delta that can already do this and actually breakthrough infections are not unusual. No vaccine is 100% effective. There always will be breakthrough cases, but there’s two issues really at hand. One is preventing breakthrough cases to stop their impact on community transmission. And two is, will the vaccines hold up against severe illness? Now, so far, what we’ve seen for the second question is that it does appear that the vaccines are remaining very, very effective in terms of preventing severe illness and hospitalization. The other issue, though, is in terms of transmission. Now, over the summer, people were very, I think, worried when the news came out that people could be infected with Delta and shed the same amount of virus as people who are not vaccinated, and that at least in a couple of cases, there had been reports of vaccinated people transmitting Delta to each other. And that has happened, but again, in most of those cases, the vast majority of those cases, people don’t go on to develop severe disease. Now it’s good to reduce cases at all as much as possible, but ultimately, if you have to get COVID, you don’t want to end up in the hospital. And this is really how we use like influenza vaccinations, for example. They’re not necessarily to completely prevent becoming infected with influenza virus, but they will keep you from getting severely ill and they may save your life. And that’s really going to be, I think, the most pressing public health question for Omicron. And finally, there may not be a reason to just say, “Oh my God, why even bother getting vaccinated in the first place” because there is a little bit of evidence that boosting can actually improve antibody neutralization. And there was some work done by a group of scientists at the Rockefeller University in New York looking at the effect of multiple spike mutations against various types of antibody repertoire. So people who had recovered, convalescent plasma, people who had been fully vaccinated, and people who had recovered from COVID and then been vaccinated—and while people who are fully vaccinated and recovered were found to have significant reductions in neutralizing antibodies to this experimental, heavily-mutated spike protein, the people who had been infected and then were vaccinated actually retained a lot of that neutralizing antibody activity. So that suggests that maybe getting another dose of immunity, essentially, from a booster shot could actually improve those neutralizing antibody responses and provide more protection against a variant like Omicron. But of course, we need to actually do the studies now to find out if this is in fact the case.


Dr. Abdul El-Sayed: We’ll be back with more with Dr. Angie Rasmussen after this break.


[ad break].


Dr. Abdul El-Sayed, narrating: We’re back with more of my conversation with Dr. Angie Rasmussen.


Dr. Abdul El-Sayed: When we had you on to talk about Delta, I thought it was really important when we talked about the potential for complete immune escape that you corrected us telling us that actually, you know, there still is SARS-CoV-2 and even though, you know, in the case of Omicron, it may be, it may render our vaccines less effective, it is extremely unlikely to render them ineffective. The analogy I always like to use for folks is if you’ve ever trained your iPhone on recognizing your face or recognizing your thumbprint, they make you put your thumbprint in a bunch of different little ways. And that’s kind of like your immune system recognizing the virus. You have to give it a couple of different looks at your thumbprint or your face before it can recognize your face or your thumbprint rather reliably. And training the immune system happens in a very similar way. The other third question that we’re starting to get rather hopeful circumstantial evidence around is severity. And is there reason to believe that Omicron is potentially less severe than Delta may have been? And what would that tell us about maybe the direction that this virus is starting to mutate toward?


Dr. Angie Rasmussen: So unfortunately, I don’t have good news about this. I don’t have bad news either, but I think it’s really premature to be concluding that Omicron is going to be milder. And if I can use this opportunity to bust a few myths that I’ve heard repeated: viruses don’t undergo selection pressure, there’s no rule that says that viruses always evolve to become less virulent. And so I think that needs to be made really clear. Endemicity doesn’t mean that a virus is less virulent. Ebola is endemic in central Africa, it has not become less virulent despite 50 years of outbreaks. So I don’t think we should expect that ever with any new variant. And furthermore, we do have some data that suggests that a lot of these cases are mild, but the interview, in particular with a scientist from South Africa who reported that was talking about a very small cohort of mostly university students who were already low risk for having severe COVID. So not only should we not assume that this virus is becoming less lethal, but we also shouldn’t try to extrapolate from groups of patients who are likely low risk anyways. I think if Omicron infects people at scale, the assumption we should make is that it’s at least as pathogenic as Delta. And you know, I think a lot of people two years into a pandemic that’s completely disrupted all of our lives say, What do you mean that SARS-coronavirus-2, isn’t that pathogenic? But it’s actually not, because the majority of people who get it don’t experience severe symptoms. There’s long COVID of course, there’s a lot of negative consequences to having SARS-coronavirus-2, but the case fatality rate overall, while it’s higher than things like seasonal flu, it’s still quite low. Fortunately, this is not even SARS classic, which had about a 10% mortality rate. But the problem is is that even in that smaller number of people who do get severe disease, this virus is so transmissible that it still means huge numbers of people dying when entire populations are infected. And so that’s why I get very worried when I hear people saying it’s mild, it’s not going to be a big deal. Even if it is mild, that doesn’t mean that we should just let it rip through the population. That still will mean thousands, potentially millions of deaths, depending on how widespread this gets. So I just want to be really clear that while we shouldn’t expect it to be more pathogenic necessarily, we shouldn’t expect it to be less pathogenic either. And really, the take-home message of all of this is get your booster if you’re eligible, which now almost everybody is—at least everybody over the age of 18. Get your booster, continue to take precautions in public spaces. You don’t want to get Delta and you don’t want to get Omicron.


Dr. Abdul El-Sayed: That is a really important point. You know, the unfortunate side effect of talking with too much hope about early, very circumstantial clinical suggestions in a very selected population of relatively young folk that Omicron could be less severe has the unintended consequence of potentially dissuading people from doing the thing that they need to do to protect themselves. And you’re right that that SARS-CoV-2 is sort of a mass effect, right? If you’re infecting millions of people and even half a percent of them get really severe illness and potentially deadly illness, that is a lot of people who ultimately die, as we’ve seen—nearly 800,000 people in our own country. One of the first things that the Biden administration did was announce this travel ban, but it was a selective travel ban for only non-citizens and listeners to the podcast know what my my opinion on this is. I want to ask because you’re actively trying to study this and so much of the flow of of material of this virus so that you can study it happens because of commercial air travel, which has nearly entirely shut down. What is your perspective on these travel bans that, you know, in a lot of ways punish South Africa for being so on the ball? What is your perspective and how is it interfered with your capacity to do science?


Dr. Angie Rasmussen: Yeah. So there are so many negative consequences to the travel bans. Before I get into talking about how it has negative consequences for me and my colleagues, I’m just going to say that we seem to have not learned anything since the beginning of this pandemic. President Trump early in 2020 imposed travel bans, selective travel bans for foreign nationals against China and against the European Union, and the US went on to lead the world in coronavirus cases for much of the last two years. These travel bans don’t work. They don’t work. Travel bans generally don’t work unless you’re imposing them before there’s any virus in your country. We already know that that’s not the case. There’s virus in Europe, there is virus in the U.S., there’s virus in Canada—and yet all of these countries—there’s virus in Israel—and yet all of these countries have imposed this travel ban against countries in southern Africa, which may not even be the countries that this variant originated in. And it really is causing huge problems both for those countries and for the rest of the world. My entire week has been spent on the phone, on Zoom meetings with people trying to figure out where we can get reagents to do research on the Omicron variants. And it’s quite clear that it’s going to be very difficult to get reagents back and forth to South Africa. Tulio de Oliveira, who is one of the leaders of genomic surveillance in South Africa, has been very outspoken on the consequences for their own country. They are running out of reagents to continue to do sequencing and cell culture experiments because those reagents are largely transported in the cargo compartments of commercial aircraft. And if there are fewer flights to South Africa, there’s going to be fewer supplies going there. And the same thing applies for vaccines for—you know, vaccines are also not just an issue of supply, they’re also an issue of providing support for the logistics of a vaccine campaign. So reaching out to people, having experts who can serve as vaccinators, having educators, having basic supplies for vaccinations such as needles and syringes, and things like that. Vaccination is not just about getting doses of vaccines, although that’s very important. So the commercial air bans have really hindered our ability to not only do research in these countries, but also to get more of their population vaccinated. And in return, that’s going to make it very difficult for us to get isolates of this virus from those countries. So me and my colleagues here in Canada, I’m sure my colleagues in the U.S. are doing the same thing—I know my colleagues in Europe are doing the same thing—are now trying to source research material basically from their own populations. And that, to me, just underscores how futile these travel bans are because we’re not dependent on South Africa to actually get an isolate of these viruses. They are already being transmitted at the community level in non-travel-associated cases within our own borders. So really, the travel bans, as you said at the beginning, I think, have no real impact other than a punitive one. They’re harmful economically, and they’re really going to slow down research worldwide.


Dr. Abdul El-Sayed: Rather than travel bans, what would you like to see in terms of a more muscular public health response to Omicron—maybe, you know, should have been the response to Delta and Beta and Alpha, and COVID before that?


Dr. Angie Rasmussen: So opposition to travel bans doesn’t mean opposition to travel restrictions. I think that vaccine passports, pre and post-flight testing, quarantine, a plane quarantine where it is warranted in the case of a positive test, having clear protocols on how to do this, making it efficient—all of those things would be much less harmful and would be much more effective at being able to track these case.


Dr. Abdul El-Sayed: As folks settle into, you know, what looks like a major extension on the pandemic, how should people be thinking about protecting themselves and their families? What should they be paying attention to as more data emerges about Omicron?


Dr. Angie Rasmussen: So I think that there’s, you know, really people don’t need to wait for new data to emerge about Omicron in the US. We are already facing huge surges for Delta. And even though these mutations might do different things in Omicron versus Delta, really, the fundamentals of reducing your risk have not changed. In fact, we do have some new tools that we could apply to make our holiday gatherings, for example, even safer. So, of course, wear masks—the same stuff we’ve been saying for ages—wear masks outside your household, physically distance, wash your hands, stay home if you’re sick, get tested when you can if you think that you’ve been exposed—all of those things are good practices. Now we are getting more access to rapid tests. And I think that that is going to be potentially a game changer. And if I can just opine for a second, I really wish that the Biden administration had gone further in their winter plan for COVID, starting with making rapid tests easily available to people just over the counter. Cut out the middle man, there’s no need for insurance reimbursement, that’s going to be a huge barrier to a lot of people. Even people with insurance aren’t going to be able to necessarily cover the upfront costs of getting those tests. I know I just spent $80 to make sure I had enough tests for our Christmas gathering in the U.S., even though I will be tested—assuming I can go to the US—prior to that trip. I think that having a group of people together, even though we’re all vaccinated, everybody’s boosted except for one child under the age of five, giving everybody a rapid test at the beginning of that is just a good way to ensure peace of mind and to make sure that our holiday gathering is just that and not a superspreader event.


Dr. Abdul El-Sayed: We really appreciate that and a lot of this clarity and perspective on how to be thinking about what evidence to pay attention to, about what it means for us personally, what it means for our public health, and really grateful for you to take your time out of what I know has been a really busy week, and really just thankful for your insights and your perspective. That was Professor Angela Rasmussen. She is a virologist, our resident virologist here at America Dissected, teaching us all about Omicron. Thank you so much.


Dr. Angie Rasmussen: Thank you so much. I appreciate you too. I’m glad to be the resident virologist.


Dr. Abdul El-Sayed, narrating: As usual, here’s what I’m watching right now. Over the next week or so, you’re going to continue to hear headlines about the Omicron variant being discovered in more parts of the United States. These headlines are going to be designed to drive views and clicks, and they’ll inevitably raise anxiety for a lot of folks. But I want you to stay calm and remember this is a virus, spreading is what it does. So as Omicron inevitably goes viral, I want you to remember that we already have the tools to protect ourselves and our families. Make sure you’re vaccinated. And by now, that means three shots for people 18 and up, and two mRNA shots for people aged five and up. Be thoughtful about what social interactions you choose to partake in: outdoor rather than indoor when you can, and masking in indoor public settings. Invest in some rapid tests and use them regularly as you engage in holiday activities. And wash your hands. These are the things that will protect us from Omicron, just like they did from Delta, Beta, Alpha and garden-variety coronavirus. From a public health containment perspective, there is a lot that needs to be done on Omicron, which is why the Biden administration’s new winter strategy is an important first step. I think it’s particularly encouraging that the administration is committed to massively increasing access to rapid testing and that they’re requiring health insurers to reimburse them. That’s great, of course, but it’s still not enough. That’s because 10% of our country is not insured in the first place. And given the inequities in COVID cases and deaths, it’s critical that these tests be made available cheaply, just as they have been across Europe. That way, we’re not just offering them to folks privileged enough to have insurance in this country, but to the people who will need them the most.


In other news, this week, the Supreme Court heard arguments in a Mississippi abortion ban case that could spell the end of Roe v. Wade and abortion access in this country overall. Though, the court is yet to rule, conservative justices showed their hand as they followed a line of questioning that suggests they could reverse the precedent set in Roe. This was Justice Sotomayor describing the potential consequences for the court should Roe fall:


[clip of Justice Sotomayor] Will this institution survive the stench that this creates in the public perception that the Constitution and its reading are just political acts?


Dr. Abdul El-Sayed, narrating: More importantly, a safe, legal abortion could be in jeopardy in 20 states in this country should the court rule against Roe. That’s it for today. On your way out, if you haven’t already rated, reviewed and shared our show, please do. And if you’re looking for a great gift for that special science loving someone, or even yourself, I hope you’ll drop by the Crooked store for some America Dissected drip. We’ve got our logo mugs and t-shirts, our Science Always Wins t-shirts, sweatshirts and dad caps, and our Safe and Effective tees.


Dr. Abdul El-Sayed: America Dissected is a product of Crooked Media. Our producer is Austin Fisher. Our associate producer is Olivia Martinez. Veronica Simonetti mixes and masters the show. Production support from Tara Terpstra, Lyra Smith, and Ari Schwartz. The theme song is by Taka Yasuzawa and Alex Sugiura. Our executive producers are Sarah Geismer, Sandy Girard, Michael Martinez, and me: Dr. Abdul El-Sayed, your host. Thanks for listening.