Q&A: COVID Variant Tests? ‘We’re Kind of Flying Blind’


Kevin Kavanagh, MD: “Throughout the history of evolution, and even through the history of mankind, you’ve seen species get wiped out. You’ve seen civilizations of man fall because of infections. And the thing that differentiates us from a tadpole is our science and our knowledge. And if we don’t take advantage of that….”

We have more than a fighting chance of getting back our normal lives, as far as Kevin Kavanagh, MD, can tell. Kavanagh, a member of Infection Control Today®’s Editorial Advisory Board, points out that the 3 different strains of coronavirus disease 2019 (COVID-19)—the variants that everybody’s keeping a wary eye on—have 3 different lineages that have developed the same mutation to dodge immunity and vaccines. “It may have plateaued in its mutation rate,” Kavanagh tells ICT®. However, Kavanagh has been a clear-eyed realist throughout this pandemic, often spotting and publicizing problems weeks before the Centers for Disease Control and Prevention or the World Health Organization. What worries him now is that not enough people seem willing to be vaccinated, and what really concerns him is the number of health care professionals who feel that way. Also, the appearance of the variants requires testing abilities that we do not at the moment possess. “In the United States, we do not have good genomic testing,” says Kavanagh. “They’re just starting to gear that up. That should have been geared up over a year ago so we could test for these variants. You want to test at least 5% to 10% of all positive cases so you can test for different strains and how this virus mutates. Right now, we’re kind of flying blind.”

Infection Control Today®: Last year when most health care experts and the media were saying that the SARS-CoV-2 virus probably wouldn’t mutate, you were one of the few experts to say that you hadn’t seen enough data to make a determination about that. In fact Doctor Kavanagh … well, I’ll let you tell it, Doctor Kavanagh. What did you say last year before anybody else said it?

Kevin Kavanagh, MD: Well, it was quite obvious that this was an RNA virus, and it was mutating. Even the initial strain, which we had in the United States, quickly mutated into a more infectious strain, which was the D614G strain. And although the narrative at that time was it wasn’t really more infectious, now people are saying that yes, it was more infectious. And that was a significant mutation. And if you looked at the website called nextstrain.org, you can see all of the mutations that the virus was undergoing. And they track those over time and over distance. Now, the vast majority, or almost all of these mutations, are inconsequential. The mutation has to involve the spike protein area to have a maximum effect on the vaccines or our immunity. But those certainly could occur during that time. And as the virus spread within our population and throughout the world, more and more people became a laboratory for causing viral mutations to occur. And finally, and unfortunately, we’ve had now a number of mutations. First, the UK strain, which is the B.1.1.7, which is more infectious and may be slightly more lethal than our current strain. But even more worrisome is a set of mutations which have occurred in Brazil, in South Africa. It also has been noticed in the United Kingdom, and also in a patient up in Boston, Massachusetts. All having similar mutations and escape mechanisms, which may make these vaccines less effective.

ICT®: When you say less effective, what do you what do you mean exactly?

Kavanagh: Well, you have to realize that the vaccine is targeted to making antibodies to the spike protein of the virus. And that’s the same region that our body makes its immunity to. Our effective antibodies to kill the virus. And the spike protein is also the key to our antigen, and our PCR testing. So, if the virus mutates in such a way that that spike protein is changed, then that can affect the vaccine’s ability to kill that virus, along with affecting our ability to detect it. You may have false negatives now coming about from some of these variants. And we will not know that the patient actually has COVID-19 by a laboratory test. Because the new laboratory tests, which will be adapted to that virus similar to the vaccines, I’m sure are under development, but they’re not out yet. When a vaccine is to the original virus, it makes a whole plethora of

Kevin Kavanagh, MD

Kevin Kavanagh, MD

antibodies, all sorts of different types. And the majority of those will not be able to effectively kill this new variant, but some will. For example, with the Moderna vaccine, it is felt that it will lose probably five-sixths of its effectiveness. In other words, it will fall six-fold in effectiveness, which is a lot. But those vaccines are so highly efficacious, that they feel that it will still give patients protection. And so that’s important. And it will especially give you protection for severe disease such as would require hospitalization, or ventilation, or death. And so that is a big plus. But it does not look like either the Pfizer/BioNTech or the Moderna vaccines will give protection that will prevent mild to moderate diseases. Now AstraZeneca in Oxford because of these new, more severe mutations, have put their vaccine on hold. I assume they’re retooling and Pfizer/BioNTech and Moderna are making a booster now. So, when I look back and thinking what it would take to get out of this pandemic, at one point it was getting one shot to get a vaccine, then in order for the vaccines to be effective, you needed two shots. Now it looks like the majority of people are going to get two shots, plus a booster. And the biggest worry is this virus mutating faster than what you can make vaccines and boosters to. And of course, that’s on a lot of people’s minds. And I would like to give a little bit of encouragement in that all of these latest escape mechanisms—in other words from Brazil, South Africa, from the UK, and we’re not talking about the UK variant in the United States, but this is now a further mutation of that variant that’s only found in Great Britain, and also, it’s been detected in a patient in Boston, Massachusetts—all of these variants have a similar type of mutation. And because these mutations occur randomly, and they’re all a similar escape key. Maybe this is the last type of mutation that virus can easily do to avoid the vaccines. It may have plateaued in its mutation rate. And I really do hope that this will be a plateau in the mutations. And it also means that it may be possible to get a single booster that will effectively give you immunity to all of these different variants. And so that’s on the good news. The bad news is you’re going to, in my case, have to have three shots, and I don’t like shots.

ICT®: Says the doctor.

Kavanagh: Yes. I don’t I don't like them. My grandkids don’t like them. They didn’t like the idea of getting one vaccination. Now, if they have to get three, they will not like that at all.

ICT®: Well, this has actually given me some uplift because you’ve been such a clear-eyed realist throughout this pandemic. You’ve been calling things months before the Centers for Disease Control and Prevention and the World Health Organization have called things. But now you’re spotting a ray of sunshine. You’re saying that we can get out of this pandemic because the mutations so far that you’ve seen and everybody’s seen, can be handled by the vaccines at least to some extent.

Kavanagh: Well, and that’s correct. But we do need to encourage people to get vaccinated. One of the problems is, is that about a third of the health care workers don’t want to get vaccinated. In Kentucky, we had a report that over 50% of the nursing home workers did not want to get vaccinated. And at this point, that probably isn’t a good decision. You cannot mandate vaccinations at this point, because it hasn’t undergone a formal FDA approval process. It’s just has an emergency use authorization (EUA). But data are coming in. And the longer we go, the more and more data we have. And these vaccines appear to be very safe. Several months ago when we only two months of data, you were a little bit more hesitant giving that type of advisement, as we are now when you have five or six months’ worth of data. Certainly, at this point, people should be getting a vaccine. And here’s the thing, throughout the history of evolution, and even through the history of mankind, you’ve seen species get wiped out. You’ve seen civilizations of man fall because of infections. And the thing that differentiates us from a tadpole is our science and our knowledge. And if we don’t take advantage of that, then as a species or a society, we’re going to be in the same situation as a tadpole, when these infectious diseases are raging. And so, we need to follow public health advice. And we also need to get vaccinated. Both of these are needed, because they’re all layers of armor, and none of them will be 100% effective.

ICT®: You’re retired now. For how long did you practice medicine?

Kavanagh: Almost 30 years.

ICT®: So, it blows my mind a little bit that health care professionals are hesitant to get vaccinated. Now, you know the health care world. You were a practicing physician for almost 30 years. You had ties to hospitals, and I know that you lecture and talk about medicine. Does it shock you that health care professionals are not standing in line to get get vaccinated?

Kavanagh: Well, it really does. And in some places that is the case, especially in some of the smaller rural areas. But you have to remember this pandemic, and along with science, has been both discredited and very much politicized in social media and in certain circles whereby people are almost brainwashed when it comes to trying to talk to them about this pandemic or about the vaccines. Another big fallacy is that people feel that these vaccines were rushed to market. That they were developed in under a year. Well, that’s not the case. They’ve been working on these vaccines for a coronavirus for almost a decade now. We had MERS [Middle East Respiratory Syndrome], we had SARS [severe acute respiratory syndrome]. This was a known risk. And of course, that led to conspiracy theories that this was made in a lab and was purposefully released because people were doing research. But they were doing the research because it was evident and predicted that this coronavirus would be one of the most likely candidates to cause a very severe pandemic. And so, because of that you had vaccines that were already made, such as those of Madonna and Pfizer/BioNTech. They already had the types of technologies and machines ready to go to make vaccines to particular coronaviruses. And when this coronavirus came along, they received the genetic sequence of the spike protein, they could put it into their machine and essentially print out a vaccine. These vaccines by these initial companies are totally man-made. And that has a big advantage on speed. The disadvantage is, of course, they’re not all that stable and have to be stored in ultra-cold storage. And that makes it problematic on getting them out to the masses. But it does get you a vaccine out there quite quickly for these types of variants. It’s almost like the flu. We get a flu shot every year and no one says, “I’m not going to get this flu shot because they’ve only been developing it for a year.” No, they’ve come out with it every year. And with the companies working on vaccines for coronaviruses, it’s the same thing. They just switched the type of coronavirus they were making it for and that will be the same thing for the booster. They’ll get that out quite quickly. But nevertheless, quite quickly means a couple of months and revaccinating the entire United States is not an easy task. Wearing masks is of utmost importance, as is social distancing and obeying public health advice. I just can’t stress that enough.

ICT®: As we talk at the moment, the latest figures I’ve seen seem to suggest that the holiday surge is that last subsiding. Hospitalizations are going down. Do you see the possibility of another surge? And I guess you do, if we don’t vaccinate faster than the new variant spreads, right?

Kavanagh: Well, that’s correct, because if the UK variant is actually more infectious, and more lethal, and we do not have a large portion of our population vaccinated, we could get another surge. Especially with the pictures I’ve seen on the Super Bowl spreader events. It can be quite distressing. I mean, the surge that we went through was from Christmas and New Years. And we may get this again because of the Super Bowl parties, which involves shouting, alcohol, eating and people intermingling in bars, restaurants, and even with home parties. We’re at risk for another surge. And unfortunately, the Brazilian and South African variants along with a new variant in the UK, those viruses, they can cause reinfections because they evade the body’s immunity. And we may not even know they’re spreading because they may also possibly cause false negatives on your tests. In the United States, we do not have good genomic testing. They’re just starting to gear that up. That should have been geared up over a year ago so we could test for these variants. You want to test at least 5% to 10% of all positive cases so you can test for different strains and how this virus mutates. Right now, we’re kind of flying blind. If the Brazilian and South African variant—we’ve had a few cases in the United States—and if it is spreading, that can be very problematic because we cannot detect right now, with any degree of accuracy, how fast those variants are spreading. Hopefully, they won’t be. The UK variant, if it spreads very fast and people are following public health advice, maybe those other variants won’t spread as much. But they certainly can be problematic. And they’ll cause reinfections. That’s been reported out of Brazil, out of South Africa. And that is of utmost concern right now.

ICT®: We always circle back to what infection preventionists should do in situations. And you’ve always said basically that they should educate, educate, educate. And I imagine you’re saying they should educate their fellow health care professionals at the moment, right?

Kavanagh: Well, yes. Because right now, it’s hard to educate the public when they’ll say, “But a third of the people at your hospital isn’t getting vaccinated.” You need to get the hospital workers vaccinated first. I think there’s no question about that. And they not only need to be offered the vaccine, but they should be setting an example for the community. Because regardless of the risks of the vaccine, the risk of the virus is so much many fold higher than what the vaccines are. I mean, we have given out tens of millions of doses at this point in the United States. And there are maybe one or two possible cases which are related in time as far as having a fatality that is associated with the vaccine. And when you talk about one or two cases out of tens of millions of vaccinations, that’s an extremely low number. So low that they might have occurred anyway. In other words. it may be totally unrelated. And that’s what I suspect is happening. I would not at this point be very concerned about the problems with the vaccine, as I would be much more concerned about the problems with getting COVID-19. Especially as these new variants are more infectious. And one of the final things that infection preventionists should be stressing is that all the advisements we’ve been giving with the initial strain, need to be upped for the new strains. We’re not sure why they’re more infectious: If they can aerosolize more, if the patient is spreading more viruses into the environment, if they survive in the environment longer. It’s almost like going back to base one. We need to be very, very cautious. We need to up the cleaning, the environmental sanitization. We need to be very careful regarding airflow air exchanges, air sanitization. And whenever possible, we need to be wearing N95 masks and goggles. This needs to be stressed in hospitals in high-risk settings. For the public, until this is sorted out, I would suggest relying on either takeout or curbside pickup or delivery as far as getting your food and your staples. That is very important to be doing. Try to wear a well fitted mask so it’s not leaking air around the sides and make sure that it is double layer. If it is surgical grade, that’s good. Three or more layers, even better. If it’s a cloth mask…. Of course, cloth masks aren’t as good as surgical masks. A surgical mask would be preferable. And if you can get an N95. Preferably, please get that and wear that if you’re going into a high-risk setting. As far as double-masking, my beliefs are if you have a very well fitted mask on as your initial mask, double-masking may provide you with additional protection. But if that first mask isn’t well fitted, and you’re leaking air around the sides and you put on an obstruction on the front end, you’re just going to leak more air around the sides. It might make things worse. I would be careful about double-masking. I would more stress getting that first mask well fitted and making sure it’s of high grade. It’s not under your nose, you’re not leaking air around the sides. You want to have multiple layers if it’s a cloth mask. If you can get a surgical mask that will get you more protection, and an N95; better. That’s just partial protection. It’ll make things safer, not totally safe. You’d have to wear goggles, gowns, everything else to be even safer than what a mask will give you. You can still get the virus, which is why you should socially distance plus wear a mask. Not one or the other.

ICT®: Is it possible that hospitals will mandate that their employees get vaccinated against COVID-19?

Kavanagh: Well, probably not. I hate to say that, at this point, because the vaccine has not been approved by the FDA. It’s just been authorized in the EUA. As more data gets in, then that may happen. And certainly, I think in a setting, let’s say, a nursing home, if you have a mother that’s 90 years old, and she’s in a nursing home, you would want to have her taken care of by people who were vaccinated. I think that at some point, it may come to that especially if we need to get about 85% of this population immune in order to get herd immunity. That’s going to be hard to achieve without strong encouragement for people to get vaccinated. We will probably need 70% to 75% of the people vaccinated with added to that then those that have natural immunity to come up with anything close to 85%. And we’re going to have to maintain that because as I said before, this virus is in reservoirs and people around the world. And unfortunately, it also resides in our animals. We’re always probably going to have to get a yearly shot, or bi-yearly shot or a shot every other year, in order to maintain our immunity to this virus.

ICT®: We might need many more infection preventionists to pull this off and hopefully some of the people out there watching this and watching the pandemic unfold, will think about infection preventionist as a career. I know APIC [Association for Professionals in Infection Control and Epidemiology] is trying to push that as a career path in colleges and universities.

Kavanagh: Oh, yes, definitely. And I mean, let’s face it. Two years ago, infectious disease and public health was kind of on the back burner. Especially public health. Epidemiology was like: “What? Why are you going into that?” They were being cut. Health departments were down 50% over a decade with their funding. It was a disaster. And now it’s at the pinnacle of importance. Everybody can see how, without a well-functioning, well-funded and staffed health department, we’re not going to be able to be competitive in the world. Because you cannot go through life by always closing down businesses, by isolating and shutting down your economy. That’s not compatible with life. What we need to do is we need to do what was done in South Korea, Taiwan, New Zealand, Australia. To have a robust health department that intervenes, the public follows the advice and interventions. And those countries are largely back to normal right now, as we’re still in the midst of this pandemic. And even though many states have not shut down their economy, the virus has done it for them. The virus is really what will decide if the economy opens or closes, and to control the spread of viruses and other dangerous pathogens, we need to have a robust public health care system.

This interview has been edited for length and clarity.

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