A&M virologist: New reason to think vaccines can beat variants
Virologist Ben Neuman was one of the world’s top experts on coronaviruses long before most of us had ever heard of them. He’s now chief virologist at Texas A&M’s Global Health Research Complex, and regularly updates us on coronavirus science.
You’re at Texas A&M. What are you seeing on campus?
Texas A&M is somewhere near the middle of what American universities are doing. You’ve got some, out on the East Coast in particular, that are testing students once a week, mandatory, and faculty once or twice a week, mandatory. That’s a really good way to figure out where the virus is and keep very close tabs on it.
A&M is in the midst of a great big testing push. We’re doing one big test at the beginning of term, and then there may be additional tests throughout term.
So there are a lot of people to go through. I’ve been helping to run some of these samples through. It’s a lot of saliva, and I’ve got to say, saliva is very unpleasant.
How reliable are those tests?
As reliable as the nasal swab — the poke-yourbrain kind of PCR.
According to published studies, they’re a lot more sensitive than the antigen detection tests like the BinaxNOW card. It takes physically a lot more virus particles to generate a positive on an antigencapture test, as opposed to a PCR test, because with the antigen-capture test, you can only work with however many particles you have right there on the card.
But a PCR test amplifies. You start out with a few particles and you build it up until you have enough that you can see it.
So if I’m taking a test, I’d rather spit than have a swab poked way up my nasal passages. But if I’m the one processing the
test...
Yeah! As far as results go, the spit test and the poke-your-brain test are equivalent.
But saliva is disgusting to process. You want to not be the guy running the de-capper. When those samples have been sitting out in the Texas sun for an hour or two, and then you open that… [Shudders.]
It’s like popping garbage bags at the dump.
How optimistic are you that this delta wave will peak soon — that the rate of spread will stop growing and then drop back off?
I’m not at all optimistic about that. But I am opti
mistic that we can control delta as well as anything else.
Here’s why, and I think it’s the key to all of this. Look at all of the Greekletter-named variants — the variants of concern, the variants of interest — plus two other variants that are seeming to spread that don’t have names yet. A very small set of mutations that is shared between them.
By my count, only six mutations are popping up in the receptor-binding domain of the spikes. That’s the part of the spike that makes contact with the cell. So that is the part where you want antibodies to bind, because an antibody will interfere with that contact.
When we see these new variants with new names, it seems like they’ve got a completely different receptor-binding things. But all of those come from the same set of mutations — those same six mutations are just popping up on different genetic backgrounds. Different branches of the family tree have come to exactly the same conclusion.
It’s kind of like Twitter, where a person has this amazing thought that everybody else has had but still puts it out there anyway. (Laughs.) Twitter for viruses, that’s what we’re dealing with.
A nice paper maybe two weeks ago looked at what’s going on not just with the spike, but also the nucleoprotein inside of the virus. The spike is the outside of the virus, the nucleoprotein is inside, and there’s a protein in the middle that isn’t changing much, so we’ll pretend it’s not there.
It turns out that in the variants, the changes on the outside of the virus seem to be making the protein a little bit creepier, a little bit better at grabbing onto cells. And in the process, they’re changing some of the parts that, if you’ve been vaccinated, your immune response recognizes. So the virus wins and wins.
But it also loses. That’s the important part here. The mutant versions of the spike that you find in alpha, beta, gamma, delta, are all much less efficiently loaded onto virus particles. So the virus runs into a logistics problem and cannot deliver enough of the stuff to the place at the time.
The change that that they discovered in this paper is that the nucleoprotein is changing in a way that dramatically increases efficiency. You might say, “All right, this is why we have problems. This is why we have delta.” But it’s actually reasonably good news.
The way I look at it, based on the current data, there are only so many ways you can change a spike and still be a competitive virus, a good-enough virus. Any additional oomph has to come from other parts of the virus — essentially, by improving various infrastructure parts that just hold the thing together, or that roll more units off the assembly line. We do see those changes.
But the vaccine is based only on the spike. In terms of how well a vaccine is going to work, it doesn’t matter whether there’s been a change to any other part of the virus as long as the spike is somewhat constrained.
And now, it looks like
the spike is splashing around in a very shallow gene pool. This makes me very happy. We have a chance to get out of this thing.
So this means the vaccines will hold up against new variants?
It’s good news for the vaccines holding up.
Of course, they don’t work very well in the bottle. They have to be in somebody’s arm. That’s the difficulty.
People are asking, “Even though I’ve been vaccinated, are we back to Square One? Is it like 2020? Should we be hermits again?” So could we run through some scenarios, and you’ll rate them for risk: red, yellow or green?
Yeah! Come on, give me some.
Eating outdoors at a restaurant: How risky is that? Red, yellow or green?
Green. There’s some risk. But not enough to make me shy away from it.
Visiting friends who are fully vaccinated?
Outdoors that’s green to yellow. Indoors that’s yellow to red. We are seeing quite a number of cases in vaccinated people where the virus does seem to get through a little bit. So we want to stay on the safe side?
Eating indoors at a restaurant?
I don’t like that at all. I mean, I love restaurants, and I love food. But taking your mask off in order to put things into your food hole really exposes the body to other things that come in through that food hole.
Sending vaccinated kids to school?
Twelve- through 18-year-olds, I guess, since they’re eligible for the vaccine? The problem there is that most kids are not vaccinated. So for the vaccinated kids it’s fine. But for the others you have whatever is the opposite of herd immunity — herd susceptibility, perhaps — particularly in the younger age groups.
So the vaccine is going to help, but there is still a lot of room for exposure in a school setting, and something needs to be done there. So that is yellow to red — even though you’ve done everything right, it’s still a problem.
Sending unvaccinated kids to school?
Oh, my gosh, why would you do that to people? And to yourself ? Just invite COVID into your house. Invite COVID over for a drink!
The problem is some kids can’t even get vaccinated: Lots are under 12, and some have medical issues.
With the little ones, you can send them with a mask to school, but are they going to wear it? I hope so.
For all our sakes, it would be much better if they did.
Going to a sporting event? The Texans have their first preseason game soon.
If you get to sit in that cushy owner’s box or something like that, where it’s just you, and the front is open: That could be okay. You should definitely push for that. (Laughs.)
But if you’re in the stands? That’s one of those situations that people are going to think is low risk. But because there are going to be so many people there, it’s probably going to be much higher risk than you would think.
And I don’t know that I’ve been to any kind of sporting game where I did not end up putting some kind of hot dog or beverage into my mouth. So I don’t know that masking would be an option.
And, frankly, under the hot Texas sun, I don’t think masking would be a pleasant option. So I’m gonna have to stay home watch on TV.
Going to a wedding or a funeral?
Those have both been superspreader events in the past. When people are dealing with extreme grief and extreme joy, they are not going to be thinking about the CDC’s guidelines. So it’s risky.
But humans need to interact at these important moments. I guess I’d be outside, like in that scene in “The Graduate.” That would be me on the outside of the wedding, banging on the window — but I’d be cheering them on.
What do we know about vaccines’ effectiveness waning?
The last set of papers that I saw — the one-year-on studies — showed that there’s a very sharp drop in the amount of antibodies and reactive white blood cells, and then it sort of levels out.
That news is more positive than I expected. Like so many others, when I first saw that initial drop, I just completed that little dotted line right down to zero and said, “Well, yeah, things are gonna be bad in six months to a year, and probably for a lot of people.” But it turns out that the immunity may be a little more durable.
Since you and I talked last, we’ve been hearing that people will need a booster shot eight months after being fully vaccinated.
The effectiveness of the COVID-19 vaccines is roughly on par with the polio vaccine. It takes four polio vaccine doses to get a person up to what turns into lifelong durable immunity. The first dose gets you about 40 percent immunity, which is about what the first dose of a COVID vaccine gets you. The second one will get you close to 90 percent, which is where the mRNA vaccines are with two doses.
The third dose of polio vaccine gets you to 99 percent. And the fourth one gets you to immunefor-life.
With the COVID vaccines, the initial studies looked at only two doses, because that was the simplest protocol to write up and put into effect. They didn’t know if they would need more doses at the time, and it would have taken longer to get anything approved if they waited until they had tried out two, three, four, five or six doses at various intervals.
So right now, with the boosters they are trying to figure out how many doses we’re going to need. I look at it not as a “booster,” but as completing a set of vaccinations that was probably always going to be more than two.
Something like four may be reasonable for coronavirus. But there’s still a lot of work that needs to be done to see exactly how durable that is, to see whether all the components of immunity stay strong for a long time afterward.
Is the durability different for people of different ages?
The studies show that on average, the older you are, the lower the antibody levels start, and the faster they drop off — but that’s not uniform at all. With the younger age groups, you get a much narrower spread: Everybody gets pretty darn good immunity and it lasts pretty long.
With older groups, you get a few people who look like they’re a young person — young at heart, young immune system — and you get other people whose response drops off, boom!, straight off the edge of a cliff. That spread means that you wouldn’t be able to tell whether someone is protected based solely on the amount of time since their last vaccine or the number of vaccines taken.
So eventually, we’re going to have to move to some kind of system where we look at a marker of immunity. Antibodies are probably the easiest and cheapest way to do that. Then we would say, “When you drop below this antibody level, then it’s time to time to go fill up the gas tank.”
Some people are arguing that the FDA approved the Pfizer vaccine too quickly. What do you think?
They say there’s been too much progress?!
I don’t see that. It was approved faster than vaccines had been before, but this particular approval has a lot more data behind it, and a lot more careful analysis of things like side effects.
VAERS — the Vaccine Adverse Event Reporting System, the thing that everybody reports their side effects through — is new. That was not in place when the measles vaccine came out, for example, or for the polio vaccine. Personal computers were still way off into the future.
You really can’t hold a modern vaccine to old vaccine standards. The process that we’ve seen for this one is more rigorous.
Based on the data, I have got to say, the FDA could have made the call on this one a month ago or or more. They were being cautious. That is their job. They’re here to certify that a thing is safe.
But no, I don’t think they were too fast. If anything, I would argue that they were a little on the slow side.