02/12/2021

Some People Had COVID-19 For So Long That It Mutated Inside Them

12:07 minutes

an illustration of a Black man sitting on the ground with his arms up the air, with a cat near his feet, and various covid particles circling around him
Credit: Shutterstock

This story is part of Science Friday’s coverage on the novel coronavirus, the agent of the disease COVID-19. Listen to experts discuss the spread, outbreak response, and treatment.


COVID-19 variants have been front and center in the news over the past few months. Mutations are a natural part of the course of life for viruses. But to us humans, they’re adding more unknowns to an already stressful time.

Groups of researchers around the world have found something interesting in a select few COVID-19 patients: individuals who seem to be reservoirs for coronavirus mutations. Essentially, these patients were infected with COVID-19 for so long that the virus was able to mutate inside them. Experts are scratching their heads at these strange cases, and now are looking into what this means for our efforts to fight the virus.

Meanwhile, South Africa has suspended the use of the AstraZeneca vaccine because it doesn’t clearly stop the coronavirus variant that originated in the country. This is a problem for AstraZeneca and the University of Oxford, which planned on deploying this vaccine en masse in developing countries.

Joining Ira to break down these stories and other science news of the week is Maggie Koerth, senior science reporter for FiveThirtyEight.


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Segment Guests

Maggie Koerth

Maggie Koerth is a senior science reporter with FiveThirtyEight.com. She’s based in Minneapolis, Minnesota.

Segment Transcript

IRA FLATOW: This is Science Friday. I’m Ira Flatow. Later in the hour, we’re going to talk about the CDC’S new guidance on double masking, but first, we’ve been hearing a lot about COVID-19 variance. For viruses, mutations are a natural course of life, but for people mutations are unsettling unknowns to an already stressful situation.

And now comes another wrinkle. Researchers have found something really intriguing. In a few specific COVID-19 patients, people who seem to be reservoir’s for coronavirus mutations. Here with me to break down this fascinating news is Maggie Koerth, senior science reporter for 538 based in Minneapolis. Welcome back Maggie.

MAGGIE KOERTH: Hi. Thanks for having me.

IRA FLATOW: So what do we know about these people who seem to be reservoirs for mutations?

MAGGIE KOERTH: Well, so what we’re finding is that these are usually chronic patients. So they’re not people who are those COVID long-haulers, who have symptoms persisting after an infection past. These are people whose infections never went away.

So one of these patients is a man in the United States who had had an active COVID infection for 154 days before he finally died from it. He was infectious that entire five months or so. And the doctors could watch the virus evolve resistance to various treatments over time that he was getting. So it was mutating faster than they had seen SARS-CoV-2 do anywhere else. And by the time he died, it was starting to fight off even things like monoclonal antibody medications.

IRA FLATOW: Wow. I’m hoping this is a really uncommon situation.

MAGGIE KOERTH: I mean, it is both uncommon and not unique. Like this is not something that happens everywhere, but it is something that they have identified in multiple places. You know around the same time, there was another person in the UK, a man whose illness lasted about 102 days before he also died.

And doctors found the same sort of hyperphosphatemia mutation happening in COVID in his body. So these cases, there are more than one. And they’re important, because they’re showing us where these new easily transmissible and vaccine-resistant variants are likely coming from.

IRA FLATOW: Are they able to track these people or the mutations that are happening in terms of then they’re these reservoirs, but the reservoirs then leak out of the patient and that’s where we get some of the new mutations?

MAGGIE KOERTH: That is what some of the speculation is right now. We don’t know that for certain, but that seems to be pretty likely, because these patients that they have identified do seem to be having mutations in some of the same places as the new variants. So right now we know that we can identify some of them, but the assumption is that there are probably some people out there who weren’t identified as these type of patients. And from there, the mutated versions kind of got out into the world.

IRA FLATOW: Something new to worry about, but I’m not going to let it keep me up at night more than any of the rest of COVID-19. OK, let’s move on to another COVID-19 story. This one out of South Africa, South Africa has suspended the use of the AstraZeneca vaccine there. Why?

MAGGIE KOERTH: Yeah, that is because it seems to be significantly less effective in that country down to the point that it no longer clears the hurdle of what effectiveness means to actually be used. So they’ve been really struggling with vaccine rollouts in South Africa, because the COVID variant that has become the dominant variant in that country is one that is resistant to the vaccines. And it’s resistant to all of the vaccines that we have to varying degrees.

So for instance, in South Africa, the Johnson and Johnson vaccine has been shown to be about 57% effective against mild and moderate disease, whereas in the US, it’s 72% effective. Novavax was even lower than that in South Africa, about 49% effective against mild and moderate disease, but this AstraZeneca situation is even worse than that. So in the first few months of a trial that began in June, researchers were seeing really good results. So AstraZeneca then was getting about 75% effective, which was results on par with other countries, but more recently as that new variant has spread throughout South Africa, the results dropped to less than 25% effective. And that was when the South African government stopped rolling out AstraZeneca there.

IRA FLATOW: So where is it being used? I know it’s not being used here in the US.

MAGGIE KOERTH: Right. It is being used in the UK right now. And there are a couple of other places also. It is kind of a big problem though to have this kind of resistance. This level of resistance built up to AstraZeneca, because that was supposed to be the vaccine that would be widely available in developing countries, like some of South Africa’s neighbors.

IRA FLATOW: But the World Health Organization did just recommend the use of this vaccine, even in places with variants. It seems like there might be conflicting information out there. No?

MAGGIE KOERTH: So this is where it gets complicated, because when we’re talking about these studies, what we’re usually talking about is effectiveness against mild and moderate disease. So you know, how many people is the vaccine preventing from getting the sniffles? How many people is the vaccine preventing from having a couple of bad days at home, right?

But the vaccine can be not so great at preventing that, but still pretty good at preventing severe illness and death. And we know that with, for instance, the Johnson and Johnson vaccines in South Africa, they have not been super great at preventing mild and moderate disease, but still been nearly 100% effective at preventing severe illness and death. So we don’t have the answers for that around AstraZeneca yet, because the trial of it was small and mostly involved young healthy people, but there is reason to assume that it would also still have effectiveness against the most severe disease.

IRA FLATOW: Yeah, and that seems to be the good news with the other vaccines is that they may not be most effective at the top level, but they’re effective enough that they keep you from dying from it.

MAGGIE KOERTH: Right. Yeah, exactly. It kind of comes down to, what are you most concerned about preventing?

IRA FLATOW: Yeah. I want to remind our listeners that on last week’s show, we had a whole segment about the new COVID-19 variants and how effective our vaccines are against them. And you can go back and listen to our show on our website sciencefriday.com/variants. Let’s move on to some epidemiological news, new information about why some place in the US have Lyme carrying ticks but don’t have Lyme disease.

MAGGIE KOERTH: This is super interesting. So I did not actually realize this until the study came out. They’re blackleg tick that lives all over this country, but the Lyme disease that it can carry only really has a significant impact on humans in the Northeast and more recently in North central parts of the US. And why some parts of the country have ticks that can carry Lyme, but not Lyme disease has been this huge mystery. And scientists may have figured out part of what’s going on here now.

That’s because some researchers spent two years just studying the heck out of ticks. They looked at how they lived. They looked at where they lived they looked at what kinds of hosts they were sucking. And they basically found like this clear line south of Virginia, where the ticks are just different.

IRA FLATOW: You mean that ticks are different or where the Lyme disease is being carried by perhaps different creatures?

MAGGIE KOERTH: A little bit of both. So in the Northeast, you have these ticks that have these behaviors, like climbing up trees and bushes to look for hosts. And they also have a favorite meal in the little white footed mouse, whereas in the South, the ticks prefer to dine on lizards.

And they stay down in the underbrush on the forest floor, where those lizards are most likely to be. And both of those differences have a big impact on how much access the ticks have to people and on how likely they are to get the Lyme bacteria themselves. Mice are really good at transmitting it, lizards not so much.

IRA FLATOW: That’s interesting, very interesting, because Lyme disease can be really devastating. Could this new research cue us into the future of this illness, perhaps, and how it spreads?

MAGGIE KOERTH: I think what it does is sort of direct our attention to how the environment affects the transmission of this disease, because we know that climate change is already altering the patterns of Lyme disease in this country. You know, we’ve already seen those Northeastern ticks expanding their range into the upper Midwest and bringing those behaviors and Lyme disease with them. So any change to climate is likely to change things like how ticks live and what they’re eating.

IRA FLATOW: Yeah. I want to go on to a story that is kind of really cute, I want to say, because it’s really fun. It turns out some rocks have been trying to dupe us into thinking they’re fossils.

MAGGIE KOERTH: Yes. Yes.

IRA FLATOW: Oh, there go those rocks again.

MAGGIE KOERTH: Oh, those rocks. It is really awesome when you get these rocks that have evidence of really ancient life, things like fossilized bacteria, things single-celled organisms in rocks. But it turns out that some of those fossils, and maybe even most of them might not actually be fossils at all. These scientists did an experiment in their laboratory, where they replicated the process of making a type of rock called chert.

And they had bacteria in some of this. And they had no bacteria in others. And what they found was that as that rock solidified, it flattened and deformed the bacteria to the point that you couldn’t even tell what that had been. But meanwhile, these squiggly crystal structures that were not alive, but were very easily mistaken for bacteria, kept their shape.

So they came through the process ready to be misidentified as doomed fossil brethren. And it is a problem that scientists were aware of already, but they hadn’t really known how serious the problem was. And that’s going to have an impact on how we interpret, not just rocks found here on Earth, but also any that we bring back from Mars.

IRA FLATOW: You know, that’s exactly what I was going to say, because in the back of my mind, I remember a story of Martian rocks that were found here on Earth. And they were looking at these little squiggly round knobs on them and thinking, hey, these are fossilized remnants of mycobacteria that might once have grown on Mars. And that was a big news story about it.

MAGGIE KOERTH: Yes.

IRA FLATOW: Remember that? So this is what this is what you’re talking about, I guess.

MAGGIE KOERTH: This is exactly the kind of thing we’re talking about. And it is going to take a lot of work I think for scientists to figure out if there’s any way to tell which is the actual bacteria and which is just sneaky, sneaky rocks going around looking like bacteria.

IRA FLATOW: Oh, those rocks they’ll do it every time. Thank you, Maggie.

MAGGIE KOERTH: Yeah, thank you.

IRA FLATOW: Maggie Koerth, senior science reporter for 538 based in Minneapolis, Minnesota.

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Kathleen Davis is a producer at Science Friday, which means she spends the week brainstorming, researching, and writing, typically in that order. She’s a big fan of stories related to strange animal facts and dystopian technology.

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Ira Flatow is the host and executive producer of Science FridayHis green thumb has revived many an office plant at death’s door.

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