How Covid mutates and why that might be a good thing

There’s good and bad news about the way Covid mutates, and it’s all wrapped around the same bit of information. 

Like most non-experts, I use the word mutate loosely. If something genomeish leads to change, I think it’s a mutation. Which goes to show you what I know.

Covid, it turns out, doesn’t just mutate, it also recombines, meaning it mixes large chunks of its genome, not just single genes. If a mutation’s a typo, recombination is a cut-and-paste error, dumping a largish chunk of text in the wrong place. And while the virus proofreads typos fairly well, it doesn’t catch cut-and-paste problems as effectively.

I’ve had that problem myself. I still wince at something quite horrible that I let go into print because the spelling was right and my eye didn’t pick up the change in meaning. And I’m larger and (I like to think) more complicated than a virus.

Most of those recombination errors, like most mutations, make a mess and that particular virus doesn’t get to leave little virette progeny behind. But some of them work and the virus changes.

Irrelevant photo: One of Janey’s crocuses.

Is recombination what’s happening with Covid? Possibly. The Kent variant has more than a dozen mutations and they seemed to appear all at once. Emphasis on seemed. A lot of what goes on happens in the kitchen while we’re out front cleaning the dining room. Feng Gao, a virologist from China, says we don’t yet have proof of recombination. “Diversity, no matter how much, does not mean recombination. It can well be caused by huge diversification during viral evolution.”

So let’s not get carried away with this. We’re dancing at the edges of what’s known. But (damn, that tune’s catchy, so I’ll do a few more steps) recombination may be how viruses that infect one species jump to another species: by swapping a bit of genetic code .

It’s possible that recombination means a more dangerous virus will appear–either a new one or a more dangerous form of Covid. So there’s our bad news. 

But the good news is that experiments with a mouse coronavirus show that blocking a single enzyme keeps the virus from correcting its typing errors and recombination events happen much less often. If this holds for Covid, the right drug might be able to block recombination and (or maybe that should be or) push the virus to mutate so badly that it ends up in something called error catastrophe–basically, the evolutionary equivalent of falling off a cliff. While dancing to that catchy little tune.

As a way to treat Covid, blocking the enzyme could make antiviral drugs more effective.

The enzyme goes by the name of nsp14-ExoN, which isn’t particularly catchy. If we’re going to be spending time with it, it needs a nickname. But whatever we call it, it’s common in coronaviruses, so if this works it opens up the possibility of curing other coronavirus diseases as well. 

 

Covid variants

If Britain didn’t end up with the world-beating test and trace system Boris Johnson promised us–and believe me, it didn’t–it may have come up with a world-beating strain of Covid instead: the Kent variant; the variant I mentioned that has all those mutations. Sharon Peacock, the director of the Covid-19 Genomics UK consortium tells us it looks likely to sweep the world.

And unlike the test and trace system, we didn’t pay a penny for it.

Go Britain!

The consortium is testing the genomes on a randomly selected 5% to 10% of all positive Covid samples in the country but aims to test them all in order to keep track of how the virus is mutating.

And speaking of variants, the World Health Organization says the small trial that found the AstraZeneca vaccine to be largely ineffective against the South African variant was inconclusive. They’re not saying the vaccine’s definitely effective against it, only that it isn’t definitely ineffective. 

Which is better than nothing. 

 

Covid and Coca Cola

How much space would all the Covid viruses in the world take up if they could be packed neatly for shipping? They’d fill a Coke can

They’d also fill a can of supermarket brand fizzy orange-flavored sugar water, but Covid’s a brand-name kind of virus. Coke it is. So in the scene where someone yells, “Don’t open the can!” for pete’s sake, don’t open the can. You know what happened when Pandora didn’t listen to the warnings?

I’m not telling. But I did give you a link.

 

Spreading the virus

More than half of all Covid cases are spread by people who have no symptoms. They may be less infectious than people who are sick, but they could well make up 80% of the total number of people carrying the disease. And they’re wandering through the world shedding viruses, not lying in bed at home.

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A study by the U.S. Centers for Disease Control found that wearing two masks can reduce the chance of getting Covid by 90% or more. Yes, not just transmitting but catching the damned thing. 

The study had its limits. It tested a tight-fitting cloth mask over a surgical mask, not two surgical masks and not two cloth ones, and it only looked at one type of cloth masks, although the world’s awash with different types just now. And as the article where I first read this put it, it also didn’t consider “men with beards or children.”

Does having children interfere with the fit of men’s masks more than women’s? Hard to say. The study didn’t test that. 

To keep everything in perspective, an engineering professor says that the only reason to wear two masks is to get a better fit. But the masks most of us wear do fit loosely, so double masking might be worthwhile, no matter who’s right.  

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Two weeks after U.S. states introduced mask mandates (they haven’t all), the weekly growth in hospitalization rates dropped by 2.9% among people who are 40 to 64. After three weeks it dropped 5.5% among people 18 to 64.

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Every so often, you’ll find someone saying that Covid’s no more dangerous than a bad outbreak of the flu. So do we have any figures on how much more dangerous it is? 

Yup, some. The risk of death is 3.5 times higher. That number comes from comparing people who are hospitalized with the Covid against those hospitalized with flu. It ignores whatever long- term effects Covid has on the unhospitalized, so I’d say it’s undercounting. Still, it’s a number, and numbers help. 

At least they help most people. 

Covid patients also had one and a half times greater use of the intensive care unit and one and a half times longer hospital stays. And they were more likely to need a ventilator.

In case you think Covid’s only a problem for the old and the ill, not many of the hospitalized Covid patients had other illnesses and 21% were younger than 50. People under 50 made up 24% of the intensive care admissions.

As far as I can see, that doesn’t address the problem of how easily Covid spreads compared to flu. It only compares hospitalized patients.

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Worldwide, the number of reported Covid cases is down for the fourth week in a row. Take a deep breath. The drop is uneven, it doesn’t count unreported cases, and we forgot to get a guarantee that it won’t go back up, but we have to take our good news where we can get it. This is good news.

 

Is there any news on curing the thing?

In a small study, a common asthma treatment, budesonide, cut the need for hospitalization and urgent care by 90%, and people who took it within seven days of showing symptoms recovered more quickly than the control group. Better yet, it cut the number of people with symptoms that lingered after twenty-eight days. 

As usual, it was a small study–146 people–so it’s preliminary, but budesonide is a well-known and well-studied drug, which would speed the process if it’s adopted.

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The U.S. Food and Drug Administration has approved a combination of two monoclonal antibodies that can keep high-risk patients from developing Covid that’s severe enough to hospitalize them. A similar drug had already been approved. Both take Covid antibodies and synthesize them so they can be given to patients as a drip. 

And it’s that drip business that’s causing trouble. Initially, getting them from vial (or whatever they come in) into human took an hour. It can now be done in sixteen minutes. But some hospitals have been so overwhelmed they haven’t had time to deal with it. 

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A team of researchers in China has identified six drugs that the FDA has already approved for other uses that could be repurposed to treat Covid. They whittled that down from 3,769. They still need to be tested in the real world, but already having FDA approval for other purposes means that if they work they could be put to use quickly.

After that, the article went over my head, but it has to do with proteases and substrates, not to mention clades. Have fun.

 

Your feelgood story

New York software developer Huge Ma tried to make his mother a Covid vaccination appointment and discovered that not only did the city and state have different systems that weren’t talking to each other but that there were dozens of separate websites, each one demanding that you sign up a different way.

So he took a couple of weeks and made a free website, TurboVax, that compiles information from the three main city and state sites and sends information on available appointments to Twitter.

It cost him $50 to make.

The difficulty of booking an appointment is one reason–although far from the only one–that vaccines are going disproportionately to white New Yorkers. 

“It’s sort of become a challenge to myself, to prove what one person with time and a little motivation can do,” he said. “This wasn’t a priority for governments, which was unfortunate. But everyone has a role to play in the pandemic, and I’m just doing the very little that I can to make it a little bit easier.”

Covid variants, vaccines, and all our clean hands

An assistant professor of food science says that all the hand washing, surface cleaning, and food washing we’re doing may or may not keep Covid in check but has kept us from spreading salmonella, e.coli, and listeria.

It’s not what we’re trying to do, but it is good for us.

There’s no evidence that Covid is spread through food, although that’s not the same as saying that it isn’t spread that way. 

But having (with her team) overdosed on US and Canadian internet videos telling us how to clean everything in sight, Yaohua “Betty” Feng reports that a bunch of them have it wrong. Of the videos telling people how to wash their hands, only 41% of the presenters used soap. The remainder, presumably, relied on good wishes and intense looks. Less than 33% mentioned hand sanitizer. And how many of us, since the start of the pandemic, can get through a day without mentioning hand sanitizer?

Like–I’m going to assume–you, I thought I knew how to wash my hands. I’ve been doing it for better than 70 years now, most of the time without supervision, but there’s no predicting what people will feel the need to learn in these difficult times. Maybe I’ve been doing it wrong. Maybe, for instance, I’ve mistaken my hands for some other body parts.

Irrelevant photo: The first spring violets.

Other videos were about washing produce, and 16% of the presenters used soap while 12% used other chemical cleansers. That sounds promising, but they’re both no-nos. If you don’t rinse them off completely, they can cause diarrhea.

Feng didn’t say this, but you might draw the conclusion that random internet videos aren’t the best places to look for reliable information. Or you might not. 

 

British and (eek!) foreign Covid variants

The British Covid variant, which to make things more complicated is now called the Kent variant, after the part of England where it was first found–

Let’s start that over: The Kent Covid variant has mutated since it was first identified. That’s standard operating procedure in the viral world. Every new infection is a chance for the disease to pick up a mutation. Some of those won’t work well for it and will die out and others will make the disease better at hiding from the immune system. Those are the ones that will spread.

So the Kent variant has picked up a new mutation, and it’s similar to one of the mutations on the South African variant. The going theory is that it evolved the change on its own rather than picking it up like an STD after a one-night stand with the South African variant. Which basically means that two strains of the virus have found the same way to partially evade the human immune system. 

There’s been a lot of focus on stopping, or at least getting control of, the imported Covid variants. In parts of the UK, house-to-house testing is looking for the South African variant.

But that may be a sideshow. Virologist Julian Tang wrote, “Unfortunately, the lack of control of these different variants in the UK may lead this population to become a melting pot for different emerging SARS-COV-2/COVID-19 variants–so we really need to reduce our contact rates to reduce the opportunities for viral spread/replication to reduce the speed with which these different virus variants can evolve.

“Closing borders/restricting travel may help a little with this, but there is now probably already a sufficient critical mass of virus-infected people within the endemic UK population to allow this natural selection/evolution to proceed . . . so we really need to stick to the COVID-19 lockdown restrictions as much as possible.”

In other words, the more the people get infected, the more times the virus gets to mutate, and the more times it mutates the more chances it has of presenting us with a more difficult problem.

There’s something tempting about focusing on imported strains of the virus–Eek! South African! Argh, Brazilian!–but all Covid infections are dangerous. That’s what we need to focus on. 

 

Symptoms

In England–possibly in all of Britain, but don’t trust me on that; I’m at least as confused as you are–the only way to book a Covid test is to claim at least one of three symptoms: cough, loss of smell or taste, and a high temperature. But a GP and senior lecturer in primary care, Alex Sohal, writes that the list should include a runny or blocked nose, a sore throat, hoarseness, muscle pain, fatigue, headache, vomiting, and diarrhea. She’s seen patients come in with them and go on to test positive for Covid.

“These patients have frequently not even considered that they may have Covid-19 and have not self-isolated in the crucial early days when they were most infectious.”

She advocates telling “the public, especially those who have to go out to work and their employers, that even those with mild symptoms . . . should not go out, prioritizing the first five days of self-isolation when they are most likely to be infectious.

“This will help to get—and keep—us out of this indefinite lockdown, as Covid-19 becomes increasingly endemic globally. Ignoring this will be at our peril.”

As it stands, if you have good reason to book a Covid test and don’t have the magic three symptoms, the best thing to do is lie. And almost none of us recognize the full list she gives as possible Covid symptoms.

 

The bad news

Some of the recent Covid mutations have outpaced the monoclonal antibodies we’d all been counting on as a treatment in case we did catch it. 

Mono-whats? 

Okay, if you have to ask, that says we haven’t all been counting on them, but let’s pretend we were so I can explain what’s happening.

Basically, monoclonal antibodies are human antibodies that have been cloned. In this case, they’re antibodies to Covid, and they’ve been used to treat serious Covid cases. The problem is that the humans who developed them did so in the presence of one form of Covid, not all of them. As the virus mutates, they can get left behind.  

They also have another problem, which is that they’re expensive and not easy to make. Other than that, though, they’re great.

 

The good news

At the beginning of February, after a 25-day lockdown, the Isle of Man (population 84,000) lifted almost all  its Covid restrictions. The exceptions are its border controls, which–well, I was going to say they take no prisoners, but in fact taking prisoners is exactly what they do. Someone who tried to get onto the island on a jet ski was jailed for four weeks. 

They seem to have eliminated the virus. Before the lockdown, the island had 400 cases and it’s had 25 deaths. 

The Isle of Man is in the water somewhere between Scotland and Northern Ireland. It’s a self-governing British crown dependency, and don’t ask what that means because it’s complicated and we’re running out of space here in the infinite internet.  

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Two bits of news about the AstraZeneca vaccine. 

One, a single dose (which is what the UK is focused on at the moment, with the second one delayed for up to twelve weeks) is still 76% effective after three months. That’s not as good as the 82% protection it offers after the second dose, but it ain’t bad, and there’s finally some data backing up the government’s decision to focus on getting an initial dose to as many people as possible–at least for this vaccine.

Delaying the second dose may strengthen the protection, but that’s not definite.

Two, the vaccine may reduce the number of Covid transmissions by two-thirds. That’s not definite–it’s still preliminary–but it’s promising. 

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A late-stage trial reports that Russia’s Sputnik V vaccine is both safe and 92% effective. It can be stored in a normal refrigerator and comes in two doses, but the second dose is slightly different than the first one. They use different vectors–the neutralized viruses that they ride on. The idea is that this will give the immune system an extra boost and protect people for longer.

 

The little-bit-of-both news

Britain’s vaccinated over 10 million people with at least one dose of one vaccine or another, and the number of hospitalized Covid patients is coming down, but it’s still higher than it was during the first peak of the pandemic. England’s chief medical officer, Chris Whitty, said infection rates are also coming down“but they are still incredibly high.” That may mean, in the American tradition of Groundhog Day, that we get six more weeks of winter. Or lockdown.