Monday, June 22, 2020

Explaining the Covid-19 Virus

A friend who is a science editor for a national publication posted this explanation of the Covid-19 virus on his Facebook page yesterday.  It is reprinted with his permission and apologies for the informal style. 

The most interesting work to me has been molecular and evolutionary. There are many reasons why we can be confident COVID-19 was not designed in a lab, but some of the most compelling are that it is too strange to have been invented by a person. Some of the mechanisms it uses barely work at all. Virologists say that the structure the virus uses to connect to ACE receptors—this is the way it infects cells—is unlike anything they have ever seen.

 When they first modeled it, they couldn’t even figure out how it works, because the arrangement of proteins is novel and peculiar. There are alternatives that bind to human ACE receptors much more selectively and effectively, so if you were designing a bioweapon, you would never use this strange contraption. Nature is always an accidental designer, and many mechanisms in living things do not work in some “ideal” sense. They merely work well enough. Scientists are intrigued by COVID-19’s crappy but “good enough” machinery, but it is nothing anyone would invent.

The structure in question helps to reveal the promiscuous evolutionary history of the virus. One of the best (and extremely difficult Science) papers I’ve read on the virus was a detailed analysis of its RNA and evolutionary history. The analysis shows that COVID-19 has heritage from both pangolin and bat coronaviruses. Different strains of virus in the same host often exchange genetic material, in the closest viruses can come to having sex (recombination). Analysis of conserved RNA suggests that COVID-19 got its novel traits when these different strains of coronaviruses came into contact, probably in the body of a bat. Bat coronaviruses infect pangolins and evolve to be better at infecting pangolins. Then they get back into bats and the viruses recombine. The new viral strain has a mosaic of traits of both.



But this also gets at what makes COVID-19 especially terrifying. It is unusually promiscuous for a virus. It can infect a wide variety of mammals, including dogs, tigers, and minks. A major reason why is that the equipment it uses to infect cells is crappy but versatile. It connects to many different varieties of ACE receptors. They are killing more than 5 million minks in Europe now, after minks in fur farms became infected with COVID-19 by their human handlers. The worry is that if COVID-19 spreads to wild mink populations they will never be able to eliminate it completely. The wild mink population could become a new viral reservoir, causing wave after wave of infection. This is a much larger potential problem than people have properly contemplated. We have no idea how many different types of mammals COVID-19 can infect, or even how many mammals may be infected right now. If it can infect squirrels, God save us all.

We still don’t know how COVID-19 crossed from bats to humans. It may have involved another unidentified species. It may have crossed directly from bats, though this has not been demonstrated for other viruses. But there is a terrifying bit of information that deserves more attention.

Years ago, scientists went into bat caves in China and took samples. They identified many novel coronaviruses. Any one of these new strains might have the potential to infect humans. So the scientists tried to warn the world, to no avail.

But they also went into areas near the caves and tested people for antibodies to bat coronaviruses. They found that a small percentage of the population already has such antibodies. This indicates there is hidden, unrecorded crossover of bat coronaviruses into rural human populations, where they apparently burn out because of isolation. Regardless of whether there is another, unidentified bridge species, or more than one, coronaviruses are “leaking” out of their reservoirs.

We would be very foolish to tell ourselves that eliminating or reforming wet markets will save us. The problem is human encroachment on wild places. The more time humans spend around these wild bat populations, the likelier it is that there will be zoonotic events (when viruses cross over from animals to humans). So we should expect additional outbreaks of novel coronaviruses in the near future.

That is, the next pandemic is probably just around the corner. There is no reason to think we will contain that one better than we did this one. So we must aggressively explore interventions that can combat any type of coronavirus, if such interventions exist, and strive toward a universal vaccine. We have been lucky with previous outbreaks because those viruses (SARS, MERS) were deadlier and caused symptoms around the time the victim becomes infectious, greatly simplifying isolation. COVID-19 is ultimately far deadlier because it is a chameleon, eliciting a variety of responses from human immune systems, including not much of a reaction at all, which is great for the person and terrible for everyone else, because they spread the virus asymptomatically. This turns out to be great for the virus too.

What will the next viral outbreak bring? Maybe we will be lucky, and it will be easy to contain. But maybe it will be more like COVID-19. Or maybe it will be even worse, with a longer incubation period but a higher death rate.

It should be obvious to everyone by now that our luck has run out when it comes to zoonotic viruses. We need to stop hoping for the best and begin a sustained, well-funded effort to anticipate a variety of viral pandemics. And we need much better monitoring of known viral reservoirs. There are bat caves all around the world, but viruses have crossed over from many different kinds of wild animals. If we will not stop encroaching on wild areas—and it is obvious that we just won’t stop—then we need to prepare for viral pandemics as a natural consequence. This is not the last major pandemic you will witness in your lifetime. It’s the first.

11 comments:

Anonymous said...

1. Like all living things, viruses evolve over time. Some strains are worse than others.
2. Once a virus has evolved, it's hard to get rid of it.
3. There will be new sources of epidemics in the future, just as there have been since the time of Adam and Eve.
4. Epidemics strike animals other than humans and can be transmitted between humans and animals.
5. We're all going to die---old, fat, sick folks are the most vulnerable to the Covid-19 strain.

Anonymous said...

“It should be obvious to everyone by now that our luck has run out...” That just about sums up everything going on in this world of ours today.

Anonymous said...

I'm sure our response to the next virus will be the same as this one, complete apathy by a large percentage of the U.S. population.

Anonymous said...

It's worth mentioning a "you know who" advisor was on the Sunday shows again claiming China engineered this virus. Just a relentless stream of bullshit from the top.

Anonymous said...

The problem in China is that they kept it hidden for months and allowed the Wuhan population to travel internationally. We must bring back manufacturing of key strategic pharmaceuticals and medical supplies, or at least diversify production to include numerous sources, particularly Central America.

The Chinese Communist Government joined with the Democrats in attempting to blame America and President Trump for the virus and the media has joined in with them. China is a major threat, both economically and militarily to the US and are already interfering in our Presidential election. Democrats are welcoming them.

Anonymous said...

@12:21
1. A virus is not alive.
I stopped reading your post after #1

Kingfish said...

Some readers are trying to refight the election in the comments. Stick to the subject of the post.

Anonymous said...

This is good science writing.

Calm Down said...

While I don't see any evidence that China engineered the virus, I do believe they were studying similar viruses in the lab and attempting gain of function manipulation. The most likely scenario is an accidental contamination and release from the Wuhan lab, which China then obviously attempted to cover up.

Overall, a pretty depressing read.

Anonymous said...

Oy vey! Clearly this wasn’t made in a lab with the nanotech help of Dr. Charles Lieber PD Harvard University

Green Acres said...

Anyone who believes this coronavirus was made in a Wuhan lab must also believe that Lyme disease, Ebola, hanta virus and Aids were invented in labs, too.

Meanwhile the other day, The Wall Street Journal published a photo of a young woman holding a peanut between her teeth and feeding it to a squirrel that she befriended during the lockdown. All I could think was YUCK - yet another opportunity to transfer a new disease from a wild animal, a tree rat no less, to humans.

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