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Fri Apr 3, 2020, 03:39 PM

Bad News Wrapped in Protein: Inside the Coronavirus Genome

Source: New York Times

Bad News Wrapped in Protein: Inside the Coronavirus Genome

By Jonathan Corum and Carl Zimmer April 3, 2020

A virus is “simply a piece of bad news wrapped up in protein,” the biologists Jean and Peter Medawar wrote in 1977.

In January, scientists deciphered a piece of very bad news: the genome of SARS-CoV-2, the virus that causes Covid-19. The sample came from a 41-year-old man who worked at the seafood market in Wuhan where the first cluster of cases appeared.

Researchers are now racing to make sense of this viral recipe, which could inspire drugs, vaccines and other tools to fight the ongoing pandemic.

A String of RNA

Viruses must hijack living cells to replicate and spread. When the coronavirus finds a suitable cell, it injects a strand of RNA that contains the entire coronavirus genome.

The genome of the new coronavirus is less than 30,000 “letters” long. (The human genome is over 3 billion.) Scientists have identified genes for as many as 29 proteins, which carry out a range of jobs from making copies of the coronavirus to suppressing the body’s immune responses.

The first sequence of RNA letters reads:

-snip-

Read more: https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html

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Response to Eugene (Original post)

Fri Apr 3, 2020, 03:45 PM

1. I can't wrap my mind around the fact that they say viruses are not living things

How can anything that replicates itself not be alive?

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Response to Sucha NastyWoman (Reply #1)

Fri Apr 3, 2020, 03:51 PM

2. It doesn't eat. It doesn't grow. It doesn't reproduce itself.

It uses your cells to reproduce.

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Response to Sucha NastyWoman (Reply #1)

Fri Apr 3, 2020, 04:18 PM

5. They are not living organisms

They do not carry out metabolic functions.

They do not require nutrition or produce wastes

They are mindless infective particles

Be afraid

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Response to jpak (Reply #5)

Mon Apr 6, 2020, 09:37 AM

15. reminds me of the quote from the original Terminator movie...

"It can't be bargained with. It can't be reasoned with. It doesn't feel pity, or remorse, or fear. And it absolutely will not stop, ever, until you are dead."

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Response to Sucha NastyWoman (Reply #1)

Fri Apr 3, 2020, 04:26 PM

6. A biovirus isn't alive for the same reason a computer virus isn't a computer

Like a computer virus, a biovirus is more like a rogue program expressed in protein and nucleic acid. Without an actual living cell to infect it's just an inert particle. Just as a computer virus is nothing but meaningless data until it is expressed by being run on a computer, at which point it corrupts the functionality of its host machine to make more of itself.

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Response to Sucha NastyWoman (Reply #1)

Fri Apr 3, 2020, 04:32 PM

7. It's a very specific chemical reaction

Crystals also grow and replicate, but it is not alive. It is a specific reaction... I guess a chemical one. But crystals are not alive.

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Response to krispos42 (Reply #7)

Sat Apr 4, 2020, 01:05 AM

11. Except crystals don't mutate and evolve

Viruses exist in the in-between, on the cusp of living and dead: they're absolutely subject to natural selection, can absolutely be classified taxonomically (IIRC they're the most genetically diverse group known) — but at the same time they don't metabolize, can't reproduce, have no independent nutritional requirements as such, a simple fleck of lipids and nucleic acids.

There's probably some kind of metaphysical discussion to be had here but it's far too late for that kind of thing.

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Response to sir pball (Reply #11)

Sat Apr 4, 2020, 10:41 AM

12. Crystals are much simpler because they're typically inorganic.

Don't have to be, but usually are. There's also not a lot of room for evolution--their structures are determined by the properties of the ions that make them up. There's no real chemical reaction involved, the best you can get are deformations due to impurities or different pressures.

In that sense, crystals are a bad analogy. Viruses do interact and do undergo chemical processes. When the RNA and proteins are copied, there can be errors, and that changes the properties of both (random mutations). Sometimes it makes them completely useless and their constituents get removed or recycled. Sometimes it makes them better adapted, and the hosts that they are in live longer (there's one source of the evolution).

Even then, viruses need something living to provide both the mechanisms for mutations and the actual change in frequency in the population.

There's nothing metaphysical about it.

You can run evolution simulations in software, and I've seen examples where drug companies used "evolution" to produce better drugs: They have complex compound with some antibacterial properties, and they shove it into an algorithm that makes a lot of small, random changes or "mutations". Then they analyse its structure and properties against receptors in the bacteria they're targeting. They keep the best candidates, and make more random changes. Mutations + natural selection. They synthesize the top candidates and test them against reality.

They're close to being living--except they lack a lot of the crucial bits. Think of them as mobile stripped down genomes. Everything alive needs a genome; not every genome has to be alive. If we tweaked the definition of "living" then they'd qualify. (It's the same kind of thing as to why Pluto isn't a planet or how many species of Echinofossulocactus their are--you pick your definition and that sets up the categories that things fall in. Some change the categories, i.e., the definitions, when it helps their field become more descriptive or highlight important things, some outside the field want the definitions changed to suit ideas of fairness or salience outside the field.)

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Response to Eugene (Original post)

Fri Apr 3, 2020, 04:00 PM

3. This is absolutely fascinating.

Thanks for posting. Much food for thought here.

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Response to Eugene (Original post)

Fri Apr 3, 2020, 04:12 PM

4. Absolutely fascinating

Absolutely fascinating from a scientific point of you. Incredibly clever ways of replicating itself by using the human body. We are indeed our own worst enemy.

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Response to Eugene (Original post)

Fri Apr 3, 2020, 07:16 PM

8. You know I am wondering if the source might really be something from the rivers and or lakes.

I know, they found a related virus inside pangolins and pangolins mainly eat ants and termites but on the other hand pangolins also will eat other insect larva if they find them and they do swim and so since this was at a fish market maybe the real source is something in the water? Maybe naturally found inside an insect larva for example that also infected the pangolins but also that a fish ate and then people ate the fish with the same virus thus it infected humans as well as the pangolins?

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Response to cstanleytech (Reply #8)

Fri Apr 3, 2020, 10:17 PM

9. The prevailing theory seems to be that it came from a bat....

...from an open market in Wuhan. I haven't really followed the chain of evidence for the theory, just parroting what I've read..

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Response to lastlib (Reply #9)

Sat Apr 4, 2020, 10:47 AM

13. Bat, pretty sure.

It's coronavirus heaven, and bats with genomes very similar to SARS-CoV-2 have been found near Wuhan. But also in other places.

Similarity gets up into the high 90s for bat-originated coronavirus in some pangolins.

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Response to lastlib (Reply #9)

Sat Apr 4, 2020, 11:10 AM

14. Probably not. It is believed to have come from pangolins according to a paper in Nature Medicine:

The proximal origin of SARS-CoV-2 (Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry, Nature Medicine (2020). https://doi.org/10.1038/s41591-020-0820-9)

Pangolins are widely trafficked in China for, ironically, "traditional medicine" purposes, since the scales of the animal are believe in folk medicine to have curative properties.

Pangolin "products" were being sold in the Wuhan market from which the virus is believed to have spread.

We know these species popularly as "anteaters."

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Response to Eugene (Original post)

Fri Apr 3, 2020, 10:55 PM

10. That mutation corresponds to the protein sequence Pro-Arg-Arg-Ala. It should be cleaved by trypsin.

This should mean that it doesn't survive very well in the alimentary canal. Of course, it infects one before it gets there.

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