Two articles on the coronavirus

These two articles in the New York Times will give you a decent understanding of how the Covid-19 virus works and what it looks like. The first, by Jonathan Corum (the NYT’s graphics editor) and science journalist Carl Zimmer, explains how the virus’s genome is put together and shows a 3-D reconstruction of the 29 proteins it makes.

Covid-19 is an RNA virus, meaning that its genetic material isn’t DNA but RNA. It injects its RNA into a cell, and that RNA, besides replicating itself, also begins producing proteins that do various things. These include making the virus’s own protein coat, which, when put together with the newly replicated RNA, makes new viruses that then enter other cells using a “spike protein” that latches onto human cells. I won’t go into detail about this, as you can read about it in many places (e.g., here).   Click on the screenshot to read the collaborative article:

The viral proteins do these things (among others):

  • Slow down the production of the infected cell’s proteins so that it can make more viral protein
  • Tag the human cell’s proteins so they persist when they are scheduled for destruction; this may make cells more susceptible to infection
  • Make fluid-filled bubbles inside the cell where new viruses are made
  • Helps the virus’s RNA replicate itself
  • Camouflage the virus’s genes so they don’t get detected and destroyed by our bodies
  • Detect and remove errors (mutations) that occur when the virus’s RNA replicates itself inside the body
  • Destroy leftover virus RNA to hide it from the cell’s antiviral  defenses.
  • Change the internal environment of the cell to make it easier for the virus to replicate
  • And, of course, produce the protein coat of the virus.  The coat is made of four proteins, including the dreaded “spike protein” that targets a human protein, ACE2, on cell surfaces in the our airway. As the link above explains:

The cells that SARS-CoV-2 prefers to infect have a protein called ACE2 on the outside that is important for regulating blood pressure.

The infection begins when the long spike proteins that protrude from the virus particle latch on to the cell’s ACE2 protein. From that point, the spike transforms, unfolding and refolding itself using coiled spring-like parts that start out buried at the core of the spike.

The reconfigured spike hooks into the cell and crashes the virus particle and cell together. This forms a channel where the string of viral genetic material can snake its way into the unsuspecting cell.

Here’s a 3-D reconstruction from the NYT article showing the virus’s spike protein, in red, latching onto human ACE2 (yellow)

Source: Yang Zhang’s Research Group, University of Michigan.

 

Note that all these functions evolved by natural selection to propagate the virus’s genome. Everything can be understood as ways to facilitate the reproduction of the virus and then to pass it on to other cells and then to other humans. It’s not to the human’s advantage, of course, but to the virus’s. It’s a pathogen—an intracellular parasite that hijacks the cell’s machinery to make more of itself.

Now most biologists wouldn’t consider viruses to be “alive” in the sense that they are not autonomous organisms with both a way to replicate and to metabolize. This, of course, depends on your definition of “life,” and most biologists don’t worry too much about that. What’s important for evolution—and for those wanting to understand Covid-19 or any virus—is that it has a way of replicating itself, even if it has to use another organism to do so. Once it’s a replicator, and has a heredity material, then it can evolve by natural selection, undergoing mutation and accumulating those mutations that facilitate its survival, replication, and transmission.

The article below tells you how the familiar picture of the coronavirus was put together. The red bits on the surface are those spike proteins that latch onto human cells.

h/t: cesar

18 Comments

  1. GBJames
    Posted April 6, 2020 at 1:32 pm | Permalink

    I’m hoping somebody figures out how to use CRISPR to mess up this thing’s ability to harm people.

    • EdwardM
      Posted April 6, 2020 at 3:40 pm | Permalink

      Hmmmm. What would you target?

    • merilee
      Posted April 6, 2020 at 4:40 pm | Permalink

      +1

  2. Filippo
    Posted April 6, 2020 at 1:48 pm | Permalink

    If I may, here’s this, on the outside chance any reader here is not aware of it.

    covid19.healthdata.org.

  3. E.A. Blair
    Posted April 6, 2020 at 1:53 pm | Permalink

    Those red triangles on the blob’s spikes are actually clusters of MAGA hats.

    • sted24
      Posted April 6, 2020 at 2:13 pm | Permalink

      If you live elsewhere other than the USA, I am not sure that is a very appropriate joke.

      • phoffman56
        Posted April 6, 2020 at 6:38 pm | Permalink

        As a non-USian, I’d say the opposite, as the harm likely to be done to future generations OUTSIDE US (and inside as well of course) by Drumpf and his cronies is pretty certain to be very grave.

        Perhaps I misunderstand.

      • Gayle C Ferguson
        Posted April 8, 2020 at 7:31 am | Permalink

        I thought it was a good joke. Made my laugh anyway.

  4. Vaal
    Posted April 6, 2020 at 2:06 pm | Permalink

    These articles remind me:

    It’s been…bizarre…trying to map the religious, especially Christian, explanations for Natural Evils like the COVID 19 epidemic to the scientific study of and battle against the virus.

    The Pandemic has been flushing Christians and theologians out of the bush, having to try to make sense of faith in a Good God at these times.

    One of the more common theodicies I’m seeing these days to explain natural evils are that earthquakes, plagues etc aren’t God’s doing.
    No, of course not. God is Perfectly Good!
    Rather, it’s another form of the Free Will defense; in this case God has allowed the Free Will of spiritual beings to choose to do harm, just as He allows this of humans. (Examples being the devil and his minions).

    So there is the “cosmic battle” theodicy: we are engaged, along with God, in a battle against unseen spiritual entities exercising their malign free will to harm us, and THEY are behind natural evils like COVID 19.

    Well…how does that WORK, exactly? I put it to a Christian promulgating this theodicy:

    How, precisely, does this relate to natural evils such as the COVID 19 pandemic?

    Is the COVID 19 virus caused by these evil “spiritual powers?”

    If so..how? We would need to know these things if we are going to combat the virus. Scientists are devising strategies based on the virus being a natural phenomenon – following blind, non-sentient, predictable natural laws. But if the virus is instead created or influenced by unseen sentient spiritual powers, how can we predict how the virus may act? If a biologist working on a candidate vaccine maps the protein spike profile of the virus, might he come in the next morning to find the protein spike has been completely re-arranged by the tricky spiritual beings? If so..how could we possibly work out strategies against such unseen powers?

    If the scientist should NOT assume evil spirits may influence the virus in such unpredictable ways… why not?

    What ARE the rules here, for how this “spiritual influence” works in regard to natural evils like viruses or anything else?

    The fact is that any natural evil you can name, from earthquakes caused by the movement of tectonic plates, to killer viruses, seem to operate on nothing more than blind, natural laws, and the only successes we achieve in predicting and mitigating natural threats to our well-being works from that assumption.

    Unless the Christian can show how adding an evil spiritual power in the causal chain aids our ability to understand and predict such phenomena, that proposal is shaved away by parsimony.

    And for the same reason, as a theodicy, the proposal that “evil powers” are behind natural evils seems inert. It just hangs in the air as a vaguely expressed proposal without detail or real explanatory power. It’s an illusory and unsatisfying “explanation” that doesn’t really explain anything.

    Some Christians are also saying the Pandemic is a “wake up call” from God.
    It’s absurdly vague…wake up to what exactly? It doesn’t seem like any clear message anyone is getting…and at what cost?

    But the implications are the same as for the Cosmic Battle scenario: If the virus is being created or abetted by an Unseen Entity of unknown power…let alone Omnipotence…how in the world are we supposed to expect to use science to help predict and mitigate the virus?

    These are just thin mental band-aids for Christians. Just enough to cover their cognitive dissonance and place the “problem” on the shelf so they can get on to the good stuff of prayer and worship. It’s not cut out to do the work of convincing the not-already-convinced.

    • Filippo
      Posted April 6, 2020 at 2:18 pm | Permalink

      Perhaps at least a few Christians consider the coronavirus a “vehicle,” in the same sense they so consider Trump.

    • phoffman56
      Posted April 6, 2020 at 6:46 pm | Permalink

      IIRC, recently I’d read a number of around 44% of USian adults believe ‘the world will end before 2050’, whatever that’s supposed to mean. Presumably jesus will be swooping down and wreaking carnage is a part of that meaning for most of them.

      So reconciling Covid with most evngelical nonsense might not be all that difficult.

  5. Posted April 6, 2020 at 2:29 pm | Permalink

    I thought Covid-19 is God’s punishment to the world for America’s sin of electing the Anti-Christian known as Donald tRump. In the same vein as AIDS was God’s punishment for homosexuality.

  6. rickflick
    Posted April 6, 2020 at 3:21 pm | Permalink

    The Zimmer article looks worth a read. He always put things into readable language.

    • phoffman56
      Posted April 6, 2020 at 6:52 pm | Permalink

      Yes, Zimmer’s really good.

      By contrast, though I support them, WAPO’s science articles seem exceptionally anemic.

      Similarly poor often are NYTimes’ related to human diet and physical exercise (never Zimmer). The ‘jockstrap’ Faculties in a lot of North American universities are unimpressive, except to a few NYT columnists.

  7. merilee
    Posted April 6, 2020 at 4:39 pm | Permalink

    Sub

  8. James A Walker
    Posted April 6, 2020 at 8:35 pm | Permalink

    While deadly, viruses fascinate me – they show that the boundaries between life and non-life are fuzzy.

    • merilee
      Posted April 6, 2020 at 11:39 pm | Permalink

      Me, too.

  9. dd
    Posted April 6, 2020 at 10:18 pm | Permalink

    Of one protein the article says:

    “Human cells have antiviral proteins that find viral RNA and shred it. This protein works with NSP16 to camouflage the virus’s genes so that they don’t get attacked.”

    I thought about cancer cells ability to evolve in such a way as to short-circuit apoptosis.

    Does anyone know whether that protein that I refer to in the quotation above is common in viruses?

    Is there any connection to cancer cell’s ability to short-circuit apoptosis?


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  1. […] am not a biologist so read about the virus from someone who is. What interests me is this: viruses change by mutation, and the principle of natural selection (and […]

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