Virus science

Tomorrow, midnight, is the end of the quarter at Leg Iron Books and author royalties (if any) will go out on time. The anthology is going ahead too, it will close for submissions on March 31st although editing and publication will be delayed because of my father’s funeral. The delay on that has also put a complete stop on my own writing and on any kind of marketing.

I’m estimating mid to late April for publication on Anthology 11. It doesn’t affect this one too much since it’s not tied to a specific event like the Halloween and Christmas anthologies. It will be the Spring anthology, just a little later than usual. Spring is going to be delayed too, if there is any accuracy in the weather forecasts.

Anyway, science. I am/was a bacteriologist, not a virologist. I specialised in intestinal disease, pro- and prebiotics and in developing farm animal feeds mainly. Also, intestinal simulations, so I could run experiments on gut contents without animals messing it all up. So this is going to look a bit simplistic to a virologist who will have studied this in far more detail than me.

The current coronavirus is generating all kinds of conflicting reports, from ‘oh it’s just the flu’ to some serious tinfoil-hatted conspiracy theories. I read one that claimed the Spanish flu was bioengineered, some 30 years before Watson and Crick and around 70 years before DNA sequencing became a viable lab procedure. This somewhat dented the credibility of that story.

First, it is not the flu. The first round apparently has mild flu-like symptoms and will kill maybe 2% of those it infects. I have seen heartless bastards on Twitter type ‘yeah, but it’s just the elderly and the sick who die’. Will they say the same if their parents get it? Oh, and the doctor in Wuhan who died was 33 and in fine health.

The problem with this one, as compared to flu, is that it has a long incubation period where an infected person can shed the virus for around two weeks (or possibly more) without showing symptoms. Flu doesn’t do that. It also seems to have a gene or two from HIV which means it’s much more likely to infect anyone it comes in contact with.

It also appears that you don’t develop immunity, as with the common cold. You can catch it again. This means that even if someone does develop a vaccine it will be irrelevant. You simply do not develop immunity. The vaccine will achieve nothing. Or… it could make things much worse.

This one seems to do most of its killing on the second round of infection. It seems to be able to use antibody-dependent enhancement which means that the second time it infects, your immune system can’t kill it even though it’s trying to. This might or might not be the case, there is still a lot nobody really knows about this thing.

As Delphius says, it is possible that the first ‘infection’ was really normal flu or a cold, misdiagnosed. That would be understandable. The Chinese medics are overwhelmed and the authorities are dragging anyone with a temperature or a cough into the coronavirus hospitals. So, maybe they only caught the coronavirus after they arrived. The deaths could then be due to already-sick people getting stuffed in with those infected with coronavirus, and simply being overloaded with two respiratory infections at once.

So it is not flu. It has a remarkably long incubation period during which it is infectious and it is much, much easier to catch than flu. If it is true that you cannot develop immunity and that the second infection is far more serious than the first, then it really is nothing at all like flu. It’s too early to be certain on those last two points.

So, is it a bioweapon? Well it would be a really good one but only an idiot would release such a bioweapon in this age of global travel. You could get several times around the world before showing symptoms. Bioweapons are not going to stay where you put them, that should be obvious. There is a very good chance it will come back to bite you.

A bioweapon should not have a high kill rate. Your victims would simply bury or cremate the bodies and move on. A bioweapon should debilitate, while killing just enough to scare the crap out of everyone else. Loads of sick people will have exactly the effect we are seeing – medical facilities overwhelmed,infrastructure collapsing, travel and supply chains shut down…

The theory that it is a bioweapon comes from the HIV-like genes in it. Could that have been made in a lab? Oh hell yes. Building a strand of viral DNA or RNA is no problem. There isn’t much of it and we have machines that can do it overnight. It has in fact been done – poliovirus has been created in a lab. But that doesn’t mean someone made it, only that they could.

The other option – could it arise naturally? Viruses do not mate within their own species, much less with other species. They only reproduce within a host cell. They change due to mutations and errors in copying their genetic code and in assembling new viruses.

When a virus infects, it dumps its genetic code into the cell. That code, DNA or RNA, then uses the cell’s own mechanisms to read its genes and assemble new viruses. It’s like someone getting into a factory with a set of blueprints and making their own stuff using the factory’s tools.

The thing is, they are idiots. They have the blueprints to make new copies of themselves but the mechanisms they are using are not set up to make viruses. Oh each cell might make hundreds of viruses, in an infection there might be billions of new viruses produced but a lot of them will be wrong.

In the case of this Coronavirus it will create protein coats and stuff RNA into them. Some of them will be missing genes and won’t be viable. Some protein coats won’t have any RNA in them. Some will be filled with RNA from the host cell. Some will have a mix of virus and host RNA. These will attach to other cells and inject whatever they have inside, which will do… nothing, usually. This happens with all viruses. They make loads of copies in each cell but a good proportion of those copies are failures. Doesn’t matter, as long as they make enough good ones.

This has actually been considered as a treatment for some genetic ailments, such as cystic fibrosis. Create viruses containing the host’s missing gene and hope the cells take it up. I haven’t heard any more on that for years so I don’t know whether it progressed.

Right, so how does it get HIV genes?

HIV is a retrovirus. It contains RNA, but on entering a host cell it uses an enzyme that’s only found in retroviruses, called reverse transcriptase, to turn its RNA into DNA.

I should digress a little here… Living cells above viruses store their genetic information in DNA. The proteins it codes for are made on little machines called ribosomes. The cell has to get copies of the blueprints (DNA) to the machines (ribosomes) without using up its only original copy, and if it wants to make a lot of one particular protein it will need more than one copy anyway. This involves an enzyme called transcriptase which makes RNA copies of the DNA blueprint. The ribosomes use the copies, not the original, to make proteins. There’s a lot more to it but I’m retired from lecturing 😉

So, HIV gets its RNA in, turns it into DNA and now it has a master copy to make multiple RNA copies for the ribosomes.

But wait – HIV has another trick. Once it’s turned into DNA it can get into the host DNA and hide there. It can then send out a few copies as RNA to make just a few viruses at a time. The host doesn’t get sick, doesn’t even know it’s there, possibly for many years.

Now, if a coronavirus infects a cell that’s already infected with HIV, and the HIV is currently making a few copies to send out into the world, it is possible that a few of the protein coats contain full coronavirus RNA plus a few genes from the HIV RNA. Most of them will contain genes that don’t help but a few might contain the genes that give it a new site of attachment to the host cell.

Attachment is coded into the protein coat, how it sticks to cells depends on the proteins on its surface. If it picks up the right HIV genes, its next infection will produce protein coats with the HIV attachment sites built in.

It really doesn’t need more than one per billion to get this new virus going. Out of the billions sneezed out, only one single enhanced virus needs to get into a new host and the new host will sneeze out billions of the new virus. It has an advantage over its ‘parent’ in that it is now better at attaching to host cells.

Yes. It could have arisen naturally. Mutation and development of any creature is simply a numbers game and viruses produce numbers that will make an astrophysicist’s head hurt.

That just leaves the long incubation period.

The classic school-level teaching of viruses is very basic. Virus gets in, makes loads of copies of itself, bursts the host cell and infects other cells. Many viruses do this.

Not all. Some viruses ‘bud off’ their copies from the host cell so the host cell stays alive longer and therefore makes more copies of the virus before it dies. A HIV virus hiding in the host DNA will do this for years, and we already know the new coronavirus has acquired some HIV genes.

So – and this is pure theory – suppose it’s budding off viruses but not killing cells for a few weeks before it goes – ahem – viral. You don’t get sick yet. It doesn’t have all of HIV’s genes, so it can’t do this for years, only weeks. It has the gene that makes it a more efficient infector and maybe a gene or two for the slow release mechanism. That could have been engineered without much difficulty using modern equipment but it could also have arisen by pure chance.

If the chance of it arising is one in a hundred billion… that’s one infected HIV patient. Just one.

It’s not flu. This is far more dangerous.

The biggest problem is governments. Governments are fixated on money and viruses don’t care about money. Governments have no idea at all how to control a new virus, they only know about ‘the economy’. I am not talking about any particular government. I’m talking about all of them.

There is much wailing and gnashing of wallets over stock markets plummeting. The virus does not care. You can’t bribe this thing any more than you can bribe the climate. Oh they’ll try throwing money at it. It will achieve nothing at all.

If it has a reinfection level like the common cold then vaccines will not work. If second infection is really worse than first infection then vaccines will kill you. The vaccine counts as the first infection.

Nobody cares as long as they make money.

I wonder what they think they’ll spend it on?

12 thoughts on “Virus science

  1. “vaccines will kill you” nothing new there, then. Further, I think the MSM are missing an obvious trick here. “Coronavirus linked to HIV”, “Another virus targets gays”, “Have you visited China or had unprotected sex lately?” I need to apply to be a headline writer!

    On a serious note, thank you for the real science on viruses – it makes a change from all the pretend science we’re bombarded with.

    Liked by 4 people

  2. Because I did biochemistry, many folks round here ask me for adivce now about this matter.

    I am saying that I don’t think there is very deep cause for alarm, so long as people are hygienic, wash hands and faces regularly with proper soap and possibly disinfectants and detergents), try not to contact people that have come from suspect places, be careful about opening food packaging (!) (Chinese goods from China!, for example) and so on.

    Oh and don’t go to swimming pools. The sort of people that go to pools and thrash about orgasmically may well be the sort that travel widely. it kinda goes together in my mind.

    Liked by 1 person

  3. The only one that’s consistent and updated regularly is this table that’s tracking stats from China.

    https://www.worldometers.info/coronavirus/coronavirus-age-sex-demographics/

    It shows that the mortality rate is highest amongst older people, however we tend to have preexisting conditions and that involves drugs to treat whatever it/they are – and some can play havoc with immune systems. I had to take chemo tablets 12 years ago, so some experience.

    That’s true of people of all age groups and special needs children have awful problems with their lungs, some so bad they need to be fed direct into their stomach, because they can’t swallow.

    To an extent President Trump is correct; based on what he’s been told, to make it simple. If you’re in good health you’ll be fine – any age.

    Regards these people who comment that it just kills the old and infirm, the irony is one helluva lot of those commentators are themselves old, defined as being 60 and up!

    The psychopaths who actively wish harm on others, well we’re surrounded by them, smokers especially. As long as they stick to comments.

    Not this

    https://www.liveleak.com/view?t=kpL8j_1581427266

    Woman deliberately spits on elevator buttons, under 60 seconds video.

    Like

    • Well, in just over a month I move from the 50-59 group into the 60-69 group and my risk triples 😦

      On the plus side, I don’t have any pre-existing conditions and take no medication.

      I’m still avoiding contact with people, but I always did anyway.

      Liked by 1 person

  4. I haven’t heard any more on that for years so I don’t know whether it progressed.

    Maybe this is the progression and it escaped.

    Like

  5. Thanks for the mention, but my theory about the first infection being flu seems to be a bit premature. There is a female patient that has been tested as positive for NCOVID-19 and then clear, but then tested positive again. This time in Japan where the medics tend to be a bit more thorough. So I tend to believe the reports.

    The ability of NCOVID-19 to re-infect or stay dormant within the body somehow seems to be more likely given the new reports. What that does for infection rates and effective quarantine measures in anyone’s guess.

    A long incubation period, the ability (possibly) to lay dormant and re-emerge, the high transmission rates…. NCOVID-19 is a bloody nightmare.

    I didn’t mention it previously as the ability to re-infect wasn’t proven, but there are further rumours that the initial NCOVID-19 infection can leave the person with cardio-vascular issues. So the second infection can be more deadlier than the first due to the underlying issues the first leaves the patient with.

    I see the number of cases in the UK, just virtually doubled. I’d be surprised if today’s total hasn’t doubled again by this time next week.

    The ability for a patient to test negative and then positive a week later looks bad given people that have tested positive have been let out into the population already. The protocol may need to change and the release date after a negative test may need to extend quite a while before a patient can be released. Or we go for the North Korea option: shoot anyone that tests positive.

    This may be a good year to become a hermit and live in a cave for the next decade or so.

    Like

    • Way ahead of you. I’ve always been an antisocial old grump and already live in the middle of nowhere 🙂

      Dengue fever is another that does the reinfection thing. It’s not unprecedented. Heck, the common cold does it.

      I think this one could be a long term issue.

      Like

  6. One of the points I didn’t mention to keep my post short was the difficulties of containing NCOVID-19. Given the issues we already know about the virus, containment is going to take a whole lot more than the measures currently in place.
    If it remains dormant in a host and can re-emerge at any point in the future, then the protocol may change to keep hosts in permanent isolation until they are no longer transmissive. I leave it up to you what that means.
    It certainly looks as if current measures do not match the virus’ abilities. Unfortunately science’s plan is to watch and react to the virus as facts emerge. It may be things are too far gone before adequate measures are put in place.
    Considering the ease at which the virus is transmitted, I’m surprised there’s been no word about contacts of virus carriers being put in isolation.
    I also blogged about financial pressures on the low-paid and how people may be tempted to not get checked and still go to work because they can’t afford to stay off work for two weeks.
    The government needs to get a lot more serious about this virus, that’s for sure.
    Maybe the outcome of this is the People of North Sentinel Island get to inherit the world.

    Like

    • When I worked as a janitor I was paid by the hour. No sick pay – you don’t turn up, you get no pay. I saw people come to work when they were sick as hell.

      A lot of people are in that situation and they will not take days off for something that looks like a cold or mild flu.

      An awful lot of them work in the food industry.

      Like

  7. Here’s a ray of hope: there are some readily-available existing drugs, which are potent anti-virals and which are active against corona virus, AND which are currently available.

    Two interesting ones are chloroquine (an anti-malarial so old that most malaria parasites are resistant to it) and a derivative, hydroxychloroquine which the Chinese say is three times more active against corona virus than is chloroquine.

    I have duly ordered a couple of boxes of chloroquine. It is quite readily available at the moment, and can be bought off-prescription; we can expect this to rapidly change when the Great UnClued get wise to this.

    Like

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