Virus mutation by artificially guided selection

[artis]

I came across an article on CNN on a bunch of scientists researching the dangers of very old viruses that have been "paused" within the northern permafrost and their prospects of causing infection due to their release which might happen as the permafrost decreases.

https://edition.cnn.com/2023/03/08/world/permafrost-virus-risk-climate-scn/index.html

In 2014, he managed to revive a virus he and his team isolated from the permafrost, making it infectious for the first time in 30,000 years by inserting it into cultured cells. For safety, he’d chosen to study a virus that could only target single-celled amoebas, not animals or humans.

The more knowledgeable folks, could you please comment about this in terms of taking a virus found in nature and putting it within artificially prepared cell cultures within a lab or lab like environment, how does that "speed up" the process of evolution?

My current understanding is that in the wild a virus can only mutate if it has a host that can serve as the "breeding ground" where the virus can live and mutate as it lives. If the virus is outside a host it either dies or as in the permafrost case it stays within the animal that died and became frozen in which case it gets frozen in time as it seems. Either way the process of mutation and natural selection stops.

Now I would think that a virus in the wild does have a rate of evolution but that rate can be increased by taking it and artificially putting it into certain cell cultures where it can have beneficial climate in which to mutate.

I guess I'm asking , whether with today's knowledge and technology certain people with knowledge and technical ability can take such old viruses and artificially speed up and "guide" their evolution in a certain direction where they could potentially make them fit for , say humans for example" and then they would pose a great risk or could be turned into potent biological weapons ?PS. To formulate the question in different terms - if a virus cannot interact with certain cells does the likelihood of it adapting/mutating to be able to interact with those cells increases if it is artificially or naturally kept into contact with those cells, does that increase the chance or a favorable mutation to appear to help it establish interaction ability?

 

[BillTre]

I think you are confusing some things.
In almost all cases, mutations occur randomly without respect for their possible success or where they are.
Natural (or other kinds of) selection selects among the the variants in a population for those can survive and reproduce.
Except for the presence of mutagens of possible triggers of mutagenesis (like maybe triggering transposon activity), the environment would not be expected to affect the production of new mutants.
Environments, like being in a cell where they might reproduce, can select for the mutations that could possible thrive there.
Certainly, a virus won't survive long (unfrozen) without a cell in which to reproduce, but the cell does not cause new mutations to make it better suited for infecting those kinds of cells, but it is not causing the mutations. Its more like it provides a place where further mutations might occur from which variants better suited to that kind of cell can be selected.
The selection among the variants is what is doing the guiding of which you write.

If you were to further mutate the viruses artificially (in a cell or not) you could speed up the rate of evolution by increasing the variety of variants available for selection to pick among.
This would not have any "guiding" function unless the mutagenesis was skewed in some way toward certain mutations (perhaps by a transposon insertion bias).

 

[artis]

In almost all cases, mutations occur randomly without respect for their possible success or where they are.
Natural (or other kinds of) selection selects among the the variants in a population for those can survive and reproduce.

Sure I know it's random, but artificially giving the virus a beneficial ground to thrive is not random, this increases it's likelihood of survival and therefore the chances of it arriving at a particular mutation that either allows for better survival or allows for jumping to new species.
The way I see it is like keeping a wild animal as a pet, the chance of it biting your head off is random of course but by living together in the same room one increases that chance by alot.

the environment would be expected to affect the production of new mutants.
Environments, like being in a cell where they might reproduce, can select for the mutations that could possible thrive there.

So essentially one could "grow" the virus and then introduce it to the "target cells" of choice and then make as many parallel such cell cultures as possible which would increase the likelihood that in one of them a mutation occurs that allows it to become adapted to the target cell?
I assume the more parallel "dishes" of the same virus within the same target cell culture the higher the chance that of all the parallel mutations taking place one would hit the "jackpot" ?

This is what I had in mind by artificially guiding the evolution process, sure the mutations stay random and natural selection selects for the most potent ones, but if one spreads out this process in a largely parallel way where the same virus is allowed to "randomly experiment" as many times as possible it does seem to increase the chance of shortening the time it would otherwise take to adapt if ever.

If you were to further mutate the viruses artificially (in a cell or not) you could speed up the rate of evolution by increasing the variety of variants available for selection to pick among.

I guess I was saying this.

It seems to me it's like trying to pick a code (of a certain target mutation for a target cell culture) where you randomly go through all possible numbers but the chance of arriving at the right one increases with increased parallel guesses per time.

 

[BillTre]

Sure I know it's random, but artificially giving the virus a beneficial ground to thrive is not random, this increases it's likelihood of survival and therefore the chances of it arriving at a particular mutation that either allows for better survival or allows for jumping to new species.

Agreed, this is what I said.

The way I see it is like keeping a wild animal as a pet, the chance of it biting your head off is random of course but by living together in the same room one increases that chance by alot.

Not a comparison I would make.

So essentially one could "grow" the virus and then introduce it to the "target cells" of choice and then make as many parallel such cell cultures as possible which would increase the likelihood that in one of them a mutation occurs that allows it to become adapted to the target cell?
I assume the more parallel "dishes" of the same virus within the same target cell culture the higher the chance that of all the parallel mutations taking place one would hit the "jackpot" ?

Makes sense.

This is what I had in mind by artificially guiding the evolution process, sure the mutations stay random and natural selection selects for the most potent ones, but if one spreads out this process in a largely parallel way where the same virus is allowed to "randomly experiment" as many times as possible it does seem to increase the chance of shortening the time it would otherwise take to adapt if ever.

Yes, but in explaining things your should use the terms correctly, or people will get the wrong idea.

I made a mistake when I said:
"the environment would be expected to affect the production of new mutants."
It should have been:
"the environment would not be expected to affect the production of new mutants."
Sorry, left out a word.
Have edited it.

I guess I was saying this.

It seems to me it's like trying to pick a code (of a certain target mutation for a target cell culture) where you randomly go through all possible numbers but the chance of arriving at the right one increases with increased parallel guesses per time.

 

[Tom.G]

where you randomly go through all possible numbers but the chance of arriving at the right one increases with increased parallel guesses per time.

"Chance" as used here is generally defined as the likelihood of a stated outcome for a given total number of experiments/instances.

That said, the "Chance" of something specific occuring depends not on the elapsed time but on the total number of experiments/instances observed.

What does decrease with multiple concurrent experiments is the clock time expected for the stated outcome to occur.

 

[artis]

What does decrease with multiple concurrent experiments is the clock time expected for the stated outcome to occur.

Exactly, so essentially a speed up of what naturally might take much longer due to the rare occurrence of necessary conditions.

 

[BillTre]

It is likely that natural infected populations of cells (in wild animals) would be much larger than the number of test situations you could set up in a lab.
This could result in a greater likelihood of viruses accumulating mutations in wild animals than in lab tests of the same cells that would result the viruses become more successful in infecting those kinds of cells.

 

[Rive]

It is likely that natural infected populations of cells (in wild animals) would be much larger than the number of test situations you could set up in a lab.

I'm not so sure. A petri dish culture does not have an immune system to clean up the added viruses and also: not much of a wild population will be infected (with a virus not specific for the species).

You need a virus which is by default already not strictly specie-specific (like flu or Covid) to see any widespread infection 'in the wild'. But for a specie-specific virus to jump species you need a really bad luck with singular events.

 

[BillTre]

I'm not so sure. A petri dish culture does not have an immune system to clean up the added viruses and also:

Working against an immune system could be thought of as providing a better homing of an effective virus in an intact animal (with immune system). In a petri dish, any existing adaptations for dealing with immune systems ight even be lost due to lack of selection for it.

not much of a wild population will be infected (with a virus not specific for the species).

You need a virus which is by default already not strictly specie-specific (like flu or Covid) to see any widespread infection 'in the wild'. But for a specie-specific virus to jump species you need a really bad luck with singular events.

There have been for example cases of COVID-19 infections in non-human animals:

• Big cats
• Otters
• Mink
• Non-human primates
• White-tailed deer
• Spotted hyenas
• Hippos
• Ferrets
• Bearcats (binturongs)
• Coatimundis
• Fishing cats
• Manatees

The deer population's infection is pretty extensive I think. There are probably more wild deer than there are cultures containing cells intentionally infected with viruses.

Also notable is that this is a wide ranging group of infected vertebrate taxa (species and larger than species groups, like genera, classes etc.).
There does not seem to be a phylogenically inherited susceptibility to the virus. Its a scattered group (unless it can infect alll vertebrate species, but has not yet shown to) containing carnivores, primates (many), hippos (related to pigs), and at least one species of deer (artiodactyls, even toed large herbivores).

There are a lot of viruses, many unknown. Their infectivity across different host species is not well known. This is why there has been so much confusion about coivd19 history.
Figuring that out would require an extensive combined field and lab operation. Not going to happen without a good economic reason (like human health or agriculture).
Viruses, as with most infections, are mostly known in humans, some pets, and agricultural animals.

I have long worked with zebrafish. This is a relatively new research animal among thousands of other fish species. As it became a well established research animal (more than a thousand labs), we wanted to be more knowledgeable of what might be infecting them (in order to make more perfect experiments).
20 years ago, not much was known about zebrafish pathogens, including viruses. Now there are lot of academic and industrial fish vets working on them (I probably know 10 personally). Many of these vets came from the aquacultural world, some from a more general research background. Both of these have a long standing economic reason to acquire this knowledge. Aquacultural species might number 40-60 species, but the most common ones might be about 20 species.

Some pathogens can infect widely among different sized groups of fish species, some are very specific. Some can even infect people.

 

[artis]

It seems based on the many random variables and time it takes and other reasons mentioned in this thread that the route labs typically chose is "gain of function" am I right?
In this way one doesn't have to wait for the lucky moment one can change the virus side stepping evolution a little to make it infectious to the target cell culture to see the result.

It depends on the goal of course whether they simply want to see how fast the virus will on average arrive at the needed change naturally or whether it can become infectious to certain target cells and therefore to the hosts of those cells, because it seems the latter is the result usually sought after then gain of function seems like a good avenue to find that out ?

As for Covid, @BillTre refresh my memory but IIRC, before the Covid pandemic set off we had no data on any Covid or Covid like virus spreading on a large scale within the very animals you mentioned ?
If we assume Covid came about naturally , it should have been present in the species that served as the intermediary (pangolins?) between the original source (bats? RatG 13?) and humans?

Sure enough I doubt pre Covid anyone would have been interested to regularly test various animals for respiratory viruses within China, although assuming they did have a big database of Coronaviruses it seems likely they did routine safety checks.What does make me suspicious among other things is that Covid managed to jump species so fast and be so fit at the same time, sure respiratory viruses mutate fast but given it's capability of transmission wouldn't the likelihood that it would be seen in the intermediate animal before it jumped to humans be high?
Unless of course it made no symptoms within those animals and given it couldn't be outwardly checked nobody cared enough to do blood tests for those animals.
What you know @BillTre ?

 

[BillTre]

Human directed gain of function mutations will only be effective if it is understood what is needed molecularly before hand. Otherwise, it will just be random guesses.
this kind of knowledge is not always available.

Others probably know more about this than me.
However, there have been other covid type viruses that infected humans and some kind of animal.

All seven HCoVs have a zoonotic origin from bats, mice or domestic animals 2,20. Multiple lines of evidence support an evolutionary origin of all HCoVs from bats, where viruses are well adapted and non-pathogenic but show great genetic diversity.

As for Covid, @BillTre refresh my memory but IIRC, before the Covid pandemic set off we had no data on any Covid or Covid like virus spreading on a large scale within the very animals you mentioned ?
If we assume Covid came about naturally , it should have been present in the species that served as the intermediary (pangolins?) between the original source (bats? RatG 13?) and humans?

Yes and yes.

 

[artis]

Yes and yes.

Ok, but then let's say SARS Cov-2 came originally from a bat, before it infected the first humans in Wuhan, what would be the average time it had to spend within the intermediary species?

I understand this is hard to determine as random mutations can take forever to "crack" the right mutation along the way randomly or they can hit the jackpot very soon, but I assume there are some statistical averages for respiratory viruses to mutate to adapt to new host species, I would assume it's not days more like months ?

What I'm trying to understand is how realistically Covid could have hid within the intermediary without anyone noticing which it seems would very much depend on the time it was there.

Here is a research paper analyzing among other things the genetic sequences to see the closest intermediary , but it says that the pangolins the were infected did show signs of infection and some even died
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9408936/

CoV-infected pangolins showed clinical symptoms of the disease, and 14 infected animals died within a span of 1.5 months

It also turns out pangolins are the most trafficked mammal in the world...
https://www.cambridgeconservation.org/the-plight-of-the-pangolin-the-worlds-most-trafficked-mammal/

plight of the pangolin – the world’s most trafficked mammal.

So it seems that , say for example, Covid had to stay in pangolins for at least few months before it jumped to humans, it seems someone should have noticed something was off, not claiming but it seems likely.

 

[BillTre]

Ok, but then let's say SARS Cov-2 came originally from a bat, before it infected the first humans in Wuhan, what would be the average time it had to spend within the intermediary species?

Not easily determined.

In infected animals, recombination can occur between the genomes of two different viruses if they aare in the same cell at the same time. This could also be between two different kinds of viruses.

Many viruses may present no symptoms in different species and therefore easy to overlook.

 

[artis]

In infected animals, recombination can occur between the genomes of two different viruses if they aare in the same cell at the same time. This could also be between two different kinds of viruses.

By that you mean , a freak accident where two viruses happen to be there at once and create a mutation that otherwise wouldn't come along therefore allowing the new mutated virus to immediately jump species once it gets the chance (contact etc) ?

Why it's called recombination if those two viruses never before met at the same cell before? Seems more like simply combination?

 

[BillTre]

By that you mean , a freak accident where two viruses happen to be there at once and create a mutation that otherwise wouldn't

I would say would be unlikely to come along

come along therefore allowing the new mutated virus to immediately jump species once it gets the chance (contact etc) ?

It could result in any new phenotype. Not necessarily jumping species, but that could be possible.

 

[Rive]

Working against an immune system

The keyword there will be the 'working', I think. The virus already needs to be able to actually infect the host (just just being injected/exposed won't do) so new viruses could be produced for any adaptation to happen.

If no actual infection happens then the immune system will just clean up the unknown trash and then the experiment ends.

In a petri dish there will be a longer, undisturbed exposure (and more, controlled tools/means/circumstances might be available) for species-jumping to happen.

It's about two different approaches for different purposes.