Delta variant... convergent evolution?

[PeterB]

Delta now present in at least 37 states. What's interesting (not in a good way) is that it seems to be arising independently in different countries, and also we're already seeing additional mutations (what is now being referred to as "delta plus"). It's been described as coronavirus on steroids.

https://www.cnbc.com/2021/06/16/who-says...ating.html

https://www.livemint.com/news/india/new-...65835.html

[pdq]

Yup, as I’m sure PeterB knows, that’s the way evolution works. If there’s a way of increasing transmissibility, given enough time and coronaviruses in the wild, life will find a way, often repeatedly.

Increased pathogenicity doesn’t typically benefit the virus though, so we can hope that drift will make for a less deadly, albeit more contagious virus. But that’s just hope at this point.

[pdq]

PS- I’ve seen this (kind of) story so many times now I’m ready to puke:

Texas man who declined COVID-19 vaccine speaks out after undergoing double lung transplant

The Texan is hoping to inspire others to get the shot now.

…”COVID ended up attacking my lungs," Garza, of Sugarland, told ABC News.

No! Your lungs? Ya don’t say. Couldn’t see that one comin’.

:RollingEyesSmiley5:

Yup. One hundred and thirty thousand healthcare dollars later this guy is here to say that it turns out the Coronavirus is really real.

Thanks, buddy.

[PeterB]

pdq wrote:
Yup, as I’m sure PeterB knows, that’s the way evolution works. If there’s a way of increasing transmissibility, given enough time and coronaviruses in the wild, life will find a way, often repeatedly.

Increased pathogenicity doesn’t typically benefit the virus though, so we can hope that drift will make for a less deadly, albeit more contagious virus. But that’s just hope at this point.

What's really concerning to me is that they're already seeing the secondary mutations ("Delta plus", etc.) ... lending credence to my idea that the longer you give this virus to cook, the more likely we'll be seeing something where the vaccines are largely or wholly ineffective. This particular virus seems to mutate at a frequency a bit higher than you'd expect for a coronavirus. The fact that it's apparently independently developing the same mutations in separate strains, suggests that there is indeed a selection process going on with this virus.

As for pathogenicity -- from the virus perspective, increased transmissibility and pathogenicity are advantageous. The virus just wants to make more copies of itself, and increased pathogenicity generally means that you're doing exactly that. So long as the pathogenicity doesn't interfere with transmissibility, that you don't kill the host before you've had plenty of time to develop new mutations and transmit yourself to other hosts. Also, it occurs to me that there's a very good chance that someone infected with these variants might inadvertently pass to an animal host, and then mutate and pass back to a human host. Hasn't happened yet, so far as we know, but it's just a matter of time...

[Ca Bob]

Well, the RNA dependent RNA polymerase that replicates the Covid-19 genome gets it right 9999 times out of 10,000 which means that in an average replication, there are 3 mutations on the average (most probably neutral) and in an average human case there will be something like billions or trillions of new copies of the virus. This presumably means that every single nucleotide in the viral genome gets changed at least once as it goes through any human with severe illness. Some runs of nucleotides get changed. There is also evidence for a kind of strand switching in which one viral genome ends up mixed with another. So there is a lot of mixing and switching and mutating going on. Probably the only thing protecting us from an immediate super virus is that there is only so much that this one little genome can do and, in addition, the virus particles that escape a sick individual to infect someone else are going to be the ones that replicate effectively and find their way into exhaled vapors and cough particles. Mutations that damage these processes will be lethal to the virus. On the other hand, a mutation which works a little more efficiently in a particular population will get the edge when there are thousands of new cases.

[sekker]

We are playing the horrible game of 'Pandemic Russian Roulette' until we truly stop the virus from growing.

The only good news I've heard is that the non-B cell immunity seems to effective against all of the known common variants.

We will see whether COVID-19 is more like polio, where a single vaccine will work for years (even though all viruses can mutate), or whether it will be like the seasonal flu.

[PeterB]

Ca Bob wrote:
Well, the RNA dependent RNA polymerase that replicates the Covid-19 genome gets it right 9999 times out of 10,000 which means that in an average replication, there are 3 mutations on the average (most probably neutral) and in an average human case there will be something like billions or trillions of new copies of the virus. This presumably means that every single nucleotide in the viral genome gets changed at least once as it goes through any human with severe illness. Some runs of nucleotides get changed. There is also evidence for a kind of strand switching in which one viral genome ends up mixed with another. So there is a lot of mixing and switching and mutating going on. Probably the only thing protecting us from an immediate super virus is that there is only so much that this one little genome can do and, in addition, the virus particles that escape a sick individual to infect someone else are going to be the ones that replicate effectively and find their way into exhaled vapors and cough particles. Mutations that damage these processes will be lethal to the virus. On the other hand, a mutation which works a little more efficiently in a particular population will get the edge when there are thousands of new cases.

To add to this-- mutations in the RNAD-RNA Pol itself can reduce replication fidelity, so that we end up with even more mutations, plus the fact that the virus has known mutational hotspots. And the strand swapping to which you're referring can happen with a person who is co-infected with more than one coronavirus, which one could see happening especially in cold-weather months (see below). So yeah, we're dealing with a "when", not an "if", kind of situation here.

sekker wrote:
We are playing the horrible game of 'Pandemic Russian Roulette' until we truly stop the virus from growing.

The only good news I've heard is that the non-B cell immunity seems to effective against all of the known common variants.

We will see whether COVID-19 is more like polio, where a single vaccine will work for years (even though all viruses can mutate), or whether it will be like the seasonal flu.

My guess is that it will be the latter. Coronaviruses make up an estimated 10-20% of all "common cold" cases, and someone -- sooner or later -- might get co-infected with both viruses. Then all hell breaks loose. (The difference, as I see it, is that polio is not running around rampant right now...)

Non-B cell immunity is good, but not for everyone... there are the immunodeficient/immunocompromised to think of. Also, even non-B cell immunity wanes over time... the estimate for MERS and SARS was that immunity might last 2-3 years at most.

And yes, we need to keep this damned virus from replicating. The 60% or so in my state who refuse to get vaccinated aren't helping matters...

[Filliam H. Muffman]

Didn't it used to be standard theory that a virus/bacteria always eventually selected higher transmission and lower mortality? I guess in modern populations that include immune compromised people with some form of vaccine antibodies, that this virus hasn't hit the lower mortality phase yet...

[Janit]

Filliam H. Muffman wrote:
Didn't it used to be standard theory that a virus/bacteria always eventually selected higher transmission and lower mortality? I guess in modern populations that include immune compromised people with some form of vaccine antibodies, that this virus hasn't hit the lower mortality phase yet...

That could happen in this case too, but it may take some time. Moreover, additional factors now complicate the trajectory involved in achieving equilibrium: international travel, modern medicine, etc.

The virus/bacterium is not the only thing that changes. One route to lower mortality can be that the most susceptible humans die, and the survivors represent those who are genetically more hardy in face of the infection. Their progeny may be more disposed to experience milder symptoms. It is more useful to think in terms of a co-evolution between humans and the bugs.

[PeterB]

Janit wrote:
[quote=Filliam H. Muffman]
Didn't it used to be standard theory that a virus/bacteria always eventually selected higher transmission and lower mortality? I guess in modern populations that include immune compromised people with some form of vaccine antibodies, that this virus hasn't hit the lower mortality phase yet...

That could happen in this case too, but it may take some time. Moreover, additional factors now complicate the trajectory involved in achieving equilibrium: international travel, modern medicine, etc.

The virus/bacterium is not the only thing that changes. One route to lower mortality can be that the most susceptible humans die, and the survivors represent those who are genetically more hardy in face of the infection. Their progeny may be more disposed to experience milder symptoms. It is more useful to think in terms of a co-evolution between humans and the bugs.
There's been a suggestion that the co-evolution thing occurs at least partially in response to human behaviors, such as hand-washing (or lack thereof), social distancing (ditto), etc.

Also, again there has been a suggestion that the mutations are most frequently cropping up in patients who are persistently infected with the virus, which suggests that there either might be some co-infection going on (as I've proposed) or just the fact that you have a virus continuing to replicate in the face of various drugs and treatments is effectively causing an in-the-body evolution/selection for particular mutations.

It will be interesting (not in a good way) to see what happens with Delta in those states, like mine, where the majority are still unvaccinated and do not plan on getting vaccinated. Not only would I expect to see an explosion in cases and deaths, but the very real possibility of new, secondary mutations such as Delta plus. If one or more of these mutations causes the vaccines to be substantially or wholly ineffective, then we're all up the creek.