Evolution of Covid Strains.

[studiot]

We are (all?) washing our hands etc more and doing so with chemicals we hope will degrade coronavirus.

So would this lead to the demise of less resistant variants and development of those strains that are more resistant ?

[CharonY]

Unlikely. A virus has only limited features that would change their physical properties. Moreover even more complex bacteria do not appear to become resistant to physical disruption in any meaningful way.

 

[Janus]

Washing your hands is more about physically removing the virus from their surface than it is about killing the virus.

[ahmet]

55 minutes ago, Janus said:

Washing your hands is more about physically removing the virus from their surface than it is about killing the virus.

so, does this mean that in fact, we did not need to use soap? 

interesting.

if not; how do we remove viruses from the surface of our hands?

addition: I was almost forgetting bacteria.sorry. but the question still stands.

1 hour ago, studiot said:

We are (all?) washing our hands etc more and doing so with chemicals we hope will degrade coronavirus.

may I ask a question: I remember you had said that we would have a probability to face a new diseaase (i.e. pandemic) in a thread.

now turkish media announces a mutated version of covid19?

if this case satisfies your (or proves that you were right in your prediction), how did you reach that information?

Edited December 22, 2020 by ahmet

[swansont]

Soap does, in fact, kill COVID 

https://healthmatters.nyp.org/how-does-handwashing-with-soap-kill-the-coronavirus/

and helps remove it from your skin

https://www.uchealth.org/today/why-soap-and-water-work-better-than-hand-sanitizer-to-remove-the-coronavirus/

“Soap disrupts the sticky bond between pathogens and your skin, allowing the pathogens to slide right off. Not only are you neutralizing the virus with the soap, but you’re also physically knocking it off your hands,” Pastula said. “Hand sanitizer doesn’t do all of that.”

[CharonY]

With regard to OP, there are several strains of SARS-CoV-2 and one of them (B.1.1.7) seems to spread significantly throughout southern England, which carries around 23 new mutations compared to the original strain. There is evidence that it is more contagious, and potentially more infectious to children than the original. There is currently no evidence that it impacts lethality or vaccine efficacy.

[MonDie]

On 12/22/2020 at 10:07 AM, CharonY said:

Unlikely. A virus has only limited features that would change their physical properties. Moreover even more complex bacteria do not appear to become resistant to physical disruption in any meaningful way.

 

Hmmm, what about disinfection via tanning booth?  I wonder.

[StringJunky]

8 minutes ago, MonDie said:

Hmmm, what about disinfection via tanning booth?  I wonder.

You would need uvc and that's extremely dangerous to skin.

[TheVat]

Silence of the lambda may be over,  and researchers in Tokyo are asking the WHO to label it a variant of concern....

https://www.infectioncontroltoday.com/view/more-data-point-to-lambda-variant-s-potential-lethality

Quote

The World Health Organization (WHO) says that the lambda variant—or C.37 variant—has been the COVID-19 carrier in about 81% of infections in Peru since April. The variant was first identified in Peru in August 2020. The WHO declared the lambda variant a variant of interest (VOI) on June 14, a designation that means that it could cause a greater risk than the wild-type variant.

That’s an understatement, according to the investigators at the University of Tokyo, who want the WHO to label the lambda variant a variant of concern (VOC) to put health care systems around the world on notice that this might be their next big challenge. They write that “because the lambda variant is a VOI, it might be considered that this variant is not an ongoing threat compared to the pandemic VOCs. However, because the lambda variant is relatively resistant to the vaccine-induced antisera, it might be possible that this variant is feasible to cause breakthrough infection.”

 

[PhilGeis]

To the orignal questioin - washing hands and "chemicals" will not drive variant development.

[studiot]

18 minutes ago, PhilGeis said:

To the orignal questioin - washing hands and "chemicals" will not drive variant development.

Thank you for the reply, but you did not say why not.

[PhilGeis]

studiot - viral "evolution" is the result of mutation and selection.  Washing with soap or surfactants disprupts an essential general element of the virus the basic structure of the lipid coat - mutation in that aspect would be lethal.  "Chemical" - assume you mean alcohol, hypochlorite and other disinfectants.   These have similar primary and general denaturing effects.  

In any case, these factors would be less than de minimis in context of a global pandemic where mutation and potential selection are constant and exponential.

[studiot]

1 hour ago, PhilGeis said:

studiot - viral "evolution" is the result of mutation and selection.  Washing with soap or surfactants disprupts an essential general element of the virus the basic structure of the lipid coat - mutation in that aspect would be lethal.  "Chemical" - assume you mean alcohol, hypochlorite and other disinfectants.   These have similar primary and general denaturing effects.  

In any case, these factors would be less than de minimis in context of a global pandemic where mutation and potential selection are constant and exponential.

Thank you for the reply.

Your first paragraph makes a sensible and coherent point, but I could not understand your last line.

In the minimal amount of microbiology I did, they stressed the idea that 'killing' and entire population is not instantaneous in normal environments, you need a 'nuclear option' for that.

Some of a population will survive for a suprising amount of time in a hostile environment, even if degraded.

The degraded survivors may go on to deliver their payload, whereby a mutation may occur.

Some such mutations may 'evolve' into viable virii, more resistant than their parents, to the degrading agent.

[CharonY]

3 hours ago, studiot said:

In the minimal amount of microbiology I did, they stressed the idea that 'killing' and entire population is not instantaneous in normal environments, you need a 'nuclear option' for that.

Some of a population will survive for a suprising amount of time in a hostile environment, even if degraded.

The degraded survivors may go on to deliver their payload, whereby a mutation may occur.

Some such mutations may 'evolve' into viable virii, more resistant than their parents, to the degrading agent.

A few points here, viruses do not die, they are either intact particles, and capable of infections, or not. If they are degraded, they do not function anymore. Mutations occur when the virus replicates in their hosts, which, to re-iterated requires an intact particle to happen.

I.e. it would require random mutations to change the viral structure significantly to make them more resistant. As pointed out earlier, viral particles are comparatively simple structures and there is not a ton of room to add functions in such a fundamental way. 

Also note that even if such mutations could occur, they do not rise in response to stressors such as soap. Rather, it would be a selective pressure and in which already resistant strains would propagate faster than their non-resistant peers. 

 

[studiot]

6 hours ago, CharonY said:

A few points here, viruses do not die, they are either intact particles, and capable of infections, or not. If they are degraded, they do not function anymore. Mutations occur when the virus replicates in their hosts, which, to re-iterated requires an intact particle to happen.

A few points ?

So how did this virus, alllegedly exactly and perfectly tailored to the human race, suddenly arise from nowhere ?

6 hours ago, CharonY said:

Also note that even if such mutations could occur, they do not rise in response to stressors such as soap. Rather, it would be a selective pressure and in which already resistant strains would propagate faster than their non-resistant peers. 

Again where did these already resistant strains come from ?

 

I think also that you may not have fully understood my English.

 

Edited August 13, 2021 by studiot

[CharonY]

2 hours ago, studiot said:

So how did this virus, alllegedly exactly and perfectly tailored to the human race, suddenly arise from nowhere ?

Viruses are not perfectly tailored to anything. In fact, how would you measure that in the first place? The pathogens are piggybacking on many of our very conserved mechanisms, which are shared e.g. among mammals. In this case the first step is docking on the ACE2 receptors which many species carry.

2 hours ago, studiot said:

Again where did these already resistant strains come from ?

For soaps there are no known mechanisms. But if we take for example better known examples, such as antibiotics resistances, they have many different mechanisms. For some, it is simply a matter of having a point mutation, which changes the structure of the target protein of a given antibiotics (for example the ribosomes). Even in the absence of antibiotics those mutations occur. They could be neutral, but if they are not, they tend to be rare, as they may reduce the fitness of its carrier. However, in presence of antibiotics those mutations are now beneficial (are under positive selection) and they multiply more effectively than their counterpart. In other words, the strains come from mutations (but also via horizontal gene transfer for example) but it is because of positive selection they start to outcompete those that do not carry it. It is not that they develop those mechanisms as a response to a given stimulus.

2 hours ago, studiot said:

I think also that you may not have fully understood my English.

Quite possible, but the way you wrote it does seem to imply a Lamarckian mode of evolution. If that is not what you meant, an elaboration would be appreciated.

[studiot]

15 hours ago, CharonY said:

18 hours ago, studiot said:

Again where did these already resistant strains come from ?

For soaps there are no known mechanisms

Here is a good example of misreading my English.

All I did was quote your exact words "already resistant strains" and ask where they came from.

Your response did not contain the answer to that question.

15 hours ago, CharonY said:

Viruses are not perfectly tailored to anything.

So what is the response of other mammals to covid19 ?

In particular since they are posited to have started in bats or pigs or somesuch how do they affect these mammals?

[StringJunky]

25 minutes ago, studiot said:

Here is a good example of misreading my English.

All I did was quote your exact words "already resistant strains" and ask where they came from.

Your response did not contain the answer to that question.

So what is the response of other mammals to covid19 ?

In particular since they are posited to have started in bats or pigs or somesuch how do they affect these mammals?

Luck and environmental selection pressure brings them into dominance, They can come from anywhere. Wherever there is a virion, a mutant can arise from its replication. They don't have to 'learn' to be resistant, derived from a series of external pressures, a perfectly resistant mutant can also just happen to be spontaneously generated... it got lucky.

Edited August 14, 2021 by StringJunky

[CharonY]

1 hour ago, studiot said:

All I did was quote your exact words "already resistant strains" and ask where they came from.

I might not have been sufficiently clear. SJ has provided the answer perhaps more succinctly, but overall they are already there because we have genetic diversity. Some genetic factors result in resistances to things (but may be detrimental with respect to other situations). So while I tried to answer the question, I was not clear what your basic assumptions are that I needed to address.

1 hour ago, studiot said:

So what is the response of other mammals to covid19 ?

In particular since they are posited to have started in bats or pigs or somesuch how do they affect these mammals?

Quite a few mammals are susceptible to SARS-CoV-2 (the virus responsible for COVID-19). The most dramatic examples are minks, as whole farms needed to be culled due to infections in the Netherlands and Denmark, and infections have been reported for dog, cats, pigs, voles, hamsters, ferrets, macaques  and I am sure quite a few other animals.

However, if an infection leads to disease as well as the severity of disease depends on a lot of factors, most of which are still unknown, though at the fundamental level the immune system and inflammation responses will play a crucial role (which is why in humans we have the whole range of asymptomatic to severe disease, for example). 

Obviously, biological differences can also play a role, a simple model is the abundance of the receptors targeted by the virus in different tissue types and organisms. Macaques, for example have effective replication in higher and lower respiratory tracts, a varied range of disease severity and have clear lesions, similar to humans. I think for cats deaths have been reported. Hamsters, whose ACE2 receptors are very similar to ours have also reported extensive lung injuries.

SARS-CoV-2 is not related to viruses found in pigs, but is closely related to bat coronaviruses and somewhat related to those found in pangolins. Those coronaviruses tend to cause few symptoms in their respective hosts (similar to human coronaviruses in humans). From what I remember bats could get infected, but did not had any clinical symptoms, which is an expected finding for reservoir hosts.

As noted elsewhere on this forum, often a long co-evolution between host and pathogen results in infections that are less lethal for the host, if the overall fitness of the pathogens increases that way. However, zoonotic outbreaks, where viruses jump hosts can sometimes lead to high lethality, in part because our immune system does not react well to the new disease (sometimes overreacting, resulting in cytokine storms). It is important to note that this is not always the case, though. As such, the assumption of a "perfectly tailored" virus does not make much sense to me from a scientific standpoint.

What would be considered better tailored to a host? A virus that replicates very fast in its host but ultimately kills it? One that has bouts of dormancy but spreads slowly but steadily and is very hard to detect? How about a virus that integrates into our genomes but ultimately loses its ability to infect, but is now transmitted via offspring? 

 

 

[studiot]

 

47 minutes ago, CharonY said:

I might not have been sufficiently clear. SJ has provided the answer perhaps more succinctly, but overall they are already there because we have genetic diversity. Some genetic factors result in resistances to things (but may be detrimental with respect to other situations). So while I tried to answer the question, I was not clear what your basic assumptions are that I needed to address.

 

2 hours ago, StringJunky said:

Luck and environmental selection pressure brings them into dominance, They can come from anywhere. Wherever there is a virion, a mutant can arise from its replication. They don't have to 'learn' to be resistant, derived from a series of external pressures, a perfectly resistant mutant can also just happen to be spontaneously generated... it got lucky.

In other words we don't know.

But none of this is inconsistent with what I said.

You get some covid virus on your hands.

As String Junky said, some may be more resistant to soap than others or I suggest perhaps better protected by the destroyed (since you object to the word dead) outer virii.

Whatever the mechanism the protection is not perfect so the soap acts as a selective environment.

Exactly as I said, and you said and SJ said.

 

Yes we know that covid has jumped species.

Fear of that, as opposed to the welfare of the mink, was the reason for the mink cull.

Yes there was a report of a man who caught covid from his dog.

 

Again my 'assumption' of a perfectly tailored virus was taken from your first answer.

Not word for word but this certainly implied to me that

On 8/13/2021 at 5:47 PM, CharonY said:

A few points here, viruses do not die, they are either intact particles, and capable of infections, or not. If they are degraded, they do not function anymore. Mutations occur when the virus replicates in their hosts, which, to re-iterated requires an intact particle to happen.

 

A virus that is right for a pig or bat cannot be an 'intact particle' in your words or 'exactly tailored' in my words for humans.

Which is why I asked for justification.

 

[CharonY]

18 minutes ago, studiot said:

In other words we don't know.

But none of this is inconsistent with what I said.

You get some covid virus on your hands.

As String Junky said, some may be more resistant to soap than others or I suggest perhaps better protected by the destroyed (since you object to the word dead) outer virii.

Whatever the mechanism the protection is not perfect so the soap acts as a selective environment.

Exactly as I said, and you said and SJ said.

That is not how I read what you wrote:

Quote

The degraded survivors may go on to deliver their payload, whereby a mutation may occur.

Some such mutations may 'evolve' into viable virii, more resistant than their parents, to the degrading agent.

This to me implies that the resistance develops either in response or at least in the following generation. I.e. in your scenario exposure happens and only after that do you get mutations and new traits.

 

44 minutes ago, studiot said:

In other words we don't know.

I do not know what kind of answer you are looking for. What would you answer to the question "where do blonde folks come from"? That would help me figure out how yo think about these types of questions.

 

45 minutes ago, studiot said:

A virus that is right for a pig or bat cannot be an 'intact particle' in your words or 'exactly tailored' in my words for humans.

Which is why I asked for justification.

I do not comprehend how you could take that from my answer. AI suspect you have something different in mind if you think about the term "intact particle". n intact particle is just that, a full functioning virus. An intact particle refers to a structurally intact virus (e.g. depending on the virus having the genetic material, capsid, potentially membrane, and other structural proteins). If it not intact, e.g. lacking these structures, it is not able to infect and replicate successfully. It does not matter what its host is, or whether it has a broad or narrow host range.

 

Quote

Yes we know that covid has jumped species.

Fear of that, as opposed to the welfare of the mink, was the reason for the mink cull.

Yes there was a report of a man who caught covid from his dog.

Not sure what your wanted to know with regard to your question then:

 

3 hours ago, studiot said:

So what is the response of other mammals to covid19 ?

 

[TheVat]

https://www.npr.org/sections/goatsandsoda/2021/11/05/1052961177/new-coronavirus-likely-from-dogs-infects-people-in-malaysia-and-haiti

We found a coronavirus," he says. And not just any coronavirus, but one that many scientists believe may be a new human pathogen — likely the 8th coronavirus known to cause disease in people. Turns out, this coronavirus in the Haiti travelers has cropped up previously, on the other side of the globe.

Back in May, scientists at Duke University, reported they had detected a nearly identical virus coronavirus in children at a Malaysian hospital.

The researchers found the virus in the upper respiratory tract of 3% of the 301 patients they tested in 2017 and 2018.

The genetic sequence of the Malaysian virus suggested it likely originated in dogs and then jumped into people. "The majority of the genome was canine coronavirus," virologist Anastasia Vlasova told NPR in May.

Although the findings sounded alarming, the researchers had no evidence that the virus could spread between people or that it was widespread around the world.

"These human infections with ... canine coronaviruses appear to be isolated incidents which did not lead to extensive human transmission," virologist Vincent Racaniello wrote on the Virology Blog. 

Now Lednicky and his colleagues have found an almost identical virus infecting people 11,000 miles away-- at the same time. The genetic sequence of the virus in Haiti is 99.4% identical to the one in Malaysia. Lednicky and his colleagues reported this past Sunday in the journal Clinical Infectious Diseases.

And the big question is: How does a dog virus in Malaysia wind up in doctors and nurses in Haiti?

(sorry about the enormous font -- cut/paste here seems to force weird font sizes on you and I don't know how to switch it off) 

[Peterkin]

Disaster relief missions, probably. It might stow away undetected in the medical personnel themselves, or in their equipment and/or vehicles. 

[PhilGeis]

On 11/6/2021 at 11:19 AM, TheVat said:

 

And the big question is: How does a dog virus in Malaysia wind up in doctors and nurses in Haiti?

 

Think this is the paper by Lednicky et al. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab924/6413759?login=true - you can download the entire pdf.  It's always a good idea to read the actual report if possible rather than taking second hand interpretation from media.

 

They did not say it (viral RNA from one sample) was the same virus but that it was closely related to Vlasova et al. Malaysian virus that appeared to be ancestral.  So an interesting journey - and/or maybe recombination in the one host.

"We report here identification of a coronavirus of canine origin which is closely related to the Malaysian virus reported by Vlasova et al, albeit isolated in this instance from a visitor to Haiti, and with a further recombinational history."

RNA viral mutation rates of 10E4 to 10E6 and coronavirus rate is reportedly much greater.  It's not just limited to the existing genome but is extended by recombination.  ".... Vlasova et al reported isolation of an Alphacoronavirus of apparent canine origin, with evidence of recombination with a feline coronavirus, from patients with pneumonia in Malaysia [6]. "

Edited November 19, 2021 by PhilGeis

[CharonY]

As much of the world still remains unvaccinated, new strains continue to emerge. Recently a new variant of concern (B1.1.259, omicron). It carries 32 mutations compared to the original strain in the gene coding for the spike protein, raising worries that current vaccines might be less effective against this variant.

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

It is yet another reminder that the pandemic is far from being over.