Coronavirus

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As suggested in a previous link, the immune system won't put much selection pressure on the virus during the initial infection. But vaccination while the virus is circulating will force the virus to evolve. This was confirmed by Sir Patrick Vallance in January 2021 during a press conference. So notwithstanding the efficacy of the vaccines, it seems to me that mass vaccination will still lead to an increase in the infection rate.

If that's really the case then it's also made the virus milder. Another benefit of mass vaccination.

[Anchorman]

But to paraphrase the leading headline in yesterday's Telegraph, "We can't jab the whole planet every six months. Future vaccination will have to be limited to those who are most vulnerable"

     


Sorry; the Torygraph isn't on my reading list.
However; the Christ-like thing to do would be to use our God-given ability to vaccinate as many, as often, as our reasources allow.
It's part of the 'Love one another' thing.

[Udayana]

As suggested in a previous link, the immune system won't put much selection pressure on the virus during the initial infection. But vaccination while the virus is circulating will force the virus to evolve. This was confirmed by Sir Patrick Vallance in January 2021 during a press conference. So notwithstanding the efficacy of the vaccines, it seems to me that mass vaccination will still lead to an increase in the infection rate.

It is just not true that "vaccination while the virus is circulating will force the virus to evolve". What did Vallance say exactly? - If he said that - it wouldn't be the first time he has made a misleading statement in a press conference. 

The virus is always "evolving" - new variants arise and spread or not - those that are better at spreading  - will spread more than other variants. These usually start in cases where someone with an immune system issue has become infected and a variant that can escape some natural anti-bodies takes hold.

All the main variants so far arose in populations with low levels of vaccination. For Omicron the most likely case is that it "evolved" in someone suffering, being treated for, or recovering from HIV.

The vaccines and vaccination programs are designed and tested so as to minimise infection rates and spread as well as effects of the disease. If you want to claim that because they don't do that perfectly, infection rates will be higher than in populations that have not been vaccinated you need to provide a mathematical model and estimated parameters that show that. Speculation on what "might" happen is useless without considering the probabilities of the possible sequence of events. 

[Maeght]

Bulgaria and Ukraine, 26% and 28% fully vaccinated, have both past the peak of their third wave. Cases in Russia also seem to be declining - good news. Perhaps things are moving more slowly there due to lower temperatures (currently -13` in Moscow)

Cases in Bulgaria rising rapidly again sadly.

https://ourworldindata.org/explorers/coronavirus-data-explorer?zoomToSelection=true&time=2020-03-01..latest&facet=none&pickerSort=asc&pickerMetric=location&hideControls=true&Metric=Confirmed+cases&Interval=7-day+rolling+average&Relative+to+Population=true&Color+by+test+positivity=false&country=~BGR

[Spud]

Cases in Bulgaria rising rapidly again sadly.

https://ourworldindata.org/explorers/coronavirus-data-explorer?zoomToSelection=true&time=2020-03-01..latest&facet=none&pickerSort=asc&pickerMetric=location&hideControls=true&Metric=Confirmed+cases&Interval=7-day+rolling+average&Relative+to+Population=true&Color+by+test+positivity=false&country=~BGR

Omicron has been detected there, so that could be the cause. If so then mortality should remain low, unless there is more to come from O than what we are currently seeing. I saw a study this morning concluding that "Protection from reinfection decreases with time since previous infection, but is, nevertheless, higher than that conferred by vaccination with two doses at a similar time since the last immunity-conferring event. A single vaccine dose after infection helps to restore protection." . This could explain why Bulgaria's third wave declined steeply despite low vaccination.
https://www.medrxiv.org/content/10.1101/2021.12.04.21267114v1

[Spud]

If that's really the case then it's also made the virus milder. Another benefit of mass vaccination.

I've been pondering this possibility for a while.

[Spud]

It is just not true that "vaccination while the virus is circulating will force the virus to evolve". What did Vallance say exactly? - If he said that - it wouldn't be the first time he has made a misleading statement in a press conference. 

I think this is it:
https://twitter.com/itvnews/status/1346510188107472898

[Udayana]

I think this is it:
https://twitter.com/itvnews/status/1346510188107472898

Well, Vallance was speaking very loosely - trying to get a general point across. It's not strictly scientific and  not be taken literally.

He implies that evolutionary pressure from vaccination will "cause" mutation, that the mutation will occur when vaccination levels are high, and that the virus will "struggle to work out what to do" - all of which is nonsense.

This is disappointing from a very successful scientist but on a par with his fall back to "herd immunity" in an earlier press conference, closer to the start of the epidemic. At least he is not as useless as Harries when she was on.

Whitty is better, suggesting that wider vaccination with single doses will help contain the disease even though there is a slightly higher risk of an escape mutant emerging in the longer gap before the second dose.

 

[Spud]

Well, Vallance was speaking very loosely - trying to get a general point across. It's not strictly scientific and  not be taken literally.

He started off by saying, "the more you vaccinate, the more you put evolutionary pressure on the virus."

[Udayana]

He started off by saying, "the more you vaccinate, the more you put evolutionary pressure on the virus."

Indeed he did, and it is correct that "the more you vaccinate, the more you put evolutionary pressure on the virus". But what do you think that means?

[Spud]

Indeed he did, and it is correct that "the more you vaccinate, the more you put evolutionary pressure on the virus". But what do you think that means?

Immune pressure on it will make it hard for it to replicate, but if the immune pressure is not enough to completely neutralize it, transmission continues, often asymptomatically, allowing mutation to continue. Then a mutation in the spike protein that enhances its ability to infect cells gives that virus a competitive advantage and a new wave of infection occurs.

[Maeght]

Immune pressure on it will make it hard for it to replicate, but if the immune pressure is not enough to completely neutralize it, transmission continues, often asymptomatically, allowing mutation to continue. Then a mutation in the spike protein that enhances its ability to infect cells gives that virus a competitive advantage and a new wave of infection occurs.

Mutations happen due to things such as antigen drift and i haven't seen anything to suggest that this process is sped up by vaccinations. As a layman one could imagine that vaccinations would mean that those mutations which get round the antibodies would be selected preferentially - but the paper i linked to earlier says that the antibodies etc act to prevent intermediate stages in the development of new variants so act to reduce the likelihood of new variants developing.

What you talk about here is just as likely with natural infection as with vaccination as far as I can see - since the immunity from natural infection isn't neutralising either - and new variants formed prior to vaccinations.

[Udayana]

Immune pressure on it will make it hard for it to replicate, but if the immune pressure is not enough to completely neutralize it, transmission continues, often asymptomatically, allowing mutation to continue. Then a mutation in the spike protein that enhances its ability to infect cells gives that virus a competitive advantage and a new wave of infection occurs.

Great, we can agree on that (with a small note that "competitive advantage" for an rna virus is different to one we normally consider in evolution).

Now, a "mutation in the spike protein that enhances its ability to infect cells" is not an inevitable event but a matter of probability, and the probability of that mutation occurring in a vaccinated individual will be equal to or less than it occurring in an un-vaccinated person.

So, suppose the whole population is vaccinated with a vaccine that is 70% effective - that leaves 30% of the people vulnerable to infection. Suppose now that 10% of people are exposed to enough of the virus to guarantee infection by the virus. Then, of the vaccinated population, 3% will become infected and become possible incubators for a mutated virus. If no-one was vaccinated, 10% of the population would be infected and be possible incubators - roughly three times as many. 

[Spud]

Mutations happen due to things such as antigen drift

Other way round - genetic variation arises as a result of accumulation of mutations.

and i haven't seen anything to suggest that this process is sped up by vaccinations.

I've seen it stated somewhere that viruses can increase the rate of mutation when under immune pressure.

As a layman one could imagine that vaccinations would mean that those mutations which get round the antibodies would be selected preferentially - but the paper i linked to earlier says that the antibodies etc act to prevent intermediate stages in the development of new variants so act to reduce the likelihood of new variants developing.

Yes that is interesting - the research is quite complicated - but it appears to me that when a more infectious variant appears, of course the diversity of variants will decline. That this correlates with increasing vaccination suggests that no vaccination would keep the diversity high. That implies less rapid spread of more infectious variants.

Note also that the more rapidly the more infectious variants spread, the more they will affect unvaccinated people, hence the reason for the higher morbidity and mortality among unvaccinated is that the vaccines have accelerated spread of these variants.

What you talk about here is just as likely with natural infection as with vaccination as far as I can see - since the immunity from natural infection isn't neutralising either - and new variants formed prior to vaccinations.

Innate immunity is very effective - that;s why children and young, healthy adults were generally asymptomatic during the first wave (when the infection rate was lower, so re-infection was less likely). Adaptive immunity is also very effective, but also wanes over time. The problem is the more pressure we put on the virus, the more infectious it has to become.

I'm talking in this post about last year's VOCs, Alpha etc. As far as the less severe Omicron goes, it has been suggested that it arose when a strain similar to Wuhan jumped into mice and then evolved in them, before jumping back to humans. Something to do with mouse ACE 2... remaining questions are, did the vaccines cause that, and if so, will the overall cost to human life of everyone being infected be worth paying?

[Spud]

Great, we can agree on that (with a small note that "competitive advantage" for an rna virus is different to one we normally consider in evolution).

Now, a "mutation in the spike protein that enhances its ability to infect cells" is not an inevitable event but a matter of probability, and the probability of that mutation occurring in a vaccinated individual will be equal to or less than it occurring in an un-vaccinated person.

So, suppose the whole population is vaccinated with a vaccine that is 70% effective - that leaves 30% of the people vulnerable to infection. Suppose now that 10% of people are exposed to enough of the virus to guarantee infection by the virus. Then, of the vaccinated population, 3% will become infected and become possible incubators for a mutated virus. If no-one was vaccinated, 10% of the population would be infected and be possible incubators - roughly three times as many.

But we need to account for changing levels of naturally induced immunity in the absence of vaccines.

[Udayana]

But we need to account for changing levels of naturally induced immunity in the absence of vaccines.

Can you account for them? What is the scientific basis for any significant difference in immunity in vaccinated and non-vaccinated individuals? The most significant difference would seem to be fatality in those whose natural immune response goes into overdrive and kills the patient!

[SteveH]

It seems that the Omigod variant may be good news. It's transmissibility means that it is becoming the dominant strain, and it is usually mild in its symproms. It may become endemic, and no more worrying than flu or colds.

[Maeght]

Other way round - genetic variation arises as a result of accumulation of mutations.

Yes, sorry - antigenetic drift  is due to a build up of mutations. I worded it badly and think I was getting confused with genetic drift! As i say below - I don't really know enough about all this, though am trying to learn.

[Maeght]

I've seen it stated somewhere that viruses can increase the rate of mutation when under immune pressure.

Can you find a link?

Yes that is interesting - the research is quite complicated - but it appears to me that when a more infectious variant appears, of course the diversity of variants will decline. That this correlates with increasing vaccination suggests that no vaccination would keep the diversity high. That implies less rapid spread of more infectious variants.

That's not what the paper said though I think. It was complicated though.

Note also that the more rapidly the more infectious variants spread, the more they will affect unvaccinated people, hence the reason for the higher morbidity and mortality among unvaccinated is that the vaccines have accelerated spread of these variants.

How has vaccination accelerated the spread?

Innate immunity is very effective - that;s why children and young, healthy adults were generally asymptomatic during the first wave (when the infection rate was lower, so re-infection was less likely). Adaptive immunity is also very effective, but also wanes over time. The problem is the more pressure we put on the virus, the more infectious it has to become.

Everything I have read says that the innate immune system is limited in it's effectiveness. You have stated this before as if fact but haven't seen any supporting links for it. I may have missed them but do you have any?

I'm talking in this post about last year's VOCs, Alpha etc. As far as the less severe Omicron goes, it has been suggested that it arose when a strain similar to Wuhan jumped into mice and then evolved in them, before jumping back to humans. Something to do with mouse ACE 2... remaining questions are, did the vaccines cause that, and if so, will the overall cost to human life of everyone being infected be worth paying?

I heard that it came from Delta but have seen nothing definitive. Again, any links to support what you have just said? No one I have read has claimed that Omicron resulted from use of the vaccines.

Edit: Have seen there is a Chinese study which says this but also found this which says many scientists have been sceptical of the animal cause of Omicron since Sars-Cov-2 isn't good at infecting mice. It says that scientists have modified Sars-Cov-2 to make it infect mice in labs so ......

https://www.iflscience.com/health-and-medicine/did-omicron-come-from-mice-chinese-scientists-believe-so/

I don't really know enough to debate this any further but, I have asked several times, with no answer, why you think the vast majority of experts in the field support mass vaccination? They are surely aware of the sort of things you are talking about. Why do you think we aren't seeing the majority of virologists and the like crying out to stop the vaccine roll outs?

[Aruntraveller]

It seems that the Omigod variant may be good news. It's transmissibility means that it is becoming the dominant strain, and it is usually mild in its symproms. It may become endemic, and no more worrying than flu or colds.

Less severe - not mild.

[Udayana]

It seems that the Omigod variant may be good news. It's transmissibility means that it is becoming the dominant strain, and it is usually mild in its symproms. It may become endemic, and no more worrying than flu or colds.

The previous variants were also usually mild.

In some ways flu can be worse - imagine what would have happened if we had been exposed to flu as a novel virus to which we had not been previously exposed - as happened in the Americas from the 16th century. 

How  is Omicrom wrt. long covid?

[ad_orientem]

It seems that the Omigod variant may be good news. It's transmissibility means that it is becoming the dominant strain, and it is usually mild in its symproms. It may become endemic, and no more worrying than flu or colds.

I think some of the medical experts over here suggested a similar thing, in which case I struggled to understand why politicians are shitting their pants and living up yet more restrictions. We have a pretty decent vaccine. We need to get back to normal.

[Udayana]

I think some of the medical experts over here suggested a similar thing, in which case I struggled to understand why politicians are shitting their pants and living up yet more restrictions. We have a pretty decent vaccine. We need to get back to normal.

Twitter thread explaining what "endemic" means.

(though I did find the gifs unnecessary and annoying) 

If we can keep the effective reproduction number under 1 - eg. by improved vaccines, it will disappear and we can get back to normal.

 

[ad_orientem]

Twitter thread explaining what "endemic" means.

(though I did find the gifs unnecessary and annoying) 

If we can keep the effective reproduction number under 1 - eg. by improved vaccines, it will disappear and we can get back to normal.

We already have a vaccine and which can be tweaked every season. The vaccine was supposed to be the way out. People are getting tired.

[Maeght]

I think some of the medical experts over here suggested a similar thing, in which case I struggled to understand why politicians are shitting their pants and living up yet more restrictions. We have a pretty decent vaccine. We need to get back to normal.

Because it is an unknown. We didn't know if it was milder and if so how much. With it being so transmissible even being milder the potential number of hospitalisations is high. It was, and is, about being cautious and trying not to overwhelm the NHS. We will get back to normal(ish) soon but need to get through the winter.