Evolution of Covid Strains.

[beecee]

2 hours ago, CharonY said:

While the data could be biased due to ongoing efforts, preliminary data suggest that in SA omicron might be outcompeting delta.

And that would be a favourable outcome?

[CharonY]

On 11/30/2021 at 2:13 PM, beecee said:

And that would be a favourable outcome?

No, generally not. Competition against delta is a bit of a benchmark as it is currently the dominant variant in most areas. Something able to inch it out is a matter of concern. The only favourable outcome I can think of is if omicron turns out to be causing only mild symptoms. In that case you would want it to replace delta.

[studiot]

21 minutes ago, beecee said:

And that would be a favourable outcome?

 

10 minutes ago, CharonY said:

No, generally not. Competition against delta is a bit of a benchmark as it is currently the dominant variant in most areas. Something able to inch it out is a matter of concern. The only favourable outcome I can think of is if omicron turns out to be causing only mild symptoms. In that case you would want it to replace delta.

 

I have heard the proposition that it is an unfavourable outcome for a virus to exterminate (or nearly so) its host.
As a result more successful viruses evolve to be less pathogenic towards their hosts.

I understand this happened in time with Spanish flu, and even the common cold.

[StringJunky]

13 minutes ago, CharonY said:

No, generally not. Competition against delta is a bit of a benchmark as it is currently the dominant variant in most areas. Something able to inch it out is a matter of concern. The only favourable outcome I can think of is if omicron turns out to be causing only mild symptoms. In that case you would want it to replace delta.

If Omicron has mild effects, would that be evolutionarily beneficial or harmful for its perpetuation in the population? 

[studiot]

12 minutes ago, StringJunky said:

If Omicron has mild effects, would that be evolutionarily beneficial or harmful for its perpetuation in the population? 

I would suggest beneficial.

Although it would be even more benficial for humans if it died out altogether.

Edited November 30, 2021 by studiot

[Arete]

Just now, studiot said:

 

 

I have heard the proposition that it is an unfavourable outcome for a virus to exterminate (or nearly so) its host.
As a result more successful viruses evolve to be less pathogenic towards their hosts.

I understand this happened in time with Spanish flu, and even the common cold.

As general rule, yes - with a significant number of caveats. Again, as a general rule virulence (i.e. how sick you make your host) is correlated with replication rate, but negatively correlated with transmission (i.e. the sicker you make your host, the fewer other susceptible hosts they will encounter). As a result, a pathogen will generally evolve to favor high transmission and low virulence over time, unless - 

1. Multiple infection: if an individual is infected with multiple strains, the fastest replicating strain will generally outcompete those that replicate slower, thus the predominant strain of the pathogen will generally end up being the most virulent. 

2. Multiple hosts: if a pathogen infects multiple hosts, its virulence in an  individual host plays a lesser role in governing transmission, thus there is less downward selection pressure on virulence. 

3. Partially vaccinated population, non-sterilizing vaccine: If a pathogen's virulence is lowered in a part of the host population via vaccine acquired immunity, there is less downward selection on virulence, as vaccinated individuals can contract and transmit the virus effectively, even if the virulence is high in unvaccinated hosts. 

[CharonY]

5 minutes ago, Arete said:

2. Multiple hosts: if a pathogen infects multiple hosts, its virulence in an  individual host plays a lesser role in governing transmission, thus there is less downward selection pressure on virulence. 

I would also like to posit that this may already be the case within the human population. Younger folks tend to have milder or no symptoms, while being able to transmit the disease (and young adults tend to be also on the more mobile side). 

One should therefore be careful to assume that lower virulence is inevitable or that it may happen on a quick timeline. There are also some other features (e.g. transmissibility prior to symptom development, as well as asymptomatic transmission) that could make it stay lethal for quite a while.

[TheVat]

51 minutes ago, Arete said:

 

 Partially vaccinated population, non-sterilizing vaccine: If a pathogen's virulence is lowered in a part of the host population via vaccine acquired immunity, there is less downward selection on virulence, as vaccinated individuals can contract and transmit the virus effectively, even if the virulence is high in unvaccinated hosts. 

 Are you saying our present situation (especially in the US, with its anti-vax cohort) could change the selective pressure towards more virulent strains?  

This seems to point to a need for the vaccinated to mask up zealously, in order to protect the anti-vaxxers from their own foolishness and/or paranoia. 

 

[CharonY]

2 hours ago, TheVat said:

 Are you saying our present situation (especially in the US, with its anti-vax cohort) could change the selective pressure towards more virulent strains?  

This seems to point to a need for the vaccinated to mask up zealously, in order to protect the anti-vaxxers from their own foolishness and/or paranoia. 

 

Actually, the logic goes the other way around. If everyone is vaccinated, then it would effectively mean that the virus has already a reduced virulence and kills fewer people. As such there is less pressure to reduce virulence than in an entirely unvaccinated population where hosts are killed at a higher rate.

However, one should take those arguments with some caution- these are only general trends. What actually happens in a population is obviously more complex and depending a combination of factors the there might be local optima for a certain combination of virulence and infectiousness. Or to put it differently, it is difficult to predict which trajectory a given virus is going to take at any given time. What we can say is that with a higher reservoir of folks carrying and producing the virus, we have a higher chance of continuously seeing new variants.

[CharonY]

Another thing that comes to mind when looking at how fast new  variants spread, is how impossible it is to stop a virus with these characteristics.

Even with tests in place, we are unable to contain worldwide spread, which does not bode well for the next possible pandemic.

[studiot]

On 12/6/2021 at 7:21 AM, CharonY said:

Another thing that comes to mind when looking at how fast new  variants spread, is how impossible it is to stop a virus with these characteristics.

Even with tests in place, we are unable to contain worldwide spread, which does not bode well for the next possible pandemic.

 

Do you know of any solid evidence (yet) that confirms whether or not a lateral flow test does detect the new omicron variant ?
That is does it produce a positive result even if it doesn't distinguish variants?

 

[CharonY]

24 minutes ago, studiot said:

 

Do you know of any solid evidence (yet) that confirms whether or not a lateral flow test does detect the new omicron variant ?
That is does it produce a positive result even if it doesn't distinguish variants?

 

We had a briefing recently suggesting that lateral flow tests are likely not compromised, however as of last week I have not seen any larger scale data (the presented report was only on a handful of positive patients).

I should add, that part of the careful optimism in that regard is because omicron only has few mutations in the nucleocapsid gene. Two seem to be specific to omicron (PI3L and Del31/33), so there is some effort to check out whether those could alter the results, whereas the two other commonly observed mutations were already found in alpha, for example.

[studiot]

41 minutes ago, CharonY said:

We had a briefing recently suggesting that lateral flow tests are likely not compromised, however as of last week I have not seen any larger scale data (the presented report was only on a handful of positive patients).

I should add, that part of the careful optimism in that regard is because omicron only has few mutations in the nucleocapsid gene. Two seem to be specific to omicron (PI3L and Del31/33), so there is some effort to check out whether those could alter the results, whereas the two other commonly observed mutations were already found in alpha, for example.

Thanks for this.  +1

As regards checking, might it not be prudent to simply persuade a bunch of folks who have tested omicron positive with a pcr or a spit test to take a lateral flow in the interests of society?

Edited December 9, 2021 by studiot

[CharonY]

To some degree that is being done, but it takes a while to verify omicron cases as most cases need to be verified via sequencing, which has a significant delay (frequently around a week) before the data comes out. 

Edit: I should add that some producers of rapid tests have come out and said that their product will detect omicron, but I have not seen independent studies or results so far.

[studiot]

3 hours ago, CharonY said:

To some degree that is being done, but it takes a while to verify omicron cases as most cases need to be verified via sequencing, which has a significant delay (frequently around a week) before the data comes out. 

Edit: I should add that some producers of rapid tests have come out and said that their product will detect omicron, but I have not seen independent studies or results so far.

Thank you, it's good to have a rational discussion with someone.

[CharonY]

A pre-print from the UK https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+Omicron+variant+of+concern.pdf/f423c9f4-91cb-0274-c8c5-70e8fad50074

suggests that the effectiveness of vaccines against symptomatic disease caused by omicron is further lowered compared to delta. For the AstraZeneca vaccine there was no protection after 15 weeks and for two-dose BioNTech vaccine the effectiveness to around 34-37% after 15 weeks. After booster the effectiveness increased to 75.5%. However, the case numbers were fairly low and they could not ascertain protection against severe disease outcomes.

[CharonY]

On 11/30/2021 at 2:24 PM, CharonY said:

No, generally not. Competition against delta is a bit of a benchmark as it is currently the dominant variant in most areas. Something able to inch it out is a matter of concern. The only favourable outcome I can think of is if omicron turns out to be causing only mild symptoms. In that case you would want it to replace delta.

I should add that my comment really only makes sense if there are virtually no or a massive reduction  of hospitalizations associated with omicron. If it spreads to many more folks, even a milder on average outcome might still cause a net increase  in hospitalizations.

[CharonY]

A non-peer reviewed article from Imperial College suggests over 5-fold higher reinfection rate with omicron compared to delta. Clinical data is still limited for omicron but in their analysis they did not see lower severity (based on risk of hospitalization or symptoms). So not great news from that data slice.

https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2021-12-16-COVID19-Report-49.pdf

[CharonY]

Comparing ongoing omicron infections with the previous wave it seems that in most areas we got data, we have lower hospitalization:infection ratio with omicron in many areas. However, it does not necessarily mean that omicron is intrinsically more harmless, it could for example reflect higher overall vaccination status. However, as transmission is higher, it could still mean that we might end up with overall more hospitalizations without additional measures to slow down transmission.

[J.C.MacSwell]

On 12/24/2021 at 2:28 PM, CharonY said:

Comparing ongoing omicron infections with the previous wave it seems that in most areas we got data, we have lower hospitalization:infection ratio with omicron in many areas. However, it does not necessarily mean that omicron is intrinsically more harmless, it could for example reflect higher overall vaccination status. However, as transmission is higher, it could still mean that we might end up with overall more hospitalizations without additional measures to slow down transmission.

Is it statistically less harmful in the unvaccinated (and/or not previously covid infected population, though I doubt we have good data on that)?

You meant less there, correct?

[CharonY]

 

14 minutes ago, J.C.MacSwell said:

Is it statistically less harmful in the unvaccinated (and/or not previously covid infected population, though I doubt we have good data on that)?

You meant less there, correct?

I don't think so, but I think it would be less confusing if I had said "less harmful" instead (more harmless is just weird).

And exactly that data is missing, but may be incoming and only I have missed it. The latest data I have seen was mostly big picture view, i.e. how many folks infected and how many ending up in hospital. The affected cohorts were mostly vaccinated and young, so likely skewing the results. I.e. at this point it would be safer to assume that disease severity might be similar to Delta. In fact, considering that vaccine protection is lowered, as a whole it might be a bit worse, actually.

There is in-vitro data suggesting at a mechanism while it is milder, but it is still difficult to be sure. Generally, higher transmissibility results in much higher number of net infections in the absence of interventions (as the spread sees exponential growth), so the much higher infection rates puts medical folks on high alert.