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In case anyone thinks omicron is milder


studiot
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I think one important bit is that because more vaccinated folks are getting infected now due to reduced protection against infection, but it still provides decent protection against severe symptoms. As a result the ratio of infected to hospitalized persons looks better, compared to the Delta wave, but given the fact that current tests seem to severely underestimate infections, we will end up with an overrun health care system. I believe the WHO has given out a similar warning, since quite a few folks seem to misinterpret the milder outcome of Omicron. 

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15 minutes ago, CharonY said:

I think one important bit is that because more vaccinated folks are getting infected now due to reduced protection against infection, but it still provides decent protection against severe symptoms. As a result the ratio of infected to hospitalized persons looks better, compared to the Delta wave, but given the fact that current tests seem to severely underestimate infections, we will end up with an overrun health care system. I believe the WHO has given out a similar warning, since quite a few folks seem to misinterpret the milder outcome of Omicron. 

Does the  suspected  great underreporting of cases mean that the overall ratio of hospitalizations to cases could be actually  lower than  what it appears from the raw statistics?

 

If so that would indicate an intrinsically  less virulent disease ? (esp as it seems to be accepted that it is less effective  at attaching to the cells in the lungs themselves)

 

Or was there similar underreporting in earlier wages as well?

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9 minutes ago, geordief said:

Does the  suspected  great underreporting of cases mean that the overall ratio of hospitalizations to cases could be actually  lower than  what it appears from the raw statistics?

Potentially. In many areas we have got extremely high test positivity rates, but that is also skewed by the fact that quite a few areas have been switching to symptom-only testing. But all evidence still point to the fact that we undertest more than we did before.

11 minutes ago, geordief said:

If so that would indicate an intrinsically  less virulent disease ? (esp as it seems to be accepted that it is less effective  at attaching to the cells in the lungs themselves)

Not necessarily. The issue is that due to increasing vaccinations, the baseline susceptibility of the population shifts. I.e. we do see more vaccinated folks getting infected, but since the vaccine still prevents more serious damage, it might appear milder. What we need to check is basically the outcome among the unvaccinated, but as the number is getting smaller, it is also getting more biased. We have generally more unvaccinated among the younger population, for example, who generally have better outcomes. So we would need to look at unvaccinated folks in an age matched cohort. However, we do not have the data (yet). It would also be important to figure out risk among the elderly, especially if vaccine protection wanes. Moreover, the lung studies were conducted on animal models. So why they provide clues, it is not entirely clear whether it can be translated directly to humans. And especially elderly people are difficult to simulate in animal models. 

Together, I would still be somewhat more careful in declaring Omicron less virulent, so far we are looking at milder outcomes, but it may not (solely) because of the properties (i.e. virulence) of the virus, but external factors (vaccination, age) are almost certainly contributing. I am fairly certain that we will get an update relatively soon.

18 minutes ago, geordief said:

Or was there similar underreporting in earlier wages as well?

Yes, there is always underreporting. The reported clinical cases are always the minimum known numbers. Depending on testing situation, testing strategies and also willingness to get tested the accuracy of reports has likely varied quite a bit. There is evidence that we have more underreporting than before, though.

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Posted (edited)

Thank you for the replies.

There is another more worrying possibility that is the reason I posted.
I note no one has replied to my comment.

5 hours ago, studiot said:

Note how the hospitilisation and then deaths lag behind the cases, but they are now catching up.

 

We had a long period of level or slowly declining cases, hospitalisations and deaths until 3 - 4 weeks ago.

Too many thought that meant it was the beginning of the end and began to relax.

Then the case rates skyrocketed, but the hospitilisations did not go up.
3 weeks ago I watched the hospitalsations go through the 6000 barrier.
Deaths still steady at about 50 per day.
Then hospitilisations started rising fast but deaths kept steady.
Last week deaths started rising into the low hundreds.
3 days ago we had 1000 deaths and are now in the higher hundreds.

Furthermore we now have several treatment drugs in use that were unavailable in the first two waves.

Looking at the small amount of current data I wonder and fear that omicron simply takes longer to work it harm.

Edited by studiot
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3 hours ago, studiot said:

Looking at the small amount of current data I wonder and fear that omicron simply takes longer to work it harm.

I don't thinks so. All clinical data I have seen suggest that folks might have symptoms earlier, but do not remain sick longer. I.e. within roughly 10 days or so folks either recover or become seriously ill. The more likely explanation is the lag now longer because more folks need to be infected in order to have persons ending up in hospital. Another thing to add, I believe that in contrast to previous waves in the UK folks are only PCR tested when they show symptoms (and referred to rapid testing otherwise). I am not sure when that was implemented, so one cannot directly compare the rates easily.

Edit: a thought that I had with regard to @geordief's question was to compare hospitalization rates of children who are not yet eligible for vaccines (0-4 years). Here we see that in the US as well as UK the hospitalization per 100,000 individuals have been increasing compared to the earlier waves. This is of course not conclusive evidence especially as it is still a very rare event. Nonetheless it indicates that at least for young, unvaccinated children there is no evidence that the disease is actually milder. For children 5-14 years the rate has been steady despite vaccinations, but the vaccination rate is overall low.

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4 hours ago, CharonY said:

I don't thinks so. All clinical data I have seen suggest that folks might have symptoms earlier, but do not remain sick longer. I.e. within roughly 10 days or so folks either recover or become seriously ill. The more likely explanation is the lag now longer because more folks need to be infected in order to have persons ending up in hospital. Another thing to add, I believe that in contrast to previous waves in the UK folks are only PCR tested when they show symptoms (and referred to rapid testing otherwise). I am not sure when that was implemented, so one cannot directly compare the rates easily.

Edit: a thought that I had with regard to @geordief's question was to compare hospitalization rates of children who are not yet eligible for vaccines (0-4 years). Here we see that in the US as well as UK the hospitalization per 100,000 individuals have been increasing compared to the earlier waves. This is of course not conclusive evidence especially as it is still a very rare event. Nonetheless it indicates that at least for young, unvaccinated children there is no evidence that the disease is actually milder. For children 5-14 years the rate has been steady despite vaccinations, but the vaccination rate is overall low.

I think I have heard that ,insofar as this now seems to be more of a disease of the upper airways than the lungs themselves that younger ("very young",was it?) people  are more liable  to more serious  illness on that account. 

 

Perhaps that ,if true would  be  relevant?

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18 minutes ago, geordief said:

I think I have heard that ,insofar as this now seems to be more of a disease of the upper airways than the lungs themselves that younger ("very young",was it?) people  are more liable  to more serious  illness on that account. 

So that is a bit more complicated and I am not a specialist for that. For the most part upper respiratory infections are more likely to cause complications and children and the elderly, whereas in adults they tend to be more self-limiting. However, complications are more common in areas with limited access to healthcare. Moreover, one of the complications is that the pathogen can also eventually colonize the lungs and thereby cause severe issues. i.e. if Omicron was mostly self-contained in the upper respiratory tract, it would not necessarily expected to cause more issues in children. Moreover, the rate of serious illness in the very young is still lower than in adults. I.e. they are actually still at lower risk. However, it now seems that with omicron the risk might have increased very slightly or at least it does not seem to have been reduced as some data on (vaccinated) adults might suggest.

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11 hours ago, CharonY said:

Another thing to add, I believe that in contrast to previous waves in the UK folks are only PCR tested when they show symptoms (and referred to rapid testing otherwise). I am not sure when that was implemented, so one cannot directly compare the rates easily.

Testing in the UK is far more complicated that this and has been subject to different rules at different times throughout.
Further the government has just announced that the lateral flow chromatography will now be accepted instead of PCR, for the political expediancy that it failed to provide
suficient proper tests which are now being rationed.

I say proper tests rather than PCR because up to 1/2 million health workers and 1.5 million social care workers are regularly using an alternative to PCR  -  a saliva test - as a matter of course several times a week.
This is still a laboratory test but results are returned much more quickly.

Also the UK has remained very open to travellers in and out during the whole pandemic.
This has been 'controlled ?' by a PCR testing regime, more stringent than for the general population at large.

Finally some employers have been funding their own worker testing regimes.

 

However the tests are conducted, the results are all supposed to be reported to the government, though not everyone does so.

 

 

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I made some of these points last monday in my OP "Why is Omicron apparently less virulent?"       

Especially the one about more vaccinated people catching it, and skewing the figures because they get less sick. 

My Sister got Omicron about eleven days ago. She was the last person I expected to get it, because she is so careful. She is immune suppressed, because she takes arthritis drugs, so she was very wary but she still got it. She had the two plus booster vaccines, and basically just got a fairly heavy cold from it. But she is still testing positive, after eleven or twelve days, although the positive line is now quite feint. 

The UK deaths have gone up, but it's hard to say if that's due to Omicron, or the winter rise in cases. They could easily give out a breakdown of who is dying, from what variant, but they don't. Omicron hasn't been the dominant variant for very long, so it's reasonable to suppose that the current deaths are still mostly Delta cases. But that's a guess. It probably won't be too long before they can confirm either way.

The outbreak in South Africa seems to have confirmed that Omicron is less virulent, but I'd still like to see the figures for people my age, before I start feeling confident.

        

 

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6 hours ago, studiot said:

Testing in the UK is far more complicated that this and has been subject to different rules at different times throughout.

Yes, that is an issue for direct comparisons in many areas. Testing regimen have changed and while e.g. Canada has started using more rapid tests, the reporting mechanisms are very inconsistent to non-existent in the various provinces.  In the UK there is a more centralized way, but uptake has been spotty and in a recent meeting the folks who record the data mentioned that even health professionals often do not submit the data as they felt that it was pointless. They have started engaging people more which improved data submission but obviously different time periods will have different accuracy. That as a whole introduces uncertainty in the analyses of the data sets. That being said, the UK still has one of the best reporting and testing systems, especially compared to North America and many parts of Europe (we often use UK data to figure out oddities elsewhere, if we can).

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16 minutes ago, CharonY said:

even health professionals often do not submit the data as they felt that it was pointless.

I disagree.

Even in the best achievable system, some data will go astray.

But in the NHS the standard is to undergo their test twice a week for non frontline staff and up to daily for sharp end covid staff or they may not/cannot go into work.

The sample kit is collected from the hospital/clinic/surgery with a serial number and attributed to a particular staff member via a scanned QR code or similar, which then attaches to that staff member and test.
The log goes automatically to the controlling system.
The staff member cannot 'not submit' for very long before action is taken.

So the amount of data going astray will be very small indeed, rather than 'often' as you portray.

 

 

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7 minutes ago, studiot said:

I disagree.

Even in the best achievable system, some data will go astray.

But in the NHS the standard is to undergo their test twice a week for non frontline staff and up to daily for sharp end covid staff or they may not/cannot go into work.

The sample kit is collected from the hospital/clinic/surgery with a serial number and attributed to a particular staff member via a scanned QR code or similar, which then attaches to that staff member and test.
The log goes automatically to the controlling system.
The staff member cannot 'not submit' for very long before action is taken.

So the amount of data going astray will be very small indeed, rather than 'often' as you portray.

 

In that case I may have misunderstood or misremembered what I heard in the presentation from the NHS staff. They were talking about the implementation and the issues they had and the original system was apparently quite annoying even to NHS staff. Upon re-reading I should not have stated "often", I started the sentence thinking of the broader population, in which (at least when we had the briefing, which is a while back) the uptake was spotty, but then switched half-way through to the NHS staff part, which apparently had a lot of complaints (e.g. the need to put in all your information every time at the beginning). So my apologies for that.

But it is great that things are seemingly eve more streamlined now. I wished we would follow suit.

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11 minutes ago, CharonY said:

In that case I may have misunderstood or misremembered what I heard in the presentation from the NHS staff. They were talking about the implementation and the issues they had and the original system was apparently quite annoying even to NHS staff. Upon re-reading I should not have stated "often", I started the sentence thinking of the broader population, in which (at least when we had the briefing, which is a while back) the uptake was spotty, but then switched half-way through to the NHS staff part, which apparently had a lot of complaints (e.g. the need to put in all your information every time at the beginning). So my apologies for that.

But it is great that things are seemingly eve more streamlined now. I wished we would follow suit.

Sure.

Two members of my family are engaged in that routine so we have a pretty good idea of what goes on.

The response and efforts by properly trained technical staff in the UK NHS has been oustandingly good.

The support provided by the politicians has been considerably less effective, even to the point of getting in the way sometimes.

Just before last Christmas, I had an operation at a specialist clinic that had been set up some years a go as a public- private partnership that has been outstandingly successful.
The clinic, some 50 miles from me, was set up to relieve pressure on routine operations being displaced by emergencies at local general district hospitals.
The regime at the clinic is even stricter, and they proudly told me they'are a green site' which means they have no covid, nor have they ever had any.
In order to be allowed through the entry door I had to drive to a temporary shack just ouside ( a bit like a bus shelter) just for them to take a PCR sample.
They would not accept anyone else taking or processing the sample.
I then had to wait 3 days for the results (they actually came in 2) and self isolate whilst I was waiting so that the were sure I was clear on the day of the op.
 

Needless to say their careful procedures extended to the op itself which went smoothly according to plan.

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Started to get runny nose and loads of sneezing and light headed on Wednesday. Tested positive on Thursday morning and have been isolated since. Symptoms started to disappear yesterday, and have now all but gone...feeling pretty good while still isolating until Thursday morning. 2 astra zeneca shots, plus Moderna booster were my defence. I am also 77 years old. 

ps: no confirmation as yet as to what variant I had.

A symptom I did forget to mention, was a loss of appetite, although taste OK.

Edited by beecee
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1 hour ago, beecee said:

Started to get runny nose and loads of sneezing and light headed on Wednesday. Tested positive on Thursday morning and have been isolated since. Symptoms started to disappear yesterday, and have now all but gone...feeling pretty good while still isolating until Thursday morning. 2 astra zeneca shots, plus Moderna booster were my defence. I am also 77 years old. 

ps: no confirmation as yet as to what variant I had.

A symptom I did forget to mention, was a loss of appetite, although taste OK.

+1

Well I hope you recover better than this 9 year old girl.

https://www.bbc.co.uk/news/uk-england-somerset-59842304

 

GET WELL SOON.

:)

 

 

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It's probably a bit early, but I have a feeling that the Omicron wave has peaked in the UK. The reporting of cases and deaths has been a bit intermittent over the Christmas/New Year period, but it's seemingly back to normal now, and the new cases have apparently began to drop. Only a few days, but it's better than nothing. 

I would be really interested to know what's happened to Delta cases, since the Omicron virus became dominant. It would be great to know if the new variant suppresses the spread of the old one, or just adds to the total over the top. 

PS, glad you had a mild dose Beecee, and hope you don't get any lingering after-effects.

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1 hour ago, studiot said:

+1

Well I hope you recover better than this 9 year old girl.

https://www.bbc.co.uk/news/uk-england-somerset-59842304

 

GET WELL SOON.

:)

 

 

Yeah sad, poor little thing.

Everything is OK with me at this time...appetite well and truly back, no light headeness, no runny nose, cough near gone...no temperature,( even in the early days) Again, considering my age, it shows the effectiveness of the vaccines and booster. 

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On 1/8/2022 at 5:14 AM, CharonY said:

So that is a bit more complicated and I am not a specialist for that. For the most part upper respiratory infections are more likely to cause complications and children and the elderly, whereas in adults they tend to be more self-limiting. However, complications are more common in areas with limited access to healthcare. Moreover, one of the complications is that the pathogen can also eventually colonize the lungs and thereby cause severe issues. i.e. if Omicron was mostly self-contained in the upper respiratory tract, it would not necessarily expected to cause more issues in children. Moreover, the rate of serious illness in the very young is still lower than in adults. I.e. they are actually still at lower risk. However, it now seems that with omicron the risk might have increased very slightly or at least it does not seem to have been reduced as some data on (vaccinated) adults might suggest.

That raises a question: the virus seems to work by binding to ACE2. I had thought ACE2 was most abundant in the lungs, rather than in the nose and throat. Yet Omicron typically gives a runny nose and sore throat, like other upper respiratory tract viruses. Do these also work via ACE2? If so why do they not also invade the lungs? Or do they work another way, and if so, does it suggest Omicron may also now be gaining entry by a different mechanism?   

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On 1/8/2022 at 10:26 PM, mistermack said:

 

I would be really interested to know what's happened to Delta cases, since the Omicron virus became dominant. It would be great to know if the new variant suppresses the spread of the old one, or just adds to the total over the top. 

PS, glad you had a mild dose Beecee, and hope you don't get any lingering after-effects.

Apparently** practically  all cases  in Ireland  are now Omicron. 

Seems to me Delta will go the way  of the earlier variants. 

 

**no source  just something  I read on social media.

Edited by geordief
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3 hours ago, geordief said:

Apparently** practically  all cases  in Ireland  are now Omicron. 

Seems to me Delta will go the way  of the earlier variants. 

 

**no source  just something  I read on social media.

That is very likely to be true. In our own analyses we found that within ~2.5 weeks of showing up it has pretty much replaced Delta.

3 hours ago, exchemist said:

That raises a question: the virus seems to work by binding to ACE2. I had thought ACE2 was most abundant in the lungs, rather than in the nose and throat. Yet Omicron typically gives a runny nose and sore throat, like other upper respiratory tract viruses. Do these also work via ACE2? If so why do they not also invade the lungs? Or do they work another way, and if so, does it suggest Omicron may also now be gaining entry by a different mechanism?   

So there are a few things related to that. First, yes ACE2 receptors are docking sites of the virus and in Omicron one piece of the puzzle seems to be that the spike protein-ACE2 receptor interaction is much tighter than with earlier variants. However, the upper respiratory tract has also high levels of ACE2 receptors (as well as other organs) and the upper respiratory tract is known to be an entry point also for earlier variants (the often reported loss of smell is one of consequences). The question then becomes why it does not spread or colonize the lungs that efficiently. There are are several lines of investigation underway to look at that.

 In vitro studies suggested (Zhang et al., cannot recall the journal of the top of my head) found that two additional serine proteases promote the entry of SARS-CoV-2 (TMPRSS2 and 4). Conversely, Omicron seems not to use that pathway to enter, instead using a TMPRSS2-independent endosomal fusion  pathway (i.e. a different way to enter after docking). These proteases are abundant in the lung, but much less so in the upper respiratory tract which would at least explain much higher efficiency in colonizing the upper respiratory tract. That being said, this data alone does not entirely explain why they seem to colonize lungs somewhat less efficiently yet. 

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1 hour ago, CharonY said:

That is very likely to be true. In our own analyses we found that within ~2.5 weeks of showing up it has pretty much replaced Delta.

So there are a few things related to that. First, yes ACE2 receptors are docking sites of the virus and in Omicron one piece of the puzzle seems to be that the spike protein-ACE2 receptor interaction is much tighter than with earlier variants. However, the upper respiratory tract has also high levels of ACE2 receptors (as well as other organs) and the upper respiratory tract is known to be an entry point also for earlier variants (the often reported loss of smell is one of consequences). The question then becomes why it does not spread or colonize the lungs that efficiently. There are are several lines of investigation underway to look at that.

 In vitro studies suggested (Zhang et al., cannot recall the journal of the top of my head) found that two additional serine proteases promote the entry of SARS-CoV-2 (TMPRSS2 and 4). Conversely, Omicron seems not to use that pathway to enter, instead using a TMPRSS2-independent endosomal fusion  pathway (i.e. a different way to enter after docking). These proteases are abundant in the lung, but much less so in the upper respiratory tract which would at least explain much higher efficiency in colonizing the upper respiratory tract. That being said, this data alone does not entirely explain why they seem to colonize lungs somewhat less efficiently yet. 

Aha. Thanks very much. (I experienced 6 weeks of anosmia myself, without any apparent lung infection, with the plain vanilla original variant, back in March 2020). 

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1 hour ago, exchemist said:

Aha. Thanks very much. (I experienced 6 weeks of anosmia myself, without any apparent lung infection, with the plain vanilla original variant, back in March 2020). 

It's great that it wasn't more severe. Looking at the current spread we are somewhat lucky that it only arrived after vaccines were available and more expertise in treating patients have been developed. If the first or second wave happened at that speed, the outcome would have disastrous, even if severity was lower on the individual level.

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The new cases in the UK have been dropping now for six days, it looks like the peak of the Omicron spike has passed. Unfortunately, the deaths look like they are in the sharply rising phase, matching the beginning of the Omicron spike. 

If that's the case, then it seems to indicate that Omicron is certainly a killer, maybe at a lower percentage,  but it's certainly capable of having an effect on the death figures. It would help, if the government would release a breakdown of the death figures, showing what strain of Covid was involved. 

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  • 2 weeks later...



I hope the at-home antigen tests can keep improving, given how immediate results are often extremely helpful.  I have had a nasty bug since Friday, which matched the symptoms of omicron, so I took a rapid antigen test and got a negative.  But now am hearing that it's less sensitive to omicron, so false negatives are higher, so I feel the need to take it again.   In the UK, they recommend you do the second one with swabbing your throat instead of your nares, because omicron seems to concentrate there more. (my USA test instructions rule out throat swab, but I've seen a couple preprint studies saying omicron may be three times as concentrated in throat!)  I want to get this right because the spouse has an important meeting this week and she does not want to be a spreader.  And there is a pregnant woman in the group that's meeting. (The PCR test does me no good, because results here in the American outback take 3-5 days, and the meeting is in two days)

Edited by TheVat
Pyto
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