The Omicron variant

corkie

"Results today suggest that approximately 14% of our cases are due to the Omicron variant."

@CMOIreland

Twitter

& Tony's account tweeting again

Ireland 544 Probable Omicron today.

EU figures are well out but none from UK yet.

TefalBrain

Very worrying situation

Rebelbrowser

https://www.boards.ie/discussion/comment/118321321#Comment_118321321

I thought I read somewhere that Moderna's share price, and this guy's personal wealth through share/share options, went up considerably when he talked up Omicron last week. He may not be the most objective suffice it to say....

is_that_so

https://www.boards.ie/discussion/comment/118321072#Comment_118321072

Definitely not this side of Christmas but a slim chance in January or February!

Economics101

This may have been on another thread already, but the UK authorities have just abolished the Red list after only a few weeks and also MHQ. The reason: as omicron is already well-established in the community measures to keep it out are pointless. I wonder how long it will take for us to make a similar decision: one week for NPHET to consider it, one week for the Cabinet to consider what NPHET says, and another week for actual implementation.

Deeper Blue

https://www.boards.ie/discussion/comment/118321736#Comment_118321736

Add another 2/3 months to that I'd say, mainly due to our penchant for Covid theatre, abundance of caution and not wanting to be like the UK

is_that_so

https://www.boards.ie/discussion/comment/118321736#Comment_118321736

Actually Donnelly was very fast on that once NPHET recommended it, it was gone in days but with the season upon us it'll probably be there till January at least.

ginoginelli

https://www.boards.ie/discussion/comment/118321736#Comment_118321736

Yes. not much point for it at this stage. I would like to see mandatory pcrs reintroduced though, as a temporary measure, until we see how the lay of the land is. Antigens only make sense if they are made that day. preferably just before or after a flight. 48 hours before is pointless.

corkie

https://twitter.com/UKHSA/status/1470829785534418952

^^^ Please note: data processing delays occurred for England in the last 24 hours and additional data will be available tomorrow.*

https://twitter.com/ECDC_Outbreaks/status/1470766076401225731

total (worldwide) 13,205 (~78,092)

Economics101

To-day the CMO says that about 14% of Covid cases are the Omicron variant. Out of a running total of about 4,000 cases per day that is equivalent to 720 Omicron cases daily. Yet last night the Dept of Health is reported as saying that has identified 18 cases (cumulative total). Both of these numbers are reported by RTE to-day.

Can anyone explain this? I know the HSE are bad at data but this seems ridiculous.

corkie

https://www.boards.ie/discussion/comment/118319542#Comment_118319542

https://www.boards.ie/discussion/comment/118322449#Comment_118322449

See above post where I linked the explanation on S-gene dropout on PCR tests.

To confirm test's there are sent for genome sequencing which is expensive.

14% is the number of tests results that had the S-gene dropout making probable omicron cases.

Only Confirmed GS tests are been reported and not the probable cases. That is how the world is reporting them.

Amirani

https://www.boards.ie/discussion/comment/118322449#Comment_118322449

14% of sequenced cases are Omicron, but not all cases are sequenced.

If the sample is representative, then about 14% will be Omicron. But we can't give an exact number for anything other than the sample.

Economics101

https://www.boards.ie/discussion/comment/118322494#Comment_118322494

Thanks for that, all is now clear! But the reporting could have made it clear in the first place!

Pussyhands

Do they sequence every test?

If they do, how come they never discovered omicron until now?

dominatinMC

https://www.boards.ie/discussion/comment/118321593#Comment_118321593

So you keep saying, but do you not feel safe in your nuclear bunker?

PicardWithHair

https://www.boards.ie/discussion/comment/118321593#Comment_118321593

Indeed.

Hold firm, just once we get the boosters out to everyone we will be out of this.

#betterDaysAhead...

#weAreInThisTogether

Bikerguy

https://www.boards.ie/discussion/comment/118323068#Comment_118323068

I have the same question...as they are/were sequencing between delta and alpha....i wonder if they were only looking for delta and assumed the rest is alpha....etc...otherwise it doesnt make sense.....

Omicron looks set to be most of the cases next week and of the cases follow the omnicron growth they will grow exponentially. Worst week to happen as well, people visiting relatives across 2-3 days.

quokula

Completely anecdotal, but I am regularly in touch with a bunch of people in London through work and while the odd person now and then has caught covid over the course of the pandemic, in the last week practically everyone I know there has caught it (about a couple of dozen people), and I know a few who have had their kid's nurseries closed because of large numbers of staff testing positive. I'd assume it's omicron from the seemingly rapid spread.

Nobody's had serious symptoms, but these are all relatively young, healthy and well vaccinated people.

Lumen

https://www.boards.ie/discussion/comment/118321415#Comment_118321415

If by "2x as infectious" you mean growth rate is 2x, then no.

Effectively what happens is the wave is unflattened, like everyone is socializing more than they actually are.

So we basically get a replay of last Christmas's case spike, but with even more infections.

As I'm not seeing anyone vulnerable over Christmas I'm trying to decide whether it's worth negligently catching Omicron to give me better protection against catching and passing it on after Christmas and against a possible future more pathogenic variant.

edit: I just spoke to someone who had covid last month and has only just recovered his sense of smell/flavour, so screw that. A Christmas without flavour would be baaad.

deholleboom

https://www.boards.ie/discussion/comment/118323569#Comment_118323569

I hear ya. But i do expect those high number cases to happen in January in Ireland. It would be good for vulnerable people to be really careful over Christmas and the other people meeting them to stay away. I would even go as far as saying that vulnerable, immuno compromised people would be better off not going to family christmas gatherings. There is an impression created that boosters are going to be a cure and will stop Omicron. It does not mean people w bad immune systems will be sufficiently protected because it is not a 'top up' but instead only goes to 100% of the existing immune system which may be running at 30%. And neither does it leave people w good immune systems without protection when not taking a booster as your T and killer cells trained by a vaccine will in most cases take care of the virus. So, i will wait for the results to come prior to deciding to get a booster shot.

I am a little bit in dubio about this. Let me explain: a booster will, well, boost my immune system. Probably not needed w Omicron so catching Omicron and let the immune system take care of it might be the best way to handle it and have it over and done with. What it will certainly NOT do, Lumen, is protect you against a more transmissable and more lethal version as that cannot happen. A following variant will be more transmissable and LESS harmful. But getting Omicron will protect you against the latter of course.

If something worse comes along it will be a different virus and current vaccines wont work.

I know some anti vaxxers who hope Omicron will be mild and solve their problems and aim to get it which is likely, get over it and get the stamp of approval. Then the others wont have to treat them as pariahs any more..

Lumen

@deholleboom wrote

I am a little bit in dubio about this. Let me explain: a booster will, well, boost my immune system. Probably not needed w Omicron so catching Omicron and let the immune system take care of it might be the best way to handle it and have it over and done with. What it will certainly NOT do, Lumen, is protect you against a more transmissable and more lethal version as that cannot happen. A following variant will be more transmissable and less harmful. But getting Omicron will protect you against the latter of course.

Viruses do not evolve to become less harmful; our immune systems develop to make them less harmful.

Why would you expect immunity from Omicron infection to be less useful against Omicron and its future variants than a vaccine developed several variants ago?

I don't think I'm advocating skipping a booster and getting infected, but boosters are not available to my age group (40s) yet AFAIK so my choices are purely behavioural: catch it deliberately and then be protected in the new year, or hide from it and then hope antigen tests work before I see vulnerable parents in January.

dominatinMC

https://www.boards.ie/discussion/comment/118323725#Comment_118323725

"Viruses do not evolve to become less harmful"

Are you sure about that? I read an article from a virologist in Stanford (I think!) which stated the contrary. Can't find it now, but if he's a professor of virology in Stanford, I'm sure he's not the only one with this hypothesis.

dominatinMC

https://www.boards.ie/discussion/comment/118323408#Comment_118323408

Agree with a lot of this, but why mention the 20 - 40 year olds when they, in general, are not at threat from the virus. And kids are certainly not susceptible. As another poster said, maybe it's the old, infirm, and immunocompromised that need to heed the abundance of caution advice and stay at home for the festive period.

kevthegaff

https://www.boards.ie/discussion/comment/118321253#Comment_118321253

Grand simple graph

Russman

https://www.boards.ie/discussion/comment/118323831#Comment_118323831

I assumed this to be the case too (albeit I had never once considered it prior to all this !), but there was a seemingly reputable piece posted on one of the threads here reasonably recently, suggesting that viruses always evolving to be less harmful was a bit of a myth apparently. The jist was that its often the case but doesn't necessarily follow. I'm struggling to find the actual post, but it was an interesting piece.

Mango321

https://www.boards.ie/discussion/comment/118322494#Comment_118322494

This is wrong. See Corkie's explanation above.

S-gene target failure is a very reliable proxy/indicator of Omicron from the actual PCR test (where the 14% figure comes from).

Whole genome sequencing is done on a proportion of cases, takes longer but confirms that it is omicron (where the 18 confirmed cases figure comes from).

deholleboom

It might be useful for people to dive in a little deeper into the way viruses behave. What we can summise is that a virus appears somewhere and doesnt raise its head above the water until through variation it starts spreading to more people. It becomes more virulent and people start to have symptoms which indicates it has already been going around for some time. More spread, more mutations and finally reaching its peak effectiveness both through higher, faster transmissability, replication and improved cell invation. We think Delta is that peak. Omicron seems to be more transmissable but so far less severe though there is an amount of uncertainty about that. If it is more transmissable AND more virulent we are in trouble but i think we would have already seen that happening.

It is true that our immune systems are better coping with virus variants due to vaccination and immunity through prior infections so the effective mutations have to find a way around it to spread otherwise they die. A variant is in competition with other variants and we can see the Darwinian selection taking place usually resulting in a milder variant form as a slightly stinky fellow traveller over time. So, in a way we COULD say that our immune systems have an influence on variants by providing a hurdle for them to try and jump over, or around..

Now, on the subject of less vs more harmful the valid argument has been made that, while a variant might be less harmful to each individual, due to a higher number of infected people the spread will be so big that it actually becomes more harmful by the sheer numbers involved. That is the fear at the moment. However, that equation is quite complex with multi variables in play. Nobody really knows. Not the best virologists nor any other scientist working in the field. We will know or better said have better information..in hindsight.

The efficacy and the need for restrictions is a related but different matter with even more complex equations. A bit like the climate change debate..

seamus

https://www.boards.ie/discussion/comment/118323327#Comment_118323327

My understanding of the latest data is that they're not sequencing every test, but Omicron has a feature of an earlier strain which Delta does not - "S-gene dropout". Don't ask me what that is, I don't know.

While full sequencing is the only way to say for certain what strain a person has, my understanding is that there's a shortcut for identifying this S-gene dropout through the PCR test, which allows us to identify how many PCR tests are returning an S-gene dropout without actually having to sequence every single one.

So, we can't say for certain that there isn't some other variant with S-gene dropout that is spreading rapidly, but the odds of that are basically nil. Thus we can track the spread of Omicron in near-realtime by tracking S-gene dropouts in PCR tests. We didn't have this with Delta, so it's really helpful.

TonyMaloney

https://www.boards.ie/discussion/comment/118324309#Comment_118324309

The alpha (Kent) variant had the s-gene thing. So we were able to track it.

Delta didn't, so we were able to track it because the alpha variant was dominant when Delta first arrived.

And now we're able to track omicron because Delta didn't have the s-gene dropout but omicron does.

In this one small area of the pandemic, we've been quite lucky. Thank you Jesus.