Omicron variant concerns

PeterWick said:

And I was just thinking this thread could sink down as the omicron variant seemed as challenging as a 35 mph fastball. There's a new omicron type going around. No word yet on whether it is more dangerous or spreads faster.

This was originally published in Business Insider according to a note at the end of it. The implications of this are not clear, only that they've found this thing in Africa, Australia, and North America so far. The taxonomy discussion is definitely on the geeky level but suffice to say it is different. There's a dropped section that easily flags the "first" omicron variant but this one doesn't have it. There are many different mutations between them even though they're in the same lineage. So far, it looks like they will still be distinguishable by PCR testing.

https://www.sciencealert.com/a-new-omicron-variant-has-been-found-and-it-s-now-even-harder-to-identify

What distinguishes a variant vs a lineage vs a subtype etc? Or I suppose the simplest way to phrase the question, what merits a Greek letter?

PVW said:

What distinguishes a variant vs a lineage vs a subtype etc? Or I suppose the simplest way to phrase the question, what merits a Greek letter?

I definitely don't know about that stuff in viruses. It seems arbitrary to me but the naming convention follows the way taxonomy classifies other species, like all the different kinds of sparrows. Or better yet, how many different kinds of irises or roses are there? They're mostly created through deliberate breeding but I don't know how they're characterized - subspecies, accessions, and varieties.

I suppose they look at the first major difference, A. Then another one comes along with new differences. If that new still has A along with some others, maybe it is A-something, etc. If it doesn't have A, maybe it becomes B, etc. Kinda like how learning about outlines drove me a little nuts as a kid. You get used to it in medicine though. We used to think there was only one type of adrenalin receptor, alpha. Then they discovered beta receptors. Then for each one, there were alpha-1, alpha-2, etc. Then they determined that there were alpha-1a, alpha-1b, etc.

Omicron variant more resistant to vaccine but causes less severe covid, major South African study concludes (WaPo)

[T]he study, released Tuesday, found that the vaccine from U.S. pharmaceutical giant Pfizer and German partner BioNTech provided just 33 percent protection against infection, much less than the level for other variants detected in the country. At the same time, the vaccine provided 70 percent protection in fully vaccinated individuals against severe complications that would require a patient to be hospitalized, the study found, calling that “very good protection.”

Variants ‘haunt’ world with vaccine imbalance between rich and poor nations

Children appear to have a 20 percent higher risk of hospital admission with complications during the fourth wave of coronavirus cases than during the first, despite a very low absolute incidence, the study found.

However mild or severe it is, and however fast the Omicron wave proves to be (some recent reports out of South Africa suggest that the Omicron wave there may already peaked), it is important to emphasize masks now more than ever.  I say this because at every crowded indoor gathering I've been to in the last six months, people were overwhelmingly unmasked based, apparently, on the comfort that if everyone in the place is vaccinated, all are relatively safe.  But that is so yesterday with Omicron.  The Omicron spreader events in the west so far have all involved heavily vaccinated crowds.  Have a good mask and make sure it is well sealed (I've seen plenty of people wearing good masks in half-assed ways).

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I find it pretty amazing that they're able to discover and track the new variants.  

jamie said:

I find it pretty amazing that they're able to discover and track the new variants.  

Yes, now there is a big push to analyze samples to keep a close eye on the possible emergence of new threats. South Africa has a robust system there.

I haven't delved too deeply into it but cities like Boston have been monitoring their sewage as a way to track COVID-19 viral levels as a reflection of the rate of COVID-19 infections in the area. Check out that graph. There was a sharp spike in December higher than any previous data points. That's most likely due to omicron variant infections. The wastewater data closely match the huge spike in current active cases there.

https://www.mwra.com/biobot/biobotdata.htm

Anyway, more places are doing similar things to monitor the progress.

A (vaxxed but often not, in my opinion, so Covid-conscious) friend mentioned yesterday he was at a wedding over the weekend, 150 guests, no proof of vaccination, no masks. I truly cannot remember the last time I was stunned into silence. (But that did it yesterday.)

Well, this explains a lot:

https://www.theguardian.com/world/2021/dec/15/omicron-found-to-grow-70-times-faster-than-delta-in-bronchial-tissue
but it still won’t convince people to wear masks properly let alone ‘bother’ with vaccinations… (someone supposedly highly educated in the health sector harangued my D today, telling him that it’s the vaccinated people who spread the virus. Huh??! Isn’t the point that that we all can spread it vaxxed or not? But if we’re vaccinated we have much milder episodes, and so less chance of spreading serious/fatal disease?)

joanne said:

Well, this someone supposedly highly educated in the health sector harangued my D today, telling him that it’s the vaccinated people who spread the virus. Huh??! Isn’t the point that that we all can spread it vaxxed or not? But if we’re vaccinated we have much milder episodes, and so less chance of spreading serious/fatal disease?)

I wasn't there but that person might have been saying that unvaccinated people are behaving more freely and are open to going without masks because "I'm protected now and you're not, you unvaccinated idiot." Now we know that's not a good idea because omicron is more transmissible but there was a good 3 weeks or more when it could spread easily. Blaming vaccinated people for part of this makes some people feel better.

H’m. From the way he recounted the conversation, I don’t believe it’s anything as well thought out as that explanation.

It's interesting how the Dr. in South Africa who discovered the Omicron variant has been repeatedly critical of what she perceives to be the overreaction to Omicron, especially in the UK.  She keeps emphasizing the mild presentation of Omicron cases vs, what she saw/sees with Delta.   She does not seem to be an anti vax kook at all, FWIW.  Also said that the course of Omicron cases was about five days, a lot shorter than the earlier variants I think.

I don't know what to think.  Everyone should be as careful as possible until we see what the next few weeks bring.  But I do hate to see businesses taking another gut punch because of this.  

As mild as omicron infections appear to be, what isn't so benign is its ability to spread. We now know that the more people it gets into as hosts, the more chances this thing gets to reproduce with possible/probable replication mistakes, some that lead to new viable variants.

My wife's job continues to have 2 or 3 new COVID cases in just her part of the workforce APPEAR. EACH. DAY. She's on the phone with a division manager right now to support two buyers who met with a group of vendors in person on Monday and are now positive even though they've been vaccinated.

https://www.yahoo.com/news/an-explosion-of-likely-omicron-cases-at-cornell-shows-whats-next-for-the-us-154703602.html

There's certainly no question it spreads fast and triple vaxxing is not a wall.  There's nothing like a good mask yet I continue to see unmasked people indoors everywhere.

I went to see a band at the shore on Saturday night and almost everyone in the crowded club was unmasked.  

My daughter’s college has also had a huge uptick in cases…students are trying to finish finals and get home but going into quarantine instead.

bub said:

It's interesting how the Dr. in South Africa who discovered the Omicron variant has been repeatedly critical of what she perceives to be the overreaction to Omicron, especially in the UK.  She keeps emphasizing the mild presentation of Omicron cases vs, what she saw/sees with Delta.   She does not seem to be an anti vax kook at all, FWIW.  Also said that the course of Omicron cases was about five days, a lot shorter than the earlier variants I think.

I don't know what to think.  Everyone should be as careful as possible until we see what the next few weeks bring.  But I do hate to see businesses taking another gut punch because of this.  

I wonder if there is information on the severity of Omicron infections based on a persons history - vaccinated, never vaccinated but previously infected, not previously infected, etc.  I wonder how many people have had Covid where the infection was truly asymptomatic.

tjohn said:

I wonder if there is information on the severity of Omicron infections based on a persons history - vaccinated, never vaccinated but previously infected, not previously infected, etc.  I wonder how many people have had Covid where the infection was truly asymptomatic.

I would add to your list:  Which vaccine(s) they had and how long since their last shot the infection occurred.

A sliver of good news:  https://www.dailymail.co.uk/news/article-10308473/Good-news-Omicron-hospitalisations-South-Africa-Delta-level.html

bub said:

A sliver of good news:  https://www.dailymail.co.uk/news/article-10308473/Good-news-Omicron-hospitalisations-South-Africa-Delta-level.html

milder disease seems to be in play with Omicron. Certainly good news if early data holds true. However,  We may have come to a place where we no longer can run and hide from Covid. Like a cold or Flu, do all you can to avoid it, certainly mask up when appropriate, boost up too but understand that this mutation is just to damn slippery not to catch it but hopefully it remains a mild version of Covid and it’s the beginning of the end of the pandemic unless of course it mutates into something quite deadly. For now, let’s just hope mild remains what doctor’s on the ground are reporting. We catch it, we build more immunity and most importantly we survive it. 

I will be pretty unhappy if I get sick but will be really unhappy if it kills me.

Meanwhile, am boosted and still wearing mask in grocery stores and Home Depot.

PS: I noticed yesterday that a lot more of the Home Depot shoppers are maskless now than were just a couple weeks ago.

The NYT Daily podcast is about Omicron today. 

steel said:

I will be pretty unhappy if I get sick but will be really unhappy if it kills me.

Meanwhile, am boosted and still wearing mask in grocery stores and Home Depot.

PS: I noticed yesterday that a lot more of the Home Depot shoppers are maskless now than were just a couple weeks ago.

I'm right there with you. I guess I'm still taking my cues from the people who work in places my wife and I go to. If the employees are wearing masks, I will as well. It might still be official store policy in these places but part of me thinks those workers are protecting themselves rather than complying with an order.

This is good.

https://www.bloomberg.com/news/articles/2021-12-17/s-africa-says-hospitalizations-in-omicron-wave-much-lower?srnd=premium

Thing is, it doesn’t matter how mild it is once you get it… and there are so many more of us than people realise.

They're expecting to see a sudden rise in COVID infections this month.

https://www.cnn.com/2021/12/17/health/us-coronavirus-friday/index.html

This is New Jersey's graph of daily new cases, taken December 17th. Thankfully, the daily deaths graph hasn't followed that spike. That daily new case graph is close to matching the highest rate New Jersey has had in this whole pandemic.

I was in midtown NYC a few evenings ago, and it was a holiday madhouse atmosphere, almost like pre-covid.  Traffic driving in was severely backed up like the old days.  Sidewalks were crowded, with as many unmasked as masked.  Inside restaurants and waiting lines appeared full, with many unmasked.  It seemed as if people were in denial, or had decided to just take their chances; or going through a final fling before things shut down again.

PeterWick said:

 Thankfully, the daily deaths graph hasn't followed that spike. 

But death is a trailing indicator. If Omicron is half as deadly but five times as infectious as Delta, the deaths will eventually exceed previous rates.

I have a vaccine question.

Vaccines like those for polio or measles work by mitigating transmission so that once you vaccinate enough people, the virus essentially goes extinct because there are no new hosts to go to. (I'm simplifying, and re-reading this, it might not be quite correct, but I think it's close enough.)

Is it unusual to have vaccines like the ones for COVID that don't seem to affect transmission rates? And is there hope that new vaccines will be developed that do affect transmission? 

If not, and given that COVID transmission so far is mostly unaffected, are we doomed to COVID having free reign over us to transmit itself and mutate forever?

Or am I just off-base regarding the vaccines affect on COVID transmission?