Covid-19 #41: Collateral Damage

[A Horse Named Stranger]

Interesting that we've reached Omicron. Last time we talked about naming, we are at Lambda and Mu. Didn't hear anything about the Nu or Xi variant. But we have now apparently passed two thirds on our way to Omega.

[Zorral]

Much appreciation for you further explaining this matter for people like me, who knows very little of the technicalities and math of these things.

[Paxter]

On the positive side, this latest variant seems to have been detected and added as a VoC much sooner (months?) than Delta was.

[felice]

16 minutes ago, Impmk2 said:

The issue is that this is an average and they'd have to be entirely unique. So each persons needs to be completely different from each other persons. Near everyone would have to be spreading and incredibly fleeting pre-symptomatic contacts would have to be infectious. Even then I'm not sure. The dynamics would be mind boggling.

Surely people living in cities typically walk past more than 30 strangers on the street in a week? And there's no guarantee people are isolating as soon as they become symptomatic. But the R_e would drop rapidly as the local area runs out of uninfected people to spread it to.

The big question is how deadly Omicron is. If it's significantly less deadly than Delta, then its spread might actually be a good thing.

[A Horse Named Stranger]

Well, we now have to wait for two weeks before we know whether the vaccines are still working or whether they need to be tweaked a bit.

Two sad takeaways.

1. The vaccination rate in Africa is just sad. ZA with 25% is rather on the upper end on the continent.

2. How much of that mutation horror could'Ve been avoided with a fairer vaccine distribution.

Of course the virus would mutate in a vaccine free enviroment.

[Fragile Bird]

2 hours ago, Fragile Bird said:

Damn that edit button!

[Impmk2]

36 minutes ago, felice said:

Surely people living in cities typically walk past more than 30 strangers on the street in a week? And there's no guarantee people are isolating as soon as they become symptomatic. But the R_e would drop rapidly as the local area runs out of uninfected people to spread it to.

It's the uniqueness I struggle with. They need to be an entirely different 30 people from Bob who I caught it from, and all the people they infected too. And if Jill stayed home because she was unwell then suddenly its more people. If you and your partner go most places together? Even more people. You'd need a lot of very mobile people in a very dense environment. NYC perhaps? We're talking double the most infectious disease we know of.

Anyway I don't want to get caught up in the semantics of this -  even if it is technically possible I don't think it's plausible based on the genetic evidence and the cases outside of South Africa. But I am worried about this one in a way I haven't been about most of the others. Not so much on the data of spread which is so limited and subject to noise at the moment, but just the sheer number of significant mutations this has amassed.

[Zorral]

Well, I live in NYC, and we literally locked down in a way nowhere else in the US did, when we interacted with very people human beings in person at all -- not even in the street, with curfews and NOTHING open and no tourists, no students, no office workers, etc.

Today, I was in the supermarket, the wine shop and the shirt laundry.  One guy in the supermarket without a mask and standing around drinking coffee told me I didn't need to wear a mask, so why was I?  I responded honestly: 1) to protect myself against people who don't mask, because they often aren't vaccinated either; 2) there's a new variant said to be even worse than Delta, maybe; 3) I have nearly died twice from flu back in the day, so I know how awful respiratory sickness can be; 4) the mask also protest against flu and other contagious illnesses; 5) to do a bit to protect the wonderful people who work here and have worked here all through the pandemic.  He looked at me as if I were an idiot and walked away in disgust.  He was the only unmasked person in the supermarket that I saw.

But I interacted one way or another with Partner, a couple of stockers, that maskless jerkwaddie, the checkout person, and two people who were also checking out, and kept coming back to ask questions while we were trying to fill our bags not to mention all the other shoppers in the aisles.  Two people in the shirt laundry who work there (both masked). All four of the bro-owners in the wine store, just chatting, etc., and their 6 deterrent guys who hang out there all day (lots of daylight, gun robberies, you know and cops not bothering to do anything), plus there were five other customers in there.  The sidewalks and streets were packed.  We stood on intersection corners among 10 - 15 people (none of whom are inhabitants of our current very highly vaccinated, very low positivity rate, no hospitalizations or deaths, and very few cases) at least four times. How many people is that in just 40 minutes or so?

In the meantime the stocks for Peloton and Zoomed and the Pharm companies, um, zoomed today, in reaction to announcement of Omicron -- gads that sounds like one of of really awful Vought International superheroes doesn't it?

[Clueless Northman]

R0 of 30 is bonkers. It would be a world record, by a very large margin. Sounds actually impossible, to be honest. The highest R0 around is measles, and it's more or less half of that. Heck even Delta is a top-tier, there's just a handful of really nasties that have a worse reproduction rate. So, I'm quite skeptical. Most likely, like original covid back in the first few months of 2020, it begins by spreading silently across younger people and visible cases grow slowly at first, before exponential growth does its trick and it's an explosion of sickness all around.

In 2-3 weeks, we'll know more about the seriousness of the issue: how infectious it actually is, how lethal it actually is, to which extent vaccines can stop it.

  

6 hours ago, Zorral said:

and also flu is really bad.

So, it's a bad flu season this time, after 2 very mild years? Makes some sense. A good thing my mom got it a few weeks ago (got my shot last week).

[felice]

51 minutes ago, Impmk2 said:

It's the uniqueness I struggle with. They need to be an entirely different 30 people from Bob who I caught it from, and all the people they infected too.

R0 is the number for an uninfected and unimmunised population specifically. If the R0 was that high (and I agree it probably isn't), R_e would drop very quickly precisely because of the shortage of unique people. With more reasonable R0 numbers, the difference between R0 and R_e is typically much less drastic, eg for R0=2 Bob gives it to you and one other person, and there are still 29 people you could potentially spread it to even if you're both encountering the same 30 people, and it will take a long time for R_e to drop significantly below 2.

[Impmk2]

7 minutes ago, felice said:

R0 is the number for an uninfected and unimmunised population specifically. If the R0 was that high (and I agree it probably isn't), R_e would drop very quickly precisely because of the shortage of unique people. With more reasonable R0 numbers, the difference between R0 and R_e is typically much less drastic, eg for R0=2 Bob gives it to you and one other person, and there are still 29 people you could potentially spread it to even if you're both encountering the same 30 people, and it will take a long time for R_e to drop significantly below 2.

Sure thanks, always enjoy learning new things. I'm not an epidemiologist, and any classes I had which touched on it are over a decade ago now so my terminology is almost certainly completely off. I guess the R0 in that case would become pretty pointless metric as the uninfected population you can pass it to would drop so rapidly that the spread would simply be unsustainable. 

I mean this would also be a complete departure from the current infection model where a minority of superspreaders are responsible for approximately 80% of infections. A superspreader in this case would have to be infecting 500+ people. Goddamn it I wasn't going to get caught up in this.

[Zorral]

21 minutes ago, felice said:

R0 is the number for an uninfected and unimmunised population specifically

Which would make my neighborhood quite safe -- except huge numbers come to it from Elsewheres, and many of them are not vaxxed and refuse to wear masks.  Though they end up needing to if they want to do any shopping because the shops around here are rigid about shoppers doing so.  Uniqlo and some others provide masks if you don't have one; they also have several strong people standing about unobtrusively to remove shoppers who won't adhere to the safety rules.  But there are others that don't.  It's such a weird mix.  A tiny packed counter-only sushi place on Houston has people shoulder to shoulder eating.  The Blue Note has people wearing masks even at the bar, allowing the masks to rise when taking a swallow -- nor did they resume serving food.

[Padraig]

Did they skip nu to avoid comediennes having a field day with the new variant being called the nu variant?  Even if it isn't pronounced new.  Or did they give nu to a less concerning variant elsewere?

The fact that Omicron became a variant of concern straight away says something.  But we don't know much more.

The earliest sample they have found so far is from the 9th Nov.  But who knows when it first emerged.  I don't know how much genetic testing is carried out in South Africa.   I would have thought they'd be missing a lot of cases when it comes to normal COVID testing but their positivity rate was 1%, which is very good.  Unless it was circulating in niche populations, who weren't getting tested.

Anyhow, one day of way too much speculation over.  The media will hopefully take a breath now.

[Fragile Bird]

You may remember I was making comments at the end of September about how well Poland was doing, with daily cases just in the hundreds, but that numbers had started creeping up. I noted that last year when my SiL went to Poland in September cases were far lower than in Canada, and then seriously spiked during the eight weeks she was visiting her mom. 
 

Well, dammit, hasn’t the same thing happened all over again. Poland was doing so much better than Canada, and boom! I took my eye off the numbers and Canada is averaging 3,000 or fewer cases a day and Poland is in the mid to higher 20,000s. We have the same population, 38 M or so. Canada has never hit 10,000 cases a day, except in days combining a few days because of holidays. 
 

It makes me worried about December through March, when we had our third wave last year and this year. Our vaccination record is way better, so maybe we won’t struggle as much this winter, but the other day when we had 750 cases in Ontario the province announced half the people were fully vaccinated. Today we had more than 900 cases.

I’d love to think Delta will burn itself out, but I fear Omicron will be worse. Like many other countries we’ve banned flights from South Africa, but I suspect the horses have left the barn.

[williamjm]

43 minutes ago, Padraig said:

Did they skip nu to avoid comediennes having a field day with the new variant being called the nu variant?  Even if it isn't pronounced new.  Or did they give nu to a less concerning variant elsewere?

I don't know if they've said why but they have apparently skipped nu completely. I suspect they probably didn't want something that people would try to pronounce like 'new variant'.

46 minutes ago, Padraig said:

The earliest sample they have found so far is from the 9th Nov.  But who knows when it first emerged.  I don't know how much genetic testing is carried out in South Africa.   I would have thought they'd be missing a lot of cases when it comes to normal COVID testing but their positivity rate was 1%, which is very good.  Unless it was circulating in niche populations, who weren't getting tested.

I've read that South Africa do a comparatively large amount of genetic sequencing, much more than other African countries and more than many others as well. It's possible that the variant could have originally emerged in a neighbouring country which does less testing.

[Paxter]

2 hours ago, Fragile Bird said:

You may remember I was making comments at the end of September about how well Poland was doing, with daily cases just in the hundreds, but that numbers had started creeping up. I noted that last year when my SiL went to Poland in September cases were far lower than in Canada, and then seriously spiked during the eight weeks she was visiting her mom. 
 

Well, dammit, hasn’t the same thing happened all over again. Poland was doing so much better than Canada, and boom! I took my eye off the numbers and Canada is averaging 3,000 or fewer cases a day and Poland is in the mid to higher 20,000s. We have the same population, 38 M or so. Canada has never hit 10,000 cases a day, except in days combining a few days because of holidays. 
 

It makes me worried about December through March, when we had our third wave last year and this year. Our vaccination record is way better, so maybe we won’t struggle as much this winter, but the other day when we had 750 cases in Ontario the province announced half the people were fully vaccinated. Today we had more than 900 cases.

I’d love to think Delta will burn itself out, but I fear Omicron will be worse. Like many other countries we’ve banned flights from South Africa, but I suspect the horses have left the barn.

Yeah, closing borders to particular countries can buy you time, but that's about it. You need a 2020 Australia or NZ-style border closure to actually have any hope of keeping variants out. 

Ontario...we are averaging about 50 daily cases per million inhabitants. That is the best COVID record of any region in the US or Canada, barring Atlantic Canada and Nunavut. Fingers crossed we can keep it that way, but undoubtedly there will be a build up from now until Christmas, fueled by indoor festive gatherings and waning immunity. 

[Paxter]

2 hours ago, williamjm said:

I don't know if they've said why but they have apparently skipped nu completely. I suspect they probably didn't want something that people would try to pronounce like 'new variant'.

I've read that South Africa do a comparatively large amount of genetic sequencing, much more than other African countries and more than many others as well. It's possible that the variant could have originally emerged in a neighbouring country which does less testing.

My understanding is that Omicron shows up in PCR tests. There is no need for sequencing. 

[Kalbear]

7 hours ago, A Horse Named Stranger said:

Well, we now have to wait for two weeks before we know whether the vaccines are still working or whether they need to be tweaked a bit.

Two sad takeaways.

1. The vaccination rate in Africa is just sad. ZA with 25% is rather on the upper end on the continent.

2. How much of that mutation horror could'Ve been avoided with a fairer vaccine distribution.

Of course the virus would mutate in a vaccine free enviroment.

To be clear, right now SA is literally turning back vaccine supply because no one wants them. While its true that better fairer vaccines would help, a big problem is vaccine adoption. 

[Fragile Bird]

I see Canada has banned flights from 7 southern African nations, not just South Africa.

[Impmk2]

40 minutes ago, Paxter said:

My understanding is that Omicron shows up in PCR tests. There is no need for sequencing. 

Unless they've changed substantially in the last year (and a quick google tells me they haven't) not all PCR tests.

You need to be screening for the spike protein to see the drop out. For example I see CDCs combined flu / covid PCR panel screens for the SARS-CoV-2 Nucleocapsid & RdRP gene but not spike.