monkey wrote: Wed Dec 15, 2021 4:58 pm
If the Omicron is localised, isn't that what you'd expect? Delta is carrying on doing its thing of not going down, but Omicron is increasing in hotspots within the area of interest. It'll only take over when it spreads from the hotspots to the notspots.
(Not suggesting this is the case, just thinking out loud).
You can maybe get an idea how localised it is from this graph from the Omicron daily overview:
Omicron by region, 6pm 14th Dec.png (61.56 KiB) Viewed 11329 times
I'm finding that 6pm label particularly worrisome; as if the situation is moving so fast just the day isn't enough...
But back to how localised it is, looks like London & the SE are getting hammered so far, with the East Midlands catching up. And those are confirmed cases, so I'm guessing there's a lag factor of some days, with SGTF being the quick and dirty upfront count.
Re: B.1.1.529 Omicron variant
Posted: Wed Dec 15, 2021 11:47 pm
by monkey
I was thinking sub areas/towns within those areas. Like it might be popular in East Kent, but hasn't got fashionable anywhere else in the South East yet.
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 12:09 am
by raven
Ah, for that you'd need to look at this spreadsheet of Omicron cases by local authority.
It is huge and rather unweildy.
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 12:33 am
by OffTheRock
lpm wrote: Wed Dec 15, 2021 5:58 pm
Chris Whitty is giving a very different opinion to the Prime Minister.
Calling for voluntary restrictions and hammering away at how people must "de-prioritise" social events.
It was the clearest example yet of having two separate press conferences in one. We need to just edit Boris out next time.
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 3:44 am
by Woodchopper
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting the possibility of host-jumping. The molecular spectrum (i.e., the relative frequency of the twelve types of base substitutions) of mutations acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients, but was highly consistent with spectra associated with evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.
raven wrote: Wed Dec 15, 2021 11:41 pm
I'm finding that 6pm label particularly worrisome; as if the situation is moving so fast just the day isn't enough...
monkey wrote: Wed Dec 15, 2021 4:58 pm
If the Omicron is localised, isn't that what you'd expect? Delta is carrying on doing its thing of not going down, but Omicron is increasing in hotspots within the area of interest. It'll only take over when it spreads from the hotspots to the notspots.
(Not suggesting this is the case, just thinking out loud).
You can maybe get an idea how localised it is from this graph from the Omicron daily overview:
Omicron by region, 6pm 14th Dec.png
I'm finding that 6pm label particularly worrisome; as if the situation is moving so fast just the day isn't enough...
But back to how localised it is, looks like London & the SE are getting hammered so far, with the East Midlands catching up. And those are confirmed cases, so I'm guessing there's a lag factor of some days, with SGTF being the quick and dirty upfront count.
Increasing-precision timestamps are the Jaws theme of incident reports.
ETA: Ninja'd
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 12:27 pm
by lpm
The Daily Mail presented it as Boris vs Scientists this morning.
The Queen has listened to the scientists instead of her Prime Minister.
People will hear the Queen's signal and react.
There was a silly Sheldrake argument where he claimed only a govt legal lockdown was a lockdown. We're about to see how far a people-led lockdown will take us.
Interesting - the insane Tories have noticed Whitty has reset the policy and overruled Johnson.
They're not wrong that it's a bit problematic. But what else can be done when Johnson is running the show.
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 8:14 pm
by Grumble
Well, my brass band have taken Whitty’s advice, not Johnson’s, and cancelled our remaining indoor activities. We’ll still do a couple of outdoor carolling jobs. The numbers are just astounding right now, after so long bobbling along at about the same level.
Re: B.1.1.529 Omicron variant
Posted: Thu Dec 16, 2021 10:13 pm
by wilsontown
lpm wrote: Thu Dec 16, 2021 12:27 pm
The Daily Mail presented it as Boris vs Scientists this morning.
The Queen has listened to the scientists instead of her Prime Minister.
People will hear the Queen's signal and react.
There was a silly Sheldrake argument where he claimed only a govt legal lockdown was a lockdown. We're about to see how far a people-led lockdown will take us.
This narrative that "the scientists" are just another special interest group lobbying for influence in Whitehall might be the most pernicious outcome of this whole disaster.
lpm wrote: Thu Dec 16, 2021 12:27 pm
The Daily Mail presented it as Boris vs Scientists this morning.
The Queen has listened to the scientists instead of her Prime Minister.
People will hear the Queen's signal and react.
There was a silly Sheldrake argument where he claimed only a govt legal lockdown was a lockdown. We're about to see how far a people-led lockdown will take us.
This narrative that "the scientists" are just another special interest group lobbying for influence in Whitehall might be the most pernicious outcome of this whole disaster.
They used to say that about climate change, too. Literally the same people in a lot of cases.
It turns out the issue wasn't that climate change was too abstract or long term or complicated or whatever: denialists gonna deny even with hundreds of deaths a day.
raven wrote: Wed Dec 15, 2021 11:41 pm
I'm finding that 6pm label particularly worrisome; as if the situation is moving so fast just the day isn't enough...
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting the possibility of host-jumping. The molecular spectrum (i.e., the relative frequency of the twelve types of base substitutions) of mutations acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients, but was highly consistent with spectra associated with evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.
lpm wrote: Thu Dec 16, 2021 12:27 pm
The Daily Mail presented it as Boris vs Scientists this morning.
The Queen has listened to the scientists instead of her Prime Minister.
People will hear the Queen's signal and react.
There was a silly Sheldrake argument where he claimed only a govt legal lockdown was a lockdown. We're about to see how far a people-led lockdown will take us.
This narrative that "the scientists" are just another special interest group lobbying for influence in Whitehall might be the most pernicious outcome of this whole disaster.
They used to say that about climate change, too. Literally the same people in a lot of cases.
It turns out the issue wasn't that climate change was too abstract or long term or complicated or whatever: denialists gonna deny even with hundreds of deaths a day.
It is likely that climate change is killing as many people as covid. Of course you don't see climate change on the death cert. And like covid it s killing people in poor countries who don't have the resources to properly record deaths and cause of.
Millennie Al wrote: Wed Dec 15, 2021 3:24 am
by making people self-test and self-isolate we are putting strong selection pressure on the virus to be infectious earlier so that people test negative due to low viral load but it increases fast enough that they infect others before they next take a test. So I would expect that eventually we would see a variant which spreads as fast as possible. Omicron may not be that variant, but it seems very likely that it is at least a step in that direction.
Further to that, I remembered I bookmarked this excellent Epidemic Calculator ages ago. Playing with the sliders on that, I don't think incubation period has much effect on doubling times. But R0 definitely does.
I think that model is too simple to show it as it takes no acount of people changing their behaviour.
* - other reasons to be in hospital exist. But not for much longer.
Omicron was already resulting in large numbers of NHS staff being off ill, especially in London.
Cos literally nobody predicted that having hospitals fuller than usual for the time of year going into winter would be an issue. And it’s definitely not going to be the government’s fault when it goes tits up, it’ll be omicron because no one could possibly have foreseen that either.
* - other reasons to be in hospital exist. But not for much longer.
Omicron was already resulting in large numbers of NHS staff being off ill, especially in London.
Cos literally nobody predicted that having hospitals fuller than usual for the time of year going into winter would be an issue. And it’s definitely not going to be the government’s fault when it goes tits up, it’ll be omicron because no one could possibly have foreseen that either.
Is flu non-existent?
Heard nothing about it and I'm assuming no news is good news. A lot of vaccines plus a few weeks of voluntary lockdown is going to crush it, surely.
Re: B.1.1.529 Omicron variant
Posted: Fri Dec 17, 2021 1:13 pm
by lpm
I've been off looking for good news. The flu thing is all I've got. Sorry.
Re: B.1.1.529 Omicron variant
Posted: Fri Dec 17, 2021 3:25 pm
by Woodchopper
A piece of the jigsaw from South Africa, some age disaggregated data on Omi severity.
Across all ages, deaths among hospitalized pts are 2/3 lower in Omicron wave.
This means that lower hospital admissions compared to Delta and Beta probably aren't explained by there being much fewer older patients this time.
However, we don't know whether this is due to Omi meeting a population which already has antibodies, or whether Omi is intrinsically less virulent.
Well, that's some (cautious) good news then.
There's some tracking of reinifections in section 9 of this document which shows them running at about 1% of cases for Delta in the UK population. That's only updated monthly, last one 18th November, so the next might show some indication of what reinfection will be with Omicron.
Re: B.1.1.529 Omicron variant
Posted: Fri Dec 17, 2021 4:11 pm
by raven
lpm wrote: Fri Dec 17, 2021 1:08 pm
Is flu non-existent?
Heard nothing about it and I'm assuming no news is good news. A lot of vaccines plus a few weeks of voluntary lockdown is going to crush it, surely.
Pretty much, as far as I can tell from the latest surveillance report. There's some about, but it's just bumping along at the bottom of the graph really.
Flu admissions.png (23.39 KiB) Viewed 10903 times
Sari Watch Flu.png (15.91 KiB) Viewed 10903 times
Re: B.1.1.529 Omicron variant
Posted: Fri Dec 17, 2021 6:44 pm
by Woodchopper
Report 49 - Growth, population distribution and immune escape of Omicron in England
Summary
To estimate the growth of the Omicron variant of concern (1) and its immune escape (2–9) characteristics, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England excluding those with a history of recent international travel. We undertook separate analyses according to two case definitions. For the first definition, we included all cases with a definitive negative S-gene Target Failure (SGTF) result and specimen dates between 29/11/2021 and 11/12/2021 inclusive. For the second definition, we included cases with a positive genotype result and specimen date between 23/11/2021 and 11/12/2021 inclusive. We chose a later start date for the SGTF definition to ensure greater specificity of SGTF for Omicron.
We used logistic and Poisson regression to identify factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. We explored the following predictors: day, region, symptomatic status, sex, ethnicity, age band and vaccination status. Our results suggest rapid growth of the frequency of the Omicron variant relative to Delta, with the exponential growth rate of its frequency estimated to be 0.34/day (95% CI: 0.33-0.35) [2.0 day doubling time] over the study period from both SGTF and genotype data. The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta.
Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta.
To estimate the impact of Omicron on vaccine effectiveness (VE) for symptomatic infection we used conditional Poisson regression to estimate the hazard ratio of being an Omicron case (using SGTF definition) compared with Delta, restricting our analysis to symptomatic cases and matching by day, region, 10-year age band, sex and ethnicity. We found a significant increased risk of an Omicron case compared to Delta for those with vaccine status AZ 2+weeks post-dose 2 (PD2) , Pfizer 2+w PD2, AZ 2+w post-dose 3 (PD3) and PF 2+w PD3 vaccine states with hazard ratios of 1.86 (95%CI: 1.67-2.08), 2.68 (95%CI: 2.54-2.83), 4.32 (95%CI: 3.84-4.85) and 4.07 (95%CI: 3.66-4.51), respectively, where PD3 states are categorised by the dose 1/2 vaccine used. Depending on the Delta VE estimates used (10), these estimates translate into Omicron VE estimates of between 0% and 20% PD2 and between 55% and 80% PD3 against Omicron, consistent with other estimates (11). Similar estimates were obtained using genotype data, albeit with greater uncertainty.
To assess the impact of Omicron on reinfection rates we relied on genotype data, since SGTF is associated with a higher observed rate of reinfection, likely due to reinfections typically having higher Ct values than primary infections and therefore being subject to a higher rate of random PCR target failure. Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date and using conditional Poisson regression to predict reinfection status, Omicron was associated with a 5.41 (95% CI: 4.87-6.00) fold higher risk of reinfection compared with Delta. This suggests relatively low remaining levels of immunity from prior infection.
Probably had that xkcd at the back of my mind.