B.1.1.529 Omicron variant

[shpalman]

UK reports another 101 Omicron cases, bringing total to 437

[Woodchopper]

It seems like there's something which manages to self-limit covid outbreaks, possibly that super-spreading/clustering model which means lots of people in limited social groups infect each other quickly but infections spread less easily from one group to another. Alternatively, people take personal measures when they feel like there's lots of covid about. In the UK, the app pinging people might make a difference, but I really don't think our app here actually does anything.

Firstly, there's behaviour, as you say even without government restrictions people are taking more or less measures to limit contact with others. Behaviour is affected by many things including the weather, employment laws, changes in things school and university terms, and traditions like Christmas. People also react to rising case numbers by changing their behaviour and distancing more.

Secondly, there's immunity. Someone gets infected or vaccinated and they are less likely to be infected again and so pass on the infection to others. Immunity appears to wane over the months but it can also be boosted by another vaccination or infection.

Those combined affect the factor which is most important for serious illness and death - the number of cases among the elderly and people with serious co-morbidities. A combination of boosters and distancing in these groups can keep the number of hospital admissions and deaths down. They or people near them can behave more cautiously and avoid being infected compared to younger and fitter people who are less cautious.

So, there's a complex interaction between several variables which also affect each other. Its not surprising that case numbers in the UK have fluctuated and its very difficult to model what's happening.

The above assumes that the contagiousness of the virus is constant. But with Omicron the variables will all be dancing to a different tune.

[Woodchopper]

Omicron has increased tenfold in a week
The FM highlights the speed of Omicron's transmission.

She says that from nine cases a week ago, cases of the variant have spread tenfold.

That 4% of cases also now show the S gene drop-out which is a sign of Omicron.

Ms Sturgeon says that the doubling time for Omicron cases may be as short as two to three days, and the R number associated with the new variant may be well over two.

She repeats what the statistics have shown today, that nine of Scotland's 14 health board areas have now reported Omicron cases.

The FM expects a "potentially rapid" rise in cases in the days to come and says that from now on, the Scottish government will review the situation on a daily rather than a weekly basis.

Emphasis added.

https://www.bbc.com/news/live/uk-scotla ... type=share

[shpalman]

Scientists find ‘stealth’ version of Omicron not identifiable with PCR test

The tl;dr is that it's a version of Omicron which doesn't have the S-gene dropout.

The discovery of the new form of Omicron prompted researchers to split the B.1.1.529 lineage into standard Omicron, known as BA.1, and the newer variant, known as BA.2. Prof Francois Balloux, director of the University College London Genetics Institute, said that 42 or roughly 6% of the 709 Omicron genomes submitted to the Gisaid genome database were BA.2.

It won't be that unnoticed if it's already a covid-positive PCR result.

[badger]

Delta was clearly exponential in unvaccinated young and partially vaccinated young, but not at the 75% vaccinated national level. Omicron is going to be exponential at the national level. Cases are going to go up.

But it's NHS capacity we care about, not cases. So it all hangs on whether the ratio of hospitalisations to cases is changed by Omi.

The UK has room for two doublings of hospital patients, with the third doubling taking the NHS to the edge of breakdown.

- currently 7,500 Covid patients in hospital
- two doublings 30,000, still less than the Jan 2021 peak of 40,000
- third doubling to 60,000 takes us to the point where people are dying in the carpark

In a bad scenario of a fit Omi with the same hospitalisation ratio, the first doubling due to Omi will be very slow. It takes weeks for Omi to grow from 1,000 cases and replace Delta. At a quick look I estimate the first doubling of cases will take till the end of Jan. But the second doubling is a lot quicker as it's all faster Omi. I expect patients in hospital to hit the 30,000 mark at the end of Feb. You've got to lockdown before this point otherwise the lags in the system will guarantee you exceed the Jan 2021 peak.

Everything seems to indicate that Omicron will return us to the exponential world. Delta was only ever in balance so it doesn't take much extra to knock us into a phase transition. Dubious that boosters will be enough without lockdown measures to help.

Optimistically there might be hints that Omi puts people in hospital at the same rate but they stay there for a shorter time and need less oxygen. Obviously if hospital admissions double but length of stay halves you've not got a change in usage.

Given some of the reports and photos of ambulances queuing in hospital car parks, I wonder if there's not as much room as you think - or at least not as much as there was in Jan '21. Capacity might have changed since then (staff burnout, prioritising the non-covid stuff that got pushed last Jan etc.) and as you say Omi patients may present differently requiring different kinds and amounts of resources.

Time to re-reopen the Nightingales?

[Lew Dolby]

Time to re-reopen the Nightingales?

Which would still leave the great unanswered question from when they were first built . . .

. . . how are you going to staff them ??

[shpalman]

Time to re-reopen the Nightingales?

Which would still leave the great unanswered question from when they were first built . . .

. . . how are you going to staff them ??

Haven't they been downgraded to non-intensive isolation wards which need less staffing?

[badger]

Nah, four of the seven were closed, and I think three are now vax or testing centres. I should've put an eye roll after the question to reopen...

[Brightonian]

COVID-19: Antibodies from Pfizer vaccine may be up to 40 times less effective against Omicron, first lab tests suggest
"may", "up to", "suggest".

[jdc]

COVID-19: Antibodies from Pfizer vaccine may be up to 40 times less effective against Omicron, first lab tests suggest
"may", "up to", "suggest".

Good news that neutralising antibodies are only 20-40 times less effective. I was a bit worried we'd see no effect at all from Nabs and have to rely on non-Nabs, killer T-cells and the old memory cells.

Also, those with hybrid immunity "had much improved protection against Omicron" which is reassuring to me personally as I had a 12-week gap between 1 & 2 and I've got 3 coming up on Friday.

[jdc]

Geometric mean titer (GMT) FRNT50 (inverse of the plasma dilution required for 50% reduction in infection foci number) was 1321 for D614G. These samples therefore had very strong neutralization of D614G virus, consistent with sampling soon after vaccination. GMT FRNT50 for the same samples was 32 for Omicron, a 41-fold decline (Fig 1B). However, the escape was incomplete, with 5 of the participants, all previously infected, showing relatively high neutralization titers with Omicron.

https://drive.google.com/file/d/1YIy4Vo ... Y_wYg/view via https://www.ft.com/content/7b65c385-414 ... f98e59d8b0

(Fig 1b shows results for Pfizer alone and Pfizer + infection.)

[Woodchopper]

Detailed thread and FT article on whether South Africa data shows that Omicron results in milder illness.
https://twitter.com/jburnmurdoch/status ... 44904?s=21
https://www.ft.com/content/d315be08-cda ... 1290ad488e

tl;dr so far Omicron is associated with a smaller proportion of hospital patients needing needing oxygen or ICU treatment compared to a similar phase in the Delta wave. This could be due to pre-existing immunity rather than Omicron being intrinsically less virulent.

[shpalman]

In the UK, a further 115 cases of the Omicron variant have been reported across England, which brings the total number of confirmed Omicron cases in England to 448, the UK Health Security Agency said.

Across the UK in total, there have been 131 additional cases, bringing the total number of confirmed Omicron cases in the UK to 568.

[lpm]

101 yesterday, 131 today. 3 day doubling period. No error bars needed, a couple of data points is enough.

[shpalman]

SAGE reckons Omicron could cause hospitalizations to soar to rates similar to those of about 6 weeks ago.

[wilsontown]

Well, the 7-day case average is now as high as it's been since January 13th. If we're going to get a faster-spreading variant on top of that then it's going to have to be really mild for us to not end up in a world of hurt within a few weeks.

[Herainestold]

Well, the 7-day case average is now as high as it's been since January 13th. If we're going to get a faster-spreading variant on top of that then it's going to have to be really mild for us to not end up in a world of hurt within a few weeks.

What would a sensible government that cared about its people do? ..

[lpm]

SAGE reckons Omicron could cause hospitalizations to soar to rates similar to those of about 6 weeks ago.

I read that as 1,000 Omis plus the existing 800 Deltas, for 1,800 per day.

Which is a lot. But no chance of it happening by the end of December, that's bollocks.

More plausible might be that the case load on 31 December is enough to give this sort of level of daily hospitalisations in mid Jan after the usual lags.

[lpm]

Or does it mean cases rising from the current 750-800 to 1,000 in total by the end of the year?

Hard to tell because these SAGE leaks are being leaked through sh.t journalists.

But that's slightly more plausible - 800 Delta hospital admissions on 31 December plus 200 Omicron admissions.

[shpalman]

I would expect Omicron to increase a lot but Delta to decrease, for a net overall increase.

[lpm]

Delta doesn't decrease for weeks. It's not like there's a list of 50,000 people to infect today and if someone gets Omicron there's one less Delta.

Replacement happens via Omicron steadily building strongholds while Delta carries on generally around the country for a few weeks. Then the exponential dominates everything and Delta gets squeezed out fast.

My little spreadsheet "model" put this at the end of Jan.

[jdc]

https://www.pfizer.com/news/press-relea ... on-variant

• Preliminary laboratory studies demonstrate that three doses of the Pfizer-BioNTech COVID-19 Vaccine neutralize the Omicron variant (B.1.1.529 lineage) while two doses show significantly reduced neutralization titers
• Data indicate that a third dose of BNT162b2 increases the neutralizing antibody titers by 25-fold compared to two doses against the Omicron variant; titers after the booster dose are comparable to titers observed after two doses against the wild-type virus which are associated with high levels of protection
• As 80% of epitopes in the spike protein recognized by CD8+ T cells are not affected by the mutations in the Omicron variant, two doses may still induce protection against severe disease

[lpm]

Delta doesn't decrease for weeks. It's not like there's a list of 50,000 people to infect today and if someone gets Omicron there's one less Delta.

Replacement happens via Omicron steadily building strongholds while Delta carries on generally around the country for a few weeks. Then the exponential dominates everything and Delta gets squeezed out fast.

My little spreadsheet "model" put this at the end of Jan.

My spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.

And Plan B is obviously hilariously insufficient if the doubling time is 2-3 days. Nothing like what would be enough.

[Woodchopper]

Delta doesn't decrease for weeks. It's not like there's a list of 50,000 people to infect today and if someone gets Omicron there's one less Delta.

Replacement happens via Omicron steadily building strongholds while Delta carries on generally around the country for a few weeks. Then the exponential dominates everything and Delta gets squeezed out fast.

My little spreadsheet "model" put this at the end of Jan.

My spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.

And Plan B is obviously hilariously insufficient if the doubling time is 2-3 days. Nothing like what would be enough.

Haven’t had time to look things up. But as far as I remember 2-3 days is what has been reported in several countries. Though these are for fuzzy data and very small numbers of cases. South Africa may be slowing down a little by now. Cases can’t keep growing like that as people react and change their behaviour.

[Woodchopper]

Delta doesn't decrease for weeks. It's not like there's a list of 50,000 people to infect today and if someone gets Omicron there's one less Delta.

Replacement happens via Omicron steadily building strongholds while Delta carries on generally around the country for a few weeks. Then the exponential dominates everything and Delta gets squeezed out fast.

My little spreadsheet "model" put this at the end of Jan.

My spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.

And Plan B is obviously hilariously insufficient if the doubling time is 2-3 days. Nothing like what would be enough.

Haven’t had time to look things up. But as far as I remember 2-3 days is what has been reported in several countries. Though these are for fuzzy data and very small numbers of cases. South Africa may be slowing down a little by now. Cases can’t keep growing like that as people react and change their behaviour.

For some British data see here: https://assets.publishing.service.gov.u ... update.pdf

S gene dropout prevalence has quadrupled in a week.

Though again, it’s still small numbers and fuzzy data. But the shape of the curve looks similar to Gauteng cases.