Re: B.1.1.529 Omicron variant
Posted: Tue Dec 07, 2021 2:51 pm
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.shpalman wrote: ↑Tue Dec 07, 2021 2:30 pmIt 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.
Emphasis added.
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.
It won't be that unnoticed if it's already a covid-positive PCR result.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.
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.lpm wrote: ↑Tue Dec 07, 2021 2:47 pmDelta 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.
Haven't they been downgraded to non-intensive isolation wards which need less staffing?
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.Brightonian wrote: ↑Tue Dec 07, 2021 10:40 pmCOVID-19: Antibodies from Pfizer vaccine may be up to 40 times less effective against Omicron, first lab tests suggest
"may", "up to", "suggest".
https://drive.google.com/file/d/1YIy4Vo ... Y_wYg/view via https://www.ft.com/content/7b65c385-414 ... f98e59d8b0Geometric 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.
What would a sensible government that cared about its people do? ..wilsontown wrote: ↑Wed Dec 08, 2021 4:10 pmWell, 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.
I read that as 1,000 Omis plus the existing 800 Deltas, for 1,800 per day.shpalman wrote: ↑Wed Dec 08, 2021 3:50 pmSAGE reckons Omicron could cause hospitalizations to soar to rates similar to those of about 6 weeks ago.
- 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
My spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.lpm wrote: ↑Wed Dec 08, 2021 5:57 pmDelta 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.
lpm wrote: ↑Wed Dec 08, 2021 6:52 pmMy spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.lpm wrote: ↑Wed Dec 08, 2021 5:57 pmDelta 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.
And Plan B is obviously hilariously insufficient if the doubling time is 2-3 days. Nothing like what would be enough.
For some British data see here: https://assets.publishing.service.gov.u ... update.pdfWoodchopper wrote: ↑Wed Dec 08, 2021 8:26 pmlpm wrote: ↑Wed Dec 08, 2021 6:52 pmMy spreadsheet is obviously way off if the doubling time is 2-3 days. That's unbelievably fast.lpm wrote: ↑Wed Dec 08, 2021 5:57 pmDelta 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.
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.