B.1.1.529 Omicron variant

[jimbob]

I'm looking back on the Wuhan Coronavirus thread from March 2020. We were talking about similar doubling rates then to Omicron now in a heavily-vaccinated population.

[shpalman]

I'm looking back on the Wuhan Coronavirus thread from March 2020. We were talking about similar doubling rates then to Omicron now in a heavily-vaccinated population.

That was due to how we were suddenly discovering cases when the virus had been around a week or two already.

[Woodchopper]

The thing is that Delta became significantly less severe as a consequence of mass vaccination. As far as I remember from about 10% of cases needing hospital treatment down to about 2%.

I assume that when people talk about Omi being less severe they mean in comparison to the early phases of the other variants. I haven’t seen any evidence that Omi would be less virulent in a population without any antibodies (if such a population even exists now).

That's ratios. It's misleading and is making people go wrong.

If Delta puts 2% of cases in hospital, Omicron will put 1%, say. Far less. That's guaranteed. It's simply the outcome of the mix.

We saw it with Delta. A huge number of kids in the case numbers, the hospitalization ratio falls. A huge number of vaccinated breakthroughs and the ratio falls.

But that's just aggregation across a population and is irrelevant to real world outcomes. It's individuals and their personal risk that matter. I'm never sure what people are talking about with "milder" because they seem confused by mix vs individuals.

I'm not managing to explain it very well though. What we need to discover is individual impacts.

Take David. He is 80 years old. Two Pfizers. Likes to spend time with grandchildren.

He didn't catch Delta. Either luck or the good vaccine protection. He's now quite likely to catch Omicron, because it'll be so widespread and his Pfizers are less protective against infection.

He catches it. Has David's risk of hospitalization changed vs if he'd caught Delta?

- Higher risk, because two Pfizers are still very good protection against hospitalization, but not quite as good as before
- Lower risk, because Omicron is milder underlying virulence

It's impossible to determine individual risk from aggregated national statistics because the vax vs unvax ratio changes in such a dramatic way for Omicron. Look at any aggregated statistic and you'll see a far lower hospitalization ratio - tricking you into telling David he's got a lower risk of going into hospital now he's caught Covid. This might well be false.

We really don't know yet. When there's more cases it'll be possible to compare demographically similar large cohorts of people in Britain infected by Delta and Omicron. At that point we can get an idea about whether or not Omicron is inherently less virulent than Delta. We know that its a lot more contagious.

I haven't yet seen any data about Omicron causing fewer serious illnesses than Delta in South Africa which can't be explained by much higher levels of prior immunity in Gauteng during this fourth wave.

But Gauteng is very different to Glasgow and we'll have to wait a few more weeks to see how it pans out.

[jimbob]

I'm looking back on the Wuhan Coronavirus thread from March 2020. We were talking about similar doubling rates then to Omicron now in a heavily-vaccinated population.

That was due to how we were suddenly discovering cases when the virus had been around a week or two already.

Indeed - the actual doubling rate was probably slower - certainly judging by the increase in deaths.

[shpalman]

First people in UK hospitals with Omicron variant

The new variant of coronavirus now accounts for a third of cases in London

[shpalman]

UK changes the bulb

[Woodchopper]

There’s been some commentary on Twitter that the Omicron wave in Gauteng had peaked and case numbers were now descending. Which would be really weird given everything else we know about Omi.

It looks like the recent lower case numbers were just a reporting backlog:

Today we report 37 875 new cases, which includes 19 840 retrospective cases and 18 035 new cases. In the past 24 hours a total of 18,035 positive COVID-19 cases have been reported. The positivity testing rate today is 28.9%.

https://www.nicd.ac.za/latest-confirmed ... mber-2021/

[Stranger Mouse]

There’s been some commentary on Twitter that the Omicron wave in Gauteng had peaked and case numbers were now descending. Which would be really weird given everything else we know about Omi.

It looks like the recent lower case numbers were just a reporting backlog:

Today we report 37 875 new cases, which includes 19 840 retrospective cases and 18 035 new cases. In the past 24 hours a total of 18,035 positive COVID-19 cases have been reported. The positivity testing rate today is 28.9%.

https://www.nicd.ac.za/latest-confirmed ... mber-2021/

That was confusing the f.ck out of me

[Grumble]

I live in Stockport and not far from Stepping Hill Hospital. Now, this is only a Facebook comment, but a lady has reported trying to go to A&E there with breathing difficulties and spending 11 hours before being sent to Chesterfield. For this to make any sense Manchester must be full, and Salford, and Altrincham, and many others that would be more obvious than Chesterfield.

[lpm]

I've ventured onto twitter.

Everyone is forgetting the steepness of the age curve again. This makes me cross. In the face of this virus 80 year olds are very very different humans to 30 year olds.

A country with a fairly young population, let's call it Shouth Ashfrica, will have a hugely different hospitalisation and death profile to an ageing European country, let's call it Ununited Shitdom.

[shpalman]

At least one person in UK has died with Omicron

[bob sterman]

I've ventured onto twitter.

Everyone is forgetting the steepness of the age curve again. This makes me cross. In the face of this virus 80 year olds are very very different humans to 30 year olds.

A country with a fairly young population, let's call it Shouth Ashfrica, will have a hugely different hospitalisation and death profile to an ageing European country, let's call it Ununited Shitdom.

Indeed. To keep it mild, instead of booking boosters - we need to book appointments to change our our middle aged and elderly folk - into young South Africans with previous exposure to the Beta variant.

[Grumble]

I've ventured onto twitter.

Everyone is forgetting the steepness of the age curve again. This makes me cross. In the face of this virus 80 year olds are very very different humans to 30 year olds.

A country with a fairly young population, let's call it Shouth Ashfrica, will have a hugely different hospitalisation and death profile to an ageing European country, let's call it Ununited Shitdom.

Indeed. To keep it mild, instead of booking boosters - we need to book appointments to change our our middle aged and elderly folk - into young South Africans with previous exposure to the Beta variant.

Can we apply for ourselves? I’d quite like to be a young South African.

[raven]

Are there some graphs for Omicron cases in the UK yet?

I found a spreadsheet of data on confirmed & spike-failure cases by local authority here but my excel-fu is not up to manipulating it into a display-friendly form.

Looks like widely scattered but small clusters so far, but it only goes up to the 6th and the increases are pretty dramatic.

(ETA: found that link in the latest variants report here (linky))

[raven]

So, while I was feeding insomnia with data on Omicron last night, I came across something interesting in this technical briefing.

There's a VUI (A.Y 4.2, unnamed as yet) from October that has given the UK 15k+ of cases in the last reporting period to Delta's 96k. It seems to be outcompeting Delta from these graphs: (Delta purple, VUI dark blue)

Screenshot 2021-12-13.png (187.28 KiB) Viewed 29669 times

So is that part of what's causing this slow upward rise of cases we've seen from 30k to 50k+? (Because Omicron hasn't really got going yet.)

[shpalman]

200,000 a day!

[Brightonian]

we expect it to become the dominant Covid 19 variant in the capital in the next 48 hours.

[headshot]

we expect it to become the dominant Covid 19 variant in the capital in the next 48 hours.

Dominant in the UK by the end of the week.

[Woodchopper]

Danish data isn’t looking so good.

They have very good surveillance and the proportion of patients admitted to hospital “tested positive prior or within 48 hrs after admission” is 0.8% for Omicron and 0.7 for ‘other variants’ which means Delta.

See here page 6.
https://files.ssi.dk/covid19/omikron/st ... 22021-i30w

There are also another 9 cases where they tested positive more that 48 hours after admission. They could have acquired the infection in hospital.

[raven]

There's a VUI (A.Y 4.2, unnamed as yet) from October that has given the UK 15k+ of cases in the last reporting period to Delta's 96k. It seems to be outcompeting Delta from these graphs: (Delta purple, VUI dark blue)

So is that part of what's causing this slow upward rise of cases we've seen from 30k to 50k+? (Because Omicron hasn't really got going yet.)

D'uh. Should've just looked that variant up - that's 'Delta plus', so no wonder.

News on Omicron is not looking great. MrRaven spoke to one of his minions today (he's a Despicable Me fan, and yes, they know he calls them that). Minion tested positive, and as all his social bubble tested positive too, thinks it must be Omicron. Oxford, I think.

Meanwhile, our local area is shooting up and about to hit double the January peak.

[lpm]

Loads of random numbers seem to be going around.

There are 50,000 official Delta cases a day. Today's official figure was 1,500 Omicron cases.

But Javid says it's 20%. Using a spreadsheet I calculate that means 10,000 cases.

Javid also says it is 200,000. Same spreadsheet says this more than 1,500.

To overtake Delta by the end of the week would take 5 doublings. Spreadsheet says for this to happen in 5 days would require a pace of one doubling a day.

Or alternatively cases are currently 12,500 and we get two doublings.

On one level, forecasts are highly sensitive to starting point assumptions, e.g. if the exam question is forecasting cases on 31 December.

On the other hand it's completely irrelevant, because if you forecast 250,000 cases it doesn't matter if that happens by 31 December or three days later on 3 Jan.

[wilsontown]

200,000 a day!

I don't get this. If there are 200,000 omicron cases a day and that is 20% of the UK cases, we have 1 million cases a day. Official numbers are circa 50,000. So testing is picking up 1 in 20 infections?

What am I missing?

[shpalman]

He was actually referring to the UKHSA estimate that 200,000 people are currently infected with Omicron.

A health source has clarified what Sajid Javid meant in the Commons when he implied Omicron infections were running at 200,000 per day. (See 4.19pm and 5.2opm.)

Javid was referring to Omicron infections, not Covid infections.

But he was referring to a UK Health Security Agency estimate for the number of people who currently are infected with Omicron, not to the number who are catching the infection for the first time every day.

[wilsontown]

Yep, just seen that.

A bit of a worry that our health secretary is making statements that make no obvious sense and is apparently not clear about what the numbers he's talking about actually mean.

[lpm]

Well that's still bollocks, as any simple sense check would show.

The multiple of actual cases to official cases is unknown, obvs, but we've previously assumed 2x or 3x. There have been 4,500 official Omi cases, so call it 3x = 15,000.

All official numbers are several days old and Omi's doubling time is fast. Call it two doublings since the 15,000 number = 60,000. That's a generous estimate of Omicron cumulative infections right now. No way can it be 200,000.

Delta total infections are currently around 1,000,000 as shown by surveys.

To get from 60,000 to overtake Delta by the end of the week is four doublings.