B.1.1.529 Omicron variant

[shpalman]

THERE'S NO SUCH THING AS DECOUPLING YOU JUST AREN'T THROUGH THE LAG YET

[raven]

Of course that's a week too late. Not clear how strong the voluntary lockdown will be in the coming week - could be enough to scrape through this.

We met a friend for lunch yesterday in Southwark. Considering it was the last Friday before Christmas Eve we assumed the restaurant would be busy and had thought about cancelling. Turned out we were the only ones there apart from the staff. The tube was still pretty busy though. So a semi-strong voluntary lockdown in London.

Eldest, who's a pretty social late 20s Londoner, has cancelled all outings to protect his family Christmas. Says lots friends have tested positive, particularly those who've been going out.

This - ETA I mean people being sensible & voluntarily locking down - would make me more optimistic if we were also advising people who have cases in their household to self-isolate, but we're not. If you're vaccinated and your LFT is negative, you can go out. And you can bet some people are taking advantage of that, particularly people who will lose pay if they don't go to work.

That's not going to cut it with Omicron.


I don't know how well Test&Trace is functioning either. Don't think they've contacted my sister yet, and it's 6 days since her lad tested positive.

[raven]

Today's Omicron daily overview is sobering reading.linky

The UK has 37,000+ confirmed Omicron cases, but almost 100,000 positive PCRs showing spike failure that are probably omicron. (I guess it takes, what, 5 or 6 days to confirm that? At some point the numbers are going to be such that we can't sequence all the samples, surely...)

Doubling times by region are not encouraging either (my bold):

We are observing doubling time central estimates of less than 2 days for every region except the South West. This may be related to poor PCR gene target reporting coverage in this region.

[Gfamily]

We drove down to that London yesterday to pick up our daughter; staying at hers overnight and then back to civilisation today. #

There was a thought that we might nip into the local shop to pick up some snacks before heading home; but we reckoned it safer just to avoid any enclosed contacts at all.

We know that the 'hyper-transmissible' variant is common in London and the SE; so assume that if you've mixed with anyone there, you're a very-high-potential positive case

[Woodchopper]

Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa

https://www.sacmcepidemicexplorer.co.za ... micron.pdf

[shpalman]

12 people have died with the Omicron variant of the coronavirus, and 104 are in hospital with it

[jaap]

https://www.deccanherald.com/internatio ... 62625.html

A growing body of preliminary research suggests the Covid-19 vaccines used in most of the world offer almost no defence against infection by the highly contagious Omicron variant.

All vaccines still seem to provide a significant degree of protection against serious illness from Omicron, which is the most crucial goal. But only the Pfizer and Moderna shots, when reinforced by a booster, appear to have initial success at stopping infections, and these vaccines are unavailable to most of the world.

[shpalman]

https://www.deccanherald.com/internatio ... 62625.html

A growing body of preliminary research suggests the Covid-19 vaccines used in most of the world offer almost no defence against infection by the highly contagious Omicron variant.

All vaccines still seem to provide a significant degree of protection against serious illness from Omicron, which is the most crucial goal. But only the Pfizer and Moderna shots, when reinforced by a booster, appear to have initial success at stopping infections, and these vaccines are unavailable to most of the world.

Well the anecdotes from the lab covid club are that basically those who had two AstraZenecas but no booster caught it, and the boosted ones didn't. And this might still have been Delta.

(AstraZeneca was given to university staff earlier than the age-based rollout would have got to most of us, so generally the second dose at least six months ago by now.)

[Woodchopper]

https://www.deccanherald.com/internatio ... 62625.html

A growing body of preliminary research suggests the Covid-19 vaccines used in most of the world offer almost no defence against infection by the highly contagious Omicron variant.

All vaccines still seem to provide a significant degree of protection against serious illness from Omicron, which is the most crucial goal. But only the Pfizer and Moderna shots, when reinforced by a booster, appear to have initial success at stopping infections, and these vaccines are unavailable to most of the world.

Yes, I've seen some pretty poor results for AZ, Janssen, Sinopharm and Sputnik.

[shpalman]

Omicron may account for almost 70% of UK Covid cases

[jimbob]

Omicron may account for almost 70% of UK Covid cases

Easily by now.

Looking at this, it's up to the 17th December if my counting is correct and is 69.2%

Screenshot 2021-12-20 182146.png (149.03 KiB) Viewed 2196 times

[Woodchopper]

Omicron may be significantly better at evading vaccine-induced immunity, but less likely to cause severe disease

[…]

Spike proteins on the surface of SARS-CoV-2 bind to ACE2, a protein receptor found on the surface of cells in the lung. Both the spike protein and ACE2 are then cleaved, allowing genetic material from the virus to enter the host cell. The virus manipulates the host cell’s machinery to allow the virus to replicate and spread.

To see how effective Omicron is at entering our cells, the team used their pseudoviruses to infect cells in lung organoids – ‘mini-lungs’ that model parts of the lung. Despite having three mutations that were predicted to favour the spike cleavage, the researchers found the Omicron spike protein to be less efficient than the Delta spike at cleaving the ACE2 receptor and entering the lung cells.

In addition, once Omicron had entered the cells, it was also less able than Delta to cause fusion between cells, a phenomenon associated with impaired cell-to-cell spread. Fused cells are often seen in respiratory tissues taken following severe disease. Indeed, when the team used a live Omicron virus and compared it to Delta in a spreading infection experiment using lung cells, Omicron was significantly poorer in replication, confirming the findings regarding impaired entry.

Professor Gupta added: “We speculate that the more efficient the virus is at infecting our cells, the more severe the disease might be. The fact that Omicron is not so good at entering lung cells and that it causes fewer fused cells with lower infection levels in the lab suggests this new variant may cause less severe lung-associated disease.

“While further work is needed to corroborate these findings, overall, it suggests that Omicron’s mutations present the virus with a double-edged sword: it’s got better at evading the immune system, but it might have lost some of its ability to cause severe disease.”

However, Professor Gupta urged caution.

“Omicron still represents a major public health challenge. Individuals who have only received two doses of the vaccine – or worse, none at all – are still at significant risk of COVID-19, and some will develop severe disease. The sheer number of new cases we are seeing every day reinforces the need for everyone to get their boosters as quickly as possible.”

https://www.cam.ac.uk/research/news/omi ... y-to-cause

Paper here:
https://www.citiid.cam.ac.uk/wp-content ... AzMjUwNC4w

[Woodchopper]

Omicron update from Denmark. 47% of cases were Omicron on the 15th (5-day lag now). Test capacity has been maxed out and DK is adjusting strategy. From now on the key metric is the number of hospitalizations. Using the number of cases as an early indicator is not possible.

https://twitter.com/madsalbertsen85/sta ... 50918?s=21

[raven]

“While further work is needed to corroborate these findings, overall, it suggests that Omicron’s mutations present the virus with a double-edged sword: it’s got better at evading the immune system, but it might have lost some of its ability to cause severe disease.”

Swings and roundabouts, I guess. But that's a small chink of silver lining.

[dyqik]

“While further work is needed to corroborate these findings, overall, it suggests that Omicron’s mutations present the virus with a double-edged sword: it’s got better at evading the immune system, but it might have lost some of its ability to cause severe disease.”

Swings and roundabouts, I guess. But that's a small chink of silver lining.

The virus would probably prefer* not to cause severe disease, because then people wouldn't take so many precautions, and then it could spread even further and faster.

* To use teleological terms, because they did it first

[raven]

Today's Omicron daily overview is sobering reading.linky

Confusingly, my linky from last night is now pointing to today's overview. Should've put a link to the main page instead, like so: COVID-19: Omicron daily overview

Anyhow.

Today's figures for the UK, which go up to 6pm yesterday (19th Dec):

45,145 confirmed Omicron cases; 124,954 probable cases, aka SGTF or Spike-gene test failure on a PCR.
(The increase in confirmed cases is 8k, a little less than yesterday's 12k, but I don't know if that's a genuine slowing or if we're maxing out on the sequencing. Increases in SGTF are about the same.)

In England: 14 deaths, and 129 hospitalisations (confirmed Omicron & SGTF)

SGTF is now running at 68% of PCR tests in England, 87% in London. Most regions are 60+%, only the NE significantly lower at 44%, but doubling time is shorter there:

Doubling times by region 20 December 2021.png (44.12 KiB) Viewed 2099 times

[Woodchopper]

A good summary:

Early lab studies hint Omicron may be milder. But most scientists reserve judgment

https://www.science.org/content/article ... e-judgment

[shpalman]

About 15% of cases sequenced in Abruzzo are Omicron, according to something on the news.

[Woodchopper]

Thread: https://twitter.com/andrewlilley_au/sta ... 91912?s=20

Covers New South Wales.

NSW is the ideal setting to measure the severity of Omicron, and it is showing a CFR for Omicron that is <1/2 of Delta
Five reasons it's ideal:
*Prior infection is irrelevant (~2-3% of NSW is prior infected)
*Delta cases were steady through Nov, making a stable baseline CHR

We have observed the aggregate C[H]R fall by ~50% over the last 10 days - what does that mean for the CFR for each Delta case v. Omicron case? We can trace out the relative C[H]R based on the estimated % of cases which were made up of Omicron 5 days ago (& assuming ~0% start of Dec).

Lots more at the thread.

tl;dr Omicron cases result in about half the hospital admission rate compared to Delta. This ratio isn't confounded by prior infection or differing levels of vaccination.

IMHO he's using a five day lag between a positive test and hospital admission, which may be a bit short. But may not.

[jimbob]

Thread: https://twitter.com/andrewlilley_au/sta ... 91912?s=20

Covers New South Wales.

NSW is the ideal setting to measure the severity of Omicron, and it is showing a CFR for Omicron that is <1/2 of Delta
Five reasons it's ideal:
*Prior infection is irrelevant (~2-3% of NSW is prior infected)
*Delta cases were steady through Nov, making a stable baseline CHR

We have observed the aggregate C[H]R fall by ~50% over the last 10 days - what does that mean for the CFR for each Delta case v. Omicron case? We can trace out the relative C[H]R based on the estimated % of cases which were made up of Omicron 5 days ago (& assuming ~0% start of Dec).

Lots more at the thread.

tl;dr Omicron cases result in about half the hospital admission rate compared to Delta. This ratio isn't confounded by prior infection or differing levels of vaccination.

IMHO he's using a five day lag between a positive test and hospital admission, which may be a bit short. But may not.

I'm tending to think the evidence is starting to show that Omicron is probably less severe, but not sufficiently-less for it to not be serious.

[lpm]

Delta cases 50,000
Omicron cases 100,000
Hospitalisations 1/2

I'm sure maths comes into it somewhere.

[Woodchopper]

Thread: https://twitter.com/andrewlilley_au/sta ... 91912?s=20

Covers New South Wales.

NSW is the ideal setting to measure the severity of Omicron, and it is showing a CFR for Omicron that is <1/2 of Delta
Five reasons it's ideal:
*Prior infection is irrelevant (~2-3% of NSW is prior infected)
*Delta cases were steady through Nov, making a stable baseline CHR

We have observed the aggregate C[H]R fall by ~50% over the last 10 days - what does that mean for the CFR for each Delta case v. Omicron case? We can trace out the relative C[H]R based on the estimated % of cases which were made up of Omicron 5 days ago (& assuming ~0% start of Dec).

Lots more at the thread.

tl;dr Omicron cases result in about half the hospital admission rate compared to Delta. This ratio isn't confounded by prior infection or differing levels of vaccination.

IMHO he's using a five day lag between a positive test and hospital admission, which may be a bit short. But may not.

I'm tending to think the evidence is starting to show that Omicron is probably less severe, but not sufficiently-less for it to not be serious.

I'm tentatively nudging in the same direction. We've got some real world data on infections and some lab results. Its all early days but together they are looking like Omicron isn't as contagious as Delta.

I agree that its still a public health problem. A small proportion of a very big number is still .....

But also, even if a hypothetical Covid variant caused close to zero fatalities, it would still be a major public health hazard if it caused large proportions of essential workers to be absent from work at the same time (off sick, caring or unable to get to work because transport workers aren't at work). No one would be dying of Covid, but parts of the healthcare system would break down. That would be possible with a disease as contagious as Omicron combined with everyone acting like its 1999, and which is virulent enough to lead to working age adults to be unable to work for a week or more.

A disease like that would pose a very difficult political problem.

[Woodchopper]

Delta cases 50,000
Omicron cases 100,000
Hospitalisations 1/2

I'm sure maths comes into it somewhere.

You should perhaps read the thread.

[lpm]

What have I missed?

[KAJ]

<snnip>

I'm tentatively nudging in the same direction. We've got some real world data on infections and some lab results. Its all early days but together they are looking like Omicron isn't as contagious as Delta.

<snip>

Omicron less contagious than Delta? Is that a mistype, or do I misunderstand the meaning of contagious?