B.1.1.529 Omicron variant

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 11:32 pm

Data from South African surveillance: https://www.nicd.ac.za/wp-content/uploa ... -Final.pdf

Omi still dominant

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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Thu Dec 02, 2021 12:43 am

Sciolus wrote:
Wed Dec 01, 2021 6:02 pm
Per capita, Denmark, Portugal and Netherlands are well ahead.
Portugal caralho!! Numero um!

Most vaccinated and now most omicroned. Yet another reason to be grateful for our international football teams.
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Thu Dec 02, 2021 12:46 am

Woodchopper wrote:
Wed Dec 01, 2021 2:56 pm
Bird on a Fire wrote:
Wed Dec 01, 2021 2:49 pm
I'm supposed to be going to a conference tomorrow. Vaccine passport and recent test are both required, masks throughout and assigned, distanced seating etc etc.

Fingers crossed I guess.
You probably won't be infected. As far as I know you're young, healthy and vaccinated so if you are ill it will likely be mild or even asymptomatic. You should though be concerned about any vulnerable people you might meet later. To reduce risks to others you could get some rapid tests and check yourself every morning.
Yeah I self tested before car sharing this afternoon, and will again before going in.

TBH I'm just salty because it's my first in-person conference for two years and we're in a really cool town in north Portugal and - as per usual for the entirety of the last two years - I can't relax and enjoy it.

The next person I hear dissing vegans is gonna get a right earful.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 02, 2021 9:09 am

shpalman wrote:
Wed Dec 01, 2021 5:35 pm
lpm wrote:
Wed Dec 01, 2021 4:56 pm
Yes! The UK takes an early lead in the race! The EU is nowhere in comparison. We really are good at this.
It's because of all that sequencing you do when you get around to it.
OWID share of covid cases sequenced
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 9:30 am

Explainer: Does Omicron pose higher risks for infants than other variants?
https://www.reuters.com/business/health ... 021-12-01/

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 9:42 am


Where did ‘weird’ Omicron come from?
Mutations could have accumulated in a chronically infected patient, an overlooked human population, or an animal reservoir
https://www.science.org/content/article ... icron-come

The article looks at the different explanations, and of course concludes that we don’t know.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 02, 2021 10:20 am

having that swing is a necessary but not sufficient condition for it meaning a thing
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 1:04 pm

Woodchopper wrote:
Wed Dec 01, 2021 1:27 pm
There's been a suspected Omicron outbreak in Oslo. Someone travelled from South Africa to Norway (following all the rules), and later went to a work function involving 100 people. I assume it was a Christmas party, so probably lots of dancing, singing and talking loudly over the noise. The traveler later tested himself and got a positive result, and it looks like 30-40 others were infected (either that evening or through secondary contact over the following days).

Link in Norwegian but Google Translate is your friend:
https://www.vg.no/nyheter/innenriks/i/R ... nvarianten
Now estimated that 50-60 have been infected with more expected. The increase probably reflects secondary infections.

Omicron has been confirmed in one person and others are expected. All the people infected are vaccinated adults. Most of them are said to have symptoms but are not seriously ill. As it was a tech company Christmas party I assume that they’d probably be fairly young and generally healthy.

Link in Norwegian https://www.vg.no/i/g6R7VJ

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 3:00 pm

Woodchopper wrote:
Thu Dec 02, 2021 9:42 am

Where did ‘weird’ Omicron come from?
Mutations could have accumulated in a chronically infected patient, an overlooked human population, or an animal reservoir
https://www.science.org/content/article ... icron-come

The article looks at the different explanations, and of course concludes that we don’t know.
Similar article, leans toward the immune compromised individual hypothesis: https://www.npr.org/sections/goatsandso ... it-matters

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Re: B.1.1.529 Omicron variant

Post by Al Capone Junior » Thu Dec 02, 2021 6:02 pm

California residents have made an effort to make sure the new variant gets going good in merkinania. And succeeded.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 02, 2021 7:34 pm

Somewhere between 10 and 53,935 new Omicron cases found in the UK.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 02, 2021 7:48 pm

shpalman wrote:
Thu Dec 02, 2021 10:20 am
shpalman wrote:
Tue Nov 30, 2021 9:42 am
AVOID UNNECESSARY SOCIALISING
AVOID UNNECESSARY SNOGGING
ITS OK TO SNOG SAJID JAVIDS WIFE BUT NOT THéRèSE COFFEY

We await further updates from the alcoholic adulterer in No. 10.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 9:20 pm

A couple more threads on how much faster Omicron is being transmitted comparted to Delta:
https://twitter.com/alexselby1770/statu ... 15492?s=20
https://twitter.com/TWenseleers/status/ ... 53568?s=20

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 9:49 pm

Update from the EUCDC

Epidemiological update: Omicron variant of concern (VOC) – data as of 2 December 2021 (12.00)
https://www.ecdc.europa.eu/en/news-even ... ember-2021

Includes the following important point about infections appearing to be mild.

Among the cases reported in the EU/EEA for which there is available information on disease severity, half of the cases were asymptomatic and the other half presented with mild symptoms. No cases with severe disease, hospitalisations, or deaths have been reported among these cases. It is important to note that if the severity is similar to the Delta VOC, hundreds of cases would need to have been identified in order to see patients presenting with complications and that most of these cases were detected recently and, where symptomatic, had very recent onset of symptoms. Severity outcomes often take several weeks to accumulate and longer to be evident at population level, impacting hospital rates. Furthermore, the majority of cases detected in the EU/EEA for which there are available data on age and vaccination status to date have not been of older age and were fully vaccinated. Being travellers, they could also be assumed to be healthier than the general population.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 10:03 pm

Woodchopper wrote:
Tue Nov 30, 2021 8:11 pm
Woodchopper wrote:
Sun Nov 28, 2021 4:15 pm
Hospital admissions are the metric that matters.

You can see the South Africa data here: https://www.nicd.ac.za/diseases-a-z-ind ... ov-report/

Hospital admissions in Gauteng province have gone from 135 in week 45 to 418 in week 47 (22-28 November).

Seems to be consistent with Omicron causing severe illness. Though of course we don’t yet know the ratio.

The data on hospital admissions for Gauteng is looking worse, presumably after more data has been reported.

Now it’s:

Week 45: 136
Week 46: 279
Week 47: 647

Cases continue to rise rapidly as well.
The data has been updated again:

Week 45: 143
Week 46: 300
Week 47: 788
Week 48 (this week so far): 827

See this thread by John Burn Murdoch for some updated pretty graphs:
https://twitter.com/jburnmurdoch/status ... 92769?s=21

Right now it’s looking worse than Delta.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 02, 2021 10:31 pm

having that swing is a necessary but not sufficient condition for it meaning a thing
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 11:35 pm

I think this is the preprint:

Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
https://www.medrxiv.org/content/10.1101 ... 21266068v2

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 02, 2021 11:53 pm

Thread on why it’s very hard to know the severity of Omicron: https://twitter.com/roby_bhatt/status/1 ... 43458?s=21

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Fri Dec 03, 2021 6:44 am

Woodchopper wrote:
Thu Dec 02, 2021 11:35 pm
I think this is the preprint:

Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
https://www.medrxiv.org/content/10.1101 ... 21266068v2
And here’s a thread by one of the authors: https://twitter.com/sacemadirector/stat ... 51371?s=21

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Fri Dec 03, 2021 5:37 pm

SARS-CoV-2 variants of concern and variants under investigation in England
Variant of concern: Omicron, VOC- 21NOV-01 (B.1.1.529)
Technical briefing 30
https://assets.publishing.service.gov.u ... ing_30.pdf

Big news is that at the end of November prevalence of S gene dropout in the UK has gone up from around 0.1% to 0.2%. Still small numbers but it’s an indicator of growing community transmission back then. See pages 25-31.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Fri Dec 03, 2021 7:58 pm

Update on the situation in South Africa.
https://twitter.com/miamalan/status/146 ... 31724?s=21

The earlier observed trend of increased hospital admissions of young children appears to have continued. So that could be an effect of Omi, or it could be something else.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Dec 04, 2021 6:19 am


Omicron variant may have picked up a piece of common-cold virus

The Omicron variant of the virus that causes COVID-19 likely acquired at least one of its mutations by picking up a snippet of genetic material from another virus - possibly one that causes the common cold - present in the same infected cells, according to researchers.

This genetic sequence does not appear in any earlier versions of the coronavirus, called SARS-CoV-2, but is ubiquitous in many other viruses including those that cause the common cold, and also in the human genome, researchers said.


By inserting this particular snippet into itself, Omicron might be making itself look "more human," which would help it evade attack by the human immune system, said Venky Soundararajan of Cambridge, Massachusetts-based data analytics firm nference, who led the study posted on Thursday on the website OSF Preprints.
https://www.reuters.com/business/health ... 021-12-03/

And here’s the preprint: https://osf.io/f7txy/

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Dec 04, 2021 12:59 pm

Woodchopper wrote:
Thu Dec 02, 2021 1:04 pm
Woodchopper wrote:
Wed Dec 01, 2021 1:27 pm
There's been a suspected Omicron outbreak in Oslo. Someone travelled from South Africa to Norway (following all the rules), and later went to a work function involving 100 people. I assume it was a Christmas party, so probably lots of dancing, singing and talking loudly over the noise. The traveler later tested himself and got a positive result, and it looks like 30-40 others were infected (either that evening or through secondary contact over the following days).

Link in Norwegian but Google Translate is your friend:
https://www.vg.no/nyheter/innenriks/i/R ... nvarianten
Now estimated that 50-60 have been infected with more expected. The increase probably reflects secondary infections.

Omicron has been confirmed in one person and others are expected. All the people infected are vaccinated adults. Most of them are said to have symptoms but are not seriously ill. As it was a tech company Christmas party I assume that they’d probably be fairly young and generally healthy.

Link in Norwegian https://www.vg.no/i/g6R7VJ
Now looking like 90-100 were infected by two people who’d recently returned from South Africa. 13 have been confirmed to have Omicron, we’re awaiting test results for the rest.

Link in Norwegian https://www.nrk.no/norge/fhi_-19-tilfel ... 1.15757630

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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Dec 04, 2021 7:31 pm

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sun Dec 05, 2021 4:42 am


Tshwane District Omicron Variant Patient Profile - Early Features

There has been a significant rise in new SARS-CoV-2 infections in the Gauteng Province in the last four weeks which has been attributed to the new Omicron variant announced on 24 November 2021. The first cases of Omicron were detected in the Tshwane District and coincided with the sharp rise in new infections, heralding the onset of the fourth wave in Gauteng.

Tshwane has been the global epicentre of the Omicron Outbreak and the Gauteng Province Fourth Wave with the weekly number of cases rising exponentially over several weeks, reaching just over 8569 cases in Epi Week 47 (21 November -November 27 and 41 921 by 3 December before the end of Epi Week 48 (28 November to 4 December). The exponential rise in cases has continued with 9929 new cases reported in Tshwane in the last 5 days from 29 November to 3 December 2021 (Figure 1).

We report on the early experience of the patient profile at the Steve Biko/Tshwane District Hospital Complex in Pretoria, in the heart of the Tshwane District.

In keeping with the statistics presented by the Gauteng Department of Health on 2 December 2021 for the province as a whole, and with admissions across all public and private hospitals in Tshwane as shown in the NICD DATCOV database, we have seen a sharp rise in admissions at the Steve Biko Academic and Tshwane District Hospitals (SBAH/TDH) Complex with 166 new admissions between 14 and 29 November 2021. This makes up 45% of all Tshwane District Admissions in the public sector and 26% of all admissions in both public and private sectors for the same period.

It is essential to recognize that the patient information presented here only represents the first two weeks of the Omicron wave in Tshwane. The clinical profile of admitted patients could change significantly over the next two weeks, by which time we can draw conclusions about the severity of disease with greater precision.

Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant.

The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent. SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason.

A snapshot of 42 patients in the ward on 2 December 2021 reveals that 29 (70%) are not oxygen dependent. These patients are saturating well on room air and do not present with any respiratory symptoms. These are the patients that we would call ‘incidental COVID admissions’, having had another medical or surgical reason for admission. Thirteen (13) patients are dependent on supplemental oxygen of which nine (21%) have a diagnosis of COVID-19 pneumonia based on a combination of symptoms, clinical signs, CXR and inflammatory markers. All are being prescribed steroids as the mainstay of therapy. The remaining 4 patients are on oxygen for other medical reasons (2 previously on home oxygen, 1 in heart failure and 1 with a confirmed diagnosis of Pneumocystis Pneumonia).
This is a picture that has not been seen in previous waves. In the beginning of all three previous waves and throughout the course of these waves, there has always only been a sprinkling of patients on room air in the COVID ward and these patients have usually been in the recovery phase waiting for the resolution of a co-morbidity prior to discharge. The COVID ward was recognizable by the majority of patients being on some form of oxygen supplementation with the incessant sound of high flow nasal oxygen machines, or beeping ventilator alarms.

There are only 4 patients in high care and one in the ICU. The numbers of patients in high care on double oxygen, High Flow Nasal Oxygen or non-invasive ventilation (NIV) were noticeably higher in previous waves. This is anecdotal but confirmed by numerous clinicians who have previously worked in the COVID wards in the hospital complex.

Of 38 adults in the COVID wards on 2 December 2021, 6 were vaccinated, 24 were unvaccinated and 8 had unknown vaccination status. Of 9 patients with COVID pneumonia 8 are unvaccinated, 1 is a child. Only a single patient on oxygen was fully vaccinated but the reason for the oxygen was Chronic Obstructive Pulmonary Disease.

An analysis of 166 patients admitted to the SBAH/TDH Complex in the period 14 -29 November 2021, revealed that the age profile differed markedly from the previous 18 months. In the last two weeks, no fewer than 80% of admissions were below the age of 50 years. This is in keeping with the age profile of admissions in all public and private hospitals in Tshwane and throughout the Gauteng Province in the last two weeks as reported by the NICD and the Gauteng Provincial Government. Nineteen (19) percent were children aged 0-9 years and the highest number of admissions was in the age group 30-39 years, making up 28 percent of the total.

A key question regarding the new Omicron outbreak is whether disease severity is similar, milder or more severe than with the other variants, given the large number of Omicron mutations.

The best indicator of disease severity is measured by the in-hospital death rate. There were 10 deaths in the SBAH/TDH cohort in the past two weeks, making up 6.6% of the 166 admissions. Four deaths were in adults aged 26 – 36 and five (5) deaths were in adults over 60. One death was in a child in whom the cause of deaths was unrelated to COVID. There were no COVID related deaths among 34 admissions in the paediatric COVID wards over the last two weeks. This compares favorably to the proportion of deaths at the complex over the past 18 months which was 17%. The trend over the next two weeks will be clarified as the number of deaths is currently low, and sufficient time will have elapsed for the development of greater severity of disease and the number of deaths might be expected to increase. For now, the death rates over the last two weeks.as well as over the past 18 months at the SBAH/TDH complex are lower than the overall in-hospital death rate of 23% for the country over all previous waves, as reported by the NICD.

Figure 2 below shows the absence of any significant increase in in-hospitals deaths in relation to the dramatic rise in the case rate for the Gauteng Province as a whole. This may be due to the usual lag between cases and deaths and the trend will become clearer over the next few weeks.

Other crude indicators of severity of disease include the level of care required in hospital (ICU, high care, general ward), oxygen requirements (nasal prongs, face mask, high flow, non-invasive or invasive ventilation) and length of stay in hospital.

There were only 2 patients in the COVID ICU in the last 14 days, neither of whom had a primary diagnosis of COVID pneumonia. Sixty-three patients were admitted to high care, but our anecdotal information is that the majority of high care admissions were for a diagnosis other than COVID.

In the snapshot Table 1 above, 3 of the 4 patients in the high care ward had a primary diagnosis of severe COVID pneumonia so it could be that the more recent profile is changing to more severe COVID disease. A more detailed analysis of high care patients is being conducted and may be more revealing.

More precise measures of severity of disease in hospitalized individuals require a review of Chest X-Ray or lung Computer Tomography findings (percent of lung fields showing changes), blood gas measures, blood biomarkers and the concomitant effect of co-morbidities on the patient’s condition. Detailed studies of both the crude and more precise measures of disease severity are being done locally by several teams of researchers and the team at Steve Biko is participating in these studies.

A significant early finding in this analysis is the much shorter average length of stay of 2.8 days for SARS-CoV-2 positive patients admitted to the COVID wards over the last two weeks compared to an average length of stay of 8.5 days for the past 18 months. The NICD reports a similar shorter length of stay for all hospitals in Tshwane in its weekly report. It is also less than the Gauteng or National average length of stay reported by the NICD in previous waves.

In summary, the first impression on examination of the 166 patients admitted since the Omicron variant made an appearance, together with the snapshot of the clinical profile of 42 patients currently in the COVID wards at the SBAH/TDH complex, is that the majority of hospital admissions are for diagnoses unrelated to COVID-19. The SARS-CoV-2 positivity is an incidental finding in these patients and is largely driven by hospital policy requiring testing of all patients requiring admission to the hospital.

Using the proportion of patients on room air as a marker for incidental COVID admission as opposed to severe COVID (pneumonia), 76% of patients at the SBAH/TDH complex are incidental COVID admissions. This very unusual picture is also occurring at other hospitals in Gauteng. On 3 December Helen Joseph Hospital had 37 patients in the COVID wards of whom 31 were on room air (83%); and the Dr George Mukhari Academic Hospital had 80 patients of which 14 were on supplemental oxygen and 1 on a ventilator (81% on room air).

The exponential increase in the positivity rate in these patients is a reflection of the rapidly increased case rate for Tshwane but does not appear to be associated with a concomitant increase in the rate of admissions for severe COVID (pneumonia) based on the high proportion of patients not requiring supplemental oxygen.

The relatively low number of COVID-19 pneumonia hospitalizations in the general, high care and ICU wards constitutes a very different picture compared to the beginning of previous waves. A detailed analysis comparing the current picture with previous waves is still being conducted. This may very well be related to the early upswing of the fourth wave, with the more classical pattern becoming evident over the next two weeks. What is clear though is that the age profile is different from previous waves. It may be that this is a vaccination effect as 57 % of people over the age of 50 have been vaccinated in the province compared to 34% in the 18-to-49-year group.

The high proportion of COVID incidental adult patients and the increased number of SARS-CoV-2 positive admissions among children aged 0-9 may reflect higher rates of community transmission compared to previous waves (variants) that is not translating into higher admission rates for a primary COVID-19 diagnosis. More time is required to fully answer the questions about the severity of COVID-19 caused by the new Omicron Variant.
https://www.samrc.ac.za/news/tshwane-di ... y-features

tl;dr During the first two weeks of the outbreak (14-29 November) hospital patients were much less sick than in previous waves. Stays were shorter and fewer needed oxygen or a stay in the ICU and there were fewer deaths in hospital. But they were also much younger than in previous waves (80% under 50, 19% 9 or under).

I’ll also assume that compared to previous waves a much higher proportion had antibodies (vaccinated or previously infected).

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