Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern" & BA.2 sub-variant, XE

[kiwibird]

https://www.telegraph.co.uk/global-health/science-and-disease/south-african-doctor-raised-alarm-omicron-variant-says-symptoms/

The first South African doctor to alert the authorities about patients with the omicron variant has told The Telegraph that the symptoms of the new variant are unusual but mild.

Dr Angelique Coetzee said she was first alerted to the possibility of a new variant when patients in her busy private practice in the capital Pretoria started to come in earlier this month with Covid-19 symptoms that did not make immediate sense.

They included young people of different backgrounds and ethnicities with intense fatigue and a six-year-old child with a very high pulse rate, she said. None suffered from a loss of taste or smell.

“Their symptoms were so different and so mild from those I had treated before,” said Dr Coetzee, a GP for 33 years who chairs the South African Medical Association alongside running her practice.

On November 18, when four family members all tested positive for Covid-19 with complete exhaustion, she informed the country’s vaccine advisory committee.

Emphasis mine. The article further states that Dr. Coetzee was concerned for the six year old child but within two days the little girl was much better. This was nearly ten days ago and the variant must have been circulating in the community for longer than that. The people quarantined in Schiphol who were interviewed were not symptomatic.

https://www.telegraph.co.uk/news/2021/11/26/new-covid-variant-less-worrying-delta-says-prof-chris-whitty/?li_source=LI&li_medium=liftigniter-rhr

New Covid variant is less worrying than delta, says Prof Chris Whitty

Chief Medical Officer urges calm in face of warnings around omicron mutation, saying concern should focus on ‘immediate threats’

T

A graph of South African deaths has not shown a dramatic spike. IMO the bottom line is you do not want to get Covid - whichever variant it is.

[Emily]

https://www.voiceforscienceandsolidarity.org/scientific-blog/my-opinion-on-the-new-african-variants

November 27, 2021
My opinion on the new African variants
Geert Vanden Bossche

The world may be taken by surprise but that doesn't include us. It remains to be seen whether Omicron can outcompete Delta (to be confirmed). If that’s the case, we're definitely not in good shape.
In case of CoV, innate immunity protects the individual and the 'herd' ( sterilizing immunity, no natural selection pressure, herd immunity) whereas adaptive immunity induced with leaky vaccines has exactly the opposite effect.
THE big Q is whether such an immune escape variant could even resist naturally acquired Abs in people who recovered from C19 disease. I am, indeed, cautious and worried about ADE, even in the unvaccinated who recovered from C-19 disease as they may no longer be able to control viral infection. ADE would equal ‘enhanced virulence’. Difficult to predict.
Mass vaccination has compressed the evolutionary trajectory of the virus from a few hundred years (?) down to one year. Hope that naturally primed individuals can deal with that speed.

[Mary Wilson]

What we know about Omicron variant that has sparked global alarm

Clive Cookson and Oliver Barnes in London
YESTERDAY

... Slawomir Kubik, a genomics research expert at Geneva-based biotech Sophia Genetics, said many of Omicron’s mutations came “completely out of the blue” and had not been observed before in other strains. Therefore, scientists “have very little visibility on what these new mutations are doing to how the virus works”, he explained, adding that once it begins to spread more widely its “true fitness” will become clear. Some of the mutations indicate increased transmissibility, while changes in the genetic code make it harder for the immune system, trained by existing vaccinations or prior infection with another variant, to tackle a new strain. But it will take researchers several weeks or months to work out the interactions between them and their cumulative impact.

https://www.ft.com/content/42c5ff3d-e676-4076-9b9f-7243a00cba5e

[Mary Wilson]

Tracking COVID-19 variant Omicron

https://bnonews.com/index.php/2021/11/omicron-tracker/

BREAKING: England reports first 2 cases of new coronavirus variant

NEW: Czech Republic reports first suspected case of new coronavirus variant in returnee from Egypt

NEW: Germany reports probable case of new coronavirus variant in returnee from South Africa

[JJackson]

Re. Omicron
There is not enough data to say anything very definitive about this variant yet - not that that will stop the media from writing exciting headlines and worst case scenarios.
Speculation is all we have so lets look at what we know and what it is reasonable to infer.

It was first found less than a month ago - Given that very few positive test are fully sequenced it is very likely to have been circulating below the radar for some time and is likely to have spread to several other areas/countries by now so travel restrictions will probably not delay international spread by much.

It has a bucket load of AA changes many in the Spike - This is unusual, while the virus will be continuously making small changes in any infection most will be weeded out in that host with only one or two making it to the next host. Viruses with this many changes as a single jump are almost always dead ends except where the host is immunocompromised allowing 'damaged' viruses to keep on adding mutations until a new viable progeny is achieved. The high HIV prevalence is a suspect here but we will never be able to pinpoint the index case.
These Spike changes are almost definitely going to reduce vaccine efficacy to some degree which will increase relative viral fitness in areas with high vaccine coverage. If the virus is relying on this to out perform the Delta variant it will spread well in high vaccine/prior infection areas but not in countries that are naive.
As we have never seen all these changes in one variant before there is no way of guessing what impact they will have on transmission, virulence or other properties of the phenotype we are just going to have to wait and watch.
As with the Alpha variant it is easier to pick up by rt PCR as the Spike probe (normally 1 of 3 probes) gives a reduced signal which in turn tends to lead to more full sequencing of that hosts viral genome which will skew the data compared to random sequencing so be wary of the relative numbers of sequences deposited at GISAID.

As far as the impact on health services is concerned the key here is if, in people whose immune system is primed, there is adequate protection to limit the replication in the host sufficiently for somatic hyper-mutation to adjust the B cells' antibodies to the new virus (I wrote an explanation of B cell maturation here https://flutrackers.com/forum/forum/...701#post907701). In countries with high vaccination/prior infection rates (like mine, the UK) people have dropped their guard and are tolerating very high infection rates as it is only producing low hospitalisations. If this strain has retained its virulence and drifted away from vaccine strains enough to allow significantly more hospitalisation and we do not change our behaviour, physical distancing and masking, then our health systems hospitals are going to get swamped and will cause more lockdowns.

A first look personal opinion only based on very little information - caveat emptor.

[sharon sanders]

Please see:

ECDC - Threat Assessment Brief: Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA - November 26, 2021

[sharon sanders]

Florian Krammer

@florian_krammer
1) My gut feeling from hearing of Omicron cases in Botswana, ex-Malawi, ex-Egypt (2 now it seems) and in South Africa is, that the variant was flying under the radar in undersequenced countries for some time until Botswana and South Africa detected it and sounded the alarm.
6:04 AM · Nov 27, 2021·Twitter Web App
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Florian Krammer

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2) However, the fact that European countries only detected it in travelers after South Africa and others warned about it, probably means that many cases so far went undetected. It also tells us a lot about genomic surveillance in some high income countries.
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Florian Krammer

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3) The mutations in Omicron which seem to wipe out the majority of neutralizing antibody epitopes are very worrisome. Combined with the apparent fitness of the virus, this could be a problem. There is now a lot to do to get a better idea of the risk this virus variant poses.
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Florian Krammer

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4) We need to first figure out how widespread it is, how well it escapes neutralizing antibodies (assumption: very well), what its R0 is, how well it does against Delta and if it can cause severe disease in vaccinated or recovered individuals.
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Florian Krammer

@florian_krammer
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5) Adapted vaccines need to be tested (this has started already) etc. Also, we should not forget that non-neutralizing antibody epitopes and T-cell epitopes are likely largely intact. And even if a variant vaccine becomes necessary, we would not start from scratch....
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Florian Krammer

@florian_krammer
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6).....since it is likely that one 'variant-booster' would do the job. Our B-cells can be retrained to recognize both, the old version and the variant, and it doesn't take much to do that.
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Florian Krammer

@florian_krammer
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7) But there are a lot of unknowns, and many 'scariants' have come and gone. I assume we will have a much better idea about the actual risk in 2-3 weeks. We need to stay calm and do our work.
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Florian Krammer

@florian_krammer
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8) A shoutout and big thank you to
@Tuliodna
and many other researchers from South Africa and Botswana for sharing sequences and information in real time!

Florian Krammer

@florian_krammer
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@florian_krammer
9) There was an update on the second case from Egypt. It seems now it was not from Egypt:

[Emily]

https://twitter.com/BWGovernment/status/1464184386912501764

Botswana Government
@BWGovernment

STATEMENT ON THE NEW COVID-19 VARIANT


4:48 AM · Nov 26, 2021·Twitter for Android

[Emily]

https://twitter.com/BWGovernment/sta...74240130785280

Botswana Government @BWGovernment
MEDIA RELEASE #LetsDefeatCOVID19Together #AReFenyengCOVID19Mmogo

8:16 AM · Nov 25, 2021·Twitter for Android

[Emily]

https://twitter.com/RWMaloneMD/status/1464303315265761280

Robert W Malone, MD @RWMaloneMD

"All four had been fully vaccinated" Any assertions that the emergence of the B.1.1.529 (Nu) variant emerged in unvaccinated or HIV-infected individuals in Africa is pure propaganda. This is yet more DISINFORMATION being pushed by legacy media such as "The Guardian".



12:41 PM · Nov 26, 2021·Twitter Web App

[Pathfinder]

South Africa accuses UK and others of ‘knee-jerk’ reaction to new variant

Travel restrictions on southern African states imposed by countries after discovery of B.1.1.529 already harming economy

Nick Dall in Cape Town and Lizzy Davies
Fri 26 Nov 2021 13.09 EST
...
Should the new variant prove to be highly transmissible, there are fears that a fourth wave could materialise – and in a more dangerous form than had been anticipated.

However, Dr Angelique Coetzee, chair of the South African Medical Association and a practising GP based in Pretoria, said it was “premature” to make predictions of a health crisis.

“It’s all speculation at this stage. It may be it’s highly transmissible, but so far the cases we are seeing are extremely mild,” she said. “Maybe two weeks from now I will have a different opinion, but this is what we are seeing. So are we seriously worried? No. We are concerned and we watch what’s happening. But for now we’re saying, ‘OK: there’s a whole hype out there. [We’re] not sure why.’”

Coetzee said she would like to see the government embark on a push to get more people vaccinated, but added: “Unfortunately, it’s not only the responsibility of the government; it’s the responsibility of the public as well … You can only ask people so many times to go and get vaccinated, and if you don’t listen, then there’s consequences, and then you have to take the consequences.”
...

https://www.theguardian.com/world/20...nt-vaccination

[sharon sanders]

From:
"Media@cdc.gov (CDC)" <sohco@CDC.GOV>
To: <MMWR-MEDIA@LISTSERV.CDC.GOV>
Subject: CDC Media Statement: CDC Statement on B.1.1.529
Date: Nov 26, 2021 9:07 PM

Media Statement

For Immediate Release
Friday, November 26, 2021

Contact: CDC Media Relations
phone number redacted

CDC Statement on B.1.1.529

On November 26, 2021, the World Health Organization (WHO) classified a new variant, B.1.1.529, as a Variant of Concern and has named it Omicron. No cases of this variant have been identified in the U.S. to date. CDC is following the details of this new variant, first reported to the WHO by South Africa. We are grateful to the South African government and its scientists who have openly communicated with the global scientific community and continue to share information about this variant with the U.S. Department of Health and Human Services and CDC. We are working with other U.S. and global public health and industry partners to learn more about this variant, as we continue to monitor its path.
  
CDC is continuously monitoring variants and the U.S. variant surveillance system has reliably detected new variants in this country. We expect Omicron to be identified quickly, if it emerges in the U.S.

We know what it takes to prevent the spread of COVID-19. CDC recommends people follow prevention strategies such as wearing a mask in public indoor settings in areas of substantial or high community transmission, washing your hands frequently, and physically distancing from others. CDC also recommends that everyone 5 years and older protect themselves from COVID-19 by getting fully vaccinated. CDC encourages a COVID-19 vaccine booster dose for those who are eligible.

Travelers to the U.S. should continue to follow CDC recommendations for traveling.

CDC will provide updates as more information becomes available.

[Commonground]

November 26

SAMRC records increase in Covid-19 fragments in Tshwane and Nelson Mandela Bay wastewater

• The South African Medical Research Council says it has seen an increase in Covid-19 fragments in Tshwane and Nelson Mandela Bay wastewater treatment plants.
• The council monitors wastewater treatment plants in four provinces weekly.
• The team started noticing increases in October.

Excerpt

Dr Rabia Johnson, Deputy Director of the SAMRC's Biomedical Research and Innovation Platform, said the picture changed dramatically at the end of October.

"At the beginning of the month, levels of SARS-CoV-2 RNA fragments in wastewater were mostly low or undetectable; now we're measuring concentrations last seen during the third Covid-19 wave."

The SAMRC has warned that the rapidly increasing concentrations of Covid-19 RNA fragments in wastewater were a major cause for concern, especially alongside reports of increases in Covid-19 cases and deaths in the past week.

https://www.news24.com/news24/southa...water-20211126

[sharon sanders]

Trevor Bedford

@trvrb
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2h
Growth rate (in absolute terms and relative to Delta) will be become clearer in the following days, but at the moment, I believe we're looking at a variant that potentially has significant immune evasion and that appears to be spreading rapidly. 15/16
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Trevor Bedford

@trvrb
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The world should be immensely grateful to
@Tuliodna
,
@ceri_news
,
@nicd_sa
, the Network for Genomics Surveillance in South Africa and the Botswana Harvard HIV Reference Laboratory for discovering this variant and immediately alerting to its existence. 16/16

[sharon sanders]

Bushman Lab
@bushmanlab
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39m
The B.1.1.529 variant has a concerning collection of Spike substitutions; less remarked on, it also has the nucleocapsid substitutions R203K, G204R, which have been reported to increase genome packaging and infectivity (PMID: 34735219). Worrisome.