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PANDEMIC ALERT LEVEL
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Now tracking the new emerging South Africa Omicron Variant

Omicron variant

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Dutch Josh View Drop Down
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    Posted: November 26 2021 at 1:08pm

DJ-So it did not get the "Nu"-name, but "Omicron"...[url]https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant ;

The Omicron variant, also known as lineage B.1.1.529, is a variant of SARS-CoV-2, the coronavirus that causes COVID-19. The WHO has designated it a variant of concern and named it for the Greek letter Omicron.[1][2][3]

The first known specimen was collected on 9 November 2021 from Botswana.[4] It was also detected in South Africa;[5] one case had travelled to Hong Kong,[6][7] one confirmed case was identified in Israel in a traveler returning from Malawi,[8] along with two who returned from South Africa and one from Madagascar.[9] One confirmed case in Belgium had apparently acquired it in Egypt before 11 November.[10]

Countries that announced travel bans from southern Africa in response to the identification of the variant include JapanCanada, the European UnionIsrael, the United Kingdom, and the United States.[11][12]

On 24 November 2021, the variant was first reported to the WHO from South Africa.[1] On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution designated B.1.1.529 a variant of concern and gave it the designation Omicron.[1][2][3]

Worry about the potential economic impact of the Omicron variant led to the a drop in global markets on 26 November, including the worse drop of the Dow Jones Industrial Average in 2021, led by travel-related stocks. The price of Brent Crude and West Texas Intermediate oil fell 10% and 11.7%, respectively. This reaction was described as "overblown" due to the lack of firm conclusions by the medical community.[13]

The variant has a large number of mutations, of which some are concerning.[14] 32 mutations affect the spike protein, many of which had not been observed in other strains.[15]

The number of cases in the B.1.1.529 lineage is increasing in all areas of South Africa, mainly in Gauteng.[14] Some evidence shows that this variant has an increased risk of reinfection. Studies are underway to evaluate the exact impact on transmissibility, mortality, and other factors. Evidence regarding the implications of this variant and vaccine efficacy is still being investigated.[16][17]

DJ [url]https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern[/url] or https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern 

Wiki-page will be updated with statistics tomorrow.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote carbon20 Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 2:35pm

Giving it a Greek alphabet name means they are worried, and we are in trouble.....

Take care all πŸ˜·πŸ˜‰πŸ’‰

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Post Options Post Options   Thanks (0) Thanks(0)   Quote WitchMisspelled Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 4:01pm

Omicron even sounds ominous.  Hopefully this will come to nothing.  I'm sure we'll know more in the coming days. On that note, I put in an order for N95s to be delivered Sunday.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote carbon20 Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 4:10pm

Originally posted by WitchMisspelled WitchMisspelled wrote:

Omicron even sounds ominous.  Hopefully this will come to nothing.  I'm sure we'll know more in the coming days. On that note, I put in an order for N95s to be delivered Sunday.

Same thought crossed my mind........

And last night I was thinking about masks....

Same page must be something in the wind.....

Take care all πŸ˜·πŸ˜‰πŸ’‰

Everything we hear is an opinion, not a fact. Everything we see is a perspective, not the truth.πŸ––

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Post Options Post Options   Thanks (0) Thanks(0)   Quote WitchMisspelled Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 4:15pm

PTSD? (Pandemic Traumatic Stress Disorder)

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Post Options Post Options   Thanks (0) Thanks(0)   Quote BeachMama Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 8:10pm

I think it’s a good idea to get more masks before the run starts. Thanks for the reminder! 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 9:50pm

DJ [url]https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant will be updated several times per day these days....: 

The first known specimen was collected on 9 November 2021 from Botswana.[8] It was also detected in South Africa;[17] one case had travelled to Hong Kong,[18][19] and one confirmed case was identified in Israel in a traveler returning from Malawi,[20] along with two who returned from South Africa and one from Madagascar.[21] One confirmed case in Belgium had apparently acquired it in Egypt before 11 November.[22]

All four initial cases reported from Botswana occurred among fully vaccinated individuals.[23] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals. [24]

DJ One major worry is about immunity ; 

Many of the mutations to the spike protein are present in other variants of concern and are related to increased infectivity and antibody evasion. Computational modeling suggests that the variant may also escape cell-mediated immunity.[8]

On 26 November, the ECDC wrote that an evaluation of the neutralizing capacity of convalescent sera and of vaccines is urgently needed to assess possible immune escape, saying these data are expected within two to three weeks.[12]

DJ ; 

The variant has a large number of mutations, of which some are concerning.[6] 32 mutations affect the spike protein, the main antigenic target of antibodies generated by infections and of many vaccines widely administered. Many of those mutations had not been observed in other strains.[7][8]

The variant is characterised by 30 amino acid changes, three small deletions and one small insertion in the spike protein compared with the original virus, of which 15 are located in the receptor binding domain (residues 319-541). It also carries a number of changes and deletions in other genomic regions. Of note, the variant has three mutations at the furin cleavage site.[9] The furin cleavage site increases SARS-CoV-2 infectivity.[10

It looks like earlier CoViD infection did not offer (major) protection against "Omicron" infection. 

When you look at the cases most of them in the South Africa region and increase/explosion has started about two weeks ago (?) Very likely early slow spread could have started in October (?)

Given the collection of mutations from several earlier variants (missing segment 69/70 was seen in the Alfa/UK variant becoming major a year ago) and new mutations "Omicron" must be related to an immunity-compromised (HIV+ ?) person. That person did get the virus-I think-over 8 months+ ago. 

Since immunity failed to deal with the virus somehow all other variants came on top of Alfa...somehow the person survived all these infections (in a hospital ?).

Looking at statistics SA cases exploding, followed by a (further) explosion of CoViD-cases in Europe, US followed later it could be Omicron did allready get widespread. 

The travelhistory of the few detected cases outside Africa-with travel from Malawi, Egypt, and going back possibly before november 11 (Belgium-Egypt linked case) is alarming. 

Of course international (air)travel should not have started in this pandemic...Stopping flights now (and with lots of exceptions) to/from SA-region is a "sad joke" ...

Looking for twitter etc. info to update this story...

Masks, even more social distancing, NO TRAVEL AT ALL !!!! (STOP THE SPREAD !!!!) would be wise...If more cases get reported we may learn more on how usefull vaccines are...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 10:15pm

[url]https://outbreak.info/situation-reports?pango=B.1.1.529&loc&selected[/url] or https://outbreak.info/situation-reports?pango=B.1.1.529&loc&selected will be tracking Omnicron [url]https://newsnodes.com/nu_tracker[/url] or https://newsnodes.com/nu_tracker trying to do the same...

[url]https://twitter.com/peacockflu[/url] or https://twitter.com/peacockflu (DJ Tom Peacock UK virologist was the link between good SA sequencing and global media.) 




I should state I catagorically did not 'discover' B.1.1.529 - the first seqs were uploaded by teams from Botswana and HK, followed shortly by SA. Several other people had independently spotted this (including SA health authorities). I just posted the public Pango request first...

This extremely long branch (>1 year) indicates an extended period of circulation in a geography with poor genomic surveillance (certainly not South Africa) or continual evolution in a chronically infected individual before spilling back into the population. 4/16

DJ Omicron uild-up" started over 1 year ago ? 

[url]https://twitter.com/x2IndSpeculator[/url] or https://twitter.com/x2IndSpeculator




We have learned a lot today from anecdotal reports. It's spreading internationally at least since Nov 11. Most positives were vaccinated, one even boosted 2 months ago. Equally infects young & old. Variable latent & incubation period. Reports quote low Ct, i.e. high viral load.

DJ Point is we still have very limited numbers....Where the SA cases vaccinated ? Could the Belgian case be a false positive ? How good is testing doing ? (Some PCR tests use segment 69/70 as one of three "segments"for testing...Like with UK/Alfa "the good news" is early detection via PCR tests...the "bad news" may be if some PCR tests would be testing for other segments that also got deleted/mutated...so testing would miss cases...). 




I am 100% for vaccination. I just want public health to be transparent about what vaccines do well and don’t do well so ppl are fully informed. For too long messaging said transmission among vax was rare. This then caused confusion and loss in confidence in the vaccines.

DJ In many countries a certain level of vaccinations meant "freedom"; lifting of restrictions...while vaccines became "less good" in stopping virus spread. 

Vaccines activate natural immunity. In many ways it is a similar proces-only you do get ill from "natural infection" often...the level of (limited) protection has a lot of similarity...

Not stopping children getting infected "to create natural immunity" is criminal...Even if only 1 in a 100 did get ill it is to many...The virus-spread does not stop with children...




At least 15 people on 2 flights from South Africa test positive for coronavirus at Amsterdam Airport; number expected to rise, variant not yet known - NOS

DJ Latest info is 61 out of 600 passengers from two flights arriving from SA after 12 hrs local time tested positive...[url]https://nltimes.nl/2021/11/26/travellers-south-africa-required-quarantine-hotels-positive-covid[/url] or https://nltimes.nl/2021/11/26/travellers-south-africa-required-quarantine-hotels-positive-covid

Anyone who tests positive for coronavirus out of about 600 passengers who returned from South Africa will be required to quarantine in a hotel, the GGD Kennemerland said. It concerns only those passengers who departed on two KLM aircraft from South Africa before the Netherlands implemented a flight ban from that country, but who landed in the Netherlands after the announcement on Friday.

"The hotel isolation period will last seven days for people with symptoms,” a spokesperson said. Those without symptoms, who also do not develop symptoms during the quarantine period, will be allowed to self-isolate at home. Results of tests were still unavailable at 9:15 p.m.

DJ There are a lot of Dutch people living in Suid Afrika.....lots of travel....

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 10:20pm

Some more info on Omicron-spread etc....

[url]https://twitter.com/yaneerbaryam[/url] or https://twitter.com/yaneerbaryam




@BethPathak
·

One direct flight from Jo-burg lands in NY every day. Biden is stopping flights, but not until 29-Nov. Plenty of time for #OmicronVariant to get well-seeded in the community from each flight’s handful of likely infected passengers. No testing/quarantine of πŸ‡ΊπŸ‡Έ arriving passengers.

-

International passenger traffic from Johannesburg O.R. Tambu airport: 188,530 If the proportion of infected individuals is like the recent report from Netherlands: Almost 6,000 infected travelers in the last week. Number of airplanes: 3,246 in October, or about 733 per week.

DJ And a lot of travel may use other airports...any cruiseships allready ? Do we never learn anything ? When you would make an estimate about the number of passengers from SA flights since november 10 you would end up in the millions...




"Early evidence suggests an increased risk of reinfection compared to other highly transmissible variants, the WHO said. That means people who contracted COVID-19 and recovered could be subject to catching it again. Note: Very very likely. Almost surely.

DJ Reminds me of Manaus-Brazil getting hit twice within one year...75%+ "natural immunity" meant nothing with a new variant...Iran reporting lots of people catching CoVid 3 times...

The first order estimate would just say, transmissibility increase is just the same factor as the mortality factor. BUt the mortalities are a bit larger overall. Doing this a bit more consistently, and with uncertainty of the values we know, gives the range 3X-12X.


5

14

59


DJ The SA R0 average was around 1,5...in the Johannesburg region close to 2...with lots of restrictions, 24% (fully ?) vaccinated...(If I do get that correct R0 without restrictions, immunity "infectious strength" would have to be higher then Delta..(R0 there between 5 and 8/5,5-6,5...)

To limit cases you have to increase (contact)restrictions...(and since governments don't do that YOU have to do that !)

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 26 2021 at 10:55pm

[url]https://twitter.com/drericding[/url] or https://twitter.com/drericding may have some good info...also on the meaning of findings/news...

[url]https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern-in-south-africa?view=stream[/url] or https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern-in-south-africa?view=stream (latests) ; 

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

DJ Waste/sewage can give early indications..also statistics give indications...Since testing/sequencing is (very) limited sewage/statistics may give a hint on what regions may see (what) cases...

So for personal protection social distancing/masks may be wise...for pandemic control waste/sewage and statistics can help. 

Belgium's national reference laboratory said the infected person was a young adult woman who had developed symptoms 11 days after returning from a trip to Egypt via Turkey. She had flu-like symptoms, but no signs to date of severe disease.

That is a long incubation period!

DJ So travel from Egypt (before) november 11-via Turkey...never came south of the Sahara ...? Mild disease ? How many mild/asymptomatic spread should we expect ? 

[url]https://bnonews.com/index.php/2021/11/omicron-tracker/[/url] or https://bnonews.com/index.php/2021/11/omicron-tracker/ 

[url]https://twitter.com/Ammer_B[/url] or https://twitter.com/Ammer_BThis is incredibly worrisome. How it will look in fact if to be seen but after reading most of the updates I feel this variant could change COVID dynamics at least as much as delta did. Lets hope not, lets remain calm but further prepare a midst an already difficult situation.

DJ And that may be it for now...[url]https://www.worldometers.info/coronavirus/weekly-trends/#weekly_table[/url] or https://www.worldometers.info/coronavirus/weekly-trends/#weekly_table  Global cases +5%...US cases -20%...thanksgiving, black friday, weekend...US will be over reporting next week...

Europe cases +15%, deaths -0,6%...Africa cases +30%, deaths +6%...South Africa cases going up +218% mainly due to increased testing ! So they will find more cases...Omicron may be pushing away Delta...SA deaths +138%...

Eswatini (former Swaziland) cases +105% (0 deaths...this week). Namibia cases +97% (last week 38, this week 75) deaths +67% (3 to 5 so very limited numbers). Malawi cases +25%...Angola +9%, basic problem with most of Africa-like in India-testing is that limited statistics also are of limited use...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 5:42am

Some good info at ;[url]https://www.imperial.ac.uk/news/232217/qa-imperial-experts-discuss-variant-b11529/[/url] or https://www.imperial.ac.uk/news/232217/qa-imperial-experts-discuss-variant-b11529/The reason we are concerned about the new variant is that it appears to have mutations in all of the identified antigenic sites, both in the receptor binding domain at the tip of spike and also in the N terminal domain on the side of spike. We would predict this could impact spike protein recognition by the vast majority of antibodies, even in a polyclonal response. When a person has fewer antibodies, or when those antibodies are less well able to bind to spike, we know that vaccine effectiveness is compromised. So, we predict the new variant might be less well controlled by the vaccines we currently have. However, it is unclear as yet how much the new variant may affect our vaccines.  

DJ Some "media" are allready downplaying the risks "so economy can be saved"...

[url]https://newsnodes.com/nu_tracker[/url] or https://newsnodes.com/nu_tracker being updated with likely case from Germany, Czech Republic...also [url]https://twitter.com/drericding[/url] or https://twitter.com/drericding ; 5) because the Belgian case returned in early November, but we don’t know about #Omicron spread since then, Belgian scientists are now retroactively combing past PCR positives for S-Gene dropout signals (SGTF is a proxy for #B11529)… they have found 47 candidates! More coming.

-




I agree  ! First rate analysis as usual. Past variant experience shows (Delta!) that (outside of island defense eg New Zealand ) by the time we have found, sequenced & named a #Variant like #Omicron … It is already gotten on planes. Closing borders is not the fix.

DJ It is very unwise to have large scale airtravel during a pandemic ! How can it be 10%+ of passengers from SA arriving in Amsterdam test positive when they all were supposed to be tested before travel ???

[url]https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream[/url] or https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream latests...;

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.

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.

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.

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.

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....

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.

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.

DJ from [url]https://twitter.com/florian_krammer[/url] or https://twitter.com/florian_krammer  also; 




Is somebody looking at the role of recombination in persistently infected individuals? Replication errors can generate diversity over time, but I assume the different intra-host variants could then also recombine? Could that contribute to the genesis of variants like B.1.1.529?

Or will we see another endless discussion on "how it started" ?

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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 12:06pm

Reading that it is everywhere it seems!  Geez it traveled fast as we all know it can!  i have seen several reports that the cases are mild in africa.  Not sure how much we can trust them but wondering if you all are hearing the same.  Also brings up questions about recently when China closed down again, wondering if Omnicron had something to do with that.  so may questions and pieces of the puzzle!

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Post Options Post Options   Thanks (0) Thanks(0)   Quote carbon20 Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 2:53pm

This variant could have been out there for weeks,and not detected because the South African testing is more advanced ,and picked it up when others missed it.....

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Post Options Post Options   Thanks (0) Thanks(0)   Quote carbon20 Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 3:18pm

BBC News - Covid: Dozens test positive on SA-Netherlands flights

https://www.bbc.co.uk/news/world-europe-59442149

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Post Options Post Options   Thanks (0) Thanks(0)   Quote ksc Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 3:45pm

South African doctor says omicron variant symptoms ‘unusual but mild’

The South African doctor who first alerted authorities to the presence of the COVID-19 omicron variant reported that it presents “unusual but mild” symptoms.

Dr. Angelique Coetzee, a board member of the South African Medical Association, first noticed otherwise healthy patients demonstrating unusual symptoms on Nov. 18.

“Their symptoms were so different and so mild from those I had treated before,” Coetzee told The Telegraph.

https://1010wcsi.com/fox-health/south-african-doctor-says-omicron-variant-symptoms-unusual-but-mild/#:~:text=The%20South%20African%20doctor%20who%20first%20alerted%20authorities,healthy%20patients%20demonstrating%20unusual%20symptoms%20on%20Nov.%2018.


FILE PHOTO: A child reacts while receiving a dose of the Pfizer-BioNTech coronavirus disease (COVID-19) vaccine at Smoketown Family Wellness Center in Louisville, Kentucky, U.S., November 8, 2021. REUTERS/Jon Cherry/File Photo

“It presents mild disease with symptoms being sore muscles and tiredness for a day or two not feeling well,” Coetzee explained. “So far, we have detected that those infected do not suffer the loss of taste or smell. They might have a slight cough. There are no prominent symptoms. Of those infected some are currently being treated at home.”

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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 5:02pm

I am reading that her comments were taken out of context.  she said she was specifically talking about young health individuals and that others could have much worse symptoms.  interesting.  we shall see i guess!

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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 8:37pm

Originally posted by roni3470 roni3470 wrote:

Reading that it is everywhere it seems!  Geez it traveled fast as we all know it can!  i have seen several reports that the cases are mild in africa.  Not sure how much we can trust them but wondering if you all are hearing the same.  Also brings up questions about recently when China closed down again, wondering if Omnicron had something to do with that.  so may questions and pieces of the puzzle!

I saw something this morning that was suggesting Omicron had an 11 day incubation period. That's quite long and so could be firmly in almost any country before the alarm was raised.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 10:18pm

Due to airtravel-for-vaccinated still catching/spreading the virus -travel going on for weeks most of the Omicron cases-better in dealing with vaccinated hosts-will be outside the South Africa region...

Coming weeks may give us a hint on how bad that is/was...statistics may give indications. Will it be a short peak of cases-Omicron then ending up with more "natural immunity" in those that recover ? 

[url]https://www.worldometers.info/coronavirus/weekly-trends/#weekly_table[/url] or https://www.worldometers.info/coronavirus/weekly-trends/#weekly_table German cases still +21%, NL +12%, UK +9%...

I think there may be millions of cases on Omicron but lack of sequencing enough samples, slow proces-sequencing still takes a week ? We could have missed its spread even in "rich countries" ...

[url]https://twitter.com/florian_krammer[/url] or https://twitter.com/florian_krammer ; 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

DJ It all makes me wonder if the main goal in "pandemic strategy" is economic...not related to public health...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 27 2021 at 11:37pm

Australia reported its first two cases, travel via Qatar, 12 other passengers also from that flight (testing positive ?) "the other 260 passengers & crew" have to "self-isolate"....(NL reporting...DJ-translation-flight had 274 passengers & crew...2 tested positive with symptoms, 12 without symptoms-both in quarantine...rest could travel further...)...Will the US report its first cases today-or "on a working day"? Why hurry ? 

Some twitter; 

[url]https://twitter.com/yaneerbaryam[/url] or https://twitter.com/yaneerbaryamCommunity transmission in Italy "An Italian who had traveled to Mozambique on business landed in Rome on Nov. 11 and returned to his home near Naples. He and five family members, including two school-age children, have since tested positive"

DJ Spread in community was allowed for weeks in many countries (but only in vaccinated ?)

Omicron list: Points of origin: South Africa, Botswana, Egypt, Mozambique, Malawi. Other community transmission: Israel Travelers: Belgium, Germany, UK, Italy, Denmark, Netherlands, Czechia, Hong Kong Transit: Turkey, Dubai, Ethiopia and Jordan https://reuters.com/world/concerns-over-covid-variant-trigger-more-travel-curbs-southern-africa-2021-11-27/

DJ All countries mentioned will have community spread...




Community transmission in Israel of Omicron: Three of the new cases in Israel are not travelers. Health Ministry says 7 people in Israel suspected of contracting Omicron variant https://timesofisrael.com/liveblog_entry/health-ministry-says-7-people-in-israel-suspected-of-omicron-variant/ via 

DJ It is good community spread is being reported, not covered up (yet)...




South Africa hospitals: “We’re seeing a marked change in the demographic profile of patients with COVID-19. Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, some needing intensive care.

DJ "only mild disease-vaccines still work"....




Two years after the pandemic started: South Africa flights to Amsterdam: "passengers with a negative result and with an onward connection will be allowed to continue their journeys despite being in close contact with positive cases for many hours."

DJ NL now looking for 5,000 other passengers coming from southern Africa last week...The 61 passengers from two latest flights testing positive were put in a hotel...other hotel guest were NOT informed....Passengers had to be vaccinated-so "needed no tests" ...Only tested once 10% tested positive...(why should you not go for a second test after 24 hrs...passengers in early stages do test negative...) ...

The NL example is proberbly "better then average"...most other countries may not have even tested passengers from South Africa in 'last flights" before restictions... People with NL passport still are allowed to travel to/from SA...; Meanwhile at Heathrow, hundreds of passengers from the South African province at the epicentre of the new variant were "advised" to self-isolate and get tested, then disembarked as normal and mingled with passengers from other flights at baggage reclaim. https://twitter.com/AdamJSchwarz/status/1464150235714932742?t=Ov0hAnnstyuErD8CmIddRw&s=19

DJ Total insanity !!! How do you expect people to follow any rule if governments do all they can to spread the virus ???

[url]https://twitter.com/dgurdasani1[/url] or https://twitter.com/dgurdasani1Narratives around the variant potentially being more transmissible/more able to escape *but* milder shared today may be based on a quote taken out of context. Hopium spreads fast, but we need to wait for the data- In the meantime we need to make plans based on potential threat.

and ; 

A widely-shared quote from a South African doctor, saying Omicron causes only mild symptoms, is being taken out of context. She was referring to a small group of young, healthy people and warned of severe disease in other groups https://telegraph.co.uk/global-health/science-and-disease/south-african-doctor-raised-alarm-omicron-variant-says-symptoms/

DJ Why am I not surprised by "media" going for "the good news" ? 




One might say things will be a lot better with boosters, and potentially children being vaccinated. But this takes time, and it makes perfect sense to use effective public health measures like high-grade masks, ventilation in the meantime to contain spread.

-


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Post Options Post Options   Thanks (1) Thanks(1)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 12:09am

Copies from twitter can go wrong...point is lots of "real"news now via twitter/alternative media (embedded media more and more sort of propaganda...ignoring problems...Here in NL "news" focussed on how restrictions limited sports...not a word on the risks of Omicron...). 

[url]https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream[/url] or https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream latest (in part also falling back to twitter news...) ; This seems to support the theory that someone with AIDS (HIV, tragically, is commonly under-treated in that part of the World) acquired COVID last Spring and it spent more than a year evolving in their body until it produced Omicron.

and ; PH Dependency Question: Is there any evidence that the PH Dependency related to endocytosis has changed in this new variant? Is there any suggestion that any of the specific Spike mutations would affect Ph Dependency? Any links / resources specific to this subject in Covid? Wondering if there is any specific ph range that is more optimum for endocytosis, what the trigger ph levels at which cell penetration is mitigated? Working on some research. Any guidance / feedback appreciated.

DJ [url]https://en.wikipedia.org/wiki/Endocytosis[/url] or https://en.wikipedia.org/wiki/EndocytosisEndocytosis is a cellular process in which substances are brought into the cell. The material to be internalized is surrounded by an area of cell membrane, which then buds off inside the cell to form a vesicle containing the ingested material. Endocytosis includes pinocytosis (cell drinking) and phagocytosis (cell eating). It is a form of active transport.

PH level of the skin is a factor for skin infections...For the rest I do not have the knowledge to say more on this...

You can see the striking accumulation of mutations in the S1 domain of the spike protein just by plotting S1 mutations against time and coloring by clade (https://nextstrain.org/ncov/gisaid/africa?l=scatter&scatterY=S1_mutations…). Omicron viruses bear many more S1 mutations than previously circulating variants. 7/16

The way I read this ‘family tree’ it’s like someone reached all the way back to April 2020, plucked out an existing variant (having only the D614G mutation in common with every other clade & variant) and then somehow, magically, all by itself, came up with not one, not two, not ‘a few,’ but twenty new mutations never before seen in any other variant of concern.

https://twitter.com/trvrb/status/146...243457/photo/1

DJ So Omicron may have been "isolated" since april 2020 (?) and developed its "own route"? Somehow showed/mixed up recently and "exploded"...

An Italian who had traveled to Mozambique on business landed in Rome on Nov. 11 and returned to his home near Naples. He and five family members, including two school-age children, have since tested positive, the Italian news agency LaPresse said. All are isolating in the Naples suburb of Caserta in good condition with light symptoms.

This is 7 days before Dr Coetzee notified the South African Medical Association.

DJ Another "november 11' mention. The (first) Belgian case went from Egypt via Turkey to Belgium around that time...It is now november 28....

https://www.voiceforscienceandsolida...rican-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.

DJ If we would see [url]https://en.wikipedia.org/wiki/Antibody-dependent_enhancement[/url] or https://en.wikipedia.org/wiki/Antibody-dependent_enhancement in theory "antibodies would help spreading the virus"...Immunity would be a problem...

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.

DJ We proberbly-this coming week-will learn more on how widespread Omicron is...Since it may have been going its own way since april 2020 maybe vaccines can limit disease ? (SA has around 24% vaccination) On the other hand Omicron did pick up lots of Alpha/Beta/Delta...and mixed it with its own mutations...

Do other regions have this kind of surprises ? Should we not do much more to STOP THE SPREAD !!!

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 1:02am

[url]https://twitter.com/GrauweGrutjes/status/1464736969414656001[/url] or https://twitter.com/GrauweGrutjes/status/1464736969414656001 (NL) twitter...Indications are Omicron 500% more infectious (!!!!) ...even it it would give 50% less disease-as some like to claim...but is far from certain/science-then that high level of infectiousness sitll would result in 250% increase of disease !!!

Some indications incubation may take longer. South(ern) Africa has a younger population...so maybe it is "just a matter of time"? 

-The two Australians testing positive for Omicron (also) fully vaccinated...[url]https://newsnodes.com/nu_tracker[/url] or https://newsnodes.com/nu_tracker far from complete on "probable cases"...but at least trying to follow new cases (also with links/source). 

[url]https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant[/url] or https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant also keeping statistics...may also offer info on vaccination/natural infection status...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote ksc Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 5:16am

Blessing in the sky: Omicron variant may be ‘very positive’ news for the world if new Covid mutation kills off more lethal Delta coronavirus

Hospitals and GPs across Southern Africa are increasingly reporting that the symptoms of the aggressive new Covid strain Omicron are “unusual but very mild,” according to various media in South Africa this weekend.

Around 90 per cent of all new infections in the Johannesburg region are now caused by the Omicron strain but, so far, the Covid death rate and even hospital admissions appear not to be increasing significantly, local media report.

Some experts are therefore cautiously optimistic that – if Omicron turns out to be less lethal but more contagious and dominant than the Delta variant – the new mutation may actually be a blessing in the sky.

Mild symptoms

Hundreds of infected people across Southern Africa reportedly complain of nausea, headaches, fatigue and a high pulse rate, but none seem to suffer from a loss of taste or smell, which has been the case with most other Covid mutations.

Moreover, more and more medics across Southern Africa are confirming that most Omicron-infected patients merely have a severe headache, nausea or dizziness.

Dr Angelique Coetzee told various newspapers in South Africa: “Symptoms are so different and so mild from [non-Omicron] Covid patients I have treated before.”

A GP for over three decades, and chair of the South African Medical Association, she was the first African doctor to suggest to local authorities Covid had mutated into a new strain.

Coetzee reportedly said the symptoms “did not make immediate sense”, with patients including young people of different backgrounds and ethnicities with fatigue and a young child with a high pulse rate.


Blessing in the sky

Looking at the first data coming out of Southern Africa, virologist Marc van Ranst said this weekend that “if the omicron variant is less pathogenic but with greater infectivity, allowing Omicron to replace Delta, this would be very positive.”

The WHO warned that preliminary evidence suggests the variant has an increased risk of reinfection and may spread more rapidly than other strains, including Delta.

They said there is early evidence to suggest Omicron has an “increased risk of reinfection” and its rapid spread in South Africa suggests it has a “growth advantage”.

“It is extremely important we need to closely monitor the clinical data of Omicron patients in South Africa and worldwide,” Van Ranst stressed.

The variant has more than 30 mutations – around twice as many as the Delta variant – which make it more transmissible and evade the protection given by prior infection or vaccination.


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 5:53am

[url]https://twitter.com/BertMulderCWZ[/url] or https://twitter.com/BertMulderCWZ ; De meest recente publicatie van gesequencete data is van samples die 10-16 dagen geleden zijn afgenomen. Tussen moment van besmetting en test zit ook nog ~7 dagen. Dus 17-23 dagen na besmetting wordt sequencing data gepubliceerd.

DJ translation/summary ; "Most recent (NL) publication on sequence data is about samples that were taken 10-16 days ago...Between infection and test on average also 7 days. So 17-23 days after infection sequences get published."

This 17-23 day gap may explain why most of western Europe may have missed-so far-the explosion of Omicron. 

On "hopium" false "good news" on "milder disease etc."[url]https://twitter.com/dgurdasani1[/url] or https://twitter.com/dgurdasani1Reminder - it is not an inevitability that viruses mutate towards becoming less pathogenic and virulent. That idea (that viruses inevitably become more infectious but less virulent) has been circulating this entire pandemic but it should really be put to rest.

DJ ; COVID-19 Omicron: it's worrying because it's expected, as are the reactions to it About: 'you're scaremongering', 'wait for more information', 'it's the bloody COVID panic-mongers' TL; DR: FFS just look at everything we've seen and learnt over the last 20 months! (1/30)

"Alarmists" in this pandemic turn out to be correct over and over again...but "saving economy" remains #1 priority (and there are also so many wars to spent trillions on...just ignore the refugees..."they are better of in their own region"...). 

[url]https://nltimes.nl/2021/11/28/rivm-13-covid-infections-linked-omicron-variant-far[/url] or https://nltimes.nl/2021/11/28/rivm-13-covid-infections-linked-omicron-variant-far KLM imported cases...out of 61 further tested cases..."may become more"....(NL now at #2 for highest number of Omicron-cases confirmed after Suid Afrika...




Lots of misinformation now being floated that #Omicron is “mild”. That’s nonsense — based on out-of-context quote. Don’t fall for it — nobody know that much yet. And hospitalizations are still rising in the hardest hit #B11529 dominant provinces in South Africa πŸ‡ΏπŸ‡¦

Fake "good news" may be "used" to stop further restrictions...not in the interest of public health !

[url]https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream[/url] or https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream

Last Updated Saturday, November 27, 2021 10:48AM EST

JOHANNESBURG (AP) -- Worried scientists in South Africa are scrambling to combat the lightning spread across the country of the new and highly transmissible omicron COVID-19 variant as the world grapples with its emergence.


In the space of two weeks, the omicron variant has sent South Africa from a period of low transmission to rapid growth of new confirmed cases. The country's numbers are still relatively low, with 2,828 new confirmed cases recorded Friday, but omicron's speed in infecting young South Africans has alarmed health professionals.

“We're seeing a marked change in the demographic profile of patients with COVID-19,” Rudo Mathivha, head of the intensive care unit at Soweto's Baragwanath Hospital, told an online press briefing.

“Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, some needing intensive care. About 65% are not vaccinated and most of the rest are only half-vaccinated,” said Mathivha. “I'm worried that as the numbers go up, the public health care facilities will become overwhelmed.”

She said urgent preparations are needed to enable public hospitals to cope with a potential large influx of patients needing intensive care.

“We know we have a new variant,” said Mathivha. “The worst case scenario is that it hits us like delta ... we need to have critical care beds ready.”

What looked like a cluster infection among some university students in Pretoria ballooned into hundreds of new cases and then thousands, first in the capital city and then to nearby Johannesburg, South Africa's largest city.

Studying the surge, scientists identified the new variant that diagnostic tests indicate is likely responsible for as many as 90% of the new cases, according to South Africa's health officials. Early studies show that it has a reproduction rate of 2 - meaning that every person infected by it is likely to spread it to two other people.

The new variant has a high number of mutations that appear to make it more transmissible and help it evade immune responses. The World Health Organization looked at the data on Friday and named the variant omicron, under its system of using Greek letters, calling it a highly transmissible variant of concern.

“It's a huge concern. We all are terribly concerned about this virus,” Professor Willem Hanekom, director of the Africa Health Research Institute, told The Associated Press

DJ Even less severe disease but much more cases would be a major problem !  Not/half vaccinated does not rule out "natural immunity"...


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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 12:11pm

DJ, Maybe related;/Omicron ;

[url]https://flutrackers.com/forum/forum/africa-ac/africa-covid-19-sept-13-2020-may-31-2021/928983-botswana-government-says-omicron-first-found-in-fully-vaccinated-diplomats-from-an-undisclosed-country[/url] or https://flutrackers.com/forum/forum/africa-ac/africa-covid-19-sept-13-2020-may-31-2021/928983-botswana-government-says-omicron-first-found-in-fully-vaccinated-diplomats-from-an-undisclosed-country

https://www.visiontimes.com/2021/11/...diplomats.html
By Neil Campbell ο½œ November 26, 2021
Botswana has said that the emerging B.1.1.529 variant, also known as Omicron, of SARS-CoV-2, the virus that causes Coronavirus Disease 2019 (COVID-19), was first detected in four fully vaccinated diplomats from an undisclosed country.

In a media release published by the country’s COVID-19 Task Force on the Government of Botswana’s verified Twitter account on Nov. 25, the state noted that the strain was first discovered on Nov. 22 “among travellers who tested SARS-COV-2 positive on routine pre-travel testing.”..

STATEMENT ON THE NEW COVID-19 VARIANT


DJ So four diplomats went into Botswana november 7, tested positive preparing to leave Botswana november 11...

GABORONE (Reuters) - Botswana's health minister Edwin Dikoloti said on Sunday the country had detected 15 more cases of the Omicron coronavirus variant, adding to the four confirmed cases it declared on Friday.

The minister applauded its scientists for detecting the new variant in the country early, but stressed it did not emerge in Botswana as the four cases were found in people who travelled to the country on a diplomatic mission.

He declined to comment on the nationalities of the four people saying the country "would not want to add to the seeming trend where the variant is stigmatised".

Botswana was early among what are now 11 countries so far reporting cases of the variant, which was identified last week by South Africa's National Institute of Communicable Diseases and later designated "of concern" by the World Health Organization...

It is bizarre that "the west" did stop all air travel to southern Africa-even to countries that not yet reported cases-but keep flying to western countries with Omicron cases...(DJ-Very likely ALL western countries do have cases !).

Several vaccine-breaktrough cases in several countries, or is Omicron not yet recognized ? 

US [url]https://flutrackers.com/forum/forum/united-states-ab/united-states-covid-19-sars-cov-2-september-13-2020-may-31-2021/929061-us-295-of-the-771-patients-in-massachusetts-hospitals-are-reported-covid-19-breakthrough-cases-or-expired-vaccine-status[/url] or https://flutrackers.com/forum/forum/united-states-ab/united-states-covid-19-sars-cov-2-september-13-2020-may-31-2021/929061-us-295-of-the-771-patients-in-massachusetts-hospitals-are-reported-covid-19-breakthrough-cases-or-expired-vaccine-status  and 

[url]https://flutrackers.com/forum/forum/united-states-ab/united-states-covid-19-sars-cov-2-september-13-2020-may-31-2021/929059-us-pennsylvania-reports-breakthrough-covid-19-cases-and-hospitalizations-continue-to-rise[/url] or https://flutrackers.com/forum/forum/united-states-ab/united-states-covid-19-sars-cov-2-september-13-2020-may-31-2021/929059-us-pennsylvania-reports-breakthrough-covid-19-cases-and-hospitalizations-continue-to-rise 

India [url]https://flutrackers.com/forum/forum/india/india-covid-19-sept-13-2020-may-31-2021/929067-india-66-fully-vaccinated-students-in-karnataka-medical-college-test-positive-for-covid-authorities-have-sealed-the-two-medical-colleges-along-with-suspending-offline-classes[/url] or https://flutrackers.com/forum/forum/india/india-covid-19-sept-13-2020-may-31-2021/929067-india-66-fully-vaccinated-students-in-karnataka-medical-college-test-positive-for-covid-authorities-have-sealed-the-two-medical-colleges-along-with-suspending-offline-classes 

South Korea [url]https://flutrackers.com/forum/forum/asia-ad/asia-covid-19-sept-13-2020-may-31-2021/929066-south-korea-breakthrough-covid-19-cases-surge-november-26-2021[/url] or https://flutrackers.com/forum/forum/asia-ad/asia-covid-19-sept-13-2020-may-31-2021/929066-south-korea-breakthrough-covid-19-cases-surge-november-26-2021..............................

[url]https://flutrackers.com/forum/forum/national-international-government-ngo-preparation-response/who-oms/929090-w-h-o-statement-update-on-omicron-november-28-2021[/url] or https://flutrackers.com/forum/forum/national-international-government-ngo-preparation-response/who-oms/929090-w-h-o-statement-update-on-omicron-november-28-2021 ; Effectiveness of prior SARS-CoV-2 infection

Preliminary evidence suggests there may be an increased risk of reinfection with Omicron (ie, people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern, but information is limited. More information on this will become available in the coming days and weeks.
Effectiveness of vaccines: WHO is working with technical partners to understand the potential impact of this variant on our existing countermeasures, including vaccines. Vaccines remain critical to reducing severe disease and death, including against the dominant circulating virus, Delta. Current vaccines remain effective against severe disease and death.
Effectiveness of current tests: The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any impact on other types of tests, including rapid antigen detection tests.
Effectiveness of current treatments: Corticosteroids and IL6 Receptor Blockers will still be effective for managing patients with severe COVID-19. Other treatments will be assessed to see if they are still as effective given the changes to parts of the virus in the Omicron variant.

DJ Most international travel cases-if not all-are in fully vaccinated people. Spread to India, South Korea may be linked to Qatar/Doha airport or Dubai ? Mixing of passengers on flights ? (So cases did get infected during travel...maybe did not visit Africa themselves...) 

Recommended actions for people

The most effective steps individuals can take to reduce the spread of the COVID-19 virus is to keep a physical distance of at least 1 metre from others; wear a well-fitting mask; open windows to improve ventilation; avoid poorly ventilated or crowded spaces; keep hands clean; cough or sneeze into a bent elbow or tissue; and get vaccinated when it’s their turn.

WHO will continue to provide updates as more information becomes available, including following meetings of the TAG-VE. In addition, information will be available on WHO’s digital and social media platforms.

https://www.who.int/news/item/28-11-...ate-on-omicron

DJ I would make that "several meters distance ! 

[url]https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream[/url] or https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-new-coronavirus-variant-b-1-1529-a-variant-of-concern?view=stream latests;

Source: https://www.timesofisrael.com/livebl...ied-in-israel/

Second person carrying Omicron identified in Israel
Today, 7:27 pm

A second person in Israel has been confirmed to be carrying the Omicron variant of the coronavirus, the Health Ministry says. The woman entered Israel from South Africa recently, the ministry says. An Israeli citizen, she had been vaccinated three times, Channel 13 reports...

-

Assuming the same generation time, the transmission advantage could act at two levels: 1) increase in transmissibility, 2) immune evasion. We recently developed a mathematical framework to relate differences in growth rates to these properties. 5/15

A potential increase in transmissibility can be expressed as ρD/R_w, where X is the estimated growth advantage (0.43 per day), D the generation time (5.2 days), and R_w the effective reproduction of the previous variant (~ 0.8 in RSA during October). 6/15 https://ibz-shiny.ethz.ch/covid-19-re-international/…

This would result in an increased transmissibility of 280% (95% CI: 98-468%). With Delta having an R_0 = 5-6 in the Northern Hemisphere during winter, the R_0 of Omicron would be around 10-30. Not impossible, but such a jump seems rather unlikely. 7/15

If the transmission advantage acted via immune evasion only, the level of immune evasion would be ρD(1-Ω)/(ΩR_w), with Ω being the proportion of the population that has fully protective immunity against infection with earlier variants.

South Africa records an excess mortality of 230k during the pandemic, which corresponds to 0.39% of the overall population (https://github.com/dkobak/excess-mortality…). We earlier estimated the infection fatality ratio for the population of South Africa to be 0.35%

Hence, it is likely that almost everyone in South Africa has been infected with #SARSCoV2 and developed partial immunity against reinfection. In addition, 24% of the population have been fully vaccinated.

Thus, the proportion of the population that is fully protected (‘immune’) against infection and further transmission must be quite high. If we assume Ω = 75%, we get an immune evasion of 93% (95% CI: 32-100%), i.e., Omicron evades protective immunity in 93% of individuals.

For Ω = 90%, we obtain an immune evasion of 31% (95% CI: 11-52%) ‘only’. This clearly illustrates the current level of uncertainty about Omicron, and I want to emphasize again the preliminary character of these calculations.

Still, I do expect partial immune evasion to be the main driver of the observed dynamics, but increased transmissibility cannot be ruled out so far.

The developments in South Africa and observations from other countries during the coming days and weeks will allow us to shed more light on the properties of Omicron.

DJ R0 of Omicron between 10 and 30 would be shocking...if it also evades immunity we are in a very major (worsening of the ) crisis...Flutrackers link to [url]https://twitter.com/C_Althaus[/url] or https://twitter.com/C_Althaus source.

DJ Maybe "politics" will use Omicron as an excuse for more action...policy did not fail...blame a new variant...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 1:01pm

I wonder about that flight from SA that went to the Netherlands and then on to the UK. All passengers who boarded in SA had to have a negative PCR test result with them in order to board and yet when tested upon arrival, 60 of them tested positive. So does that mean that 60 became positive in the time it took between the PCR test and landing in the Netherlands, or, more likely, does it mean that the positive cases took a test result from someone else with them in order to travel? Is that even possible? I haven't travelled since these regulations came in so don't know if you can get away with it.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 1:15pm

KiwiMum...all the passengers needed was proof of vaccination...there was no testing...only after SA brought the news on Omicron NL-and others-had to "act like they were acting"...Even the testing that was done was a "joke" ...The Hong kong case only was detected after several tests and days in isolation...

In NL 61 of 624 passengers tested positive-and (if I did get that right) NL as final destination...so they had to move to a hotel for isolation (after waiting on the airport for hours with people that tested negative...). 

Passengers that did not have NL as final destination probably were allowed to continu their travel...

Part of the "show" was also "restricting air travel to southern Africa" ...but not for most passengers...EU citizens can still fly with EU airlines to/from SA..."vaccines will protect them" (so far all Omicron cases outside SA were in vaccinated...) ...there is no stop of airtravel to NL...

Since sequencing samples may take 2-3 weeks from time of infection to publishing sequences a lot of the spread most likely is allready done...The "explosion" of cases in Europe most likely are from Omicron...but sequencing is to slow to catch it up...

After the Wuhan-early 2020 variant in 2021 Delta and Omicron made a "worldtour"...not stopped by government inaction...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote carbon20 Quote  Post ReplyReply Direct Link To This Post Posted: November 28 2021 at 1:38pm








Wonders how many forged vaccine passes out there ??

Reap what you sow......

Take care all πŸ˜·πŸ˜‰πŸ’‰

Everything we hear is an opinion, not a fact. Everything we see is a perspective, not the truth.πŸ––

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Post Options Post Options   Thanks (0) Thanks(0)   Quote EdwinSm, Quote  Post ReplyReply Direct Link To This Post Posted: November 29 2021 at 1:57am

Community spread in Scotland  

Quote

Six cases of the new Covid Omicron variant have been identified in Scotland. 

Some of the people identified have no travel history and have caught the virus variant in the community. 

https://www.bbc.com/news/uk-scotland-59457332

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Post Options Post Options   Thanks (0) Thanks(0)   Quote CRS, DrPH Quote  Post ReplyReply Direct Link To This Post Posted: November 29 2021 at 10:22am

Originally posted by carbon20 carbon20 wrote:

Wonders how many forged vaccine passes out there ??

Reap what you sow......

Take care all πŸ˜·πŸ˜‰πŸ’‰

Yeah, a forged pass won't keep you off of a ventilator! 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 12:54pm

South Africa reports 4,373 new coronavirus cases, an increase of 404% from last week- just reported from BNO news on twitter

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Post Options Post Options   Thanks (0) Thanks(0)   Quote ksc Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 1:32pm
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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 2:07pm

I sure hope this is true and not just a rebuttal to the drug company that said the vaccine wouldn't hold up.  That caused another market dip and people weren't happy he told the truth. Jus sayin.

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Post Options Post Options   Thanks (1) Thanks(1)   Quote ME163 Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 7:09pm

I would in this case be more likely to believe the drug maker.
it is a statement against interest. 


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Post Options Post Options   Thanks (0) Thanks(0)   Quote CRS, DrPH Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 8:55pm

Like with the original Wuhan strain, it appears that Omicron has been spreading long before detection in South Africa. 

https://www.modernhealthcare.com/safety-quality/omicron-was-netherlands-days-earlier-first-thought

DJ, what are you hearing in the NL?  

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: November 30 2021 at 11:26pm

CRS,drPH [url]https://nltimes.nl/2021/11/30/testing-shows-omicron-coronavirus-variant-spreading-netherlands[/url] or https://nltimes.nl/2021/11/30/testing-shows-omicron-coronavirus-variant-spreading-netherlands ...A lot of downplay for the rest...virusses, pandemics are "difficult" items...

I did report on community spread earlier...(but as allways trying to put it in a wider perspective...lots of words...This pandemic is complex...People with a history background tend to talk a lot...). 

Stay safe !

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Post Options Post Options   Thanks (0) Thanks(0)   Quote CRS, DrPH Quote  Post ReplyReply Direct Link To This Post Posted: December 01 2021 at 12:08am

Thank you, DJ!  As always, your research is amazing!  

Stay safe, my friend....I'm not too panic-stricken by this variant right now, it is always the variant we don't predict that bites us.  Delta was like that in India. 

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: December 01 2021 at 2:13am

CRS,DrPH SAGE-UK has a different view [url]https://www.bbc.com/news/health-59484322[/url] or https://www.bbc.com/news/health-59484322 ;

The impact of the Omicron variant on the UK is "highly uncertain" but may require a "very stringent response", government advisers have said.

The BBC has seen leaked minutes of a meeting of the Scientific Advisory Group for Emergencies held on Monday.

Officials should prepare now for a "potentially significant" wave of infections while data on the variant is collected and analysed, they say.

-

The minutes, which have not yet been published but have been seen by the BBC, say that it is "highly likely" that Omicron can escape immunity caused by previous infection or vaccination "to some extent".

The existing Delta variant is already more resistant to vaccines than the original version of the virus found in Wuhan.

The advisers say that there is not currently any evidence of widespread community transmission of Omicron in the UK, as there has been in parts of South Africa. They say the impact on a country like the UK remains uncertain as it is different in terms of age structure, the numbers previously infected with coronavirus and the level of vaccination coverage.

The scientists believe that booster jabs are likely to provide protection against severe disease, hospitalisation and death from most variants in the short term.


But they note: "Any significant reduction in protection against infection could still result in a very large wave of infections. This would in turn lead to a potentially high number of hospitalisations even with protection against severe disease being less affected."

Although the size of any future wave remains "highly uncertain", the scientists say it may be of a scale that requires "very stringent response measures" to avoid unsustainable pressure on the NHS.

DJ BioNTech (German/Turkish partner of US-Pfizer) expects its vaccine still would offer (some) protection also against Omicron...I (DJ) think we soon will find out....

With allready extreme pressure on most countries healthcare systems-bringing them close to collapse allready- even without Omicron there would be more then enough reasons for further restrictions to limit such a collapse...we can no longer avoid "black scenario's", triage etc...

But maybe we can limit its duration...

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Post Options Post Options   Thanks (0) Thanks(0)   Quote EdwinSm, Quote  Post ReplyReply Direct Link To This Post Posted: December 03 2021 at 3:43am

One worrying change in age range, and one big question (how deadly is this varient) we still do not know the answer to.

Originally posted by "BBC" "BBC" wrote:

Early data from the Gauteng province [South Africa] - which has the highest number of coronavirus infections in the country - show that there is a higher number of admissions in children under the age of five than in previous waves.

Scientists have said they will try and determine why this is the case. 

In the last week, hospital admissions have steadily increased but are still well below hospital capacity. 

Epidemiologists here say it is still too early to determine if the variant will cause severe disease. They say this will become clearer in the few weeks as the surge reaches its peak and more cases present in hospitals. 

At this stage most people who have tested positive have reported mild symptoms. 

{posted on BBC's regularly updated page so a link will soon be too old - so not included}

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Dutch Josh Quote  Post ReplyReply Direct Link To This Post Posted: December 04 2021 at 8:47am

[url]https://www.nytimes.com/2021/12/03/world/botswana-diplomats-omicron-europe.html[/url] or https://www.nytimes.com/2021/12/03/world/botswana-diplomats-omicron-europe.html ;

Some of the first cases of the Omicron variant of the coronavirus to be detected in Botswana — which were among the first known in the world — were in foreign diplomats who had traveled to the country from Europe, the country’s president said.

President Mokgweetsi Masisi told CNN on Thursday that four diplomats who tested positive for the coronavirus on Nov. 11, and who were later found to be carrying the new variant, “came from a number of countries.” He added: “Yes, some had been to Europe, and some had been elsewhere.” He did not offer more details.

On Sunday, Botswana’s health minister, Edwin Dikoloti, asserted that most of the 19 Omicron cases that have been detected in his country were “imported.” Officials have not said how that determination could have been made.


Until now, Botswana had not disclosed the nationalities or other details of the four diplomats, with officials saying that they wanted to avoid stigmatizing other nations. The president’s comments highlight that scientists still cannot say with certainty where the variant originated.


DJ It most likely was not Iceland, Malta or Luxemburg.....Historic ties with UK...first almost to stop air travel to SA...(after their diplomats did bring (!!!!!) Omicron there !!!) ...

Maybe -UK having 150+ Omicron detections- the "idea to work from" is that it started in the UK ? See if there is more indications (UK hospital cases going up sooner then in other parts of Europe-indicating patients further in the proces?

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Post Options Post Options   Thanks (0) Thanks(0)   Quote KiwiMum Quote  Post ReplyReply Direct Link To This Post Posted: December 04 2021 at 12:52pm

Wow, if the UK has in excess of 150 cases of Omicron with an RO of 6.3, they'll never stop it now.

"Once you've decided that something's absolutely true, you've closed your mind on it, and a closed mind doesn't go anywhere. Question everything. That's what education's all about." ~ David Eddings
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