Just curious, anyone have a plan, or preps for global pandemic?

[AlanPater]

1 hour ago, Matt said:

 

https://www.nejm.org/doi/full/10.1056/NEJMc2108120

.. and nary a mention of vaccines/vaccination comparisons.  Much better to avoid running the gauntlet of the primary infection in the first place by vaccination.

.. or for that matter, the comparison with infection and subsequent vaccination. 

The numbers were so small that " Severe, critical, or fatal disease" and "Severe disease" results were not even significant.

Edited November 26, 2021 by AlanPater

[Matt]

New study from Harvard (pre-print)

Continued Effectiveness of COVID-19 Vaccination among Urban Healthcare Workers during Delta Variant Predominance

"We further conducted a secondary analysis limiting the study period from July 1, 2021 to September 30, 2021, corresponding to delta variant predominance in Massachusetts (4). We observed an incidence rate of 5.8/10,000 (15 events out of 25,910 person-days) for unvaccinated person-days and 1.3/10,000 (39 events out of 308,267 person-days) for 14 days after fully vaccinated, resulting in an adjusted VE of 76.5% (95% CI: 40.9–90.6%)."

"Independently, we found no re-infection among those with prior COVID-19, contributing to 74,557 re-infection-free person-days, adding to the evidence base for the robustness of naturally acquired immunity."

https://www.medrxiv.org/content/10.1101/2021.11.15.21265753v1.full-text

[Matt]

7 hours ago, AlanPater said:

.. and nary a mention of vaccines/vaccination comparisons.  Much better to avoid running the gauntlet of the primary infection in the first place by vaccination.

.. or for that matter, the comparison with infection and subsequent vaccination. 

The numbers were so small that " Severe, critical, or fatal disease" and "Severe disease" results were not even significant.

Yes, Al, as I have said many times before., If someone does not have immunity, I think they should get the vaccine. However, firing healthcare workers who have proven immunity is hardly rational.

As for numbers, I missed out the PDF:

"Reinfections were rare in Qatar. Out of a total of 353,326 individuals with PCR-confirmed infections between February 28, 2020 (the date when the first SARS-CoV-2 case was recorded) and April 28, 2021 (the closing date of the study), only 1,339 reinfections were recorded, that is
a percentage of 0.38% (95% CI: 0.36-0.40%)"
https://www.nejm.org/doi/suppl/10.1056/NEJMc2108120/suppl_file/nejmc2108120_appendix.pdf

Out of those people, the number that were serious was very small. Which is a good thing, it shows that naturally-acquired immunity is effective at preventing serious reinfection.

[mccoy]

Another aspect is that the usefulness of the 3rd shot may be jeopardized by the rise of the new SA variant.

Now, if I take a 3rd shot, after a while the new variant may spread and the 3rd shot become more or less useless. So, I'll have to take a 4th or 5th shot to fight the new variant. And a booster shot, which makes six. This in the timespan of a few months? Now, in an individual not historically susceptible to viruses infections (like myself, who apparently never took the flu with symptoms), the remedy may be worse off than the illness. It's also highly speculative, but the degree of reliability of official science presently is not encouraging.

 

https://www.nature.com/articles/d41586-021-03552-w#:~:text=Heavily mutated coronavirus,COVID vaccines’ effectiveness.

Edited November 26, 2021 by mccoy

[Gordo]

What we know about the new highly mutated Covid variant found in South Africa

 

This is being blamed for roiling markets all around the world today (big declines everywhere) although I'm not really sure I buy that story, I think the market is in an epic bubble just looking for any excuse to sell off 😉

 

The discovery of a new and potentially more transmissible coronavirus variant by South African health authorities has sparked a forceful reaction across the world with a number of countries banning travelers from several southern African countries.

The newly identified variant, currently known as B.1.1.529, appears to be spreading rapidly in parts of South Africa and scientists are concerned that its unusually high number of mutations could make it more transmissible and result in immune evasion.

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"Initially it looked like some cluster outbreaks, but from yesterday, the indication came from our scientists from the Network of Genomic Surveillance that they were observing a new variant," Minister of Health Joe Phaahla said Thursday, stressing that it is currently unclear where the variant first emerged.

It has so far been detected in South Africa, Botswana and in a traveler to Hong Kong from South Africa, Phaahla added.

Tulio de Oliveira, the director of South Africa's Center for Epidemic Response and Innovation, said the variant has "many more mutations than we have expected," adding it is "spreading very fast and we expect to see pressure in the health system in the next few days and weeks."

Viruses, including the one that causes Covid-19, mutate regularly and most new mutations do not have significant impact on the virus's behavior and the illness they cause.

The World Health Organization (WHO) will hold a meeting on Friday to decide whether the B.1.1.529 variant should be considered one "of interest" or "of concern," designations that signify the amount of risk that it could pose to global public health.

WHO added it would "share further guidance for government on actions they can take."

What we know about the new variant

Lawrence Young, a virologist and a professor of molecular oncology at Warwick Medical School in the United Kingdom, said the variant was "very worrying."

"It is the most heavily mutated version of the virus we have seen to date. This variant carries some changes we've seen previously in other variants but never all together in one virus. It also has novel mutations," Young said in a statement.

The variant has high number of mutations, about 50 overall. Crucially, South African genomic scientists said Thursday more than 30 of the mutations were found in the spike protein -- the structure the virus uses to get into the cells they attack.

Neil Ferguson, the director of the MRC Centre for Global Infectious Disease Analysis at Imperial College London, said in a statement that the number of mutations on the spike protein was "unprecedented."

"The spike protein gene [is] the protein which is the target of most vaccines. There is therefore a concern that this variant may have a greater potential to escape prior immunity than previous variants," Ferguson said.

Sharon Peacock, a professor of Public Health and Microbiology at the University of Cambridge, said that while the overall number of Covid-19 cases is relatively low in South Africa, there has been a rapid increase in the past seven days.

She said that while 273 new infections were recorded on November 16, the figure had risen to more than 1,200 cases by November 25, with more than 80% coming from Gauteng province.

"The epidemiological picture suggests that this variant may be more transmissible, and several mutations are consistent with enhanced transmissibility," Peacock said in a comment shared by the UK's Science Media Centre.

She added that while the significance of the mutations and their combination is unknown, some of those present in the latest variant have been associated in others with immune evasion.

What we don't know

Peacock, de Oliveira, Ferguson and other scientists said it was too early to tell the full impact of the mutations on vaccine efficacy.

De Oliveira stressed that the shots are still the best tool against the virus, adding that lab studies still need to be carried out to test vaccine and antibody evasion.

More studies also need to be conducted to understand the clinical severity of the variant compared to previous variants.

It is also unclear where the new mutation emerged from. While it was first identified in South Africa, it may have come from elsewhere.

"It is important not to assume that the variant first emerged in South Africa," Peacock said.

Quick reaction

Scientists have praised South African health authorities for their quick reaction to a Covid-19 outbreak in the country's Gauteng province, which led to the discovery of the new variant.

When cases in the province started to rise at a higher rate than elsewhere, health experts focused on sequencing samples from those who tested positive, which allowed them to quickly identify the B.1.1.529 variant.

Peacock said the South African health ministry and its scientists "are to be applauded in their response, their science, and in sounding the alarm to the world."

She added that the development shows how important it is to have excellent sequencing capabilities and to share expertise with others.

The reaction to the announcement of the new variant discovered by South African health authorities was also prompt. A number of countries have imposed new travel bans and markets in the US, Asia and Europe took a plunge following the news.

UK officials announced on Thursday that six African countries will be added to England's travel "red list" after the UK Health Security Agency flagged concern over the variant.

UK's Health Minister Sajid Javid said flights to the UK from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will be suspended from midday Friday and all six countries will be added to the red list -- meaning UK residents and British and Irish nationals arriving home from those points of departure must undergo a 10-day hotel quarantine at their own expense.

Speaking on Friday, Javid said it was "highly likely" that the B.1.1.529 variant has spread beyond southern Africa. In a statement to the UK House of Commons Friday Javid expressed concern that it may "pose a substantial risk to public health."

South Africa, like much of the region, has suffered through three significant Covid-19 waves since the pandemic's start. While the number of new infections across the country is now still relatively low and positivity levels are under 5%, public health officials have already predicted a fourth wave because of a slow vaccine uptake.

[Gordo]

 

Israel warns of 'emergency' after detecting new virus strain

JERUSALEM (AP) — Prime Minister Naftali Bennett said on Friday that Israel is "on the threshold of an emergency situation” after authorities detected the country’s first case of a new coronavirus variant and barred travel to and from most African countries.

The Health Ministry said it detected the new strain in a traveler who had returned from Malawi and was investigating two other suspected cases. The three individuals, who had all been vaccinated, were placed in isolation.

 

[Gordo]

+++ 13:50 Biontech is investigating a new variant - results within two weeks +++ The Mainz vaccine manufacturer Biontech is looking at the new variant of the coronavirus detected in southern Africa in tests and is expecting findings in two weeks at the latest. "We can understand the concerns of experts and immediately initiated investigations into variant B.1.1.529," said the company on request. The variant differs significantly from the variants observed so far, since it has additional mutations on the spike protein. The data from ongoing laboratory tests would provide information on whether an adaptation of the vaccine would be necessary if this variant spreads internationally. Biontech also announced that, together with US partner Pfizer, preparations had been made months ago to adapt the vaccine within six weeks in the event of a so-called escape variant of the virus and to deliver the first batches within 100 days

[Gordo]

Chart shows how quickly the new coronavirus variant spread in part of South Africa, totally supplanting Delta

 

 

 

A chart showing different coronavirus variants over time in part of South Africa. An arrow, added by Insider, points out the blue spike representing, B.1.1.529, which became dominant within 2 weeks over the Delta variant (in red).South Africa Health Department/Insider

• A new coronavirus variant, B.1.1.529, has spread rapidly in South Africa.

• A chart from the country's Health Department shows how it shot to dominance in one province.

• The variant's high level of mutations to the spike protein is causing concern for scientists.

A chart from South African officials shows how a new coronavirus variant quickly came to dominate in a province of the country, supplanting the Delta variant.

It was shown in a briefing from South Africa's Department of Health on Thursday warning about the B.1.1.529 variant.

As of Friday, the variant had been detected in South Africa, Botswana, and Hong Kong. Its origin is unclear.

Prof. Tulio de Oliveira, director of the Centre for Epidemic Response & Innovation near Cape Town, said the data in the chart is from samples taken in Gauteng province from November 12 to November 22.

In that period, B.1.1.529 completely overtook the Delta and Beta variants that were present in Gauteng. The variant has rapidly increased there and is may already be present in most of the country's provinces, he said.

B.1.1.529 — represented by the blue part — represented 75% of cases detected within just two weeks. Its ascent was much faster than the Beta (green) and Delta (red) variants, which each took months to become dominant.

de Oliveira said that the B.1.1.529 cases were drawn from 77 samples — a relatively small number, but with a clear direction of travel.

The Financial Times produced another chart illustrating the speed of the variant's rise:

The increase in infections from the variant in Gauteng "shocked" de Oliveira and his colleagues, he told the South African channel SABC News.

One of the biggest fears about the variant is that its high levels of mutation in its spike protein could inhibit the body's immune response, as Insider's Dr Catherine Schuster-Bruce reported.

Speaking to SABC News, de Oliveira said it is too early to know if the vaccine will work against B.1.1.529, but said scientists expect it to hold "against hospitalizations and deaths."

"Vaccines are the strongest weapon in our arsenal to fight that virus," he said. He also called for people to avoid mass gatherings and to wear masks as scientists track the variant.

The UK has blocked flights from 6 African countries in response to the alarm, with the EU considering similar moves.

 

Edited November 26, 2021 by Gordo

[corybroo]

MedicalXpress has an article looking at how information may be “massaged”.

COVID death data can be shared to make it look like vaccines don't work, or worse – but that's not the whole picture

Some vaccines are single-dose, others are double-dose regimens. Most jurisdictions define "fully vaccinated" as two weeks after the last required dose, but some social media posts like this one lump together anyone who has had any dose.

Let's say 95% of NSW's entire population of approximately 8,000,000 was fully vaccinated. That's 7.6 million people. Imagine 0.05% of fully vaccinated people needed to be hospitalised with COVID. That's just shy of 4,000 people.

Let's also say 1% of the remaining 400,000 unvaccinated people were hospitalised with COVID. That's 4,000 people.

So the absolute number of hospitalised vaccinated people would be similar to the hospitalised unvaccinated people.

But, less than 0.05% of fully vaccinated people are in hospital, compared to 1% of unvaccinated people—that's 20 times higher!

Another way to explain this relates to what's known as Simpon's paradox: when a very large proportion of the population is vaccinated, it is quite likely that a larger absolute number of cases will be vaccinated rather than unvaccinated. To compare effects, one must instead focus on the rates of cases and death from COVID.

And almost all countries vaccinated the most at-risk populations first. Some, like the elderly, already displayed higher death rates. Given the most likely to die are the first vaccinated, then we may see more deaths in the group vaccinated first. The vaccine will have lessened the deaths, but at-risk people were always more likely to die.

To truly discern the effect of the vaccine, then, one has to compare rates across matched levels of risk, especially age. A very good analysis matches different levels of age risk on the Israeli data and shows that even though the absolute number of vaccinated hospitalised cases was more than the unvaccinated hospitalisations, the Pfizer vaccine still showed good effectiveness against severe disease.

[From the referenced analysis:              CB]

To adjust for vaccination rates, one should normalize the counts, of severe cases in our setting, for example by computing number "per 100,000"  

After this adjustment, we see that the rate of severe cases is 16.4/5.3=3.1x higher in unvaccinated individuals than fully vaccinated individuals.   

[Saul]

The new variant from South Africa has been named the omicron variant.  The US President, on advice from Dr. Faucet, is restricting travel from several Southern Africa countries  -- including South Africa, Zimbabwe, and half a dozen or so others.

Edited November 26, 2021 by Saul

[Todd Allen]

13 hours ago, Gordo said:

The newly identified variant, currently known as B.1.1.529, appears to be spreading rapidly in parts of South Africa and scientists are concerned that its unusually high number of mutations could make it more transmissible and result in immune evasion.

Not that new, here's a story mentioning this variant from July...

https://www.weforum.org/agenda/2021/07/how-scientists-detect-new-covid-19-variants/

Quote

Scientists in South Africa have discovered a small number of cases of a new COVID variant. They’re working to understand its potential implications but told a news conference that it had a ‘very unusual constellation’ of mutations.

They’re concerned that they could help it evade the body’s immune response and make the variant - named B.1.1.529 - more transmissible.

 

[Sibiriak]

Quote

US Centers for Disease Control and Prevention has said no cases of the new Covid-19 Omicron variant detected in South Africa have so far been identified in the United States to date.

Nevertheless:

Quote

New York governor Kathy Hochul issued a Covid-19 “disaster emergency” declaration on Friday, citing increasing rates of infections and hospitalisations. An order from the governor said the state was experiencing Covid-19 transmission “not seen since April 2020” and that hospital admissions has been increasing over the past month to over 300 a day.

 

[Dean Pomerleau]

11 hours ago, Todd Allen said:

Not that new, here's a story mentioning this variant from July...

https://www.weforum.org/agenda/2021/07/how-scientists-detect-new-covid-19-variants/

No. That webpage has been updated in the past couple days to mention the new Omicron variant. Here is what it looked like back in July, when it discussed Delta as the new variant of concern:

https://web.archive.org/web/20210712172008/https://www.weforum.org/agenda/2021/07/how-scientists-detect-new-covid-19-variants/

Omicron (B.1.1.529) was first detected this week. 

--Dean 

[Gordo]

17 hours ago, Saul said:

The new variant from South Africa has been named the omicron variant.

Interesting that Omicron is an anagram for Moronic 😉

 

[Todd Allen]

19 hours ago, Dean Pomerleau said:

No. That webpage has been updated in the past couple days to mention the new Omicron variant. Here is what it looked like back in July, when it discussed Delta as the new variant of concern:

Good catch.  The possibility of a dated story being updated didn't cross my mind.  I had a deja vu'ish sense when these stories broke of a frightening new numbered variant and when a cursory search on B.1.1.529 turned up an article dated in July confirmation bias kicked in and I didn't look further.  It doesn't help that once again folks from Imperial College London are prominently sounding the alarm generating for me a bit of fool me once, fool me twice disdain.

[Todd Allen]

14 hours ago, Gordo said:

Interesting that Omicron is an anagram for Moronic

Ha ha perfect.  Curiously if we look at the unexplained skipped greek letters Nu is an anagram for Un and Xi is an anagram for Ix which together is Unix.  Bill Gates has some explaining to do.

[mccoy]

The Omicron variant is just invading Europe. We'll see if the 3rd shot has any effect on it. Government-payed virologists say a resounding YES. The party line. I am far less optimistic....

https://www.euronews.com/2021/11/27/germany-reported-first-suspected-case-of-omicron-covid-19-variant#:~:text=Germany%2C the Czech Republic%2C Italy and the UK announced on Saturday that they had detected cases of the new COVID-19 variant%2C Omicron.

[Sibiriak]

The omicron variant is more transmissible, apparently.  But it is  it any more severe/deadly?

[mccoy]

I've read the news from Italy. The man was returning from Africa. He was vaccinated with 2 shots and is in good health. his family also has the variant, but is in good health (it's not specified if all the members of the family had had vaccination shots and how many).

So far so good, if it's not more severe, we couldn't mind less. It will just contribute to the ruling paranoia. Of course, it may target different organs and systems in the body, so will know for certain in a few days, I hope.

Edited November 28, 2021 by mccoy

[AlanPater]

7 hours ago, mccoy said:

I've read the news from Italy. The man was returning from Africa. He was vaccinated with 2 shots and is in good health. his family also has the variant, but is in good health (it's not specified if all the members of the family had had vaccination shots and how many).

So far so good, if it's not more severe, we couldn't mind less.

Omicron symptoms mild so far, says South African doctor who spotted it
Dr Angelique Coetzee, the South African doctor who first spotted the new Covid variant Omicron, says the patients seen so far have had "extremely mild symptoms" - but more time is needed before we know the seriousness of the disease for vulnerable people.
Watch her tell the BBC's Andrew Marr how patients in South Africa have told her they've been feeling.
    BBC News

https://www.bbc.com/news/av/uk-59450988

[Mike41]

 

[Sibiriak]

No Severe COVID Cases Among Vaccinated Patients Infected With Omicron, Top Israeli Expert Says

 

Quote

Israel’s chief of public health services, Dr. Sharon Alroy-Preis, warned Sunday that the potential for infection with the COVID variant omicron is “very high,” but stressed that in cases where vaccinated people were infected they became only slightly ill.

Speaking at a Knesset meeting, she gave the example of a flight from South Africa to the Netherlands, where 62 out of 600 passengers were found to be infected. “This is very, very fast," Alroy-Preis said.

[...]  Prof. Dror Mevorach, head of the coronavirus department at Hadassah University Hospital Ein Karem, said the preliminary reports on the clinical condition of people infected with the new variant are encouraging.

“If it continues this way, this might be a relatively mild illness compared to the delta variant, and paradoxically, if it takes over, it will lead to lower infection rates,” and it will be easier to deal with globally.

 

[Gordo]

COVID-19: Some Omicron cases have 'mild' symptoms and experts should know more about transmission 'within days' - WHO

I'm pretty sure this is the typical progression of deadly fast spreading diseases and something similar happened over time with the flu.  So this alledgedly very fast spreading "Omicron" may actually be very good news.

Edited December 1, 2021 by Gordo

[Sibiriak]

 

1 hour ago, Gordo said:

"Omicron" may actually be very good news. 

Good news for authoritarians and big pharma?

EU must consider mandatory Covid jabs, says  Von der Leyen

Quote

The EU must consider mandatory vaccination in response to the spread of the “highly contagious” Omicron Covid variant across Europe, the European Commission president has said.

In a call to action, Ursula von der Leyen said the EU’s 27 member states should rapidly deploy booster doses and a commission communique backed countries opting to temporarily enforce pre-travel PCR tests even within the bloc’s borders.

There have been a total of 59 identified cases in the EU of the Omicron variant all of which have involved mild symptoms or been asymptomatic.

Asked whether she supported the Greek government in its imposition of a €100 (£85) monthly fine on those aged 60 and over who failed to get a Covid jab, Von der Leyen said the spread of the disease and lack of vaccine take-up in parts of the EU meant mandatory vaccination had to be on the table as a policy response.

 

[AlanPater]

Odds of Testing Positive for SARS-CoV-2 Following Receipt of 3 vs 2 Doses of the BNT162b2 mRNA Vaccine.
Patalon T, Gazit S, Pitzer VE, Prunas O, Warren JL, Weinberger DM.
JAMA Intern Med. 2021 Nov 30. doi: 10.1001/jamainternmed.2021.7382. Online ahead of print.
PMID: 34846533
Abstract
Importance: With the evidence of waning immunity of the mRNA vaccine BNT162b2 (Pfizer-BioNTech), a nationwide third-dose (booster) vaccination campaign was initiated in Israel during August 2021; other countries have begun to administer a booster shot as well.
Objective: To evaluate the initial short-term additional benefit of a 3-dose vs a 2-dose regimen against infection of SARS-CoV-2.
Design, setting, and participants: This preliminary retrospective case-control study used 2 complementary approaches: a test-negative design and a matched case-control design. Participants were included from the national centralized database of Maccabi Healthcare Services, an Israeli healthcare maintenance organization covering 2.5 million members. Data were collected between March 1, 2020, and October 4, 2021, and analyses focused on the period from August 1, 2021, to October 4, 2021, because the booster dose was widely administered from August 1 onward.
Exposures: Either 2 doses or 3 doses of the BNT162b2 vaccine.
Main outcomes and measures: The reduction in the odds of a positive SARS-CoV-2 polymerase chain reaction (PCR) test at different time intervals following receipt of the booster dose (0-6, 7-13, 14-20, 21-27, and 28-65 days) compared with receiving only 2 doses.
Results: The study population included 306 710 members of Maccabi Healthcare Services who were 40 years and older (55% female) and received either 2 or 3 doses of the BNT162b2 vaccine and did not have a positive PCR test result for SARS-CoV-2 prior to the start of the follow-up period. During this period, there were 500 232 PCR tests performed, 227 380 among those who received 2 doses and 272 852 among those who received 3 doses, with 14 989 (6.6%) and 4941 (1.8%) positive test results in each group, respectively. Comparing those who received a booster and those who received 2 doses, there was an estimated odds ratio of 0.14 (95% CI, 0.13-0.15) 28 to 65 days following receipt of the booster (86% reduction in the odds of testing positive for SARS-CoV-2).
Conclusion and relevance: Previous studies have demonstrated that vaccine-derived protection against SARS-CoV-2 wanes over time. In this case-control analysis, we showed an association between receipt of the booster dose and a reduction in the odds of testing positive for SARS-CoV-2, potentially counteracting waning immunity in the short term. Further monitoring of data from this population is needed to determine the duration of immunity following the booster.