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🦘Cacatman's Personal Coronavirus COVID-19 Update Thread

Omicron Mutation
South African genomic scientists said earlier this week the variant has an unusually high number of mutations, with more than 30 in the key spike protein -- the structure the virus uses to get into the cells they attack.

To compare, the Delta variant has 13 mutations.

Discovered Nov 9.

The discovery of the omicron variant has coincided with a spike in South African cases — a 1,124 percent increase over the past two weeks.

It also has mutations that are known to increase the infectivity, fitness, and virulence of SARS-CoV-2.

Another mutation, N501Y, appears to increase the ability of the virus to gain entry to our cells, making it more transmissible.
screenshot_278.png


Our vaccines are focused on identifying the virus based upon the genetic code of what is commonly called the “spike protein”. “SARS-CoV-2 is characterized by a spike protein allowing viral binding to the angiotensin-converting enzyme (ACE)-2, which acts as a viral receptor and is expressed on the surface of several pulmonary and extra-pulmonary cell types, including cardiac, renal, intestinal and endothelial cells.” The virus binds to the cell at the ACE-2 receptor site on the cell and then injects itself into the cell to replicate.

The strain is officially called B.1.1.529 and today the WHO designate the variant as the “Omicron variant”, using the Greek number classification system and labeled it a “variant of concern.” On the genomic epidemiology of novel coronavirus website, it is Clade 21K (see first attachment).

“Back in November 2020, when the alpha variant emerged, it was about 50 per cent more transmissible (as the Wuhan strain). This made a huge difference, and raised the herd immunity threshold from 66 per cent to almost 80 per cent. Today, with Delta, it is 85-90 per cent. The Delta variant, is more than twice as transmissible as the Wuhan strain.” “Data from South Africa’s National Institute for Communicable Diseases show how the new variant quickly crowded out the highly transmissible Delta variant over the past two weeks. It now makes up around 90% of infections in the country’s most populous province, home to its political and economic capitals of Pretoria and Johannesburg.” See the blue spike for November 2021 in the chart below.

Here are the two key issues that indicate this variant is a problem:


  1. “On the protein that helps to create an entry point for the coronavirus to infect human cells (i.e. just the receptor binding domain of the spike protein), the new variant has 10 mutations, many more than the dangerous Delta variant, Professor de Oliveira said.” (Another article said that the Delta variant had 2 changes on the receptor binding domain of the spike protein which is part of the reason for the need for the booster vaccinations. The changes in the Delta variant made is more difficult for our antibodies to easily identify the virus.) The new variant, B.1.1.529, has a “very unusual constellation of mutations,” with more than 30 in the spike protein alone, according to Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform. The new variant already accounts for 75% of the genomes tested in the country, De Oliveira said in a later tweet.” Note: “Some of the mutations have been detected in previous variants, such as Alpha and Delta, and have been associated with increased transmissibility and immune evasion. Many of the other identified mutations are not yet well characterized and have not been identified in other currently circulating variants.”

More specifically, here is a list of mutations and their potential impact:

  1. “South African scientists spotted a quirk in the testing regimen. PCR tests look for three genes in the coronavirus and amplify them. If, however, the virus was this variant they were only able to amplify two.” “This variant seems to give quirky results (known as an S-gene dropout, see also this) in the standard tests and that can be used to track the variant without doing a full genetic analysis. That suggests 90% of cases in Gauteng may already be this variant and it "may already be present in most provinces" in South Africa.”

How Did It Get Created? “B.1.1.529 is likely to have evolved during a chronic infection of an immuno-compromised person, possibly in an untreated HIV/AIDS patient.” This is believed to be the source of the Alpha variant, an immuno-compromised person patient in England. “In the United States, the Alpha variant first appeared late November 2020, grew from 1.2% in late January and became predominant around the end of March 2021.” It was then replaced by the Delta Variant. It was first detected in India in late 2020. The Delta variant was named on 31 May 2021 and had spread to over 163 countries by 24 August 2021. Note: It took six months for WHO to name the Delta Variant, it has named Omicron in three days!

The Reaction:

“Countries around the world moved to restrict travel from southern Africa on Friday in a frantic effort to keep a
newly identified, and apparently significantly evolved, variant of the coronavirus from crossing their borders.
The European Commission proposed that its members activate the “emergency brake” on travel from
countries in southern African and other countries affected to limit the spread of the new variant.
“All air travel to these countries should be suspended until we have a clear understanding about the danger
posed by this new variant,” Ursula von der Leyen, the president of the European Union’s executive arm, said
in a statement. “And travelers returning from this region should respect strict quarantine rules.”

“Late on Thursday Britain said it was suspending flights temporarily from South Africa, Botswana, Lesotho,
Eswatini, Namibia and Zimbabwe. When they start up again, British and Irish citizens returning from these
countries will be required to quarantine in government-approved hotel facilities.” “Any British residents arriving
from South Africa after Sunday morning must stay at a government approved
hotel for 11 nights at a cost of £2,285 per person.

“The Biden administration will restrict travel from South Africa and seven other African countries to try to contain the new variant of the coronavirus, senior administration officials said on Friday. Starting on Monday, the administration will prohibit travelers from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi from coming to the United States, the officials said. The travel ban will not apply to American citizens or lawful permanent residents, officials said. But they will need to show a negative coronavirus test before coming to the United States.”

Summary of Medical Impact:
  1. Effectiveness of current vaccines will not be known for about two weeks based upon what I have read.
  2. “Antibody therapies, used for immunocompromised people, could be seriously undermined.
  3. “Antivirals, however, which attack the enzymes used by the virus, will be unaffected.”

Attached are various news sources used above, with extractions highlighted. Below are some twitter references where other information was pulled from. Some quotes above pulled from webpages that are not included in PDFs:

Saliva swabs are the preferred sample for omicron detection - the pattern of viral shedding during the course of infection is altered for Omicron with higher viral shedding in saliva relative to nasal samples resulting in improved diagnostic performance of saliva swabs. This supports the ex-vivo finding of improved viral replication in upper respiratory tract tissue and possibly altered tissue tropism.5 This is an important finding as the current standard of care for diagnosis using swabs of the nasal or nasopharyngeal mucosa may be suboptimal for the Omicron variant.

The researchers found that Omicron SARS-CoV-2 infects and multiplies 70 times faster than the Delta variant and original SARS-CoV-2 in human bronchus, which may explain why Omicron may transmit faster between humans than previous variants. Their study also showed that the Omicron infection in the lung is significantly lower than the original SARS-CoV-2, which may be an indicator of lower disease severity.
 
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Vaccine use with Lung Cancer
Three doses of the SARS-CoV2 vaccine were shown to be safe and effective in patients with lung cancer, particularly in those with minimal serologic response after receiving only 2 doses, according to findings from a French study published in the Journal of Thoracic Oncology.

The results showed that most patients were immunized after 2 doses and that a third booster shot given to 11% of patients who had persistent low antibody titers induced an 88% immunization rate.
 
WHO: Meanwhile, the organisation opted against using Xi as it is a common surname. "WHO best practices for naming new diseases ... suggest avoiding 'causing offence to any cultural, social, national, regional, professional or ethnic groups'," they said.

~11 million Greeks: 😒😒😒 You’re literally using our unique alphabet for every variant…
 
WHO: Meanwhile, the organisation opted against using Xi as it is a common surname. "WHO best practices for naming new diseases ... suggest avoiding 'causing offence to any cultural, social, national, regional, professional or ethnic groups'," they said.

~11 million Greeks: 😒😒😒 You’re literally using our unique alphabet for every variant…
Yeah, but there is 1.25 billion more of us. That's why. ;)
 
Covid-19 and Myocarditis Risk
Bottom line - still get vaccinated
  • There appears to be a higher risk of myocarditis or pericarditis — an inflammation of the heart muscle or its outer lining — in people ages ages 16–30 who get an mRNA vaccine (Pfizer or Moderna).
  • The risk varies from 1–25 cases per one million mRNA vaccine doses, depending on the person’s age, which vaccine they get, and whether it’s the first or second dose. (Simplified, the risk about 1 in 50,000.)
  • It’s not clear yet if there’s an increased risk for those aged 12–15.
  • Symptoms are chest pain, shortness of breath, and/or heart palpitations that occur within a few days of vaccination.
  • More than half of people who developed this heart inflammation were male.
  • The vast majority of people have fully recovered. (It’s not possible to get a rate of full recovery yet since cases are ongoing as data is collected.)
  • The primary treatment for myocarditis is rest, and it typically goes away on its own.
  • The risk of a serious problem from myocarditis or pericarditis after vaccination is still much lower than the risk of a severe outcome or death from Covid-19, even in young people.
  • Hospitalization rates for Covid-19 have increased in teens, and a third of those hospitalized need intensive care.

Particularly in males ages 16 to 30 as something occurring with somewhat more frequency in those who get the mRNA vaccines than one might expect at baseline.

First of all, the increased risk, still, even in the group that's at highest risk, those of males in the 16 to 30 age range, the risk is about one in 5,000, roughly, because these aren't hard numbers. But the other piece of that is that there are different kinds of myocarditis. There are certain medical products or even vaccines that are associated with myocarditis that puts one in the hospital, in an ICU.

And then there is this myocarditis, which is occurring, which is a very mild issue, where it's generally been either chest pain and/or ECG changes or troponin levels where within a day people are home if they go to the hospital. And, to the best of CDC's follow-up to date, by and large these cases do not appear to be associated with any lasting effects.

So, from the CDC databases, looking at the Vaccine Adverse Event Reporting System and its other data, it looks like about 98% of the cases that show up are exactly as I've described. It is true that 2% seem to be somewhat more significant, but those are hard to tease out sometimes from other sources of myocarditis.


This study evaluated more than 4,900 adverse effects of mRNA COVID-19 vaccines in adolescents mainly reported by European countries. We found that the second dose of vaccine was associated with a 5-fold increase in the reporting odds of myocarditis and/or pericarditis compared to first dose of vaccine. This risk was higher in boys particularly for myocarditis. Our results suggest no differences according age group or type of vaccine.
https://watermark.silverchair.com/qcab090.pdf

Before COVID-19 the incidence of myocarditis was between one and 10 cases per 100,000 people per year. Rates are highest in males between 18 and 30 years old. Interestingly, most cases of myocarditis in the highest risk group are in otherwise healthy and active people.

According to the U.S. Centers for Disease Control and Prevention, the risk of myocarditis after infection with COVID-19 is much higher, at 146 cases per 100,000. The risk is higher for males, older adults (ages 50+) and children under 16 years old. Soccer player Alphonso Davies, 21, of Canada’s national men’s team, was sidelined by heart inflammation after having COVID-19.

Post-vaccination myocarditis​

Myocarditis following COVID-19 vaccination is rare and the risk is much smaller than the risks of cardiac injury linked to COVID-19 itself.

Based on a study out of Israel, the risk of post-vaccine myocarditis is 2.13 cases per 100,000 vaccinated, which is within the range usually seen in the general population. This study is consistent with others in the United States and Israel which put the overall incidence of post-vaccine myocarditis between 0.3 and five cases per 100,000 people.
 
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  1. “South African scientists spotted a quirk in the testing regimen. PCR tests look for three genes in the coronavirus and amplify them. If, however, the virus was this variant they were only able to amplify two.” “This variant seems to give quirky results (known as an S-gene dropout, see also this) in the standard tests and that can be used to track the variant without doing a full genetic analysis. That suggests 90% of cases in Gauteng may already be this variant and it "may already be present in most provinces" in South Africa.”
Why did they leave Xi out?
greekalphabet1.jpg
 
They left Nu and Xi out. Allegedly because Nu would make people think it was the "new" COVID-19, and Xi because it's an Asian surname. True story.
I've heard that about Xi, but thought it was #fakenews but apparently it isn't!
 
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