Coronavirus COVID-19 - Global Health Pandemic #90

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Just stopping in to say I Hate this curse of a virus.
I don't disdain it. I don't dislike it... I absolutely HATE this virus!
That's it. I hope all of you are safe as our entire world is in an uproar.
 
acutename said:
this educated law blogger was sent home I think more than once, wound up on a ventilator and then recovered:


'Above the Law' blogger David Lat on ventilator with coronavirus
nypost.com › 2020/03/22 › above-the-law-blog-founde...
Mar 22, 2020 — David Lat in the hospital after testing positive for coronavirus ... Lat, 44, founder of the legal blog Above the Law, has been put on a ventilator and ... Lat said he went to the emergency room but was sent home — only to return ...
Click to expand...

He became ill in March when Covid wasnt being recognized for what it was. In his case
they diagnosed the flu and put him on a Z-pack. The also put people on ventillators
which actually made many patients worse. The virus was so new then ---'
 
acutename said:
I guess it could be a legitimate question whether "over 2" means 3 yrs old, or whether it means one minute after your second birthday. The article about their NY trip discusses that. (Something I have noticed during COVID is that most adults have limited their talking, shouting and singing, but small children, in their acquiring speech phase, talk a lot, IMHO.) They, were, BTW, as per that article, going to NYC to see the tree at Rockefeller Center. This country, IMHO, is so weird- half of the country is hiding in a bunker and the other half is flying some where every week for recreation.
Click to expand...

exactly!!!
 
Updated compilation of notes on strains, mutations, variants:

Live Q&A on the new #COVID19 virus variant with WHO, @covidgenomicUK, and @sangerinstitute experts / Dec. 23, 2020
—-

Are there different strains of the SARS-CoV-2 virus circulating?
June 10, 2020

What is a virus ‘strain’?
When scientists use the word strain, they are referring to a genetically distinct virus lineage, distinguishable by one or more mutations from another strain. Strains may or may not be biologically (functionally) distinguishable from one another and some virologists use the term strain only for the former. Two strains would be biologically different if they elicited different responses from the human immune system, or if they varied in their transmission characteristics.

What are viral mutations?
When a virus infects a cell and begins making copies of itself, it starts by replicating its genetic information, which for the COVID-19 virus is encoded in an RNA molecule. More complex organisms have a variety of “proof-reading” mechanisms to ensure high-fidelity replication; however, these are less developed in RNA viruses where the process is particularly error-prone, leading to a relatively rapid accumulation of mutations over time. SARS-CoV-2 does carry some proof-reading enzymes and its mutation rate is lower than many other RNA viruses, such as influenza virus, norovirus and human immunodeficiency virus (HIV).
—-

June 15, 2020
COVID-19 Will Mutate — What That Means for a Vaccine

“More infectious

A new study from the Scripps Research Institute in Florida suggests the new coronavirus has mutated into a variant that’s more infectious.

The mutation — named “the D614G mutation” — occurred on the spike protein, the part of the virus that helps it bind and fuse to our cells. The D614G mutation makes it easier for the virus to infect our cells.

The Scripps researchers aren’t the first to identify the tiny mutation on the spike protein.

In March, researchers from the Los Alamos National Laboratory announced they detected the D614G mutation, and that it was likely responsible for most infections reported in Europe and the United States.

In total, the researchers identified 14 strains of SARS-CoV-2 and released their findings to help those working on vaccines and treatments.

That being said, the new dominant strain identified does seem to be more infectious in laboratory settings. Scientists are now trying to understand how the variation behaves in the body — which may be very different from lab settings.”
—

June 30, 2020
Mutated COVID-19 Viral Strain in U.S. and Europe 10 Times More Contagious than Original Strain | BioSpace

“The mutation does not appear to make the virus any more deadly than it already is, but it does appear to make it significantly more contagious. The original strain in China is dubbed D614, while the one found in the UK, Italy and North America by May is dubbed G614.“
—

July 16, 2020
Second Coronavirus Strain May Be More Infectious—but Some Scientists Are Skeptical

“The paper indicates that a single amino acid change from D (aspartic acid) to G (glycine) on the SARS-CoV-2 spike protein(which such viruses use to grab onto human cells) is the key to how infectious the pathogen is. “The spike protein has a critically important role in the biology of the virus,” says Bette Korber, a computational biologist at the Los Alamos National Laboratory and lead author of the new paper.

Korber and her colleagues came to this conclusion after employing multiple approaches to examine the two strains. First, they performed a statistical analysis that showed how the mutated virus—often referred to as the “G strain”—achieved dominance across multiple continents, outperforming the coexisting original version of SARS-CoV-2, or “D strain.” Then the researchers tested the amount of the virus in individuals with COVID-19 at the Sheffield Teaching Hospitals NHS Foundation Trust in England. The results showed that the G strain produced more of the virus in the human body than the D strain. But the former did not lead to a higher hospitalization rate, meaning it apparently did not cause more severe illnesses. Lastly, the team members created “pseudotype” pathogens by embedding SARS-CoV-2 spike proteins, containing either D or G amino acids, into other disease-causing viruses...”
—

Aug. 3, 2020
The six strains of SARS-CoV-2
“Source:
Università di Bologna
Summary:
The virus causing the COVID-19 pandemic, SARS-CoV-2, presents at least six strains. Despite its mutations, the virus shows little variability, and this is good news for the researchers working on a viable vaccine.“
—

Sept. 8, 2020

“In April, Korber, Montefiori and others warned in a preprint posted to the bioRxiv server that “D614G is increasing in frequency at an alarming rate”1. It had rapidly become the dominant SARS-CoV-2 lineage in Europe and had then taken hold in the United States, Canada and Australia. D614G represented a “more transmissible form of SARS-CoV-2”, the paper declared, one that had emerged as a product of natural selection.“
—

Oct. 30, 2020
Coronavirus mutation may have made it more contagious

“Source:
University of Texas at Austin
Summary:
A study involving more than 5,000 COVID-19 patients in Houston finds that the virus that causes the disease is accumulating genetic mutations, one of which may have made it more contagious. This mirrors a study published in July that found that around the world, viral strains with the same genetic mutation quickly outcompeted other strains.

A study involving more than 5,000 COVID-19 patients in Houston finds that the virus that causes the disease is accumulating genetic mutations, one of which may have made it more contagious. According to the paper published in the peer-reviewed journal mBIO, that mutation, called D614G, is located in the spike protein that pries open our cells for viral entry. It's the largest peer-reviewed study of SARS-CoV-2 genome sequences in one metropolitan region of the U.S. to date.”

[...]

“A study published in July based on more than 28,000 genome sequences found that variants carrying the D614G mutation became the globally dominant form of SARS-CoV-2 in about a month.”

[...]

“Natural selection would favor strains of the virus that transmit more easily. But not all scientists are convinced. Some have suggested another explanation, called "founder's effects." In that scenario, the D614G mutation might have been more common in the first viruses to arrive in Europe and North America, essentially giving them a head start on other strains.“
—

RAPID RISK ASSESSMENT
Detection of new SARS-CoV-2 variants related to mink
12 November 2020
https://www.ecdc.europa.eu/sites/default/files/documents/RRA-SARS-CoV-2-in-mink-12-nov-2020.pdf

“The mutation Y453F”

SARS-CoV-2 mink-associated variant strain – Denmark
6 November 2020

“Since June 2020, 214 human cases of COVID-19 have been identified in Denmark with SARS-CoV-2 variants associated with farmed minks, including 12 cases with a unique variant, reported on 5 November. All 12 cases were identified in September 2020 in North Jutland, Denmark. The cases ranged in age from 7 to 79 years, and eight had a link to the mink farming industry and four cases were from the local community.

Initial observations suggest that the clinical presentation, severity and transmission among those infected are similar to that of other circulating SARS-CoV-2 viruses. However, this variant, referred to as the "cluster 5" variant, had a combination of mutations, or changes that have not been previously observed. The implications of the identified changes in this variant are not yet well understood. Preliminary findings indicate that this particular mink-associated variant identified in both minks and the 12 human cases has moderately decreased sensitivity to neutralizing antibodies. Further scientific and laboratory-based studies are required to verify preliminary findings reported and to understand any potential implications of this finding in terms of diagnostics, therapeutics and vaccines in development. In the meantime, actions are being taken by Danish authorities to limit the further spread of this variant of the virus among mink and human populations.“

WHO / SARS-CoV-2 mink-associated variant strain – Denmark / Nov. 6, 2020

https://www.oie.int/fileadmin/Home/...E_on_Sars-CoV-2_in_Denmark_5_november2020.pdf
Nov. 5, 2020
—-

Nov. 13, 2020
Study: New Mutation Sped Up Spread of Coronavirus

“Compared to the original strain, people infected with the new strain -- called 614G -- have higher viral loads in their nose and throat, though they don’t seem to get any sicker. But they are much more contagious to others.“
—

Dec. 15, 2020
New coronavirus strain spreading in UK has key mutations, scientists say

“The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19 spreading more easily between people.”

[...]

“As of Dec. 13, 1,108 COVID-19 cases with the new variant had been identified, predominantly in the south and east of England, Public Health England said in a statement.

But there is currently no evidence that the variant is more likely to cause severe COVID-19 infections, the scientists said, or that it would render vaccines less effective.“
—

Severe COVID variant detected in South Africa, health minister says

“Known as the 501.V2 Variant, it was identified by South African researchers and details have been sent to the World Health Organization, Zwelini Mkhize said in a statement.“

[...]

“The research team, led by Tulio de Oliveira, has shared its findings with the scientific community and alerted authorities in Britain, who have “studied their own samples and found that a similar mutation… was the variant that was driving their resurgence in London,” he said.”
—

@DrZweliMkhize
Dec 18
Karim: This new 501.V2 variant has become dominant in South Africa. This new variant has 3 mutations. #SARSCOV2MediaBriefing

South Africa identifies new coronavirus strain causing surge in cases

““The evidence that has been collated, therefore, strongly suggests that the current second wave we are experiencing is being driven by this new variant,” Mkhize added.”
—

New Variant of SARS-CoV-2 Frequently Asked Questions - NICD
Dec. 19, 2020

“Q What is the new SARS-CoV-2 variant?
A This new variant of the virus was discovered through routine genomic surveillance of SARS-
CoV-2 performed by a network of laboratories around the country (Network for Genomic Surveillance South Africa, NGS-SA). The new variant has been identified in almost 200 samples collected from over 50 different health facilities in Eastern Cape, Western Cape and KwaZulu- Natal. The new variant is different from the others that were circulating in South Africa because it has multiple mutations (changes) in the spike protein – this is the very important part of the virus that binds to the receptor on the cells inside our body and that is also the main target for many of the antibodies produced during infection or after vaccination. Work is being done to understand what effect these mutations have on the behaviour of the virus and our body’s response to it - particularly whether it makes the virus spread more easily, whether it might lead to more severe COVID-19, and whether the virus can evade our immune response.

Q What is the geographical distribution of this mutation?
A The variant was first identified in Nelson Mandela Bay but has rapidly spread through the rest
of the Eastern Cape and to the Western Cape and KwaZulu-Natal provinces. Testing in other provinces is being undertaken to understand the extent of geographical spread but it is likely that this variant has spread to other provinces too.”

[...]

Q Is this the same or different to the London variant?
A It is definitely not the same variant, but there are similarities as they both share the same change in the spike protein at the 501 position. What it does tell us is that if we do not control the spread of the virus then it is likely to evolve in similar ways in different parts of the world.”
—

UK Variant:

“The variant that’s being discussed was first identified in September...” - Alex Azar | source
—

In the WHO Press Briefing from Monday, Dec. 21, 2020, Dr. Maria Van Kerkhove comments about the UK VUI / source:
  • It has a number of mutations that was identified through genomic sequencing, which is carried out across the country.

  • The Variant Under Investigation was reported to WHO on 14th December, following detail analysis that the UK had done in the southeast of England, looking at their epidemiologic surveillance data and their laboratory data, noting an increase in transmission at the end of Nov/Dec, while interventions were in place.
  • They did some file genetic analysis and identified this variant, “they’re calling it the “B-117 lineage which includes this mutation at the N501Y site”.

  • She also said the reproductive number went up by .4, increasing from 1.1 to 1.5.

  • Also note it was originally referred to as “VUI-202012/01”:
    * From above notes, “Dec. 15, 2020: New coronavirus strain spreading in UK has key mutations, scientists say “The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19 spreading more easily between people.”...“As of Dec. 13, 1,108 COVID-19 cases with the new variant had been identified, predominantly in the south and east of England, Public Health England said in a statement.“
Additionally, the reporter specifically asks if there is a connection between the two new variants from UK and South Africa:

21:00 | Dr. Maria Van Kerkhove:

“So, at the same time, there was another variant that was identified in South Africa, and it has one of the same mutations, this 501Y mutation but a different variant. They have arisen at the same time but it is a separate variant.”
 
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My 84 year old cousin described her 2020 travels in her annual letter. She lives on the east coast and has a summer cottage in New England. She traveled there twice by car for a couple of weeks each time, when I happen to know the state required a two week quarantine. She never mentioned quarantining. Friends went with her the first time and family visited the second time. She visited quite a few friends on the way home and attended a highschool reunion! She is currently taking an art class locally. SMH

She’s very smart, has a masters degree in biology and is definitely not a Covid-hoaxer or anti-masker. Am I missing something here? I’m ten years younger and I’ve been holed up since March and will continue even after getting the vaccine until Dr Fauci says I can emerge safely. Even though I believe my choices are wise, I feel a little envious of what seems to be her YOLO casual attitude. We aren’t close enough to discuss it, so it will remain a mystery.
 
10ofRods said:
Today, I read that it's the nanoparticles in the Pfizer vaccine that they think are triggering this effect. So far, no such effect noted for Moderna.

Suspicions grow that nanoparticles in Pfizer’s COVID-19 vaccine trigger rare allergic reactions | Science | AAAS
Click to expand...

Some initial notes from the beginning of the article (before getting to this “nanoparticles” business):

“Severe allergy-like reactions in at least eight people who received the COVID-19 vaccine produced by Pfizer and BioNTech over the past 2 weeks may be due to a compound in the packaging of the messenger RNA (mRNA) that forms the vaccine’s main ingredient, scientists say. A similar mRNA vaccine developed by Moderna, which was authorized for emergency use in the United States on Friday, also contains the compound, polyethylene glycol (PEG).

PEG has never been used before in an approved vaccine, but it is found in many drugs that have occasionally triggered anaphylaxis—a potentially life-threatening reaction that can cause rashes, a plummeting blood pressure, shortness of breath, and a fast heartbeat. Some allergists and immunologists believe a small number of people previously exposed to PEG may have high levels of antibodies against PEG, putting them at risk of an anaphylactic reaction to the vaccine.”

[...]

“Anaphylactic reactions can occur with any vaccine, but are usually extremely rare—about one per 1 million doses. As of 19 December, the United States had seen six cases of anaphylaxis among 272,001 people who received the COVID-19 vaccine, according to a recent presentation by Thomas Clark of the U.S. Centers for Disease Control and Prevention (CDC); the United Kingdom has recorded two. Because the Pfizer and Moderna mRNA vaccines use a new platform, the reactions call for careful scrutiny, says Elizabeth Phillips, a drug hypersensitivity researcher at Vanderbilt University Medical Center who attended an NIAID meeting on 16 December. “This is new.”

News reports about the allergic reactions have already created anxiety. “Patients with severe allergies in the US are getting nervous about the possibility that they may not be able to get vaccinated, at least with those two
vaccines,” Togias wrote in an invitation to meeting participants. “Allergies in general are so common in the population that this could create a resistance against the vaccines in the population,” adds Janos Szebeni, an immunologist at Semmelweis University in Budapest, Hungary, who has long studied hypersensitivity reactions to PEG and who also attended the 16 December gathering.

Scientists who believe PEG may be the culprit stress that vaccination should continue. “We need to get vaccinated,” Phillips says. “We need to try and curtail this pandemic.” But more data are urgently needed, she adds: “These next couple of weeks in the U.S. are going to be extremely important for defining what to do next.””

—

Also referenced in above article:

Risk of anaphylaxis after vaccination in children and adults

—

Here is the CDC report referenced above:

Anaphylaxis Following m-RNA COVID-19 Vaccine Receipt
Thomas Clark, MD, MPH December 19, 2020

—

UK Government Press Release linked above:

Press release
Confirmation of guidance to vaccination centres on managing allergic reactions following COVID-19 vaccination with the Pfizer/BioNTech vaccine
Statement by Dr June Raine, Chief Executive of the Medicines and Healthcare products Regulatory Agency on the guidance to vaccination centres on managing allergic reactions following COVID-19 vaccination with the Pfizer/BioNTech vaccine

Published 9 December 2020
 
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Lilibet said:
My 84 year old cousin described her 2020 travels in her annual letter. She lives on the east coast and has a summer cottage in New England. She traveled there twice by car for a couple of weeks each time, when I happen to know the state required a two week quarantine. She never mentioned quarantining. Friends went with her the first time and family visited the second time. She visited quite a few friends on the way home and attended a highschool reunion! She is currently taking an art class locally. SMH

She’s very smart, has a masters degree in biology and is definitely not a Covid-hoaxer or anti-masker. Am I missing something here? I’m ten years younger and I’ve been holed up since March and will continue even after getting the vaccine until Dr Fauci says I can emerge safely. Even though I believe my choices are wise, I feel a little envious of what seems to be her YOLO casual attitude. We aren’t close enough to discuss it, so it will remain a mystery.
Click to expand...
Until the shock of my aunt dying, I think my mum was also conflicted by a touch of YOLO. Like yourself Lilibet, my parents have stayed home since March. Her sister on the other hand has continued with nair and nail appointments, visits from grandchildren, lunches out with my uncle. Then my aunt died and my mum absolutely realised they are doing the best thing. It is also hitting hard that they are not going to the funeral (postponed btw as someone in my cousin's immediate family has now tested positive).

Another aunt though, on my dad's side, is IMO behaving absolutely recklessly. She is 79 and lives alone. She takes taxis everywhere - food shopping, chemist (she would easily have both food and prescriptions delivered if she wanted to). She "had" to have her nails done before visiting a friend in his care home. The latest drama is that she "needs" to see her great grandchildren at Christmas. Not only is this against our Tier rules, but her granddaughter does not want it, she's trying to protect her children from unnecessary contact. It must be terrible living alone and isolated if you are an extrovert, but with the situation here at the moment she's literally playing Russian roulette.
 
COVID-19: England bans travel from South Africa after two cases of 'more transmissible' variant

England has banned travel from South Africa after two cases of a new "more transmissible" COVID-19 variant linked to the country were found in the UK.

Health Secretary Matt Hancock warned the "highly concerning" new variant is believed to be more transmissible than the mutant strain that resulted in the creation of the new Tier 4 restrictions.

The two cases are contacts of people who travelled from South Africa over the last few weeks, Mr Hancock said at a Downing Street news conference.

Those with the new variant, and contacts of them, are quarantining.
 
California:

Gov. Gavin Newsom will enter quarantine again after coronavirus exposure
Dec. 20, 2020

—

Supermarkets in L.A. County see unprecedented coronavirus infection rates
Dec. 20, 2020

““Every single one of my managers has COVID — one of them is really sick,” said Hughes, 61. “It’s stressful, but I just tell myself: ‘You gotta go. You gotta work.’”

[...]

““The number of outbreaks is extraordinary — we’ve just never had this many,” said Dr. Jeffrey Gunzenhauser, L.A. County chief medical officer.

Of the six outbreaks at Food 4 Less locations reported to the county during the pandemic, three — including the one at Hughes’ store — were first logged this month, linked to the current surge, according to a Times analysis of outbreaks posted on the county’s website. An outbreak is defined as three or more cases among staff in a 14-day period.

There have also been new outbreaks reported in December at three Trader Joe’s locations, two Whole Foods Market stores, three Sprouts Farmers Market branches and several smaller grocery chains, county and company records show.“

[...]

““Everything becomes more dangerous than it was last month — every type of activity,” said Dr. Kirsten Bibbins-Domingo, an epidemiologist at UC San Francisco. “When 1 in 80 people in L.A. are infected, even if you’re just going to the grocery store … there’s a higher chance today than there was two weeks ago that you’ll be exposed to COVID-19.”“

[...]

“The county health department has fined more than 200 businesses since August for violating COVID-19 precautions, none of which have been grocery stores, according to county records.“

[...]

“Other food retailers that reported outbreaks recently included Gelson’s Markets in Marina del Rey, Super A Foods in Glassell Park and Superior Grocers in City of Industry. Three outbreaks at Vallarta Supermarkets were reported this month. Five of the 10 outbreaks at L.A. County Target locations since the pandemic began were reported in December.“

—

Covid-19 outbreaks reported at SoCal grocery stores

Grocery stores in Los Angeles County seeing rising number of COVID-19 outbreaks

“Using data from the Department of Public Health, the Los Angeles Times reported that there are 490 businesses under investigation for outbreaks, compared with 173 a month ago.”

[...]

“An analysis by the L.A. Times also found a jump in outbreaks this month at other essential businesses that have stayed open during the pandemic, including banks, pharmacies and hardware stores.“”
—

Morning Brief: COVID-19 Outbreaks Are Exploding at Local Grocery Stores

“» Outbreaks of COVID-19 at local grocery stores are exploding, with nearly every chain reporting multiple stores that have become hotspots. “I worry every day that I’m going to bring this virus home to my grandsons that live with me,” said Barbara Hughes, who has been a Food 4 Less cashier for 26 years.” [Los Angeles Times]
 
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Covid: Baby girl becomes Scotland's youngest death

A child under the age of one has died with Covid-19 in Scotland, official figures show.

The death of the baby girl is the youngest Covid death in Scotland and the only one under the age of 15.

National Records of Scotland (NRS) counts all death certificates that mention Covid-19, even if the person has not been tested for the virus.

The baby's death was registered between 14 and 20 December along with 202 others that week.
 
astheworldfallsdown said:
Covid: Baby girl becomes Scotland's youngest death

A child under the age of one has died with Covid-19 in Scotland, official figures show.

The death of the baby girl is the youngest Covid death in Scotland and the only one under the age of 15.

National Records of Scotland (NRS) counts all death certificates that mention Covid-19, even if the person has not been tested for the virus.

The baby's death was registered between 14 and 20 December along with 202 others that week.
Click to expand...

I wonder if she developed MIS-C.
 
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astheworldfallsdown said:
Covid: Baby girl becomes Scotland's youngest death

A child under the age of one has died with Covid-19 in Scotland, official figures show.

The death of the baby girl is the youngest Covid death in Scotland and the only one under the age of 15.

National Records of Scotland (NRS) counts all death certificates that mention Covid-19, even if the person has not been tested for the virus.

The baby's death was registered between 14 and 20 December along with 202 others that week.
Click to expand...
That is awful.
 
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