Coronavirus, The End of the Year Edition

 Coronavirus, The End of the Year Edition

By the Numbers

 

The Numbers:

The Omicron surge has been breathtaking.  From being identified to dominance in the US in under 5 weeks.

On 12/29, there were a mind numbing 465,082 new cases in the US.  Shattering the previous record of 312,939 the day before, which beat the previous the all time high logged in on 1/8/21 and is growing by 7.3% per day for the last week.  It brings the estimated number of cases to 3.9 million coming into the New Year.  

 

Pennsylvania broke its record new case number of  13,318 (12/11/2020) by over 4,000 yesterday.  And New York shattered its previous 1 day record of 18,664 last January with 43,131 Tuesday, and again with 67,226 yesterday.

 

There is no sugar coating this.

 

Omicron update:

Just hours after my previous posting.  Significant information from South Africa.

1) Full but not boosted vaccination with Pfizer drops protection down to 33% for Omicron compared to closer to 60%+ vs Delta and over 80% vs Alpha, Beta, or ancestral (IIRC), but protection vs hospitalization appears to be a 70% reduction vs unvaccinated against Omicron.

2)Those who previously contracted Delta appear to have a 40% risk of reinfections, 60% for Beta, and older/original strain 73%.

3) Adults seem to have a 29% lower risk of hospitalization, particularly if a reinfection.

4) Children appear 20% more likely to require hospitalization.  While most experience 3 days of cold like symptoms, others are hospitalized for bronchitis and pneumonia.

Why is Omicron so infectious?:
One study by the Ragon Institute, demonstrates that Omicron replicates 70 times faster then Delta in the bronchial tubes.  That alone would explain how it is out competing Delta.  While in the broncs, it is much easier spread from patient to patient with each breath.

Why does Omicron seem less dangerous?:

In the lungs, Omicron seems to replicate only 1/10th as fast as Delta.  So it seems to set up well in the door way (the bronchial tubes), but doesn't penetrate deeply into the major systems like lungs, heart, kidneys.

If you have been exposed:

I have had my first encounter with someone who tested positive for Covid.  Despite putting out these missives bi-weekly, my experience with Covid has been more theoretical than real.  

First, thank the person that called you that you have been exposed.  While some regard this as a common courtesy and obligatory, others will avoid the unpleasantness and hope for the best.  Give them some positive reinforcement.

In my case, the person that called was not the infected contact, but was also contacted by him/her.

Testing false positives are rare.  False negatives are more common.  If you test too soon, there may not be enough pathogens to be detected. 

 

The best time to test is two or three days after exposure to someone who has the virus.  In my case it was 4 days on notification, 5 to testing.  My test was negative, so I dodged the bullet.

 

So if you were exposed yesterday, you can make arrangements for a tomorrow or the day after, but today is too soon.

With the new wave of Omicron, testing centers are overwhelmed.  Doctors office's are refusing patients without a current test,  Take your temperature, self isolate and be patient.  

If you are a veteran, the VA seems to have capacity to test right now.  

 

The day after my test, my sister called me to say that she might have been exposed the previous week as well.  I didn't have contact with her directly, but had a 90 minute conversation with her husband.  

 

So 5 people contacted in total, and two possible Covid infections.

 

In the end, it is just probability. 

The year in review.

I decided to look at last years final missive and see what we got right, and what went wrong.

The drug Bamlanivimab, a monoclonal antibody drug was announced and shown to be effective.  This specific drug had been approved, then later revoked in the US.  A recent test on the drug was canceled in Denmark when it's efficacy against placebo was statistically irrelevant.

 

But other monoclonal drugs are effective against Covid, but this is the most expensive way to treat the virus.  Several shots at 3-5,000, and are effective for about a month.

 

Last Christmas Eve, there were around 5 million active cases.   The highest daily new case count was 254,000 on December 18, 2020.  The high for that surge, which was the Alpha Variant, was 301,000 on Jan 8.

The vaccine rollout had started, and the production schedule was tracking for 190 million Americans vaccinated by June.  We hit 135 million partially and fully vaccinated on May 25, 2021.  Currently we are at 240.

Anaphylaxis from the Covid vaccine was 1 in a million with the test group, but was about 10 in a million in real life.  Anti-vaxers will bring this up, ignoring that Covid will kill 2,500 per million.

Long Term Impact of Covid damage still is an under studied effect.  Last year vascular damage was between 35% and 70% of patients examined. The current number is thought to be 30%.  But we won't really know until much later.

 

“Herd Immunity” was estimated at 80% of the population.  For the USA, that is 265 Million.  We are still not there yet. 

 

It would be amusing if it wasn't so wrong:

A conspiracy group held a convention, "ReAwaken America", on Dec 10th.  This large number of this mostly unvaccinated group started having fever, chest pain, shortness of breath, headache, fatigue.  

Since Covid is just a conspiracy put out by the pharmaceutical companies, with the collusion of every government and medical system in the world, their logical conclusion is that they were subjected to an anthrax attack.

 

You can't make this stuff up. 

 

Update, Jan 3, 2022.  One of the infected members, Doug Kuzma, after 5 days of being ill, replied to a suggestion that he have a Covid test with, "no way"!  It was just his chronic bronchitis, or maybe anthrax. But either way, there was a photo of himself with a container of Ivermectin.  Is Ivermectin a proper treatment for anthrax?

He was found unconscious at his home on Christmas Eve, was hospitalized, and died 10 days later.

What went wrong?:

Obviously, the strength of the misinformation of the anti vaccine people was underestimated.  It was thought they would be ploughed under by the realities of the situation to the anti-vaxer's natural 3-5% of the population and be irrelevant.

 

No one saw that the pundits of a major political party would attack the efforts to save lives as contrary to all that was good and decent in their world view.

 

But the truth is, it's something else.  Its not the Republican banner wavers, though that is how it manifests itself in the USA (vaccination rate 73%).  In the UK (vaccination rate 76%), they have the same issues.  Often with the same arguments.  But this was largely the Tory party, their equivalent of the Republicans, and they took their cue from Boris Johnson, who's politics and attitudes is so close to Trump as to not matter.  But to the rest of the world, American foreign policy is just UK foreign policy extended.   In short, one is just like another.  

But what about France (vaccination rate 78%)?  They are having riots over vaccinations and restrictions.  And they were practically ground zero in 2020.  Germany (vaccination rate 71%) also has a strong resistance to the remaining people being vaccinated.  Their mantra seems to be "Vaccinated, recovered or dead."

All western nations, but with different cultures.  All having trouble getting over the critical threshold percentage needed to put the brakes on Covid.  

Many anti-vaxers are fed arguments attacking the science. They will listen to "Dave" on the internet, vice take their information from actual scientists who are authorities on the work.

 

They will point out that the science is inconsistent, and  therefore "Dave" is right, and none of it can be trusted.

But they will latch on studies that have failed the peer review process or haven't been replicated that reflect their world view.  Like one study showing efficacy of Ivermectin, which failed peer review, and ignored 50 other studies that showed no efficacy.  They attribute it to the conspiracy and ignore the evidence.

 

And while it is considered amoral to experiment on humans, Brazil experimented with Ivermectin on a country wide scale, mixing it with HCQ, and some vitamins and calling it "First Response", and not allowing the vaccines to be imported.  The result is the second highest body count in the world.  Sad to say, but that is also science. 

 

So we have a woman preaching that if God meant us to cover our faces, he would have given us a mask, reading from her prepared statement required her to have on her reading glasses.

I think the core of problem is a secondary school education issue.  Somehow the sciences are being reduced, and people just don't know how the scientific method works.  

They argue that the scientists are biased, have an agenda, or on a payroll, or any number of human behavior issues.  And they are absolutely correct.

People are imperfect.  That is why there is the scientific method.

If you do a study, or produce an extraordinary result in an experiment.  You have to write it all up, and subject it scrutiny.  Other scientists may have an opposing agenda, and will want to destroy it.  They will tear into the documentation and do their best.   If they succeed, the experiment will have to be redone, addressing any issues.  If they fail, we have a conclusion.  Other scientists that don't have a dog in the fight will make popcorn and read the results and come to a consensus.

It's called an adversarial relationship.  It is how science works.  It's also how the court system works.  It's how the US Government works.  It's ugly and brutal.  But it gets at the facts of the matter.  

When you read a headline that "Scientists disagree on <this or that issue>".  This is ALWAYS true.  

When someone says, "Well, not all of them believe that."  This is also ALWAYS true.  But then, there are people that believe in flat earth.  

There are always people that will not believe what is right in front of them.  But it is a failure of the education system when the percentage is so high.  In Pennsylvania, that percentage seems to be 40%.  Plenty of fertile ground for the anti-vax agenda, and unfortunately, wood for the Covid fire.

I'll put this out as an analogy.  Galileo and the Pope.  Which could be defined as new ideas vs. the status quo.  Or the scientific method vs. ignorance.  Galileo didn't just do experiments, he wrote them down, and subjected them to scrutiny, and replication.  And his observations took root in countries beyond the Papal reach.  

 

The church had to dig in it's heels because if the Catholic church, which was considered infallible, was wrong about heliocentric model of the solar system, then what else could it be wrong about?   Ignorance won out on the short run, but the scientific method on the long run.

 

This came up again with evolution.  Missing species had been in evidence for centuries.  They couldn't have died out, because that would mean God created imperfect things, which means God himself was imperfect.  So it was thought extinct species were just, "Elsewhere".  But by the late 1800's, it was obvious that the Stegosaurus wasn't hiding behind the arborvitae.  160 years later, we still have many who deny it, which is 'ok', but some actively point to fraudulent evidence "demonstrating" that man and dinosaurs coexisted at one time.

A final note:

Donald Trump, while being interviewed by Bill O'Reilly, announced his vaccination status as vaccinated and boosted.  Bill O'Reilly also made the same announcement and they both recommended everyone get the jab.  He even noted that most of the Covid hospitalized were from the unvaccinated.  They were booed from the audience.

In a later interview, Bill O'Reilly basically said the conspiracy nuts were in the stratosphere with their theories and they were wrong.

For example a Ms Candace Owens, a journalism school drop out, how claims that Trumps vocal support for vaccinations is based on his inability to use the internet to do, "proper", research.  She stated that, "He only knows what is written down, or read to him."  

 

Failing to notice that for a while, those writings were from the most prominent virologists in the land.  Doctors that actually completed college, and then some.  Then went on to spend a life time studying the medical sciences.

So Ms Owens, what qualifies you to "do" research?  Based on what I have seen of your writing, you didn't even pass, like, proper sentence structure.  To quote her, 'People oftentimes forget that, like, how old Trump is,'.  Has she read even one formal research paper on vaccine efficacy?  Or is she just repeating echo chambers?  

And you all know I would rather amputate a significant toe rather than say something good about our dear departed leader.

But he is right about getting vaccinated.

Coronavirus, The Mid December Edition

 Coronavirus, The Mid December Edition

By the Numbers

 

The Numbers:

The number of new cases continue to grow.   For the week of 12/3 to 12/10, the number daily new cases increased about 9% per day, then has settled in to about 1.5% per day for the following week.   Bringing the total number of calculated cases to over 2.2 million cases nation wide.

In Pennsylvania, the average daily new cases continues to grow, 8,556 per day last week, up from 7,423 the week before, and 5,626 before that.

 

Omicron Highlights:

Since information on Omicron is coming in fast and furious these last two weeks, my missive was updated continuously and was in the form of stream of consciousness reporting.  So I split it in two, and you can read the ramblings if you want to.

Is Omicron more infectious?  Yes.   Research released by the UK, not yet peer reviewed, that Omicron will be the dominant strain in the UK by late December.  As of 12/13, Omicron represents 40% of all new cases in London.  In the US, Omicron is already 3% of the sequenced cases, and 13% of the new cases in NY and NJ.  For a comparison, previous variants, Mu and Lambda, never hit .1% in regions where they were found.

Is Omicron deadlier?  No, so far, there has been only 1 death attributed to Omicron out of 2,500 known cases in the UK.  And no deaths in South Africa against 78,000 cases.

Does vaccination help against Omicron?  Yes, initially the Astra Zenica and Pfizer vaccines does well for about 3 months, afterwards, the effectiveness drops down to the 35-40% range.  But vaccinations, even older ones have dramatically reduced the terms of hospitalization to 35% of that of previous variants. Boosters help bring it back to 75% effectiveness.  See diagram below.

Due to Omicron, the UK Recommendations for boosters is now 3 months vice 6 months.

Does Natural Immunity help against Omicron?  No. The omicron variant of COVID-19 appears to have a "substantial ability" to evade natural immunity acquired from past COVID-19 infections.

 

Does Omicron provide natural immunity against Delta?  We don't know. It is too soon to tell.

Does Omicron cause "Long Covid"?  We don't know. It is too soon to tell.

 

Omicron Ramblings:

The first case of the Omicron variant  detected in the US is a Minnesota man  who attended an anime convention November 19-21.  Since then, half of his group of 30 have come down with Covid, but Omicron itself has not been verified in the rest of the group, but a relative of one of his group, a man in his 60's, was later infected with the Omicron variant.  He had been vaccinated and boostered, and suffered only mild symptoms.  See here.

This incident predates South Africa's announcement of Omicron's existence, proving that Omicron was world wide before it was even detected. 

 

In my last report I stated that Omicron has gone from newly detected to dominating the case numbers in major regions of South Africa.  What I could not find out then, was if the variant  Beta, formally known as "South Africa", was still the dominant strain in SA.  Since then, I have finally had evidence that Beta had succumbed to Delta in SA like everywhere else.   

Why this is important is this.  If Omicron is out performing its parent Beta, that is one thing, but Delta is another.  I am writing this only a couple of days after my last missive, and it seems like Omicron has legs.

 

The latest surge in South Africa has been dramatic.  On Nov 1, the number of daily new cases was 350.  On December 16, it was 26,000.  Most of them have been the new Omicron variant.  But so far, the anecdotal reports are that it is less dangerous.  

South African Scientists have preliminary evidence that Omicron spreads more than twice as quickly as the delta variant in that country.   And "this new variant is more capable of bypassing antibodies generated by a prior infection than previous variants".  Which means, any "Natural" immunity is now out the window.

Pfizer lab studies show that three doses of their vaccine is able to provide adequate protection from Omicron.  Statistics in the wild will need time to be acquired.  

In Denmark, over 1,280 cases of Omicron have been detected, about 5% of the total number of Covid cases.

19% of those cases were among those that have booster shots.

But little or no deaths have been attributed to this variant.  

A South African study of 78,000 Omicron cases found the risk of hospitalization is 29 per cent lower compared with the original Wuhan strain, and 23 per cent lower than Delta, with vaccines holding up well.  ICU requirements in SA is 5% the number of cases, vice 22% for delta.  That that seems high to me.  Does it mean 5 and 22 of total cases, or just those hospitalized?  I am thinking hospitalized.

An anecdotal story about Omicrons ability to spread.  November 27, there was a Christmas luncheon held for some 150 students in Viborg, Denmark.   64 were later diagnosed with Omicron.  How many people came in with Omicron is unknown.

I'm thinking of getting this tattooed on my shot arm, any thoughts?

Coronavirus, The Early December Edition

Coronavirus, The Early December Edition

By the Numbers

The Numbers: The day after my last report, the rate of daily new cases began surging. From increasing .6% per day to 3.5% per day. The doubling rate for .6% is 4 months. The doubling rate of 3.5% is just 3 weeks.

There is a statistical drop in the increases during the 5 days around Thanksgiving. The actual numbers wouldn't have dropped, but the accounting of them has. The Tuesday-Thursday numbers will probably show a commensurate jump.

Who are the infected?

The infected are still dominated by the 50+ crowd. See this image put out by Minnesota Health Services.

The hospitalization rate for the unvaccinated 50+ crowd is over 400 per 100,000. For the vaccinated, 50+ crowd, the hospitalization rate is about 20 per 100,000. 

 

This is 20-1, and in keeping with very numerous similar reports around the country I have been seeing since August, that the unvaccinated represent 95% of the hospitalizations for Covid.

Another analysis by the New York Times is they are from counties with low vaccination rates rates as well. The same counties also happened to have voted strongly Republican in the last election. See Here...

These lines represent accumulative deaths for the year to date, not a snapshot of that point in time. So in January, they were very closely grouped, but as the vaccines took affect, the spread widened.

Mentioned in the article, that the daily rate difference is growing.

I'll copy past the article snippet as my attempts to paraphrase is proving insufficient to explain properly:

"The gap in Covid’s death toll between red and blue America has grown faster over the past month than at any previous point.

In October, 25 out of every 100,000 residents of heavily Trump counties died from Covid, more than three times higher than the rate in heavily Biden counties (7.8 per 100,000). October was the fifth consecutive month that the percentage gap between the death rates in Trump counties and Biden counties widened." (Emphasis mine)

Pfizer Covid Vaccine, 12-15's Year Olds

The Pfizer test on their vaccine against 12-15 year olds was 2,200 people. Of the 1,100 vaccinated, zero cases of Covid was reported. The Placebo group of 1,100 had 30 cases.

Misuse of the Vaccine Adverse Event Reporting System

The Vaccine Adverse Event Reporting System, hereafter referred to as VAERS, is a national early warning system to detect possible safety problems in U.S.-licensed vaccines. It is being used by anti-vaxers to prove that the Covid vaccines are more dangerous than the disease.

The thing is, VAERS, is not statistical science. But more of an open source reporting system. In short, anyone can make a submission, some of the obviously false. The CDC does it's best to remove false claims, but for Covid reports alone this year, over 225,000 make this a daunting task.

But anti-vax attempts to "Game the system" is not the real problem,. It is just a blip in the numbers. The real problem is looking at the VAERS reports alone and deriving statistical conclusion. The system was meant as a trip wire for detecting early warning problems, and not a complete statistic outlook.

So when a popular anti-vax personality reported in May, 2021, that over 4,000 fully vaccinated people have died since taking the vaccine, as reported in VAERS, he was totally correct. But he was also totally misleading. What VAERS does not report is that reaction to the vaccine was a cause of death in all those 4,000.

At that point, 125 million Americans had been vaccinated, about 50%. Most of them were 50 years old or older. So out of 125 million, how many would be expected to die in a 5 month period of time? Roughly 700,000.See here.

The only surprise here is that only 4,000 were reported having been vaccinated. 

Followup note. Listening to a podcast, "More or Less: Behind the Statistics", based in the UK. It was reported using statistics accumulated by the Office for National Statistics, ONS, that deaths for vaccinated was higher than unvaccinated. And it was another case of one data point on the chart being misrepresented to the whole of the chart. For details, listen to their podcast episode, "Simpson's Paradox, How to make vaccinated death figures misleading."

It has to do with disproportionate group sizes where the age group, 10-59, where the 55+ was disproportionately, by a factor of 80 times, affecting the group as a whole.

A analog would be a statistic that people that saw original Ghostbusters in the theater, are far more likely to have died than those that saw the latest remake. And drawing a conclusion that the older movie was killing more people.

The point is, the anti-vaccine refusenicks, are international, and will stoop to any level to justify their position, which is really just "I don't want to."

Omicron.

The latest variant of interest has assigned the Greek letter, Omicron. Since it was first reported earlier last week, I have seen articles that are almost copy paste's of previous variants, and others with often contradictory information.

But the the fact that B.1.1.529 (B means it is a variant of the South Africa variant) has been assigned a letter implies the powers-that-be are concerned.

What do we know? Extracted from NPR's article last week.

In areas of South Africa where it was first detected, Omicron has gone from extremely rare to dominating the number of cases in Pretoria in about 4 weeks. Omicron is now the leading cause in the current outbreak in South Africa.

The variant has been detected in just about every major country, including the US.

Is it a vaccine breaker? WE...DON'T...KNOW... Anything you read otherwise, is hyperbole. About 25% of the adult population has been vaccinated in SA, so there is a lot of potential unvaccinated population to spread in.

Is it deadlier? More infectious? WE...DON'T...KNOW... I don't have statistics for how dominant "South Africa" was in South Africa, nor do we know if Omicron will out pace Delta in the rest of the world.

The CEO of Moderna believes that existing vaccines will be "much less effective" dealing with Omicron. And I have to assume he is talking to the experts in the field, as a number of them work for him.

FYI, South Africa, like America and Europe, has had a serious drop off rate in their vaccination numbers. Their goal was 300,000 per day, and got close to achieving that goal in August since large shipments of the vaccine arrived, but has since dropped in half starting in September.

In two weeks, we will know a lot more.