I hope to Hell I was wrong about China

From the South China Morning Post — 9:52pm, 15 Jan, 2022

“The Chinese capital reported its first community case of the Omicron coronavirus variant on Saturday, with local and imported infections of the strain now detected in about half of the country’s provinces and municipalities.”

https://www.scmp.com/news/china/politics/article/3163525/china-braces-omicron-variant-extends-its-reach-and-lunar-new-

If true, containment, quarantine, lockdowns and isolation are hopeless.  The quote implies that they’ve already failed.

I find this very worrisome for reasons listed in a post 12 December 2021, a copy of which is below.

The short answer is that the mainland Chinese are immunologic virgins to exposure to the variants of the pandemic virus.  Hopefully their vaccines will work better against omicron than those of the west, but there is no reason to think they will.

Is China following a Smokey the Bear policy on the pandemic?

China is following a prevent pandemic virus infection policy, just as Smokey the Bear followed a prevent forrest fires policy.  The latter didn’t work out well, as although fires were prevented for a while. However, when fires did occur, they were much much worse than the smaller ones Smokey prevented.  There was much more tinder and stuff to burn.

Actually Smokey has changed his tune slightly.

https://en.wikipedia.org/wiki/Smokey_Bear  SmokeyBear.com’s current site has a section on “Benefits of Fire” that includes this information: “Fire managers can reintroduce fire into fire-dependent ecosystems with prescribed fire. Under specific, controlled conditions, the beneficial effects of natural fire can be recreated, fuel buildup can be reduced, and we can prevent the catastrophic losses of uncontrolled, unwanted wildfire.”

Revision 14 December 2021 — China’s policy of prevention has resulted in a Chinese population which has been vaccinated using two killed virus vaccines (Sinopharm, Coronavac).  They have not had any natural infections with the virus (aside from the original cases) as far as we know given what China has allowed out.

Infection with the virus itself exposes you to all its proteins, with your immune system responding to all of them.   Western vaccines are just to the spike protein.

It tends to be forgotten that moist cases of pandemic viral infection are asymptomatic.

Given 800K deaths  from COVID19  in the USA, how can I possibly say this is good. Here’s how :>

If you had an infection with the virus, you develop antibodies.  Nowadays, everyone who is vaccinated has antibodies so there is no point in testing for them, but what were things like in the days before vaccines?

The following is from a post July/2020.

https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html–https://www.cnbc.com/2020/04/23/new-york-antibody-study-estimates-13point9percent-of-residents-have-had-the-coronavirus-cuomo-says.html.

New York State  randomly tested 3,000 people at grocery stores and shopping locations across 19 counties in 40 localities to see if they had the antibodies to fight the coronavirus, indicating they have had the virus and recovered from it. With more than 19.4 million people residents, according to U.S. Census data, the preliminary results imply that at least 2.7 million New Yorkers have been infected with Covid-19.They weren’t all hospitalized.

Here’s some work the same month from Queens — https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html

At a clinic in Corona, a working-class neighborhood in Queens, more than 68 percent of people tested positive for antibodies to the new coronavirus. At another clinic in Jackson Heights, Queens, that number was 56 percent. But at a clinic in Cobble Hill, a mostly white and wealthy neighborhood in Brooklyn, only 13 percent of people tested positive for antibodies.

So the disease has already to spread to half the population in some neighborhoods in Queens. If even 10% of them were sick that would have been 140,000 hospitalizations.  They didn’t happen.

OK, so a lot more people were infected than got sick.  Why is this good?

Enter the omicron variant of the pandemic virus.  It can evade the antibodies produced by all the current vaccines (in the West — protection against the Chinese killed viral vaccines CoronaVac and Sinopharm isn’t known yet).   Yet omicron doesn’t appear to produce severe disease. Thus far…

 

The CDC in the past week said of the 40+ omicron cases it knows about (there certainly are more out there, and more to come), there was one hospitalization (for two days) and no deaths.

Here is Dr. Fauci 12 December 2021 — “We’re getting anecdotal information … not necessarily confirmed yet, that the level of severity appears to be maybe a bit less than in the Delta. But there are a lot of confounding issues that it may be due to the underlying protection in the community due to prior infections,”

Source — https://nypost.com/2021/12/12/omicron-appears-to-evade-some-protection-from-covid-vaccines/

So the Chinese population may be sitting ducks for omicron having been given vaccines (Sinopharm, Coronavac) of unknown potency against omicron.  If their statistics are true there has been little or no natural infection with the pandemic virus in the Chinese population (which Fauci has just implicated is protective),.  Given that I have a son, daughter in law and two grandkids living in Hong Kong, I find this extremely disconcerting.

The pandemic of the ‘fully vaccinated’

At the end of 12 January ’22 the state of Massachusetts had 3,180 COVID19 patients in hospital.  484 were in the ICU and 278 were on respirators.  Of those 3,180, some 1,005 were ‘fully vaccinated’.  — https://www.mass.gov/info-details/covid-19-response-reporting#covid-19-interactive-data-dashboard-

Addendum 15 Jan: Thanks to MStriker for picking up the error.  1,005 above should be 1505, giving 49%.

That’s nearly 50% of the hospitalized.  This,  in Massachusetts where we believe in Science.  We’re not talking about the toothless peasantry of West Virginia.  The fully vaccinated are serious and important people; news anchors, members of congress, white house staff, not the unvaccinated riffraff we’ve heard about.  What are the faithful believers in Science of Massachusetts to do? ,

If this sounds like Schadenfreude it is.  I’ve listened and read plenty of it in the press in the past two years, with much gloating over the deaths of the unvaccinated.   .  These people died and snarkery (such as the above) is inappropriate and cruel. So let those who formerly thought they were safe worry a little (including me) and realize that science is never settled.

What can be done to restore the faith?  It would certainly be of interest to know the percentage of the fully vaccinated in the ICU or on respirators.  This might actually be evidence of some protective effect of the vaccines.

This data is certainly known to the department of health.

Also, the definition of fully vaccinated can be found (with some difficulty) on their website.  It is clearly outdated e.g. two shorts of Pfizer or the other vaccine longer than 14 days ago.  There is nothing in the definition about boosters.  The definition goes back to September 2021.

I’m sure that in the charts of all 3,180 hospitalized COVID19 patients, the presence and time of  booster administration is noted.  So the State Department has in hand evidence for the efficacy/nonefficacy of boosters, to prevent hospitalization, and when in hospital to prevent serious complications of COVID19.  This should be released immediately.

Sometimes your licked before you’ve even started

The first issue of Neuron for 2022 got off to a rather depressing start, with two papers stating that the die was cast before you leave the uterus.

The first concerned Huntington’s chorea a hereditary movement disorder which doesn’t begin for decades after birth (like many hereditary disorders).  Or does it?

Well over 10,000 papers have been written to figure out why mutations in the huntingtin protein produces neurodegeneration, primarily in a small set of neurons deep in the brain.

Now that we know the genetic cause, it is possible to study people with the mutation long before they get sick.  One finding is a thin tract of axons connecting the two hemispheres (the corpus callosum).

So a transgenic mouse was created with a typical huntingtin mutation (111 glutamines in a row instead of the normal 7 for the mouse).  Even in utero axons forming the corpus callosum were shorter and fewer.  This was due to defects in bundling of microtubules in the axon growth cone.  It was due to a deficiency not of huntingtin but of a microtubule binding protein called NUMA1 (Nuclear Mitotic Apparatus 1) whose function we thought we knew in the mitotic spindle.  Giving NUMA1 reversed the axonal defect (in tissue culture).   So the problems with Huntington’s chorea go back to fetal life.

Even worse, 4 human fetuses of 13 weeks gestation (presumably aborted because the parents didn’t want a child with the gene, showed also sorts of abnormalities in the developing brain Science vol. 369 pp. 771 – 772, 787 -792 ’20 ].  Read it if you wish, I found it rather creepy.

The second paper is on congenital hydrocephalus [ Neuron vol. 110- pp. 12 – 15 ’22 ].  Several parent child trios were sequenced, and damaging mutations were found in 25% of the probands.  All of them were regulators of neural stem cell fate.  So the ventricles got big (that’s hydrocephalus after all), because there weren’t enough neurons to keep them small.

Even worse, the most consistent macroscopic (e.g. visible) finding in schizophrenia is large ventricles.  Were they doomed from birth?

If that isn’t depressing enough here’s a Supreme Court Justice holding forth on COVID19 in children. “We have over 100,000 children, which we’ve never had before, in serious condition, and many on ventilators” due to the coronavirus.  Presumably the Justice believes in science as many of her party claim.

Who is Gabriel Leung and why you should very much care what he says

From today’s (5 Jan) South China Morning Post (SCMP)

“Fellow government adviser Professor Gabriel Leung, dean of the University of Hong Kong’s faculty of medicine, told a radio programme there were “probably five to 10 invisible transmission chains in the community. It’s a very alarming situation”.

Here is what Dr. Leung had to say almost two years ago to the day in the SCMP of 27 Jan 2020.

“As of a few days ago the virus had been found in 29/31 Chinese provinces. ” and “research shows self-sustaining human-to-human transmission is already happening in all major mainland cities.”

Clearly he was right 2 years ago, and widely ignored in the west.   I thought the US government had people watching China.

There were 38 cases of COVID19 in Hong Kong today.  Some of them have the omicron variant (if not all).

This is very scary as despite immunization with Sinopharm and Coronavac, the Chinese are basically immunologic virgins as they have had little exposure to the pandemic virus (Wuhan excepted).  Hopefully it will work better than the Western vaccines.  As of 4 January 2022 Massachusetts had 2,426 hospitalized cases of COVID19 of which 973 were ‘fully vaccinated’ e.g. 40% of cases– not sure if this means 2 shots or 2 shots plus a booster.  On 21 December we had 1621 cases in hospital and the fully vaccinated accounted for only 29%.  So it’s getting worse here.

For an elaboration of why I think the Chinese are particularly vulnerable to omicron see yesterdays post — https://luysii.wordpress.com/2022/01/04/were-about-to-find-out-just-how-good-the-chinese-vaccines-are-against-omicron/

Addendum 7 January 2022

As of 6 Jan Massachusetts had 2,637 COVID19 cases of which 42% are described as ‘fully vaccinated’.

It looks like Dr. Leung was right (again).  From today’s SCMP

“At least 18 locally transmitted cases have been reported in Hong Kong in recent days and the city is reimposing some of its toughest Covid-19 social-distancing measures.”

https://www.scmp.com/news/china/science/article/3162526/shenzhen-covid-19-cases-lower-hopes-hong-kong-border-reopening?module=perpetual_scroll_1&pgtype=article&campaign=3162526

We’re about to find out just how good the Chinese Vaccines are against omicron

A very disturbing article in the South China Morning Post (SCMP) today — https://www.scmp.com/news/hong-kong/health-environment/article/3162088/coronavirus-hong-kong-reports-first-untraceable?module=storypackage&pgtype=homepage.

First: some background. There has been an outbreak of COVID19 traced to the Moon Palace restaurant  in Kowloon recently.   It began with an aircrew member from Cathay Pacific Airways Ltd., who was subsequently found to be infected with omicron.  He ate lunch there 27 December with his family. . Five other customers later tested positive. Yesterday’s paper said that transmission occurred between the first known case and others not sitting close to each other.  I can’t find that particular article, so this is from memory.

Today’s news is particularly bad, because the current case was acquired within the community (with no obvious contact to an infected person, or time at the restaurant), His virus has two of the mutations typical of omicron (further testing is in progress).

Given how infectious omicron is and the population density of Hong Kong (mask or no mask) omicron is likely to spread widely in Hong Kong (and likely China itself).

You won’t find any schadenfreude here.  I have a son, daughter-in-law and two grandkids living there.  This is why I was able to see that a pandemic was in store 2 years ago –https://luysii.wordpress.com/2020/01/27/what-to-do-about-the-wuhan-flu/

It seems quaint now, but I the reason I was reading the SCMP regularly in 2019 – 2020 was the Hong Kong riots in the summer of 2019 their possible effects on my family.

So why am I concerned presently?  Due to the Chinese attempts at tight control, the majority of the Chinese population  have had no infectious experience with the pandemic virus (aside from Wuhan of course). This is unlike Western populations which have been exposed and symptomatically/asymptomatically infected with various strains of the pandemic virus for nearly two years.  So the Chinese are immunologic virgins as far as omicron is concerned.  We are about to see how protective the vaccines they’ve received (Sinopharm, Coronavac) are against omicron.

 

Hopefully, the Chinese are better protected than we have been by the Pfizer, Moderna, etc. etc vaccines.  As of yesterday,  37% of the 2000 or so COVID19 patients in Massachusetts hospitals are said to be ‘fully vaccinated’ (I’m not sure if this means 3 shots or the original 2).

Addendum 5 Jan ’22 — If you want to see how tenaciously the Chinese are tracing cases in the outbreak in Hong Kong — look at today’s SCMP — https://www.scmp.com/news/hong-kong/health-environment/article/3162190/coronavirus-hong-kongs-fifth-wave-has-already?module=lead_hero_story&pgtype=homepage.

Particularly fascinating is a diagram of the diners and seating arrangements in  the Moon Palace restaurant in Kowloon, the source of one outbreak — they have each confirmed case — the table they were sitting at, the times they were there.  Particularly scary is the 20 meter distance between the index case (an airline stewardess) and one of the infected.

Even scarier is the pronouncement of Gabriel Leung — he’s the MD who said the pandemic was in 31 Chinese cities  in 27 Jan ’21, so anything he says must be taken seriously.  See the link to my post  — https://luysii.wordpress.com/2020/01/27/what-to-do-about-the-wuhan-flu/

“Fellow government adviser Professor Gabriel Leung, dean of the University of Hong Kong’s faculty of medicine, told a radio programme there were “probably five to 10 invisible transmission chains in the community. It’s a very alarming situation”.

Stay tuned.   The article said that there 38 COVID19 cases in Hong Kong — it isn’t clear how many are the omicron variant.

So here’s a repeat of a post written 12 December ’21

Is China following a Smokey the Bear policy on the pandemic?

China is following a prevent pandemic virus infection policy, just as Smokey the Bear followed a prevent forrest fires policy.  The latter didn’t work out well, as although fires were prevented for a while. However, when fires did occur, they were much much worse than the smaller ones Smokey prevented.  There was much more tinder and stuff to burn.

Actually Smokey has changed his tune slightly.

https://en.wikipedia.org/wiki/Smokey_Bear  SmokeyBear.com’s current site has a section on “Benefits of Fire” that includes this information: “Fire managers can reintroduce fire into fire-dependent ecosystems with prescribed fire. Under specific, controlled conditions, the beneficial effects of natural fire can be recreated, fuel buildup can be reduced, and we can prevent the catastrophic losses of uncontrolled, unwanted wildfire.”

Revision 14 December 2021 — China’s policy of prevention has resulted in a Chinese population which has been vaccinated using two killed virus vaccines (Sinopharm, Coronavac).  They have not had any natural infections with the virus (aside from the original cases) as far as we know given what China has allowed out.

Infection with the virus itself exposes you to all its proteins, with your immune system responding to all of them.   Western vaccines are just to the spike protein.

It tends to be forgotten that moist cases of pandemic viral infection are asymptomatic.

Given 800K deaths  from COVID19  in the USA, how can I possibly say this is good. Here’s how :>

If you had an infection with the virus, you develop antibodies.  Nowadays, everyone who is vaccinated has antibodies so there is no point in testing for them, but what were things like in the days before vaccines?

The following is from a post July/2020.

https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html–https://www.cnbc.com/2020/04/23/new-york-antibody-study-estimates-13point9percent-of-residents-have-had-the-coronavirus-cuomo-says.html.

New York State  randomly tested 3,000 people at grocery stores and shopping locations across 19 counties in 40 localities to see if they had the antibodies to fight the coronavirus, indicating they have had the virus and recovered from it. With more than 19.4 million people residents, according to U.S. Census data, the preliminary results imply that at least 2.7 million New Yorkers have been infected with Covid-19.They weren’t all hospitalized.

Here’s some work the same month from Queens — https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html

At a clinic in Corona, a working-class neighborhood in Queens, more than 68 percent of people tested positive for antibodies to the new coronavirus. At another clinic in Jackson Heights, Queens, that number was 56 percent. But at a clinic in Cobble Hill, a mostly white and wealthy neighborhood in Brooklyn, only 13 percent of people tested positive for antibodies.

So the disease has already to spread to half the population in some neighborhoods in Queens. If even 10% of them were sick that would have been 140,000 hospitalizations.  They didn’t happen.

OK, so a lot more people were infected than got sick.  Why is this good?

Enter the omicron variant of the pandemic virus.  It can evade the antibodies produced by all the current vaccines (in the West — protection against the Chinese killed viral vaccines CoronaVac and Sinopharm isn’t known yet).   Yet omicron doesn’t appear to produce severe disease. Thus far…

The CDC in the past week said of the 40+ omicron cases it knows about (there certainly are more out there, and more to come), there was one hospitalization (for two days) and no deaths.

Here is Dr. Fauci 12 December 2021 — “We’re getting anecdotal information … not necessarily confirmed yet, that the level of severity appears to be maybe a bit less than in the Delta. But there are a lot of confounding issues that it may be due to the underlying protection in the community due to prior infections,”

Source — https://nypost.com/2021/12/12/omicron-appears-to-evade-some-protection-from-covid-vaccines/

So the Chinese population may be sitting ducks for omicron having been given vaccines (Sinopharm, Coronavac) of unknown potency against omicron.  If their statistics are true there has been little or no natural infection with the pandemic virus in the Chinese population (which Fauci has just implicated is protective),.  Given that I have a son, daughter in law and two grandkids living in Hong Kong, I find this extremely disconcerting.

The pandemic isn’t ending by a long shot

There’s nothing like data to change your mind.  Just 6 days ago I posted a rather optimistic take on the pandemic which I updated daily (a copy of the most recent  update 31 December ’21 is to be found after the ****

It began like this

I hope I’m not doing what I’ve seen many times, a devoted family hovering over a brain dead patient seeing signs of life when none exists because they desperately want to. Who can blame them?  They’re human beings not rational automatons.  Nonetheless, there are two signs that the pandemic is actually ending.

Well, I was doing exactly that.

The media endlessly  trumpets a surge in ‘casesm but remember a case is defined as finding the virus (in the form of a viral protein or the viral genome) in your respiratory passages.  It does NOT mean you are sick.

Example — a few days it was mentioned that 800 kids were being admitted to the hospital each day in the USA with COVID19.  However every hospital admission gets tested for the virus, and it turns out the kids were being admitted for other childhood problems — fractures, appendicitis etc. etc.  They weren’t sick with COVID19.

So I was encouraged, that despite the surge in ‘cases’ people sick with COVID19 weren’t filling the hospitals.  Hospitalizations and death are the numbers you need to know.

Here is some data from my home state of Massachusetts

Date stands for the date of the report, and includes all data up to and including the previous day — Total cases is really total cases of COVID19 in hospital.

Date       Total cases   Fully vaccinated   % fully vaccinated

21 Dec      1,621            470                       29%

22 Dec     1,632            500                      31%

23 Dec     1,595           503                       31%

So I was pretty optimistic that the pandemic could be peaking when I wrote the post on December 26.

Data proved me wrong

27 Dec       1,636         509                       31%  — essentially the same

28 Dec      1,707           529                       31%

29 Dec       1,711           572                       33%

30 Dec       1,817          631                       35%

31 Dec         1,954        686                       35%

If you’d like to follow the Massachusetts data yourself — here’s a link — https://www.mass.gov/info-details/covid-19-response-reporting#covid-19-interactive-data-dashboard-

It is updated each day (except on weekends) after 5 PM

Ditto for Florida. Here’s where I got the data — https://www.nytimes.com/interactive/2021/us/florida-covid-cases.html

Look at the Florida data carefully.  There are 4 graphs, a big one on the top of ‘cases’ from March 2020 to the present.  You can click on it at any point and see how many new ‘cases’ there were that day.

Now  below this there are 3 more graphs (but each is shrunk down to 1/3 the size of the top one to fit).  They are from left — number of tests, number hospitalized, and number of deaths.

Note the left most — the number of tests increases in December about the same way the number of cases does  — so although there is a surge, it may be due (in part) to increased testing.

Note the two right most graphs — hospitalizations and deaths.

A comparison with Massachusetts is instructive –Florida with a population of 20 million or so had only 2,005 COVID19 patients in hospital on Christmas day, while Massachusetts withs 6.7 million had 1,505.  So what has Florida done that we’re not doing up here?

Addendum 27 December — the number of COVID19 cases in hospital in Florida 26 December was 2129 a 6% increase from 25 December.

Date                     COVID cases (Florida)  Deaths

26 December           2129                               22

27 December           2228                               18

28 December           2560                              16

29  December         2963                               16

30  December          3376                              19

Given the greater than 50% increase in hospitalized cases in a few days, I think that daily deaths will similarly increase (with a 1 – 2 week time lag as is usually the case).

Then there are curve balls about the data itself

On 28 December the CDC said that it had overestimated the prevalence of omicron — According to agency data, omicron accounted for about 59 percent of all U.S. infections as of Dec. 25. Previously, the CDC said the omicron variant comprised 73 percent of all cases for the week ending Dec. 18. But that number has now been revised to 22.5 percent of all cases.– https://covid.cdc.gov/covid-data-tracker/#variant-proportions

So that means that omicron deaths won’t be as large as the initial prevalences given by the CDC implied. Revisions of data are common and unavoidable in a fluid situation like this.

The sudden shifts in data and information (sometimes incorrect, sometimes conflicting) is so typical of the early days of a new disease.  It so reminds of the early days of AIDs in the 80s when I was in practice.

In medicine, you never have the data you really want.  But you do not have the luxury of waiting for it.  You have to advise patients and families with the information you do have.  It’s difficult and frustrating, but very fit work for your intelligence.  And it’s important in a way that few things are.

Now here is the old post with all its twists and turns. You may find it interesting

********

This post is updated daily with new data — today’s is 31 December.

Addendum 30 December — nothing like new data to make you change your mind. Going from 2005 hospitalized COVID19 cases 25 Dec to 2,963 on 29 December in FLorida is a significant surge.  The fat lady hasn’t sung in Massachusetts, New York or Florida.  The pandemic is surging where it counts — hospitalized COVID19 patients.

 

I hope I’m not doing what I’ve seen many times, a devoted family hovering over a brain dead patient seeing signs of life when none exists because they desperately want to. Who can blame them?  They’re human beings not rational automatons.  Nonetheless, there are two signs that the pandemic is actually ending.

First, some background.  The media endlessly trumpets surges in ‘cases’.   Here’s the latest from Massachusetts — https://www.wwlp.com/news/health/coronavirus/covid-19-surge-in-mass-continues-to-cancel-news-years-eve-celebrations/.

Remember a case is defined as finding the virus (in the form of a viral protein or the viral genome) in your respiratory passages.  It does NOT mean you are sick

Nonetheless, there are two signs that the pandemic is actually ending.

First from Massachusetts, where ‘we believe’ in science and the adults in the room are in charge.  There is no question that the number of cases has dramatically increased in the past month — follow the following link to an excellent site which allows you to click and explore

https://www.mass.gov/info-details/covid-19-response-reporting#covid-19-interactive-data-dashboard-

If you click on various points of the curve you’ll see that a month ago the state had 750 people in the hospital with COVID19. On 23 December there were 1,595 — surge enough for anyone.

As someone well over 60 and being fully vaccinated (Pfizer) with a booster 9/21 I’me very interested in how many breakthrough infections in fully vaccinated people there are — it was 503/1595 on 23 December 31.5% hardly trivial.They don’t give an age distribution of breakthroughs at various ages, but based on past experience, it’s likely to be highest in the Medicare set.

I’ve been watching the site for the past few days and here are the numbers.  Date stands for the date of the report, and includes all data up to and including the previous day — Total cases is really total cases of COVID19 in hospital.

Date       Total cases   Fully vaccinated   % fully vaccinated

21 Dec      1,621            470                       29%

22 Dec     1,632            500                      31%

23 Dec     1,595           503                       31%

Addendum 27 Dec

27 Dec       1,636         509                       31%  — essentially the same

Addendum 28 Dec

28 Dec      1,707         529                          31%

Addendum 29 Dec

29 Dec       1,711         572                          33%

Addendum 30 Dec

30 Dec       1,817       631                            35%

Addendum 31 Dec

31 Dec         1,954     686                           35%

Not stable or decreasing — 1817 is 14% increase from a week ago 23 Dec.  Note that the percentage of the fully vaccinated is increasing.  Certainly no longer the pandemic of the unvaccinated. Florida jumped 10% today (see below) which shows why you’ve got to get figures each day and look at trends

I plan on daily updates for the rest of the week.  Things look quite stable in Massachusetts — not so much in Florida

Addendum 29 Dec — the statistics in New York State are nowhere as good — https://coronavirus.health.ny.gov/daily-hospitalization-summary

On 21 Dec there were 4200 or so COVID cases in hospital in New York State — as of the 28th there are around 6600.

Now both New York State and Florida both have about 20 million people, yet Florida’s case load today of 2560 is only 38% that of New York ! !  A smart friend thinks this is due to the far greater population density in NY (particularly in New York City).  Perhaps, but there has been a huge amount of criticism in the New York Times and other elements of the mainstream press of Florida and its Governor for they way they’ve been lax about masking, school closures, and social distancing.

Addendum 30 Dec

Comparing Florida and New York again.  Florida has a population of 21,480,00 and 62.390 deaths.  New York has a population of 19,450,00 and 58,560 deaths.   So Florida has 2% more death per capita.  Much closer than I had been led to believe by the press which basically called Governor DeSantis a murderer due to his unmasking policy.  Well, maybe he is, but then so is former Governor Cuomo for sending recovered COVID19 nursing home patients back to the nursing to infect the vulnerable

The numbers in Massachusetts are pretty stable and large enough to be significant. Now maybe this is seeing signs of life where none exist due to lags in reporting due to the Christmas holiday etc. etc.   But if it isn’t, it is good news.  I await next week’s numbers with great interest.

Addendum 30 Dec — Well it was wishful thinking.

Second — the data from Florida as of 26 December– according to the New York Times — https://www.nytimes.com/interactive/2021/us/florida-covid-cases.html

There are 4 graphs, a big one on the top of ‘cases’ from March 2020 to the present.  You can click on it at any point and see how many new ‘cases’ there were that day.

In case you can’t, here are a few numbers.

Date                 new cases

24 December  31,683

23 November   1,605

Certainly, surge enough for anyone.

Now  below this there are 3 more graphs (but each is shrunk down to 1/3 the size of the top one to fit).  They are from left — number of tests, number hospitalized, and number of deaths.

Note the left most — the number of tests increases in December about the same way the number of cases does  — so although there is a surge, it may be due (in part) to increased testing.

Note the two right most graphs — hospitalizations and deaths.  They don’t really budge in December.

In particular the deaths appear to have declined.  Again a caveat about the reporting accuracy over the Christmas holiday.

Also note that Florida with a population of 20 million or so had only 2,005 COVID19 patients in hospital on Christmas day, while Massachusetts withs 6.7 million had 1,505.  So what has Florida done that we’re not doing up here?

Addendum 27 December — the number of COVID19 cases in hospital in Florida 26 December was 2129 a 6% increase from 25 December.

Addendum 28 December — the number of COVID19 cases in hospital in Florida 27 Dec  2228 another 5% increase

Addendum 29 December — the number of COVID19 cases in hospital in Florida 28 Dec 2,560 — a big increase

Addendum 30 December — the number of COVID19 cases in hospital in Florida 29 December is 2,963 — another big increase

Addendum  31 December — the number of COVID19 cases in hospital in Florida 30 December is 3,376

I should have reported the number of deaths earlier, but didn’t, but I will start now.  It is given daily by the NYT, but the graph of deaths isn’t interactive and you can’t pick these numbers from it

There were 22 COVID19 deaths in Florida on the 26th.

There were 18 COVID19 deaths in Florida on the 27th

There were 16 COVID19 death in Florida on the 28th — increase sure to follow the increase in COVID19 cases in hospital

There were 16 COVID19 deaths in Florida on the 29th — increases sure to follow

There were 19 COVID19 deaths in Florida on the 30th  — increases sure to follow

I plan on daily updates for the rest of the week, so you’ll be able to draw your own conclusions.  Look at the third graph in the second line, it doesn’t look like deaths are surging.

But if accurate, the conclusion is inescapable — the currently extant virus variant (omicron) simply is NOT putting people in the hospital the way the earlier surges did.  Again have a look at the preceding 3 bumps in hospitalization for COVID19 since March 2020, and note how they parallel the number of cases.

Addendum 30 December — nothing like new data to make you change your mind. Going from 2005 hospitalized COVID19 cases 25 Dec to 2,963 on 29 December in FLorida is a significant surge.  The fat lady hasn’t sung in Massachusetts, New York or Florida.  The pandemic is surging where it counts — hospitalized COVID19 patients.

It is thought that the omicron variant accounts for over 50% of new infections no matter where you are, and over 90% in the NY metropolitan area.  So the surge in the new variant may actually be a good thing in that it is replacing delta (the previous dominant variant), a more virulent form of the virus, by a more innocuous one,.

Stay tuned and relax a bit.

Yet another Addendum 29 December (if you can stand it)— yesterday the CDC said that it had overestimated the prevalence of omicron — According to agency data, omicron accounted for about 59 percent of all U.S. infections as of Dec. 25. Previously, the CDC said the omicron variant comprised 73 percent of all cases for the week ending Dec. 18. But that number has now been revised to 22.5 percent of all cases.– https://covid.cdc.gov/covid-data-tracker/#variant-proportions

So that means that omicron deaths won’t be as large as the initial prevalences given by the CDC implied. Revisions of data are common and unavoidable in a fluid situation like this.

Reasoning about data as it comes in is exactly what scientists do.  I love doing this. Any guesses as to what tomorrow will bring?

Is the pandemic ending?

This post is updated daily with new data — today’s is 31 December.

Addendum 30 December — nothing like new data to make you change your mind. Going from 2005 hospitalized COVID19 cases 25 Dec to 2,963 on 29 December in FLorida is a significant surge.  The fat lady hasn’t sung in Massachusetts, New York or Florida.  The pandemic is surging where it counts — hospitalized COVID19 patients.

 

I hope I’m not doing what I’ve seen many times, a devoted family hovering over a brain dead patient seeing signs of life when none exists because they desperately want to. Who can blame them?  They’re human beings not rational automatons.  Nonetheless, there are two signs that the pandemic is actually ending.

First, some background.  The media endlessly trumpets surges in ‘cases’.   Here’s the latest from Massachusetts — https://www.wwlp.com/news/health/coronavirus/covid-19-surge-in-mass-continues-to-cancel-news-years-eve-celebrations/.

Remember a case is defined as finding the virus (in the form of a viral protein or the viral genome) in your respiratory passages.  It does NOT mean you are sick

Nonetheless, there are two signs that the pandemic is actually ending.

First from Massachusetts, where ‘we believe’ in science and the adults in the room are in charge.  There is no question that the number of cases has dramatically increased in the past month — follow the following link to an excellent site which allows you to click and explore

https://www.mass.gov/info-details/covid-19-response-reporting#covid-19-interactive-data-dashboard-

If you click on various points of the curve you’ll see that a month ago the state had 750 people in the hospital with COVID19. On 23 December there were 1,595 — surge enough for anyone.

As someone well over 60 and being fully vaccinated (Pfizer) with a booster 9/21 I’me very interested in how many breakthrough infections in fully vaccinated people there are — it was 503/1595 on 23 December 31.5% hardly trivial.They don’t give an age distribution of breakthroughs at various ages, but based on past experience, it’s likely to be highest in the Medicare set.

I’ve been watching the site for the past few days and here are the numbers.  Date stands for the date of the report, and includes all data up to and including the previous day — Total cases is really total cases of COVID19 in hospital.

Date       Total cases   Fully vaccinated   % fully vaccinated

21 Dec      1,621            470                       29%

22 Dec     1,632            500                      31%

23 Dec     1,595           503                       31%

Addendum 27 Dec

27 Dec       1,636         509                       31%  — essentially the same

Addendum 28 Dec

28 Dec      1,707         529                          31%

Addendum 29 Dec

29 Dec       1,711         572                          33%

Addendum 30 Dec

30 Dec       1,817       631                            35%

Addendum 31 Dec

31 Dec         1,954     686                           35%

Not stable or decreasing — 1817 is 14% increase from a week ago 23 Dec.  Note that the percentage of the fully vaccinated is increasing.  Certainly no longer the pandemic of the unvaccinated. Florida jumped 10% today (see below) which shows why you’ve got to get figures each day and look at trends

I plan on daily updates for the rest of the week.  Things look quite stable in Massachusetts — not so much in Florida

Addendum 29 Dec — the statistics in New York State are nowhere as good — https://coronavirus.health.ny.gov/daily-hospitalization-summary

On 21 Dec there were 4200 or so COVID cases in hospital in New York State — as of the 28th there are around 6600.

Now both New York State and Florida both have about 20 million people, yet Florida’s case load today of 2560 is only 38% that of Florida ! !  A smart friend thinks this is due to the far greater population density in NY (particularly in New York City).  Perhaps, but there has been a huge amount of criticism in the New York Times and other elements of the mainstream press of Florida and its Governor for they way they’ve been lax about masking, school closures, and social distancing.

Addendum 30 Dec

Comparing Florida and New York again.  Florida has a population of 21,480,00 and 62.390 deaths.  New York has a population of 19,450,00 and 58,560 deaths.   So Florida has 2% more death per capita.  Much closer than I had been led to believe by the press which basically called Governor DeSantis a murderer due to his unmasking policy.  Well, maybe he is, but then so is former Governor Cuomo for sending recovered COVID19 nursing home patients back to the nursing to infect the vulnerable

The numbers in Massachusetts are pretty stable and large enough to be significant. Now maybe this is seeing signs of life where none exist due to lags in reporting due to the Christmas holiday etc. etc.   But if it isn’t, it is good news.  I await next week’s numbers with great interest.

Addendum 30 Dec — Well it was wishful thinking.

Second — the data from Florida as of 26 December– according to the New York Times — https://www.nytimes.com/interactive/2021/us/florida-covid-cases.html

There are 4 graphs, a big one on the top of ‘cases’ from March 2020 to the present.  You can click on it at any point and see how many new ‘cases’ there were that day.

In case you can’t, here are a few numbers.

Date                 new cases

24 December  31,683

23 November   1,605

Certainly, surge enough for anyone.

Now  below this there are 3 more graphs (but each is shrunk down to 1/3 the size of the top one to fit).  They are from left — number of tests, number hospitalized, and number of deaths.

Note the left most — the number of tests increases in December about the same way the number of cases does  — so although there is a surge, it may be due (in part) to increased testing.

Note the two right most graphs — hospitalizations and deaths.  They don’t really budge in December.

In particular the deaths appear to have declined.  Again a caveat about the reporting accuracy over the Christmas holiday.

Also note that Florida with a population of 20 million or so had only 2,005 COVID19 patients in hospital on Christmas day, while Massachusetts withs 6.7 million had 1,505.  So what has Florida done that we’re not doing up here?

Addendum 27 December — the number of COVID19 cases in hospital in Florida 26 December was 2129 a 6% increase from 25 December.

Addendum 28 December — the number of COVID19 cases in hospital in Florida 27 Dec  2228 another 5% increase

Addendum 29 December — the number of COVID19 cases in hospital in Florida 28 Dec 2,560 — a big increase

Addendum 30 December — the number of COVID19 cases in hospital in Florida 29 December is 2,963 — another big increase

Addendum  31 December — the number of COVID19 cases in hospital in Florida 30 December is 3,376

I should have reported the number of deaths earlier, but didn’t, but I will start now.  It is given daily by the NYT, but the graph of deaths isn’t interactive and you can’t pick these numbers from it

There were 22 COVID19 deaths in Florida on the 26th.

There were 18 COVID19 deaths in Florida on the 27th

There were 16 COVID19 death in Florida on the 28th — increase sure to follow the increase in COVID19 cases in hospital

There were 16 COVID19 deaths in Florida on the 29th — increases sure to follow

There were 19 COVID19 deaths in Florida on the 30th  — increases sure to follow

I plan on daily updates for the rest of the week, so you’ll be able to draw your own conclusions.  Look at the third graph in the second line, it doesn’t look like deaths are surging.

But if accurate, the conclusion is inescapable — the currently extant virus variant (omicron) simply is NOT putting people in the hospital the way the earlier surges did.  Again have a look at the preceding 3 bumps in hospitalization for COVID19 since March 2020, and note how they parallel the number of cases.

Addendum 30 December — nothing like new data to make you change your mind. Going from 2005 hospitalized COVID19 cases 25 Dec to 2,963 on 29 December in FLorida is a significant surge.  The fat lady hasn’t sung in Massachusetts, New York or Florida.  The pandemic is surging where it counts — hospitalized COVID19 patients.

It is thought that the omicron variant accounts for over 50% of new infections no matter where you are, and over 90% in the NY metropolitan area.  So the surge in the new variant may actually be a good thing in that it is replacing delta (the previous dominant variant), a more virulent form of the virus, by a more innocuous one,.

Stay tuned and relax a bit.

Yet another Addendum 29 December (if you can stand it)— yesterday the CDC said that it had overestimated the prevalence of omicron — According to agency data, omicron accounted for about 59 percent of all U.S. infections as of Dec. 25. Previously, the CDC said the omicron variant comprised 73 percent of all cases for the week ending Dec. 18. But that number has now been revised to 22.5 percent of all cases.– https://covid.cdc.gov/covid-data-tracker/#variant-proportions

So that means that omicron deaths won’t be as large as the initial prevalences given by the CDC implied. Revisions of data are common and unavoidable in a fluid situation like this.

Reasoning about data as it comes in is exactly what scientists do.  I love doing this. Any guesses as to what tomorrow will bring?

Was omicron produced in some lab? I think so but I hope I’m wrong

Omicron appeared out the blue less than a month ago in S. Africa and is spreading very quickly.  Rachel Walensky of the CDC, said today (14 December 2021) that it currently accounts for 13% of cases in New York and New Jersey.

Where did it come from?  An analogy might help the nonvirologist. Lots of things evolve, even musical instruments.  The  Museum of Fine Arts in Boston  has a room with old instruments, some of which are decidedly weird and vanished without a trace. Others show an obvious evolution, particularly keyboard, string and wind instruments.  A cellist can see how it evolved from the gamba, and a keyboard player can see how the piano came from the harpsichord.  Omicron is so different from its predecessors that it’s like a tuba coming from a clavichord  with no intermediate steps.

This is exactly the way scientists saw it initially [ Science vol. 374 pp. 1178 – 1180 3 December ’21 ] https://www.science.org/doi/epdf/10.1126/science.acx9737

The first diagram shows it best, with a plot of the number of mutations from the original sequence in early 2020.  Gradually the number of mutations in successful viruses crept up one by one to about 15.   Enter omicron which suddenly has 30 (15 of them new).

Three possible scenarios for its appearance are given

l. The virus was evolving in a population with no surveillance

2. The virus came from an infected patient who was immunodeficient, who fought the virus to a draw allowing it to mutate for months — there is a well documented precedent for this sort of thing happening [ Nature vol. 592 pp. 277 – 282 ’21 ]

3. It might have evolved in animals, only recently spilling over to man (a la AIDS)

It was early times and the excellent author Kai Kupferschmidt whose article this is and whose articles are always worth reading, couldn’t have known about what was to appear in the 9 December Nature [ vol. 600 p. 197 – 199 ’21 ]. https://media.nature.com/original/magazine-assets/d41586-021-03614-z/d41586-021-03614-z.pdf.

A virologist engineered a viral protein with mutations which was able to evade antibodies produced by the 3 extant vaccines used in the USA.  You can read about it here — https://www.rockefeller.edu/news/31153-could-future-coronavirus-variants-fully-dodge-our-immune-system/.  They selected for the mutations in the spike protein which were resistant, and then put TWENTY of them in the spike protein.

Here is a direct quote from the article — ”

For the study, they first created a safe stand-in for the coronavirus by tweaking a different, harmless virus to express SARS-CoV-2 spike protein on its surface. As the faux coronaviruses replicated, some picked up mutations as they made mistakes copying themselves. The team then bathed the faux coronaviruses in plasma samples from people who had recovered from COVID, and selected the mutants that escaped neutralization by antibodies. A few rounds of this and the team found many mutations that were in the same locations as those occurring naturally in SARS-CoV-2 variants, including those found in Delta or other variants of concern.

The researchers then created a “polymutant” virus: a faux coronavirus sporting a spike protein featuring 20 of the worst of those mutations all at once. This polymutant showed near-complete resistance to antibodies generated by individuals who have been infected by or vaccinated against SARS-CoV-2.”

This is a far more likely (and frightening) story for the origin of omicron.  The technology is available and widespread.  The virus is so different with no intermediate viruses known that a lab origin is more likely than the 3 explanations given above.  It makes more sense to me and I hope I’m wrong; but if I’m not there will be others: and some of them could well be used as bioweapons.  It is even possible that omicron is the first (or the second depending on how paranoid you are).

Is China following a Smokey the Bear policy on the pandemic?

China is following a prevent pandemic virus infection policy, just as Smokey the Bear followed a prevent forrest fires policy.  The latter didn’t work out well, as although fires were prevented for a while. However, when fires did occur, they were much much worse than the smaller ones Smokey prevented.  There was much more tinder and stuff to burn.

Actually Smokey has changed his tune slightly.

https://en.wikipedia.org/wiki/Smokey_Bear  SmokeyBear.com’s current site has a section on “Benefits of Fire” that includes this information: “Fire managers can reintroduce fire into fire-dependent ecosystems with prescribed fire. Under specific, controlled conditions, the beneficial effects of natural fire can be recreated, fuel buildup can be reduced, and we can prevent the catastrophic losses of uncontrolled, unwanted wildfire.”

Revision 14 December 2021 — China’s policy of prevention has resulted in a Chinese population which has been vaccinated using two killed virus vaccines (Sinopharm, Coronavac).  They have not had any natural infections with the virus (aside from the original cases) as far as we know given what China has allowed out.

Infection with the virus itself exposes you to all its proteins, with your immune system responding to all of them.   Western vaccines are just to the spike protein.

It tends to be forgotten that moist cases of pandemic viral infection are asymptomatic.

Given 800K deaths  from COVID19  in the USA, how can I possibly say this is good. Here’s how :>

If you had an infection with the virus, you develop antibodies.  Nowadays, everyone who is vaccinated has antibodies so there is no point in testing for them, but what were things like in the days before vaccines?

The following is from a post July/2020.

https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html–https://www.cnbc.com/2020/04/23/new-york-antibody-study-estimates-13point9percent-of-residents-have-had-the-coronavirus-cuomo-says.html.

New York State  randomly tested 3,000 people at grocery stores and shopping locations across 19 counties in 40 localities to see if they had the antibodies to fight the coronavirus, indicating they have had the virus and recovered from it. With more than 19.4 million people residents, according to U.S. Census data, the preliminary results imply that at least 2.7 million New Yorkers have been infected with Covid-19.They weren’t all hospitalized.

Here’s some work the same month from Queens — https://www.nytimes.com/2020/07/09/nyregion/nyc-coronavirus-antibodies.html

At a clinic in Corona, a working-class neighborhood in Queens, more than 68 percent of people tested positive for antibodies to the new coronavirus. At another clinic in Jackson Heights, Queens, that number was 56 percent. But at a clinic in Cobble Hill, a mostly white and wealthy neighborhood in Brooklyn, only 13 percent of people tested positive for antibodies.

So the disease has already to spread to half the population in some neighborhoods in Queens. If even 10% of them were sick that would have been 140,000 hospitalizations.  They didn’t happen.

OK, so a lot more people were infected than got sick.  Why is this good?

Enter the omicron variant of the pandemic virus.  It can evade the antibodies produced by all the current vaccines (in the West — protection against the Chinese killed viral vaccines CoronaVac and Sinopharm isn’t known yet).   Yet omicron doesn’t appear to produce severe disease. Thus far…

 

The CDC in the past week said of the 40+ omicron cases it knows about (there certainly are more out there, and more to come), there was one hospitalization (for two days) and no deaths.

Here is Dr. Fauci 12 December 2021 — “We’re getting anecdotal information … not necessarily confirmed yet, that the level of severity appears to be maybe a bit less than in the Delta. But there are a lot of confounding issues that it may be due to the underlying protection in the community due to prior infections,”

Source — https://nypost.com/2021/12/12/omicron-appears-to-evade-some-protection-from-covid-vaccines/

So the Chinese population may be sitting ducks for omicron having been given vaccines (Sinopharm, Coronavac) of unknown potency against omicron.  If their statistics are true there has been little or no natural infection with the pandemic virus in the Chinese population (which Fauci has just implicated is protective),.  Given that I have a son, daughter in law and two grandkids living in Hong Kong, I find this extremely disconcerting.

Next up omicron itself and how it came to be.  The possibilities are even more disconcerting.

It’s the early days of AIDS all over again

Probably no one under 50 has any idea of what the first few years of AIDS were like.  Well, it is exactly like what the past 2 years of the pandemic have been.  In both cases there was/is  something out there that we don’t understand which can kill you.  The first cases appeared 40 years ago in June.  The cause (Human Immunodeficiency Virus 1 — HIV1) was isolated in 1984.  The fear until then  was palpable.  We didn’t know what it was or how it was transmitted.  Eventually it became clear that sex was  involved, and I remember reading the riot act about protecting themselves to a roomful of my teenaged sons and their friends.  It was probably one of the most useful things I ever did.

I personally knew physicians and dentists who refused to treat AIDS patients.  Sick jokes like this one were prevalent

Q. What is the AIDs diet ?

A. Pizza and Pancakes

Q. Why that?

A. Because you can slide it under the door.

It really isn’t so different from now even though we know the cause of the pandemic and we know how it is transmitted.  But we do not know what the virus will do next.  We do not know how often we need boosters, or even whether they will work against the new variant (omicron).  We are far from certain just how much to isolate ourselves (this clearly depends on our age).

One day the news is good — like this from the BBC earlier this week

There is community transmission of the Omicron coronavirus variant in multiple regions of England, Health Secretary Sajid Javid has confirmed.

He told MPs the variant was continuing to spread “here and around the world” and there were now cases here “with no links to international travel”.

There have been 336 confirmed cases of the highly-mutated variant across the UK, he said, a rise of 90 from Sunday.

There are concerns about how Omicron could interact with current vaccines.

Of the confirmed Omicron cases, 261 were in England, 71 in Scotland and four in Wales – while Northern Ireland is yet to have a confirmed case.

Mr Javid said that as far as he was aware none of those people had been admitted to hospital.

The next day it gets scary again —  from the Massachusetts Department of Public health — also this week.

“There are now 1,151 COVID patients in the state, a daily jump of 33 patients. Hospitalizations have been spiking in recent weeks, reflecting a 129% jump from 502 patients a few weeks ago.The state reported that 239 patients are in intensive care units, and 126 patients are currently intubated.

Of the 1,151 total hospitalizations, 407 patients are fully vaccinated — or about 35%. It’s the first time the state has reported more than 400 breakthrough hospitalizations on one day. Those who are unvaccinated are at a much higher risk for a severe case.”

Here’s a link to the full article — https://www.bostonherald.com/2021/12/07/massachusetts-reports-3720-new-coronavirus-cases-breakthrough-case-count-hits-record-high/

It is clear that the vaccines, while helpful are not a panacea, and a personal friend came down with it again 2 months after receiving a booster.  There is no question that the vaccines are protective to some extent, just nowhere near what they were originally billed as.