Tag Archives: pandemic virus

Virus 1 Astra Zenica vaccine 0

It’s already happened. A mutated pandemic virus has rendered a vaccine useless. This is serious — the game of cat and mouse with the mutating pandemic virus (otherwise known as natural selection) has begun. You can read all about it here

For a leisurely stroll through the background needed to understand the Science and Nature articles I’m going to essentially republish (and refurbish) a very recent  post — trying to make things as accessible as possible. 

The human species as a culture medium for the pandemic virus

Creationists or not, we are all about to get an unwanted lesson in natural selection and evolution, courtesy of the current pandemic virus (SARS-CoV-2).  This is going to be a long post, which will contain an incredible case of meningitis, thoughts on selfish genes in viruses, evolution, natural selection and why we’re in for a very, very long haul with the pandemic virus.

As you probably know, mutant pandemic viruses (all different) have emerged (in England, South Africa, Brazil).  Even worse they appear to be more infectious, and some are more resistant to our vaccines (all of which were made before they appeared).  

Here is lesson #1 in natural selection.  Viruses have no brains, they barely have a genome.  The human genome contains 3 billion positions, the pandemic virus 30,000.  So we have 100,000 times more information in our genome than the virus does. 100,000 is about the number of inches in a mile and half.  

So how is the virus outsmarting us?  Simply by reproducing like mad.  The molecular machines that copy our genome are very accurate, making about 1 mistake per 100,000,000 positions copied — that’s still enough for the average newborn to have 30 new mutations (more if the parents are older).  The viral machine is much less accurate.  So lots of genome mutations are made (meaning that the viral proteins made from the genome change slightly).  Those that elude the vaccines and antibodies we’re throwing at them survive and reproduce, most don’t.  This is natural selection in action. Survival of the fittest.  Darwin wasn’t kidding.

What is so remarkable about the British and the South African variants, is that they contain multiple mutations (23 in the British variant, at least 3 in the South African variant).  Usually its just one or two.

 You’ve probably heard about the mutation changing just one of the 147 amino acids  in hemoglobin to cause sickle cell anemia. Here’s another.  APOE is a 299 amino acid protein.  It comes in 3 variants  — due to changes at 2 positions.  One variant greatly increases the risk of Alzheimer’s disease, another decreases it.  So even single mutations can be quite powerful. 

So how did these multiple mutations come about?  We likely now have an answer due to one very well studied case [ Cell vol. 183 pp. 1901 – 1912 ’20 ] in an immunocompromised patient with chronic lymphatic leukemia (CLL). She shed the virus for 70 days.  Even so, she wasn’t symptomatic, but because the patient had enough immune system to fight the virus to a draw, it persisted, and so its genome was always changing.  The authors were smart enough to continually sequence the viral genome throughout the clinical course and watch it change.  So that’s very likely how the virus accumulates mutations, it lived for a long time in a patient who lived a long time with a weakened immune system allowing the virus to merrily mutate without being killed and allowing the weakened immune system to effectively select viruses it can’t kill. 

Could this happen again? Of course.   There are some 60,000 new cases of CLL each year in the USA.  Many of them have abnormal immune systems even before chemotherapy begins.

Here is an example from my own practice. The patient was a 40 year old high school teacher who presented with severe headache, stiff neck and drowsiness.  I did a spinal tap to get cerebrospinal fluid (CSF) for culture so we could find the best possible antibiotic to treat the organism.  This was 30+ years ago, and we had no DNA testing to tell us immediately what to do.  We had to wait 24 hours  while the bugs grew in culture to form enough that we could identify the species and determine  the antibiotics it was sensitive to. . 

As the fluid came out, I had a sinking feeling; as it was cloudy, implying lots of white cells fighting the infection. Enough white cells to make CSF cloudy (it normally looks like water) is a very bad sign. So after starting the standard antibiotic to be used in the first 24 hours before the cultures came back, I called the lab for the cell count.  They said there weren’t any.  I thought they’d seriously screwed up maybe losing what I’d sent or mislabeling it and looking at the wrong sample, and I unpleasantly stormed down to the lab (as only an angry physician can do) to see the spinal fluid.  They were right.  The cloudiness of the CSF was produced by hordes of bacteria not white cells.  This was even worse as clearly the bacteria were winning and the patient’s immune system was losing, and I never expected the patient to survive.  But survive he did and even left the hospital.  

Unfortunately, the meningitis turned out to be  the first symptom of an abnormal immune system due to a blood malignancy — multiple myeloma. 

****

Addendum 2 February — I sent this post to an old friend and college classmate who is now a hematology professor at a major med school.  He saw a similar case —

“When I was a medical student I saw a pediatric sickle anemia patient (asplenic) with fever and obtundation. When I looked at the methylene-blue stained CSF, I thought that stain had precipitated. So I obtained a fresh bottle of stain and it looked the same. Only this time, I looked more closely and what I thought was precipitated stain were TNTC pneumococci.

I urge all my immunosuppressed patient to get vaccinated for covid-19. I worry that if many people don’t get vaccinated,  those who do will not be that better off.”

Addendum 3 February– I asked him if his patient had survived like mine —

answer 

“Unfortunately, no. With the pneumococcus, If antibiotics are not started within 4 hours after recognition, the train has left the station.”

 

****

So there are millions of active cases of the pandemic, and tons of people with medical conditions (leukemia, multiple myeloma, chemotherapy for other cancer) with abnormal immune systems, just waiting for the pandemic virus to find a home and proliferate for days to weeks.  Literally these people are culture media for the virus. Not all of them have been identified, so don’t try to prevent this by withholding vaccination from the immunocompromised — they’re the ones who need it the most. 

I think we’re in for a very long haul with the pandemic.  We’re just gearing up to stay on top of the viral sequence du jour.   Genome sequencing is not routine (it should be).  The South African and British mutations were picked up because a spike in cases led people to sequence the virus from these patients.  Viral genome sequencing and surveillance should be routine in most countries and should not wait for an infection spike to occur. 

You may come across the terms B.1.351 and  507Y.V2 — they are different names for the South African virus which beat Astra Zenica.  The British variant is also called B.1.1.7

The human species as a culture medium for the pandemic virus

Creationists or not, we are all about to get an unwanted lesson in natural selection and evolution, courtesy of the current pandemic virus (SARS-CoV-2).  This is going to be a long post, which will contain an incredible case of meningitis, thoughts on selfish genes in viruses, evolution, natural selection and why we’re in for a very, very long haul with the pandemic virus.

As you probably know, mutant pandemic viruses (all different) have emerged (in England, South Africa, Brazil).  Even worse they appear to be more infectious, and some are more resistant to our vaccines (all of which were made before they appeared).  

Here is lesson #1 in natural selection.  Viruses have no brains, they barely have a genome.  The human genome contains 3 billion positions, the pandemic virus 30,000.  So we have 100,000 times more information in our genome than the virus does. 100,000 is about the number of inches in a mile and half.  

So how is the virus outsmarting us?  Simply by reproducing like mad.  The molecular machines that copy our genome are very accurate, making about 1 mistake per 100,000,000 positions copied — that’s still enough for the average newborn to have 30 new mutations (more if the parents are older).  The viral machine is much less accurate.  So lots of genome mutations are made (meaning that the viral proteins made from the genome change slightly).  Those that elude the vaccines and antibodies we’re throwing at them survive and reproduce, most don’t.  This is natural selection in action. Survival of the fittest.  Darwin wasn’t kidding.

What is so remarkable about the British and the South African variants, is that they contain multiple mutations (23 in the British variant).  Usually its just one or two.

 You’ve probably heard about the mutation changing just one of the 147 amino acids  in hemoglobin to cause sickle cell anemia. Here’s another.  APOE is a 299 amino acid protein.  It comes in 3 variants  — due to changes at 2 positions.  One variant greatly increases the risk of Alzheimer’s disease, another decreases it.  So even single mutations can be quite powerful. 

So how did these multiple mutations come about?  We likely now have an answer due to one very well studied case [ Cell vol. 183 pp. 1901 – 1912 ’20 ] in an immunocompromised patient with chronic lymphatic leukemia (CLL). She shed the virus for 70 days.  Even so, she wasn’t symptomatic, but because the patient had enough immune system to fight the virus to a draw, it persisted, and so its genome was always changing.  The authors were smart enough to continually sequence the viral genome throughout the clinical course and watch it change. 

Could this happen again.  Of course?   There are some 60,000 new cases of CLL each year in the USA.  Many of them have abnormal immune systems even before chemotherapy begins.

Here is an example from my own practice. The patient was a 40 year old high school teacher who presented with severe headache, stiff neck and drowsiness.  I did a spinal tap to get cerebrospinal fluid (CSF) for culture so we could find the best possible antibiotic to treat the organism.  This was 30+ years ago, and we had no DNA testing to tell us immediately what to do.  We had to wait 24 hours  while the bugs grew in culture to form enough that we could identify the species and determine  the antibiotics it was sensitive to. . 

As the fluid came out, I had a sinking feeling; as it was cloudy, implying lots of white cells fighting the infection. Enough white cells to make CSF cloudy (it normally looks like water) is a very bad sign. So after starting the standard antibiotic to be used in the first 24 hours before the cultures came back, I called the lab for the cell count.  They said there weren’t any.  I thought they’d seriously screwed up maybe losing what I’d sent or mislabeling it and looking at the wrong sample, and I unpleasantly stormed down to the lab (as only an angry physician can do) to see the spinal fluid.  They were right.  The cloudiness of the CSF was produced by hordes of bacteria not white cells.  This was even worse as clearly the bacteria were winning and the patient’s immune system was losing, and I never expected the patient to survive.  But survive he did and even left the hospital.  

Unfortunately, the meningitis turned out to be  the first symptom of an abnormal immune system due to a blood malignancy — multiple myeloma. 

****

Addendum 2 February — I sent this post to an old friend and college classmate who is now a hematology professor at a major med school.  He saw a similar case —

“When I was a medical student I saw a pediatric sickle anemia patient (asplenic) with fever and obtundation. When I looked at the methylene-blue stained CSF, I thought that stain had precipitated. So I obtained a fresh bottle of stain and it looked the same. Only this time, I looked more closely and what I thought was precipitated stain were TNTC pneumococci.

I urge all my immunosuppressed patient to get vaccinated for covid-19. I worry that if many people don’t get vaccinated,  those who do will not be that better off.”

Addendum 3 February– I asked him if his patient had survived like mine —

answer 

“Unfortunately, no. With the pneumococcus, If antibiotics are not started within 4 hours after recognition, the train has left the station.”

 

****

So there are millions of active cases of the pandemic, and tons of people with medical conditions (leukemia, multiple myeloma, chemotherapy for other cancer) with abnormal immune systems, just waiting for the pandemic virus to find a home and proliferate for days to weeks.  Literally these people are culture media for the virus. Not all of them have been identified, so don’t try to prevent this by withholding vaccination from the immunocompromised — they’re the ones who need it the most. 

I think we’re in for a very long haul with the pandemic.  We’re just gearing up to stay on top of the viral sequence du jour.   Genome sequencing is not routine (it should be).  The South African and British mutations were picked up because a spike in cases led people to sequence the virus from these patients.  Viral genome sequencing and surveillance should be routine in most countries  — not waiting on an infection spike. 

 

 

Good riddance 2020

It’s no good being right if nobody listens. It was clear to me in late January that we would be in a pandemic as my post of 27 January 2020 below will show. The press in those early months did not cover itself in glory. Here’s a link to a bunch of press headlines — forget that the site is a bit dicey — I remember reading many of these at the time — https://twitter.com/dbongino/status/1245341299320016897. Why the CDC didn’t figure this out is anyone’s guess. The problem wasn’t lack of staff, but lack of brains. We’re all playing the price.

What to do about the Wuhan flu

This was published 27 Jan ’20.  Nothing has been altered (other than this).

What to do about the Wuhan flu?  The short answer is to lay in a month or two of dried food and drink, and have plenty of bottled water around.

The long answer depends on whether the new corona virus (called 2019-nCOV) becomes a pandemic and if the (symptomatic) case fatality rate continues at 3.5% (based on 80 deaths in 2,800 cases as of yesterday).

With a son, Chinese daughter in law and two grandchildren living in Hong Kong, I’ve followed the outbreak ever since hearing of it 1 January.

The best and most current source of info about the outbreak is the South China Morning Post — https://www.scmp.com.  It is in English and is not a government mouth piece.

Here’s the bad news

(1) As of a few days ago the virus had been found in 29/31 Chinese provinces.  This means that confining the virus to China is nearly impossible — how do you cut off a billion or so people from the rest of the world?

(2) Here’s more from today

  • Hong Kong University  faculty of medicine dean Gabriel Leung says research shows self-sustaining human-to-human transmission is already happening in all major mainland cities.   Here’s a link
  • https://www.scmp.com/news/hong-kong/health-environment/article/3047813/china-coronavirus-hong-kong-medical-experts-call
  •  Why is this significant?  You have to know how docs operate.  When I wanted information about some issue or disease, I’d call a doc whose opinion and background I respected.  It is likely that Leung made this statement after calling med school deans he personally knew in major mainland cities.

(3) There is no treatment, in the sense of stopping the virus in its tracks.  All we have is supportive care, oxygen rest, medication for fever, bronchodilators.  This is true for the vast majority of viruses.  Remember the joke that modern medical science can cure a cold in 14 days, but otherwise it takes two weeks.

(4) We know that you don’t have to be clinically ill to transmit the disease.  Screening new arrivals for fever is well and good but that won’t totally prevent spread.

(5) Some individuals are what is called ‘superspreaders’ — one individual infected 15 hospital personnel.

(6) I wouldn’t hope for a specific treatment any time soon — look how long it took to get any treatment for AIDS, despite the huge amount of resources devoted to it.

Here is some good news. It is quite possible that there are many more cases out there with people who were either asymptomatic or  just mildly ill.  The classic example is polio, in which for every case with paralysis there were 99 cases with mild GI illness or nothing at all.

This will need to wait until we can test people for antibodies to 2019-nCOV to find out how many people have had it.  This is probably at least a month away

Vaccines (if they can be made) are even more months away.  We’ll just have to hunker down and hope for the best.

Why lay in dried food ?– in a pandemic people will panic and clear out all food they can get their hands on.  There were pictures of empty bins in a Wuhan food market last week.

People are getting serious about it.  From Reuters -“U.S. President Donald Trump offered China whatever help it needed on Monday”.  It would be nice to have some of our people from the Center for Disease Control over there. Hopefully the Chinese won’t be too proud to accept the offer.

Addendum 28 Jan — apparently the US (in the form of the CDC) is begging China to let them help out — sad — why should they have to beg?  Apparently the first overture was 3 weeks ago ! ! ! ! — https://www.scmp.com/news/china/article/3047967/china-coronavirus-washington-asks-beijing-permission-send-health-team

DON’T TOUCH YOUR MASK !!!

I am fortunate enough to have a beautiful reservoir within a half mile of my house. Over the years in the 3.5 mile circumferential stroll it requires I’ve seen 3 black bears, 20 or so American Eagles, Swans, Mergansers, deer, chipmunks and 20 billion Canada geese.

I don’t wear a mask when I’m out there, because at most I’ll see 100 or so people during the walk. Everyone is very good about social distancing and actual propinquity lasts a few seconds at most when we’re walking in opposite directions. About 80% are wearing masks, or at least have them around their neck. Those wearing them around their neck grab them and cover their mouth and (sometimes) their noses.

This is a terrible mistake. The only way the pandemic virus can cause you serious trouble is if it gets to your mouth, nose or eyes. It will never get through your skin. Unless you carefully washed your hands before leaving for the reservoir, you might have it on the skin of your hands. Do not give it a free ride to your mask where it will happily reside getting a shot at entry every time you inhale.

Amazingly, this is not generally known, and people seem genuinely surprised when I tell them this. Most of them thank me.

Places like the reservoir are among the few where you don’t need to wear a mask. So protect yourself if you wear one, and don’t touch it.

Lots of people seem to be using cell phones on the walk, which is even worse, should they contain the virus, as contact is much more prolonged than a simple mask adjustment. How many people clean their cellphones?

One happy point now that winter is almost on us in these parts. The crucial spike protein of the virus (which is how it gets into your cells) deteriorates and becomes nonInfectious after storage for a week at 4 centigrade (about 40 F). What an overnight chill does for it is anyone’s guess. This is from a non-peer reviewed preprint — https://www.biorxiv.org/content/10.1101/2020.07.12.199588v1

Health tip: how to avoid infecting yourself with SARS-Cov-2

Being closer to 85 than 80 now, I try to stay in as good physical shape as possible by walking 4.5 miles around a beautiful reservoir within a mile of my home. It takes about 90 minutes, and I usually meet 40 – 100 walkers, runners, joggers, bicyclists, mommies with kids in baby carriages, and today a lady in a motorized wheelchair.

It is the one place where you don’t need a mask (unless you know you are actively infected with the virus in which case you shouldn’t be out there in the first place). Why? Because the virus is spread as droplets as you breathe out, and they don’t hang around in the air very long, and there’s lots of air when you go outside to dilute them. It’s closed spaces and prolonged contact with the same air which causes infection. If you haven’t already done so please look at https://www.erinbromage.com/post/the-risks-know-them-avoid-them — it hasn’t been updated since May but you simply can’t do better than this. The examples he cites are convincing (and scary).

Now our skin is crawling with bacteria and viruses. Estimates go as high as 1 trillion (1,000,000,000,000) per human. But they don’t get through your skin. So if you have the pandemic virus on your skin (particularly your hands) it isn’t going to get through the skin to infect you. It will infect you if you put your hand to your nose or your mouth or your eyes, because those are the parts of you which are no barrier to the pandemic infection.

So aside from giving me dirty looks, when people raise their masks to their nose when they see me coming, they’re giving any pandemic viruses on their hands a free ride to their noses and mouths and a much better shot at infecting them.

Seriously.

If the virus makes it from your hand to the mask, and you keep the mask on, the virus stays there (and hopefully stays there rather than moving inside) as you breathe in an out. So you’re not protecting me and you are possibly harming yourselves. So don’t do it.

Put the mask on and keep it on in most other places, walking in crowded places, stores, restaurants, malls. But if you’re out walking in an uncrowded park enjoy yourself.

For those who don’t know, I’m a medical school graduate (Penn). I’m going to run this by two college classmates (both retired med school professors) and if they tell me I’m wrong, I’ll let you know. I’ll let you know even if they tell me I’m right.

Addendum — 10 November — from a retired professor of medicine at Johns Hopkins. The other one is on his farm on the Eastern Shore of Maryland and will respond when he gets back


“I totally agree with you that unless you put your fingers in or around your nose, you aren’t going to get the covid virus from surface contact. Anecdotally, I would predictably get a significant  URI every year after our annual Hematology meeting in December because I am big on shaking hands, which invariably would touch my nose at some point.  I skipped the last two annual meetings and presto, no URIs since.

As for masking outdoors, for the first 6 months, I was assiduous and furious at nonmaskers. Now, I wear a mask outdoors but only when near other people (on sidewalks etc.). I probably don’t need to when socially distanced but do so as a courtesy to others because they are masked. Bottom line, in DC we’ve gone from ~ 50 % masked to 95 % masked. So I want to encourage that.”

Addendum 11 Nov

From the other retired med school professor


    -your exercise regimen is laudatory……..but you failed to state whether you walk clockwise, counterclockwise, or alternate between the two

    -as usual, your medical analysis is well-reasoned…..at least technically, but as a physician you know the importance of instilling a feeling of comfort and safety in patients (your fellow walkers, etc), so wearing a mask (of any kind) when they approach might better address the “human condition”

Here’s is sort of an engineering analysis of why masks don’t need to be worn in the great (uncrowded) outdoors.

Figure that  the 50 people I pass on the walk are in perhaps 30 groups 20 doubles 10 singletons.  4.5 miles is 23760 feet. so I see a different group every 792 feet.  Now I’m walking at a pace of 90 *60 seconds for 23,760 feet or 4.4 feet per second  — assume they’re walking at the same pace, so every second we move about 9 feet apart (forgetting the 6 feet or more sideways distance) and we’re well out of each other’s airspace in a few seconds.  That is a miniscule dose of the virus when you consider the volume it is being diluted into (and a very short time of exposure).  Here it is very important to read Bromage, because infectivity is not just dose, it’s  dose x time. 

A paper everyone should look at

Proc. Natl. Acad. Sci. vol. 117 pp. 25237–25245 ’20 presumably is ‘freely shared’. Here’s the link — https://www.pnas.org/content/pnas/117/41/25237.full.pdf

The authors set up a mist of fine water droplets in front of a speaker and watch what the emitted air does to them (using high speed cameras). Sentences with a lot of plosives (such as p) e.g. peter piper picked a peck of pickled peppers produce a jet which barrels along for a few meters. Different sound produce air flows in different directions. The pictures are incredible. If viruses are carried along with this, the implications for the pandemic flu are obvious. Wear a mask when talking to strangers.

Here’s a quote from the paper “We show that the transport distance of exhaled material versus time, in the form of three distinct scal- ing laws, represents the typical structure of the flow, including 1) a short (<0.5 m) distance, with large angular variations, where the complexity of language is evident and responsible for mate- rial transport in a fraction of a second; 2) a longer distance, out to approximately 1 m, where directed transport occurs driven by individual vortical puffs corresponding roughly to individual plo- sive sounds; and 3) a distance out to about 2 m, or even farther, where spoken sentences with plosives, corresponding effectively to a train of puffs, create conical, jet-like flows. “

Well, those are just words — if you do nothing else, look at the pictures in the paper.

Why do some socially isolate and some don’t

The current flare in US cases (and deaths) are likely due to a failure in social isolation, rather than a loosening of restrictions on activity.  Georgia loosened its restrictions back in April.  Following this, new cases dropped for two months, and deaths dropped for nearly 3 months, before rising again to pre-lockdown levels and above.  The number of new ‘cases’ can partially be attributed to more testing, but the number of deaths can not.  For links and the exact numbers see the copy of the previous post after the ***

I think the rise is partially explainable by a failure of social distancing. Have a look at this  https://nypost.com/2020/07/18/video-shows-people-in-queens-flooding-streets-without-masks/.   It may not be a COVID party in name, but it is in fact.

That being the case, wouldn’t it be nice to know why some people social distance and others do not.

Incredibly, a paper just came out looking at exactly that Proc. Natl. Acad. Sci. vol. 117 pp. 17667 – 17674 ’20 (28 July).  It’s likely behind a paywall so let me explain what they did.

The work was conducted in the first two weeks after the 13 March declaration of a national emergency.  Some 850 participants from the USA had their working memory tested using the Mechanical Turk from Amazon — https://en.wikipedia.org/wiki/Amazon_Mechanical_Turk.  Essentially they are volunteers.  I leave it to you to decide how characteristic of the general population at large these people are.   My guess is that they aren’t.

Then the 850 were subsequently asked how much they had complied with social distancing.

But first, a brief discussion of working memory — more is available at https://en.wikipedia.org/wiki/Working_memory

Working memory is tested in a variety of methods, but it basically measures how many objects you can temporarily hold in your head at one time.  One way to test it, is to give you a series of digits, and then ask you to repeat them backwards (after a lag of a second or so).  Here’s what the authors used —

“Participants performed an online visual working memory task, in which they tried to memorize a set of briefly presented color squares for  half a second and after a 1 second delay tried to identify a changed color in the test display by clicking on it using a computer mouse.”

The more you can hold in your head for a short period of time, the more working memory you have.  There is a lot of contention about just what intelligence is and how to measure it, but study after study shows that the greater your working memory, the more intelligent you are.

To cut to the chase — here are their results.

The greater their working memory, the greater the degree of compliance with social distancing.

Here is the author’s explanation –what’s yours?

“We find that working memory capacity contributes unique variance to individual differences in social distancing compliance, which may be partially attributed to the relationship between working memory capacity and one’s ability to evaluate the true merits of the recommended social distancing guidelines. This association remains robust after taking into account individual differences in age, gender, education, socioeconomic status, personality, mood-related conditions, and fluid intelligence.”

Talk about currency and relevance ! !   If failure of social distancing explains the rise in cases, studies like this will help us attack it.

Here is the older post with numbers and links

***

The News is Bad from Georgia

This is an update on a series of post about Georgia and the effect of relaxing restrictions on activity.  If you’ve been following the story, this post is somewhat repetitive, but I’d rather not leave newcomers behind. As of 14 July Georgia seemed to be bucking the trend of increasing deaths (but not of increasing ‘cases’ however defined).  No longer.

 https://dph.georgia.gov/covid-19-daily-status-report.  Page down past the map to the chart with 3 tabs —  cases (which means daily newly diagnosed cases), cumulative cases, and death.  Clicking on the tabs will move you back and forth (or better if your screen is big enough open the link twice and compared cases vs. deaths.

Georgia has changed the way it reports cases, no longer waiting 14 days before result are secure.  I also think they changed some of the older numbers.  I don’t recall seeing over 70 deaths in a day in May and June, yet the current chart shows 4 of them.  There is no way to get the old reports from the Georgia department of health, by clicking on the links in the old posts on the subject.  They all take you to the current one.

The 7 day average of deaths back in 25 April was 35, new cases  740 based on detection of viral genome or antibodies to it — not sick people

Sadly now the 7 day average of death is now 45 and new cases 3700.

The charts allow you to see when both new cases and deaths began to rise.  The number of new cases began to spike 16 June and the number of death began to increase 19 July (eyeball the charts, and you’ll see that these are not precise numbers.  So there was about a 1 month lag between the increases.

So were the doom and gloom sayers correct?  Here they are again to refresh your memory.

From The Atlantic — “Georgia’s Experiment in Human Sacrifice — The state is about to find out how many people need to lose their lives to shore up the economy.” — https://www.theatlantic.com/health/archive/2020/04/why-georgia-reopening-coronavirus-pandemic/610882/

Possibly they were right, but deaths actually decreased for a month or two after 25 April hitting a low of 13 daily deaths on 2 July.   I don’t think any of them predicted a lag of 2 months before the apocalypse.

Most likely it was a change in behavior.  Have a look at this  https://nypost.com/2020/07/18/video-shows-people-in-queens-flooding-streets-without-masks/.   It may not be a COVID party in name, but it is in fact.

At first glance it appears that they are trying for a Darwin award, but on second glance, based purely on a cost benefit analysis (to them only) the chances of a healthy 18 – 20 year old dying from COVID19 are less than 1 in a thousand.  Libido is incredibly intense at that age.   I’m not sure what I would have done in their shoes.  Here are some statistics from Florida with numbers large enough to be significant

Here is some older data from Florida  (from their department of health) — http://ww11.doh.state.fl.us/comm/_partners/covid19_report_archive/state_reports_latest.pdf

Age  Range     Number of Cases  Number of Hospitalizations Deaths

14 – 24              54,815                                503                                    12

25 – 34             70,030                              1,315                                    34

This is a risk of death if you are a ‘case’ however defined of less than 1/2,000.

This is age range of most of folks in the video. Further more recent examples are lifeguards in NY and on Cape Cod.

Think of all the gay men who knew full well how AIDS was transmitted, still got it and died.  Libido is powerful.  The classic example is Randy Shilts who wrote the magnificent “And the Band Played On” in 1987 about the early days of the epidemic.  He knew everything there was to know about the way the AIDS virus (HIV1) was transmitted yet he himself died of AIDS.

Further examples are lifeguards in NY and on Cape Cod.

 

New Delhi has 4.4 million COVID19 cases — Run !!

New Delhi has 4.4 million COVID19 cases ! ! !  Well that’s how the US press would have handled it, generating all sorts of clicks on their websites.  Fortunately the Indians are far more intelligent, noting that they have had a total 123,747 cases of clinical illness due to the pandemic virus, using the term COVID19 case as the term was originally defined — someone clinically ill with the virus.  That’s how the term was initially used in the USA, until they began calling a positive antibody test or finding the viral genome, COVID19.

How did they get the 4.4 million figure?  Well it’s based on tests for antibodies to the virus conducted from 27 June to 10 July, with a total of 21,387 samples from 11 districts of New Delhi by the National Center for Disease Control in collaboration with the Delhi government.  Here’s a link to a very circumspect article about the study — https://www.firstpost.com/health/over-23-delhi-residents-have-covid-19-antibodies-shows-sero-survey-data-ncdc-says-77-still-susceptible-8624511.html.

I’m hardly a regular reader of the Indian press, so I have no idea of the site’s reputation or orientation.  However they do quote National Centre for Disease Control Director Dr Sujeet Kumar Singh at some length.

At any rate the 4.4 million figure comes from multiplying the overall positivity rate from the samples (23.5%) by the population of New Delhi which is around 20,000,000 !

Also noted in the article is the number of clinically ill people with COVID19. The number of currently active cases of COVID19 stood at 15,288, and the overall total since the beginning of the epidemic is 123,747.

Clearly, if the study is to be believed, infection with the pandemic virus is usually benign and asymptomatic.

Addendum 23 July — People have been tested for antibodies to the pandemic virus just about everywhere now.  Amazingly, my home state of Massachusetts had tested some 60,000 souls for it by 18 June, but they won’t say how many had the antibodies ! ! That’s insane.  Would it destroy a narrative? https://www.bostonglobe.com/2020/06/18/nation/state-has-tested-60000-people-covid-antibodies-wont-say-how-many-tested-positive/

Where are the deaths?

Our current model of the pandemic is that if the number of people testing positive for the viral genome increases, deaths will increase.   Could the model be wrong?  We’re about to find out.  The number of cases diagnosed daily has markedly increased recently in Georgia and Florida.

The number of hospitalizations for illness due to the virus (e.g. the old meaning of Covid19)  in Miami Dade county rose from 607 on 15 June to 1,062 on 28 June. https://www.miamiherald.com/news/coronavirus/article243854907.html Certainly deaths are sure to show a similar increase.  Aren’t they?

Well so far deaths are falling as diagnosed cases are rising. https://experience.arcgis.com/experience/96dd742462124fa0b38ddedb9b25e429.  has data through 28 June (a Sunday, where reporting is likely to be slow).

If anyone knows how to get these graphics into a WordPress post, please let me know (just write a comment).  Every time I try my post collapses and nothing shows up.  The WordPress Gods must be angry with me.  The links will get you there however, but even then you’ll have to root around to find what I’m talking about.  Apologies.

There is a new WordPress editor out, and I’ll try it to see if it helps.

Florida is particularly good to study because every Friday they tally the number of cases with a positive antibody test for the virus for the past week.  These are people who have recovered, and who likely have never been very sick.  There would be little reason to test someone hospitalized with COVID19 for antibodies.  Here’s a link — http://ww11.doh.state.fl.us/comm/_partners/action/report_archive/serology/serology_latest.pdf.

It boils down to the fact that about 35% of 51,982 newly diagnosed cases of infection in the two weeks ending 26 June are really positive antibody tests.

Unfortunately Florida doesn’t have available a statewide number for the total hospitalized cases of COVID19 — like Massachusetts– https://www.mass.gov/doc/covid-19-dashboard-june-29-2020/download  — but with a population more (6.9 million) than  Miami Dade metropolitan area (5.5 million), there were only 760 cases statewide.

Now on to Georgia, which I’ve been following because they were one of the first states to lift restrictions.  As of 3PM today 29 June,  the 7 day moving average of daily deaths was 15 (this number is for 16 June, because Georgia doesn’t regard its numbers as solid until two weeks have passed).  On 25 April, the day the lockdown was partially lifted, the 7 day moving average of daily deaths was 41.

The number of cases in Georgia diagnosed (using both antibodies to the virus and the genome) has risen markedly in the past 2 weeks. Unfortunately I’ve been unable to find what percentage of the positive tests in Georgia are due to antibodies to the virus.

Both Florida and Georgia are so typical for what docs face all the time.  The data you have is never quite the data you’d like to have.

Now the time from hospitalization with COVID19 to death is unknown, but it’s unlikely to be greater than a month. However, for both states, given the rise in diagnosed cases, we had better see a rise in deaths, or something is seriously wrong with our model.

Has this ever happened before?  You bet.  The nationwide rise in obesity over the past several decades was predicted to have awful effects on mortality.  Yet life expectancy continued increasing.  For details see a copy of an old post after the ****

So I’ll revisit these states in two weeks or so to see if deaths have risen.  This post is long enough, but it’s worthwhile inserting two pieces of data from family and friends.  Family spies tell me that yuppies in Brooklyn are partying in the street without any protection.  Similarly, a friend from Baltimore notes  “Not many people are wearing masks in Baltimore or Washington, particularly individuals at high risk.”

Although Trump’s medical pronouncements are rightly ridiculed, I find it improbable that the bunch described above take what he says as holy writ and that he’s responsible for their behavior.

We are currently witnessing a massive social and medical experiment which would never get past an institutional review board.

****

https://luysii.wordpress.com/2011/03/20/something-is-still-wrong-with-the-model/

Something is still wrong with the model

We’re getting fatter and fatter as a nation and with fatness comes diabetes, hypertension, elevated lipids, strokes, heart attacks and death.  That’s the model.  There’s something wrong with it however, as people in the USA are living longer and longer, and deaths are dropping. The following is one of the first posts I wrote on the blog and it got a lot of play.

https://luysii.wordpress.com/2009/08/20/something-is-wrong-with-the-model/ (I’ll reproduce it here at the end of this post)

What’s happened since?  The following year the Center for Disease Control (CDC) reported a one month dip in expectancy to 77 years and 11 months.  Last week the CDC announced that because of a computer programming error the dip didn’t happen.   They also announced new data for the most ‘recent’ year available (2009 not 2010) and life expectancy continues to increase (now 78 years and two months for a child born today).  This is probably not a statistical fluke.  The data is based on death certificates. Why in the world we don’t have data for 2010 yet and why it took 14+ months for the CDC to collate the data for 2009 I leave to your imagination.

The absolute number of deaths  dropped by 36,000.  Now docs misdiagnose a lot of things but death isn’t one of them.  So my guess is that life expectancy is even higher, because the CDC is probably using the numbers the census counts rather than the numbers of people who are actually here (e.g. undocumented immigrants etc. etc.).

As noted earlier, one self serving explanation is that medical care is just getting better and better, and certainly it is, but it is very unevenly distributed, which was one of the points in passing ObamaCare.  More likely, in my opinion, is that obesity just isn’t as bad as its cracked up to be.  This goes against years and years of experience as a practicing physician.  Next time you visit a friend in the hospital, look at what’s lying in the beds — you will find the percentage of really heavy people much higher than the people walking the streets.  How many times have I seen an obese diabetic hypertensive, hyperlipidemic patient improve all 3 (and presumably their risk of premature death) by losing weight.   Yet facts must be faced — we’re not dropping like flies even though we’re getting fatter as a nation.  Any thoughts?

 

HERE’s the old post

Back in grad school when a theory came up with a wrong prediction, we all clapped hands because it showed us exactly where a new theory was needed, and just how it failed. No casting about for something to work on. A program that crashes intermittently is very hard to fix. Once you’ve found input that consistently makes it crash the job becomes much easier.

The Center for Disease Control released new data for 2007 (based on 90% of all USA death certificiates) showing that mortality rates dropped again (by over 2%) to 760/100,000 population. It’s been dropping for the past 8 years, and viewed longer term is half of what it was 60 years ago. Interestingly death rates from heart disease dropped a staggering 5% and even cancer dropped 2%.

But the populace is fat and getting fatter. This has been going on for 30 years. You can Google NHANES for the gory details, but the following should be enough. [ Science vol. 299 pp. 853 – 855, 856 – 858 ’03 ] The data from a recent NHANES (’99 – ’00) shows that the percentage of obese (as opposed just overweight) increased from 23% in the surveys from ’88 to ’94 to 31%. This is based on the body mass index (BMI). Someone 6′ 1″ would have to weigh 225 pounds to be obese.

We are told to be prepared for an epidemic of diabetes, high blood pressure, elevated blood lipids because of this. Every doc has seen blood sugar drop, blood pressure lowered, lipids come down in people with any/all of the above when they are able to lose a significant amount of weight. These diseases are significant only if they kill people, which they certainly seem to do in my experience. The next time you’re visiting a friend in the hospital, look at what’s lying in the beds. Very likely, many more than 31% of them are obese.

So why are death rates dropping and people living longer? Something must be wrong with the model — it’s pretty hard to quarrel with the data as being inadequate. Certainly the increased incidence of obesity should have produced something by this time (it started 30 years ago).

Well, the self serving answer for the drug developers is that their drugs are better. MDs would like to think it’s due to better care. Possibly. Here’s some detail.

#1: More people are exercising than they used to. How many joggers and walkers did you see on the streets 20, 30 years ago?

#2: Fewer people are smoking. Forget lung cancer (if you can). The big risk for smokers is premature vascular disease. Normally we all have carbon monoxide in our blood (it comes from the breakdown of hemoglobin). [ Brit. Med. J. vol. 296 pp. 78 – 79 ’88 ] Natural carbon monoxide production would lead to a carboxyhemoglobin level of .4 – .7%, but normal levels in nonsmokers in urban areas are 1 – 2%. Cigarette smoke contains 4% carbon monoxide, so smokers have levels of 5 – 6%. This can’t be good for their blood vessels.

#3: Doctors know more than they did. My brother is a very competent internist. He took over the practice of a similarly competent internist after his very untimely many death years ago. Naturally he got all the medical records on the patients. He found letters (now over 25 years old) from the late MD to his patients informing them of their lab results, and assuring them that their cholesterol was just fine at 250 mg%.

#4: The drugs are better. In addition they may be working in ways that we have yet to fathom. Consider the statins — their effect on vascular disease is far greater than their effect on blood lipids (cholesterol, triglyerides) — particularly when compared to other agents that lower blood lipids to the same extent.

Any further thoughts?