Category Archives: Medicine in general

TDP43 and the anisosome

Neurologists have been interested in TDP43 (Tar Dna binding Protein of 43 kiloDaltons) for a long time. Mutants cause some cases of ALS (Amyotrophic Lateral Sclerosis — Lou Gehrig disease) and FTD (FrontoTemporal Dementia).  Some 50 different mutations in the protein have been found in cases of these two diseases.  Intracellular inclusions containing TDP are found in > 90% of sporadic ALS (no mutations) and 45% of FTD.

TDP43 contains 414 amino acids (as you might expect for a protein with a 43 kiloDalton mass).  There is an amino terminal ubiquitinlike fold, two RNA Recognition Motifs (RRMs) followed by a glycine rich low complexity sequence prion-like domain at the other (carboxy) end.  The disease causing mutations are found in the low complexity sequence. 

A  phase separated structure (the anisosome) never seen before involves  mutant TDP43 [ Science vol. 371 pp. 585, abb4309 pp. 1 –> 15 ’21 ].  It is a phase separated mass with liquid spherical shells and liquid cores.  The shells showed birefringence — evidence of a liquid crystal.  The cores show the HSP70 chaperone bound to TDP43 (which wasn’t binding RNA).

ATP is required to maintain the chaperone activity of HSP70. When ATP levels are reduced, the anisosome is converted into the protein aggregates seen in ALS and FTD.  So the anisosome is a protective mechanism. 

Biology is clearly leading chemistry around by the nose.  No chemist would ever have predicted something like this, or received a grant to mix all this stuff in a test tube not even thinking about stoichiometry and see what happened.  For more details on phase separation please see an old post — https://luysii.wordpress.com/2020/12/20/neuroscience-can-no-longer-ignore-phase-separation/

Here’s some stuff from that post to whet your appetite

Advances in cellular biology have largely come from chemistry.  Think DNA and protein structure, enzyme analysis.  However, cell biology is now beginning to return the favor and instruct chemistry by giving it new objects to study. Think phase transitions in the cell, liquid liquid phase separation, liquid droplets, and many other names (the field is in flux) as chemists begin to explore them.  Unlike most chemical objects, they are big, or they wouldn’t have been visible microscopically, so they contain many, many more molecules than chemists are used to dealing with.

These objects do not have any sort of definite stiochiometry and are made of RNA and the proteins which bind them (and sometimes DNA).  They go by any number of names (processing bodies, stress granules, nuclear speckles, Cajal bodies, Promyelocytic leukemia bodies, germline P granules.  Recent work has shown that DNA may be compacted similarly using the linker histone [ PNAS vol.  115 pp.11964 – 11969 ’18 ]

The objects are defined essentially by looking at them.  By golly they look like liquid drops, and they fuse and separate just like drops of water.  Once this is done they are analyzed chemically to see what’s in them.  I don’t think theory can predict them now, and they were never predicted a priori as far as I know.

No chemist in their right mind would have made them to study.  For one thing they contain tens to hundreds of different molecules.  Imagine trying to get a grant to see what would happen if you threw that many different RNAs and proteins together in varying concentrations.  Physicists have worked for years on phase transitions (but usually with a single molecule — think water).  So have chemists — think crystallization.

Proteins move in and out of these bodies in seconds.  Proteins found in them do have low complexity of amino acids (mostly made of only a few of the 20), and unlike enzymes, their sequences are intrinsically disordered, so forget the key and lock and induced fit concepts for enzymes.

Are they a new form of matter?  Is there any limit to how big they can be?  Are the pathologic precipitates of neurologic disease (neurofibrillary tangles, senile plaques, Lewy bodies) similar.  There certainly are plenty of distinct proteins in the senile plaque, but they don’t look like liquid droplets.

It’s a fascinating field to study.  Although made of organic molecules, there seems to be little for the organic chemist to say, since the interactions aren’t covalent.  Time for physical chemists and polymer chemists to step up to the plate.

 

The United States lost the battle with the virus by March of 2020

Two papers published this February show that the USA had lost the ability to contain the pandemic virus by early April 2020.  The first paper was submitted in July 2020, the second in August.  They would have changed our perception of what we were up against in late 2020.  Here are links to both — they are not behind a paywall, and a friend who subscribes to neither was able to access them through these links.

The Nature paper is the most damning.  10,000 blood samples from Mt. Sinai hospital in New York City accumulated from February through July 2020 were studied for antibodies to the pandemic virus (whose presence implies previous infection)

Figure 1 p. 147 shows it best, with weekly numbers of tests and cases, in two groups — people attending urgent care and (more representative of the general population) patients who visited the obstetrics and gynecology department and visits for labour and deliveries, oncology-related visits, as well as hospitalizations owing to elective surgeries, transplant surgeries, pre-operative medical assessments and related outpatient visits, cardiology office visits and other regular office and/or treatment visits.

As you might expect the ER patients had a higher percentage of antibodies.  The first PCR confirmed case in the city was 1 March, with 1000 cases by the 15th. 

It was no secret that NYC was in the middle of the pandemic.  What is quite shocking is the number of people with antibodies (hence previously infected with the virus) in the presumably healthy group.  By 5 April 33/326  (10%) of tests were antibody positive, by 19 April 46/241 (19%) where it essentially remained to the end of the study in July.  Game over. Containment impossible. 

The second paper is from Boston where the virus genomes were sequenced from March through May of 2020.  The sequence of the viral genome tells you where the virus was coming from.  There were 120 separate introductions of the virus into the Boston area.  Most were from North America.  But of those from elsewhere how many do you think were from Asia?  Amazingly only 3.  How many from Europe?  19.  It’s like Wile. E. Coyote  peering earnestly toward Asia to nab the roadrunner, while a pack of roadrunners from Europe passes him from behind without him noticing a thing. 

It isn’t the fault of the authors that this information has just come out this month.  It would have changed our perception of the epidemic and what to do about it Trump or no Trump.  

20/20 hindsight is a wonderful thing.  Here’s Dr. Fauci doing the best he could with what he knew at the time — he is NOT to be faulted to saying this — he changed quickly. 

In the clip, Dr Fauci says “There’s no reason to be walking around with a mask. When you’re in the middle of an outbreak, wearing a mask might make people feel a little bit better and it might even block a droplet, but it’s not providing the perfect protection that people think that it is. And, often, there are unintended consequences — people keep fiddling with the mask and they keep touching their face.”

Fauci made this comment on an interview with 60 Minutes on March 8, a time when NYC proven cases were surging from 1 to 1000. 

Our vaunted intelligence service and the ‘situation room’ either did  not know or did not tell Dr. Fauci about the fact that the dean of a Hong Kong medical school wrote an article in the South China Morning Post 27 January 2020 stating that  “research shows self-sustaining human-to-human transmission is already happening in all major mainland cities.”  For details please see https://luysii.wordpress.com/2020/01/27/what-to-do-about-the-wuhan-flu/

Here are the links to the two papers cited above  https://www.nature.com/articles/s41586-020-2912-6.pdf

and https://science.sciencemag.org/content/sci.371/6529/eabe3261.full.pdf

Click to access 574.full.pdf

 

600,000 Pandemic deaths in the United Kingdom ! ! !

Yes, 600,000 pandemic deaths in the UK given their attack rate of 182/100,000 and a population the size of the USA (328 million) actually it’s even worse than that because their case fatality rate is 2.9 % and ours is 1.8% — so multiply the 600,000 deaths by 1.6 and you get a million deaths in the UK given their attack rate and case fatality rate (and scaling their population to match ours).

Where are these numbers coming from — the same place that those in the previous post came from — https://coronavirus.jhu.edu/data/mortality, Johns Hopkins. 

Here are the top ten attack rates per 100,000 population from the previous post

181.70, 180.83, 158.39, 155.25, 152.49, 143.61. 142.73, 140.98, 124.72, 118.50

You were asked to guess where the USA, and the UK were.  No the USA is not at the top, but in the middle (hardly great but not as bad as the 500,000 headline would imply).  The UK is at the top. 

Here are the 10 countries (alphabetized) from which these rates were drawn

Czech Republic, France, Italy, Mexico, Peru, Portugal, Slovakia, Spain, United Kingdom, USA

Here are the case fatality rates (in percent) from the same 10 countries

8.8, 3.5, 3.4, 2.9, 2.3, 2.2, 2.1, 2.0, 1.8, 1.7

The UK is 2.9 and the US among the lowest at 1.8  

Not what you’ve likely been led to believe.  

There are worse problems afoot for the USA.  Granted the following  are 3 small and nonrandomized samples, but the minorities who need it the most aren’t getting the vaccine (and not because it is being withheld from them).

Sample #1 Yrs Trly and wife second shot yesterday —

My wife and I received the booster dose of the Pfizer vaccine today. We live in a town that is 45% Latino (mostly Puerto Rican). Both times we were there, the vaccinees were almost all Caucasian, a disaster in the making. The nurse I spoke with said that what we’d seen about Latinos not getting vaccinated was typical in her experience. She also noted misinformation going around among them, such that vaccination would make you sterile.

Sample #2 a friend who was vaccinated elsewhere (but in the same metro area)- “That was my experience at the State Curative site at XXXXXXX. Large African-American population in that area; however, only caucasians getting the vaccines on both occasions. Puzzling.”

Sample #3 a college classmate and friend –Welcome to the club. I received my vaccine through Hopkins as a practicing clinician. My wife received hers as a DC resident through the DC Government in a Black neighborhood; all of the vaccinees there were whites from Foggy Bottom and Georgetown. the DC Government then got smart and has been allocating vaccine by specific neighborhood.

Now there was a giant article in the 4 January New Yorker by Lawrence Wright blaming the magnitude of the pandemic on Trump’s not pushing mask wearing. 

Well here’s our Vice President — https://abc7ny.com/vice-presidential-debate-vp-2020-kamala-harris/6852144/

Harris was asked if Americans should take the vaccine and if she would. Harris says that if doctors “tells us that we should take it, I’ll be the first in line to take it, absolutely. But if Donald Trump tells us that we should take it, I’m not taking it.”  Well he did tell us exactly that. 

Is it her fault that minorities aren’t taking the vaccine?  Don’t wait for the New Yorker to take up the issue. 

 

500,000 US deaths from the pandemic ! ! !

My wife and I received the booster dose of the Pfizer vaccine today. We live in a town that is 45% Latino (mostly Puerto Rican). Both times we were there, the vaccinees were almost all Caucasian, a disaster in the making.

The setup was a marvel of efficiency. The time of vaccination was written on a sticky, which was to be placed on the (widely separated) chairs we sat on for 15 minutes, watched by several nurses for any symptoms.  As soon as we got up, someone (a Latino wouldn’t you know) zoomed over and sterilized the chair. The nurse I spoke with said that what we’d seen about Latinos not getting vaccinated was typical in her experienced. She also noted misinformation going around among them, such that vaccination would make you sterile.

I asked her how she though the USA was doing vis a vis other countries, and she said she thought that we were the worst, and quoted the front page of the New York Times of 21 February.

Well, we have two sets of actual statistics available. The first is mortality from the pandemic per 100,000 population and the second is the mortality rate of symptomatic cases (case fatality ratio).

Here are the top ten mortality rates per 100,000 population

181.70, 180.83, 158.39, 155.25, 152.49, 143.61. 142.73, 140.98, 124.72, 118.50

Here are the 10 countries (alphabetized) from which these rates were drawn

Czech Republic, France, Italy, Mexico, Peru, Portugal, Slovakia, Spain, United Kingdom, USA

Here are the case fatality rates (in percent) from the same 10 countries

8.8, 3.5, 3.4, 2.9, 2.3, 2.2, 2.1, 2.0, 1.8, 1.7

Your job is to match the countries with rates based on what you’ve read and what you know.  At least guess where the USA and the UK fit in. 

Answers and further commentary tomorrow 

 

The uses and abuses of molarity — II

Just as the last post showed why a 1 Molar solution of a protein makes no sense at all, it is reasonable to ask what the highest concentration of a single protein in the cellular environment could be. Strangely, it was very hard for me to find an estimate of the percentage of protein mass inside a eukaryotic cell. There is one for the red blood cell, which is essentially a bag of hemoglobin. The amount is 33 grams/deciliter or 330 grams/liter. Hemoglobin (which is a tetramer) has a molecular mass of 64,000 Daltons.  So that’s 330/64000 = .5 x 10^-3 Molar.   So all proteins in our cells have a maximum concentration at most in the milliMolar range.

Before moving on, how do you think the red blood cell gets its energy?  Amazingly it is by anaerobic glycolysis, not using the oxygen carried by hemoglobin at all.  Why? If it used oxidative phosphorylation which runs on oxygen, it would burn up.  That’s why red cells do not contain mitochondria. 

On to Kd the dissociation constant.  At least 475 FDA approved drugs target G Protein Coupled Receptors (GPCRs), and our genome codes for some 826 of them.  Almost 500 of them code for smell receptors, and of the 300 or so not involved with smell 1/3 are orphans (as of 2019) with no known ligand.  There are GPCRs for all neurotransmitters which is why neurologists and psychiatrists are very interested in them. 

The Kd is defined as [ free ligand ][ free receptor ]/ [ ligand bound to receptor]  where all the  [  ]’s are concentrations in Moles/liter (e.g. Molar concentrations). 

There’s the rub.  Kd makes sense when ligand and receptor are swimming around in solution, but GPCRs never do this.  The working GPCR is embedded in our cell membrane which topologists tell us are 2 dimensional manifolds embedded in 3 dimensional space.  What does concentration mean in a situation like this?  Think of the entropy involved in getting all the GPCRs to lie in a single plane.  Obviously not so simple.  

People get around this by using radioactive ligands, and embedding GPCRs in membranes and measuring the time for ligands to bind and unbind (e.g. kinetics), but this is miles away from the physiologic situations — for details please see

2019 Apr 5; 485: 9–19.
 
The same is true for other proteins of interest — ion channels for the neurologist, hormone receptors for the endocrinologist, angiotension converting enzyme 2 (ACE2) for the pandemic virus.  
 
I think that all Kd’s of membrane embedded receptors do is give you an ordinal ordering (e.g. receptor A binds ligand B tighter than ligand C ) but not a quantitative one.
 
Next up, how a Nobel prizewinner totally misunderstood the nature and applicability of molarity and studies on a two dimensional gas (complete with Pressure * Area = n * Gas Constant * Temperature).
 
 

 

How to get vaccinated early

Here is a completely ethical way to jump to the head of the line and get vaccinated before you should have been. I did it quite unconsciously, taking my wife in for her scheduled vaccination 1 February in the midst of a blizzard whose intensity was impressive even by Montana standards. It was toward the end of the day and the place was pretty empty. I had an appointment for the 9th and my wife asked if I could get in if there had been cancellations (which there seemed to be). So they took me.

This turned out to be ethical because they were administering the Pfizer vaccine, which has to be used after being thawed out or thrown away (it can’t be refrozen). It really is a situation of use it or lose it.

So that’s what you do — go to a place administering the Pfizer vaccine (this won’t work if they’re giving the Moderna vaccine which can be refrozen) and ask there have been any cancellations.  Do this late in the day.

At last something useful from this blog.

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

Montana girl does good, real good !

Montana is flyover country. Nobody smart lives there. We all know that.

But when I got there in 1972 an issue of Science contained an article by State Legislator about a modification of general relativity — https://en.wikipedia.org/wiki/Kenneth_Nordtvedt.  MIT grad, Harvard Junior Fellow etc. etc. 

Then there was the son of a doc I practiced with in Billings.   Honors physics at Billings Senior high school placed him in 2nd year physics at Harvard, from which he graduated in 4 years obtaining a masters in physics as well. 

Then there was a local boy, the Thiokol engineer who predicted the Challenger disaster and was over-ruled. 

The great thing about Montana was that no one ever bragged about this sort of thing.  There were so few people, that no one felt compelled to tell you about themselves, you’d find out about them soon enough.  The classic example was an excellent surgeon and friend I practiced with for 15 years.  Only on reading his obituary last year did I find out that he had a Fulbright after college.

Which brings me to Lindsay, a girl I first met when she was a high school student.  The family were ranchers with a beautiful spread on the east face of the Crazy mountains north of Big Timber.  I’m not sure how we first met — I don’t think I saw any of them as a patient.  But we all became friends and the galactic premiere of a cello sonata I wrote with a 19 year old secretary in a lumberyard was in their living room. 

The two least important things about Lindsay are that she was a centerfold and an olympic silver medalist in woman’s two person crew.  Don’t get excited about the centerfold bit, she was fully clothed, but for some reason the Harvard Alumni magazine had a 2 page picture on a field of daisys of her back in the 80’s when she was there. 

Lindsay went on to get a PhD from Cambridge and her work and that of her husband may have come up with something useful for Alzheimer’s disease.  I’ll talk about the science behind it in a future post.  But when the news broke today, the stock of her company hit 70  (it was around 7 at the beginning of the year).  For details please see — https://finance.yahoo.com/m/49fa6153-4235-3866-bff2-5a35470e54da/why-cassava-sciences-stock.html.

Couldn’t happen to a nicer girl.  Of course it didn’t just happen.  Decades of hard work went into it.  So as you fly across the country, look down.  Some people down there might be even smarter than you are. 

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. 

 

 

How wrong could I be ?

I wrote a post 13 September saying the SARS-CoV-19 virus mutations were nothing to worry about. Some 19,000 were already known, and anything bad should have happened already, so we were in the clear. You can find a copy of this post below the *****.

If there ever was a case of ‘absence of evidence is not evidence of absence’ this is it. A sample taken in England that month (but not reported until November) found the B 1.1.7 variant which is more infectious).

So it’s time to take stock about the future course of the pandemic. 

First — the new strain had all sorts of mutations (23 depending on how you count them).  This was unprecedented, and why I was so sanguine in the post.   We now understand how this might have happened due to one very well studied case [ Cell vol. 183 pp. 1901 – 1912 ’20 ] in an immunocompromised patient with chronic lymphatic leukemia, shed the virus for 70 days.  The patients wasn’t symptomatic, but because the patient had enough immune system to fight the virus to a draw, it persisted, and its genome was always changing.  Now we worry that infection in people getting just one dose of vaccine might show the same characteristics, being incubators for multiple mutations.

So it’s going to be cat and mouse with the virus for the forseeable future.  Fortunately as new mutations occur leading to more infectious and/or more virulent viruses, we’ll know exactly what they are, and can change the mRNA in the vaccine to exactly match them. 

Even better, research is now swinging into high gear to find out what the virus is doing inside cells. Several studies [ Cell vol. 184 pp. 92 – 105  ’21 ] have infected cells with the virus, and then used CRISPR to knock out a bunch of genes, the cells that survive have had a gene knocked out that the virus needs pointing to a line of attack.  Other studies (using other types of cells) have also found other  genes essential for the virus, but there is little overlap in the genes that they find.

This line of attack is good, particularly when you remember that despite 40 years of work we have no vaccine against AIDs, but we have all sorts of drugs inhibiting the virus inside the cell, so that AIDs has become a chronic manageable disease rather than a death sentence (as it was when I was in practice).

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Why the news about SARS-CoV-2 mutations is actually good

How can the latest news about mutations in the pandemic virus be good?   Simply this — there are so many known ones, that it’s almost certain that nearly every possible mutations has been formed out there, and since not much has changed about the lethality of the virus, none of them are that bad.  Not only that, but the ones that haven’t occurred must be lethal to the virus and will give us new ideas about how to attack it.

Here is a link to an article (vol. 585 pp. 174 – 177 ’20) in the current 10 September Nature — https://media.nature.com/original/magazine-assets/d41586-020-02544-6/d41586-020-02544-6.pdf.  Hopefully not behind a paywall. It’s definitely worth a read

You’ve probably heard about the D614G mutation in the spike protein of the virus.  It came out of nowhere and has taken over worldwide, even in areas where different forms of the viral genome were previously established.  D is the one letter abbreviation for aspartic acid, one of the twenty amino acids, and G stands for another one glycine.  This immediately makes bells ring for the chemist, because glycine is the smallest amino acid, having a single hydrogen atom for its side chain, while the side chain of aspartic acid contains 2 carbons 4 hydrogens one oxygen and one nitrogen atom.  So there’s a lot more room for the protein where aspartic acid used to be.

Whether or not the mutation made the virus more infectious still isn’t known.  It appears to be more infectious in studies using pseudoviruses.  Not everyone has a high level containment facility, so people work with the AIDS virus (HIV1) which doesn’t need one and simply change one of its proteins to the spike protein of the pandemic virus (yes we have the technology to do that).  Then they infect cells with the pseudovirus.  Translating this to whole organisms (us) with the real virus requires a leap of faith.  It’s a long leap, but pseudoviruses are the best thing we have at present.

Here are three quotes from the article ”

“More than 90,000 isolates have been sequenced and made public (see http://www.gisaid.org). ”

“Two SARS-CoV-2 viruses collected from anywhere in the world differ by an average of just 10 RNA letters out of 29,903,”

“Researchers have catalogued more than 12,000 mutations in SARS-CoV-2 genomes. ”

How many mutations are possible in the  viral genome?  Just 29,903 times 3, because at each position, the element normally there can change to only 3 others — the viral genome is made of RNA is a linear chain of only 29,003 nucleotides, and each nucleotide can be uracil (U), adenine (A) guanosine  (G) or cytosine (C).  That’s it.  Proteins can have 20 different amino acids at each position.

So 13% of all possible mutations have been found in the virus, out of only 90,000 completely sequenced genomes. There are now 28,000,000 cases out there, so it’s almost certain with 1,000 times more virus out there to sequence, that nearly all the other 44,000 or so possible mutations have already occurred somewhere in the world.

How can this be good news?  Because if any of them were truly horrible, we’d know about it.  It would have taken over just the way the D614D mutation did.

But there’s even more to be gleaned from this work.  Hopefully http://www.gisaid.org is continuing to accumulate more and more sequences from all over the world.  Suppose certain mutations don’t show up.   This means they are fatal to an infectious virus.  Since we know exactly what proteins the virus is making and what stretch of the genome makes each one, this should suggest  clear lines of attack into the virus.