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Coronavirus

SARS-CoV-2: Is it one virus or two?

Speculation about a link from virus DNA to severity of disease and why some people are saying it is two viruses.

This chart from the Fred Hutch in Seattle is interesting. On the left it shows all 264 cases in which the entire 30,000 letters of the virus DNA have been read. When they were read, between the end of Dec and now, goes left to right on the bottom scale. Each branch is where one of the 30,000 letters has changed, giving the virus new, usually unpredictable properties. The map on the right is color coded to let you match where in the world the virus is when it made its DNA spelling errors. The bigger the colored circle on the map the more cases in that location.

I put a yellow hand written vertical arrow at about Christmas time when, still in China, the virus made a ‘trunk’ split; a single letter DNA mistake…one letter out of 30,000. The infections then spread around the world, with the larger two-thirds coming from the top branch into Iran, Italy, and the rest of Europe and the smaller one-third bottom branch going to America and Australia. More mistakes continued to be made off of that first split as the subsequent splits indicate.

What’s interesting is the viruses in the top branch are in the parts of the world with patients with more/worse cases. This could mean the ‘Christmas DNA letter mistake’ has true clinical meaning.

I am going to watch to see if the virus in the top branch continues to be more aggressive than the one in the bottom. Matching DNA sequences and clinical outcomes is a speculative hypothesis at this point however.

Only time will tell.

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Coronavirus

What’s in a name? Sometimes a learning.

In 1976 a strange, rare pneumonia epidemic broke out at an American Legion convention (picture) at an old hotel in Philadelphia. It became known as Legionaires’ disease (or officially legionellosis), caused by a bacteria (then new) named after the meeting called Legionella. So this old military veterans group have both a bacteria and the disease it causes named after them. It was traced to the non-circulating water in the roof air conditioners in that old hotel. That is where it has been found over the decades over and over again.

To this day, when someone asks me about a cough and they live or visit in an old, tall building in a city, I picture their air conditioning system looking like the actual picture below and I suggest a diagnostic test be performed for the Legionella virus. Here the name triggers a useful memory to make me a better doctor.

Additional word associations:

Lyme’s disease, named after Lyme, CT, a wooded New England town with lots of deer. Deer = ticks = disease.

West Nile virus, a river in a hot, equatorial jungle, like Uganda where it began.

St. Louis encephalitis virus, a southern city on a river.

Japanese encephalitis virus, first seen in 1870 in Japan and still the center of it.

MERS, the Middle East Respiratory Syndrome. Jumped to humans from camels, which have surprisingly similar immune systems to us. I’ll send the link entitled, “How Camels Revolutionized the Antibody Engineering Industry.” below. Using camels as ‘antibody factories’ like we use cows for milk is a reality! As they say in the movies, no camels were hurt during the making of these antibodies.

Cocksakie virus, discovered in 1948 in a fecal specimen in Cocksakie, NY while searching for a cure for the polio virus, so I remember it affects the brain/nerves like polio. So its like polio plus GI symptoms, that was why it was in the poo.

Spanish flu of 1918, named in France and which I remember because the Spanish called it the French flu; this reminds me it had nothing to do with either country/location but more with living conditions. Here the name provides a negative association.

So in the spirit of going along I will continue to call our current nemesis by its official name, SARS-CoV-2.

But you have to admit naming it after the huge (11 million) city in Asia where it began in an open air “wet market,” selling wildlife, could make a useful mental picture of some of its characteristics without offending people.

SARS-CoV-2 just doesn’t trigger anything.

Categories
Coronavirus

Coronavirus update, 1110 GMT, 10 Mar.

Speculation about a link from virus DNA to severity of disease and why some people are saying it is two viruses.

This chart from the Fred Hutch in Seattle is interesting. On the left it shows all 264 cases in which the entire 30,000 letters of the virus DNA have been read. When they were read, between the end of Dec and now, goes left to right on the bottom scale. Each branch is where one of the 30,000 letters has changed, giving the virus new, usually unpredictable properties. The map on the right is color coded to let you match where in the world the virus is when it made its DNA spelling errors. The bigger the colored circle on the map the more cases in that location.

I put a yellow hand written vertical arrow at about Christmas time when, still in China, the virus made a ‘trunk’ split; a single letter DNA mistake…one letter out of 30,000. The infections then spread around the world, with the larger two-thirds coming from the top branch into Iran, Italy, and the rest of Europe and the smaller one-third bottom branch going to America and Australia. More mistakes continued to be made off of that first split as the subsequent splits indicate.

What’s interesting is the viruses in the top branch are in the parts of the world with patients with more/worse cases. This could mean the ‘Christmas DNA letter mistake’ has true clinical meaning.

I am going to watch to see if the virus in the top branch continues to be more aggressive than the one in the bottom. Matching DNA sequences and clinical outcomes is a speculative hypothesis at this point however.

Only time will tell.

Categories
Coronavirus

Coronavirus update, Monday 09 Mar.

A lot of what we do is what I call ‘Science in the Middle.’ You want to know something about a big population so you take a sample of the population, study it, and then extrapolate to the population. 250,000 women (the population) get breast cancer each year so to get a new drug approved you test a sample, say 1,000, and then, if it works, extrapolate to the population.

But sometimes it is a new disease, what I call ‘Science at the Beginning.’ Here you are seeing something new, never seen before, but you think it is important and so you put out a description of everything you can about it with the hope it helps people look for more cases. Sometimes it grows into a population and you can do ‘Science in the Middle’ experiments and sometimes it stays small. Some of the findings in the first few patients will become universal findings and some will be ‘red herrings,’ unique to that patient. At the time you don’t know which is which, of course. This kind of science is called ‘Case Reports.’

The first case report of HIV on Jun 5th, 1981, involved five patients in LA over eight months, with a rare infection, usually only seen in end-stage cancer patients; but they didn’t have cancer. We now have 38 million cases worldwide.

In March of that year, 1981, I wrote a case report on the third case of an unusual kind of prostate cancer. 39 years later we now have exactly 21 cases in the world! So a tiny contribution to medicine.

The first patient in the US with coronavirus is charted below. Three notable findings:

1. Cough was the first symptom not fever. In fact he had a fever only after he was hospitalized. If common, this makes spread easier as the temperature screening method used everywhere won’t find early cases and stop contact.

2. He declined very quickly, only 72 hours from being at work to being in a hospital. So if you’ve been sick for a week at home it is not like this first case and so it may be just a cold or the flu..

3. The nausea and vomiting really throughout it, is unusual for respiratory viruses. My bet is this will end up being a great science clue, this ability to infect cells in the gut and the lung by the same virus at the same time, will become some new, important science understanding. Minority Report: this patient had TWO infections at the same time and this will be the exception. Time will tell…

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Coronavirus

Coronavirus update, 0210 GMT. A good trend…

Chart 1. The serious cases are at the lowest level since Feb 6th, over a month ago. Remember my ‘rule:’ you can’t die without being a serious case somewhere in the system, so a good predictor of the next week or so. It also broke an upward tick of serious cases we had a day ago; the down today might be a weekend reporting effect (folks are less vigilant in hospitals, etc. over the weekend) so will keep an eye on it.

Graph 2. 86% of active cases still in four countries: China, South Korea, Italy, Iran. France breaks into the top four for serious cases, replacing Iran. This is entirely because Iran doesn’t report serious cases. But it does show France is struggling a little.

US serious rate at eight for eighth day in a row. Surprisingly stable. BTW, I had an idea that folks were dying of coronavirus before being diagnosed and so I checked the CDC for a spike in pneumonia deaths, which might be coronavirus deaths not reported as such. None, actually pneumonia deaths trending downward.

Graph 3. When you watch the hours of coronavirus news this weekend on TV, please remember the two MD guild rules, secret since the time of de Vinci, which I will reveal to you now:

  1. When you, as a doctor, don’t know something revert to lot’s of Latin and a few big words. Latin’s been a dead language for 1600 years and so no one will call you out; and the white coat reflects not only broad-band visible light…but patient criticisms as well.
  2. Don’t reveal that you can cure a disease in a week but if the patient just stays home and drinks orange juice and eats chicken soup, they will recover in seven days. Very bad for business.

I will now be in witness protection for this ‘reveal’ so PM me if you need something! 

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Coronavirus

Coronavirus update from Coralville, Iowa.

Because the ‘coastal folks’ dominate the gadgets, cell phones, newspapers, etc. it is easy to forget that sometimes what goes on in the middle of the country can change the world.

So what does Coralville, IA, population 18,000, have to do with the coronavirus? Everything! This rural, largely farming community is ground zero for a key part of the science of this virus

In 1987 Dr. Joseph Walder was a newly minted MD, PhD from Northwestern with a vision: to start a company specializing in making DNA/RNA, arguably the most complex molecules in nature. The company became IDT, Integrated DNA Technologies. I worked with them about 13 years ago when I was developing a piece of RNA as a drug for Rheumatoid Arthritis. The darn thing worked well but my own little Shakespearean drama prevented it from being developed…you can learn what happened when the records are unsealed in 50 years! 🙂

Joe is a solid, salt of the earth man, great scientist, a practicing Jew, who just likes to get things done!

Fast forward to early January, when the first listing of the 30,000 letters in this virus’s DNA were available. Joe’s company was among the first to make a probe, a tool, that is the key part of a testing kit. When the hair-on-fire CDC folks contacted him about helping to make a test kit for the CDC he had already finished the weeks long process of making the tools and so FedEx could get them to the CDC by 10 am the next day. His company continues to make the probes for about 100% of the test kits in the entire US!

So next time you are on your five hour flight from LA to NY, look out the window at hour three and smile down on Coralville, the world’s center of coronavirus testing kit components.

Here is an interview with Joe! A few years ago he sold this little business he started for about $2 billion and is now splitting his time between IDT and his charitable efforts. This interview below focuses on the latter efforts.

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Coronavirus

Coronavirus 1300 GMT 07 Mar.

A/K/A the [China, South Korea, Italy, Iran] Virus:

95% of total cases in those four countries 88% of active cases in those four countries 86% of new cases in last 24 hours in those four countries

US report: five days of 7-8 serious cases is encouraging. This stability means when a death takes someone off this list they are being replaced with a new serious patient at about the same rate. Personally sad of course but public health perspective encouraging. If serious number starts to grow it is serious.

The South Korea [serious]/[active] ratio, applied to the US, suggests about 1500 active cases in US. South Korea has best DNA testing data.

US testing is the gap between 335 ‘total cases’ reported here and the untested, asymptomatic 1165 or so because US testing is just coming on line. So expect an artificial ‘surge’ in US cases over next week as DNA evidence replaces clinical symptoms.

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Coronavirus

Coronavirus update, 155 GMT.

Ending today on a positive note, for the first time in human history the evolutionary changes in a community epidemic of a new virus is being tracked in real time. The color coded genealogy in the middle is tied to the colors in the map on the right of where the specimen came from. Bubble size is number of cases from that location. Time is on the x-axis and each jump/indent is a new mutation.

The diversity line at the bottom is CRITICAL to vaccine development. This is the virus on truth serum telling the humans what part of its DNA book is critical and what part is changeable. Vaccines will zero in on the parts the virus is saying it can’t ‘live’ without; the places where no vertical lines tell you a mutation has occurred. So, for example, the right end of the DNA book has too many changes to be good for a vaccine. Etc… The observation that there are few long spaces without DNA mistakes is the reason a vaccine will be so hard to come up with.

24/7, as the sun travels over the sky, scientists are ‘reading’ viruses and putting their data into this system.

This whole, worldwide project is coordinated by our very own Seattle/Fred Hutch scientist, Trevor Bedford.