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  • Mutations

    Posted by Assistant Village Idiot on April 24th, 2020 (All posts by )

    Note that Greg Cochran over at West Hunter remains pessimistic about life becoming safer. Mutations are of course already occurring in C19, just from the numbers.  Most of those will be deleterious to the virus itself, or neutral.  But sheer volume produces mutations that are also diseases, some lesser, some greater.

     

    29 Responses to “Mutations”

    1. Mike K Says:

      Then last time I looked at his blog he was discussing passages. That refers to infecting new cases, which in the case of smallpox, tended to weaken the pathogenicity of the virus. This was the technique of the “Variolationists.” Variola is the smallpox virus and there were examples going back to the 18th century of inoculating people with the virus to create resistance or immunity, which was not understood at the time. Catherine the Great hired a British inoculator to inoculate hundreds of her servants after which the weakened virus was used to inoculate her family. Her reward to the inoculator created one of the great English fortunes.

      However, passaging the virus through species, as happens with pigs and ducks in rural China, may enhance pathogenicity. This is where the annual flu epidemics begin. China has had a particularly bad epidemic among its pig population.

      African swine fever has spread to Southeast Asia and eastern Europe, with cases found in Vietnam, Cambodia, Laos, Korea, Myanmar, the Philippines, Poland, Belgium and Bulgaria. Around the globe, those countries and others that have so far sidestepped the epidemic are cracking down on travelers, increasing cargo screenings and banning meat imports.

      Now we have a virus native to bats that has infected another species, humans, and that may enhance pathogenicity. Whether passages through millions of human will affect the virus through mutation is still to be discovered. There does appear to be multiple strains created by mutation. The S and L strains have been known for months. The S appears to be less virulent and the L more so but I see nothing on PubMed yet about it,

    2. Assistant Village Idiot Says:

      Good comment. History is being neglected in much of the discussion, as people prefer to put things in categories they are familiar with, like seasonal influenza.

    3. MCS Says:

      Now that antibody tests are starting to come out, the “experts” are recapitulating their mistake of deploying them where they will give the least insight to the actual course of the epidemic. It’s great news that the infection rate in NY is 20%, it means for all the sound and fury in the media, it was the flu. It’s mostly irrelevant for the rest of the country.

      What we need to guide the decisions in all the places with low apparent rates from hospitalizations is this same underlying rate of infection. If the rate is very low, it follows that a wave of hospitalizations will follow as it works its way through the population, picking off those that are vulnerable as the rest fail to notice that they’ve even been infected.

      I know it’s been in at least one of Trent’s many posts but it’s worth remembering the story about how they decided where to add armor to the B-17. The assessors realized that the damage was distributed at random, but they were only seeing the planes that made it back to England. Therefore, the places that they didn’t see damage were where the most fatal damage was occurring and where the armor was needed first.

      Until we know what the underlying rate is in the areas away from the hot spots, any projections are just guesses and probably bad ones at that.

      After Pearl Harbor, one of the things that Admiral Kimmel was criticized for was not concentrating his long range search in the direction where the Japanese would most likely attack from. Instead he dispersed the flight paths so widely that they were completely ineffective.

      Finally: I’ve read more than once that doctors are supposed to be taught to never order a test unless the results will change the treatment. Reserving the testing to those that were already in the hospital with serious symptoms and then further restricting them to only those that had some sort of exposure to China gave exactly zero information about the actual conditions and the probable course of the epidemic. Since it didn’t actually benefit the patients either, it may have been an ethical violation as well as a waste of time and resources.

      Since we all, already have a headache that’s not going away from hitting ourselves in the head with a hammer called lockdown. It would be useful when we stop, to know whether to expect a wave of hospitalizations and be ready for them, as the virus works its way through the population or if it already has. We don’t have a choice about lifting the lockdown. Actually knowing what to expect would be helpful. To do that we have to look in the right place.

    4. The Dark Lord Says:

      chance of death in US before corona .75757% if corona kills 100k then it goes all the way up to .78787% … if you feel unsafe today then corona or not you won’t feel safe tomorrow …

    5. Mike K Says:

      I’ve read more than once that doctors are supposed to be taught to never order a test unless the results will change the treatment

      You must remember that the country is run by lawyers who know to never ask a question that answer to which you don’t know. The FDA and CDC people who pretend to be doctors think like lawyers.

      I can’t recall if I mentioned this here before but drive-in movie theaters in Florida are full. I anticipate that as malls die off, they might be replaced by drive-in theaters.

      Doctors are also taught that any test result that is a surprise, needs to be repeated.

    6. Dan from Madison Says:

      “It’s great news that the infection rate in NY is 20%, it means for all the sound and fury in the media, it was the flu. It’s mostly irrelevant for the rest of the country.” This.

    7. David Foster Says:

      Mike K…”I anticipate that as malls die off, they might be replaced by drive-in theaters.”

      I haven’t done the calculation, but intuitively, the value per square foot of a drive-in theater must be much lower than that of a successful mall. If this is correct, then such conversion very deflationary for land prices in the area.

    8. Mike K Says:

      the value per square foot of a drive-in theater must be much lower than that of a successful mall.

      I would only ask where the “successful malls” are. The Laguna Hills Mall in OC is resembling 1946 Berlin. Half torn down. The Evergreen Park Mall in Chicago, near my sister’s home, is empty. The Tucson Mall is half empty.

      In the post corona virus world, I’m not sure that many will survive. Aside from the issue of on line shopping, the attraction of large enclosed spaces is questionable. Outdoor malls, like Fashion Island in Newport Beach CA, will probably remain. The enclosed malls typical of colder climates, may not survive. I still remember the first enclosed mall I saw, in Tacoma WA, in 1965. They were a new concept.

      I’m just speculating but it seems possible.

    9. Anonymous Says:

      As regards malls, here in San Antonio over the last twenty years, I’ve seen one totally-enclosed mall torn down and replaced by open-air clusters of stores – it was directly across a major avenue to a mall which is still going strong, although I have only set foot in it a couple of times since the business that I worked in, across the road from it, some fifteen years ago. That mall is all high-end clothing, jewelry, accessories, shows and makeup. All the interesting and varied stores that I liked (like the book store, and the Museum Store, the Body Shop and Caswell-Massey) moved out.
      Another mall closed up entirely, and was taken over by Rackspace as their operational HQ. A third mall is half offices of various sorts now. (Horrible place – I had the con crud after doing an event there, as the entire inside of the place smelled musty and moldy.) And a fourth mall – the one nearest me, has always seemed about half-dead. I don’t know what keeps it staggering on, like some kind of horrible retail zombie. Once the Sears outlet closes, I don’t think it will be long for the world.
      And yet – a long and extensive retail development just miles from it, at the confluence of 35 and 1604 is doing … well, it WAS doing well before the advent of the Wuhan corona-crud. Mostly big box outlets, a Target, Hobby Lobby, Home Depot, with a nice mix of small specialty stores. Early last year, a new open-air shopping center opened, Live Oak Town Center, anchoring on an Ikea store, which is the only Ikea until you get to Round Rock, about a two-hour drive. They had just completed an Olive Garden there, when the Corona Crud hit. I don’t know what other retail outlets were planning on building in that space.
      Guess we’ll know by the end of the year.

    10. Sgt. Mom Says:

      Above comment at 4:12 was me.

    11. David Foster Says:

      Yes, I think the outdoor malls have a better choice…especially, I think, the “New Downtown” areas created by Federal Realty Trust and a few other REITs. These areas typically include stores, apartments, restaurants, offices, etc.

      They will be hurt by reduced office occupancy as work-from-home becomes more accepted, as well as by the retail and restaurant issues. But the best of the species, I think, will survive.

    12. Mike-SMO Says:

      The testing question comes from 2 worlds. Public health agencies have different needs than physicians. CDC blew the early opportunity to understand the existance and spread of the COVID-19 virus.

      Disease “mutation” is a thing but that ignores the fact that south China (Asia) has been a pest hole for new and “interesting” diseases for several millenia. Before Boeing asnd AirBus got involved, I suspect that a good number of diseases showed up along major bird migration routes (e.g. MERS). After all, the outbreak of the “seasonal Flu” comes after the Fall bird migration.

      Disease “mutation” traditionally leads to milder forms of disease since dead victims don’t help the virus/bacteria to spread. Measles was once very lethal.

      Disease “mutation” may allow for a “seasonal” form of the disease. Looks like the lab guys/gals will have lots to do.

      Disease “mutations” can be useful. The mild “Cow Pox” virus allowed the relatively safe generation of immunological resistance to the similar, but deadly “Small Pox” virus. Thus “mutation” provides “opportunity” for the smart people in the lab.

      The “work from home” thing is for paper shufflers. You don’t build and distribute from your basement. “Outdoor” malls are for the south and west. The real world has rain, snow, and freezing temperatures. Like “seasons”. HVAC (and filtration) and sanitation will matter for the future. China/Asia has tolerated death and disability from disease. The West came up with vaccination, soap, clean water, flush toilets, and garbage collection.

      “Mutation” isn’t just a viral thing. Wash your paws, and enjoy the ride. Whatever next crawls out of the south China rice paddies, where the wild animals, farm animals, and humans all drink, eat, and crap, will be worth a horror movie or two.

    13. Assistant Village Idiot Says:

      The focus on what percentage of people are dying is misguided. We do not apply that to other new problems. What percentage of Americans die in war? So, no problem then, right? Have all the wars you want. What percentage of Americans was killed in 9/11? What percentage of people die in car accidents? Drug overdoses? Shootings? So no problem right? We can just ignore those. If you use those sorts of statistics for C19 you have to apply them across the board. You will notice that we never quote those statistics because we know they are not the real issue. Therefore, trying to use them now to make a point isn’t especially enlightening.

      A new disease that kills 50,000 Americans and still going is a very big deal. It doesn’t happen very often. Additionally, that is 50,000 even with dramatic precautions. That government officials have not covered themselves in glory is not surprising. However, it doesn’t mean that it’s a free-for-all, with everyone’s opinion being equally valid.

      The history of epidemics is really ugly, and illustrate the instability of contagion. Fitting things into categories we are more familiar with is just evasion.

    14. Assistant Village Idiot Says:

      Oh, and one more thing, as Columbo used to say. Read the comments at the link. There are some very smart and deeply informed people over there. I wish we had some of them in positions of power instead of the experts we have now.

    15. Mike K Says:

      There are some very smart and deeply informed people over there.

      Most of them know more than I do and I have a virology book ordered to bring me up to date. I read that blog every few days,

    16. Gavin Longmuir Says:

      AVI: “A new disease that kills 50,000 Americans and still going is a very big deal.”

      What about all the old diseases? The ones that kill about 2,800,000 Americans in the course of a year?

      And what about the overlap between the 50,000 who die with C-19 and the 2,800.000 dying of other diseases? There is bound to be some overlap, since we know that those dying with C-19 generally have co-morbidities — serious prior medical issues. Whether the overlap is 5% or 95%, we will have to wait till the end of the year to find out.

      I am not trying to make light of the plight of those people experiencing big problems with C-19, but please let’s keep a sense of proportion. CNN won’t be carrying panic-inducing headlines about Americans suffering and dying because of the Political Class over-reaction to C-19 — but those people will exist. People were scarred for life by the experience of the Great Depression in the 1930s — and now our Betters are creating a new generation of children & young people scarred by economic privation.

      Balance! Let’s have balance.

    17. newrouter Says:

      >A new disease that kills 50,000 Americans <

      About 7000 Americans die per day(https://www.cdc.gov/mmwr/volumes/68/wr/mm6826a5.htm). In the last 30 days 210,000 deaths. Those 50,000 checked out early. Go away fear monger!

    18. Mike K Says:

      There is also the issue of annual deaths from flu, the most common communicable disease since cholera and typhoid went away. I got all the childhood diseases before most of the vaccines came along. A few were really dangerous, like measles which killed thousands of soldiers in Civil War army camps. Tetanus was not a problem in the Civil War because hose manure was not used in the locations of battlefields. In WWI it was a huge problem with war wounds. Belgium used horse manure to fertilize fields.

      Polio was the great epidemic when I was a child. Now it and smallpox have nearly been eradicated. The likelihood of a C19 vaccine by fall is iffy. It is an RNA virus and subject to lots of duplication errors, hence lots of mutations. Many will be lethal to tyhe virus but some will persist as they do in Influenza.

      The most bizarre aspect of this epidemic is the politics around hydroxychloroquine.

    19. Assistant Village Idiot Says:

      @ Mike K – hydroxychloroquine and politics, yes. I am not that hopeful it turns out to be that helpful, largely because magic seldom happens with new medicines, including new uses for old medicines. I believe the old joke among physicians was that you should take a medicine while it was new and still did miracles. After a few years the miracles seem to wear off.

      But it was never a crazy idea, and seemed at least worth pursuing. Why Trump decided he was going to get behind it should puzzle me, but it doesn’t, because that is the type of talking off the top of his head and then sticking to it that he does. I agree about a quick vaccine. There are always promising things on the horizon, but only a minority of them materialise.

    20. Mike K Says:

      I am not that hopeful it turns out to be that helpful, largely because magic seldom happens with new medicines, including new uses for old medicines.

      You really should read the history of penicillin. Sulfa drugs came first by gradual stages, beginning with Scarlet Red dye, then Prontosil.

      Back in the laboratory Domagk fought successfully against that helplessness. This year marks the 75th anniversary of Domagk’s 1935 landmark paper introducing Prontosil Rubrum, the first drug to cure bacterial infections and the first of many sulfa drugs.

      After serving in the Sanitary Service during the war, Domagk returned to medical school and later became the director of the Institute of Experimental Pathology at I.G. Farbenindustrie. Here Domagk led the research to develop treatments for common bacterial infections. After a number of unsuccessful attempts I.G. Farbenindustrie chemists repeated an old trick used to make dyes bind better to wool. They introduced sulfonamide function into azo dyes and found a promising chemical combination. The new sulfonamide successfully cured mice infected with an extremely virulent form of Streptococcus pyogenes. On Christmas Day, 1932, I.G. Farben submitted a patent application for sulfonamide dyes, one of which would be named Prontosil Rubrum.

      Penicillin came suddenly but there were problems. Fleming is often given credit, but it is Florey who really discovered it and learned how to make it. The first patient was a policemen who developed sepsis from a rose thorn scratch. He improved but they ran out of the drug and he died.

      I was a child of 6 in 1944 when I got scarlet fever, which is a reaction to streptococcus. It was quite dangerous and I was quarantined. My mother was allowed to stay. I even got a small dose of penicillin. Those were the days when they collected urine as it could be extracted from urine unchanged.

      I think we are going to learn that HCQ is effective early and about 60% or so respond. Maybe more. It is completely safe. The stuff about cardiac risk is nonsense. More politics. I have read that people taking the low dose for lupus or rheumatoid arthritis, like my wife who has taken it for three years, are protected from the virus in spite of altered immune system. It might be years before the real story is accepted.

      I compare it to the story of the Atkins Diet, which has taken 50 years to become accepted. I have a section in my medical history about that.

    21. David Foster Says:

      Penicillin…”It is Florey who really discovered it and learned how to make it.”

      I think the general public perception is that all the hard part in pharmaceuticals is in the original research, and the manufacturing is pretty trivial by comparison. I don’t know how generally correct this is.

      Based on what I’ve read & heard, the class of drugs known as Biologics is indeed pretty tricky to manufacture.

      https://www.bluelatitude.com/site/assets/files/4375/introduction_to_the_manufacturing_of_biologics_-_blue_latitude_health.pdf

    22. Mike K Says:

      Fleming made the discovery by serendipity. He left some Petri dishes he had inoculated with staph out side the incubator because he was leaving on vacation. He opened the covers for a moment to inoculate the agar gel. Someone on another floor at St Marys was working with Penicillium mold. Spores must have circulated in the building and floated into that Petri dish in the moments he had the cover off. While he was gone, London had a heat wave, which allowed the Staph to grow, then cooler weather that allowed the Penicillium to grow. It does not grow at high temps.

      When he returned, he realized what had happened as he had previously worked with lysozyme in tears, which acts similarly.

      Almoth Wright, who was the head of Fleming’s department, did not want him working on that project and he dropped it.

      Florey was years later and was told of the mold by an employee who had kept it growing for years. The news media in England did not like Florey, who was Australian and resisted publicity. There was a serious effort to deny him the Nobel Prize and give it only to Fleming.

      The story is in my book.

    23. Grurray Says:

      Yesterday Bannon interviewed Dr Zelenko about hydroxychloroquine

      https://youtu.be/QHFNJpRMlpg?t=276

      Although I’m skeptical of his claims of how zinc fits into the whole combination, you can’t argue with results. He says that most medical staff on the front lines are now taking it for prevention, including him, and I believe that.

    24. MCS Says:

      We all seem to be lagging far behind the current standard of care. I am informed by no less than the wife of someone on television that all you need is I.V. vitamins administered by a doctor that makes house calls in a hazmat suit, bathing in a dilute Clorox solution, the application of some sort of energy charging device and other assorted woo. And we were all wasting time on ventilators and masks.

    25. Mike K Says:

      I didn’t listen to the whole video but he is right to treat early. As early as possible.

      There was a story in the Tucson paper about a month ago about the first death from the virus.

      The woman was 54 and was an example of how to NOT treat this.

      Her illness kept getting worse over a few days. She tested negative for the flu and then eventually found out she had pneumonia. A lung X-ray prompted her doctor to order a COVID-19 test.

      Three days later, her test result came back positive. And within minutes of arriving at Tucson Medical Center, the 54-year-old woman became Tucson’s first known coronavirus-related fatality.

      For most people, the new coronavirus causes mild or moderate symptoms, such as fever and cough that clear up in two to three weeks. For some, especially older adults and people with existing health problems, it can cause more severe illness, including pneumonia and death.

      She could not get an appointment for several days, then waited three days for the test result. The elderly couple in California had an MD son who started them on HCQ immediately. They did fine even at ages 88 and 92.

    26. MCS Says:

      How is that even competent treatment for pneumonia?

    27. Mike K Says:

      Some interesting ideas on how the virus might be treated,.

      It pertains a bit to the furor over Trump’s briefing where he apparently mentioned using disinfection methods., Of course it was blown up into him telling people to inject bleach but there are some novel concepts. Here is one.

      The virus is reported to colonize the nose, somewhat the way Staph does, and this can be a period of days or weeks. During this time, the host can be a spreader of the virus.

      Clinical applications of antimicrobial PDT to localized viral infections caused by herpes and papilloma viruses, and nonviral dermatological infections such as acne and other yeast, fungal and bacterial skin infections are covered. PDT has been used to treat bacterial infections in brain abscesses and non-healing ulcers. PDT for dental infections including periodontitis and endodontics has been well studied. PDT has also been used for cutaneous Leishmaniasis. Clinical trials of PDT and blue light alone therapy for gastric Helicobacter pylori infection are also covered.

      How about the use of Photodynamic Therapy in the nose in those whose nasal swab tests positive ? PDT has been used for years for esophageal cancer. The therapy requires the use of a porphyrin that is injected and which concentrates in the area to be treated.

      The initial studies of antimicrobial PDT, in the 1970s, involved clinical treatment of viral lesions [3] but this practice ceased when a paper in New England Journal of Medicine [4] claimed that the procedure was ineffective. Also concern was raised about the treatment being a possible cause of cancer [5]. Thus, in spite of a 100 years of discovery, the progress in the field of antimicrobial PDT has been rather slow. But with the recent rise in antibiotic resistance throughout the world, there has been renewed interest in alternative antimicrobial therapies. Antimicrobial PDT also known as photodynamic inactivation (PDI), lethal photosensitization, photoactivated disinfection (PAD) or photodynamic antimicrobial chemotherapy (PACT) represents an alternative treatment for drug resistant pathogens and has made a comeback as a possible approach to treat multidrug resistant infections.

      I have no idea if this was what Trump was referring to but it is an interesting approach to the issue of the carrier.

    28. miguel cervantes Says:

      Justin hart, did a comparative analysis of influenza, pneumonia fatalities, over the last four years, he found the combination of the first two factors have been nearly the covid totals, this year they made up a little more then half of cases undifferentiated from covid,

    29. Soviet of Washington Says:

      Grurray said “Although I’m skeptical of his claims of how zinc fits into the whole combination”…

      You might want to watch the 10 min Dr. Sehault video (episode 32) linked below that describes the theory and (in vitro) research behind behind the hydroxychloroquine/zinc combination.

      https://youtu.be/Eeh054-Hx1U?t=172

      Here’s a link to one of the papers referenced regarding the zinc research:

      https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001176

      Also, Chris Martenson has been going on about the ‘bad science’ being reported on both hydroxychloroquine effectiveness and the side effect warnings this week.