Further Adventures of Avian Influenza

This week the USDA reported the first infection of dairy cows with the strain of Avian Influenza H5N1 that has been consistently found in birds in the US. It is believed, based on molecular evolution models, that a single cross over event in Texas one year ago between bird and cow initiated the infection of our dairy herds. That strain of the virus, called genotype B3.13, has spread steadily across the country, and efforts of the USDA and CDC have failed to interdict it. Another distinct genotype of the virus, D1.1, has been responsible for infection of wild birds in North America and the massive losses of many millions of domestic poultry—again with efforts to control the spread failing pretty miserably. What’s the practical difference from our point of view between these two strains you might be wondering? The short answer is, we don’t know—but the 69 Americas who we know contracted the cow strain of the virus had mild to moderate disease, and of the two who contracted the bird version D1.1, one died and the second, a healthy teenager, had critical life threatening disease, and barely survived. The USDA is expressing cautious optimism that they will be able control the spread of this virus within the dairy herds, and tout the discovery of the virus in Nevada as a result of their bulk milk testing. What’s your guess—will they do better this time around than over the last year? Will people in the dairy industry soon be contracting a potentially more dangerous genotype of H5N1, and will co-infection with routine human seasonal influenza increase the odds that D1.1 will pick up the genes which currently allow seasonal influenza to spread rapidly among humans?

Vladimir, thanks for sharing!

Personally I’m not confident that the lackadaisical approach of our government over the last several years as a new clade of H5N1 spread massively around the world, killing billions of birds and demonstrating an unparalleled ability to infect and kill a huge number of different mammalian species, is likely to improve now. Today the governor of New York ordered all live bird markets in NYC and surrounding areas closed because of detection of infected birds at seven locations throughout the city. Authorities in Chicago this week reported that a mass die off of hundreds of ducks, geese, and also hawks due to H5N1 is occurring along the shores of Lake Michigan. This began in late December but appears to be accelerating. Like it or not, we are immersed in what is the greatest zoo-pandemic ever seen, and this has been unfolding around the world over the last three years with basically a governmental shrug of the shoulders. If a human pandemic of a virus with a HIGH mortality rate appears (not the paltry case fatality rate of COVID, but say 10% across all age groups) mRNA vaccines appear to be our best defense. Anti-virals will have comparably minimal impact, and trying to shutter society and hide will predictably fail again. My bet is that quite a few individuals who are convinced that mRNA vaccines are the work of the devil will be rolling up their sleeves when they see healthy folks carted off to the morgue in droves. It may be inappropriate to look for silver linings in a pandemic, but it’s a biological fact that not only does herd immunity arise to that particular virus, but also at least partial immunity to other closely related viruses. There is also the possibility of improvement of the gene pool through selection of whatever group of genes control what we refer to as “common sense”.

Evolution favors common sense as a survival tool

I just made a pretty strong claim that anti-virals will have minimal impact on the course of an Avian Influenza pandemic—is there evidence for that? A systematic review and meta-analysis of 73 randomized and controlled studies was just published in JAMA Internal Medicine, looking at results of a combined 34,000 patient’s response to treatment of Influenza with the four drugs currently available in the US. The meta-analysis included only patients with “non-severe” Influenza—but the definition they used was, the patients had not required hospitalization in the first two days of symptom onset. The normal clinical evolution of Influenza suggests that many people included in these studies were in fact destined to have very severe disease. The conclusions are clear.

Oseltamivir (Tamiflu) and zanamivir (Relenza) had little to no effect on mortality, hospitalization rates, or symptom duration. Peramivir (Rapivab) had little to no impact on mortality rates and symptom duration, and had no data available for its effect on hospitalization rates.

One available anti-viral, baloxavir (Xofluza) fared slightly better, “Baloxavir (Xofluza) reduced hospitalization rates for high-risk patients but with a ‘low certainty’ of evidence, and it reduced symptom duration by a day compared with standard care or a placebo with moderate certainty. The drug had no effect on mortality.”

Antiviral Medications for Treatment of Nonsevere Influenza A Systematic Network Meta-Analysis and Review.

https://jamanetwork.com/journals/jamainternalmedicine/article-abstract/2829156

How is it that drugs approved by the FDA to be “safe and EFFECTIVE”, can have such incredibly mediocre performance? I think the answer lies in the disconnect between what transpires in a clinical trial and the “real world”. A clinical trial is structured to maximize the possibility of finding the drug under development is effective. There is (ideally) no cheating, just stringent controls that define exactly the clinical status of each patient, the exact nature of their symptoms and laboratory parameters, other baseline medications, and precise compliance with the dose regimen. Not so in the world of medicine at large. Whenever you find that a drug has some incredibly minimal effectiveness, even if “statistically significant”, you should keep this phenomena in mind. Conversely, we never needed a randomized controlled trial to show that penicillin was a total game changer for pneumococcal pneumonia and sepsis. In any event, I think this should be sufficient to dispel belief that available anti-virals would make a large impact on an Avian Influenza pandemic mortality.

Let’s return now to the topic of polio, which is currently a quarter century past the date originally proposed for its eradication by the Global Polio Eradication Initiative in 1988. Although Europe has been certified polio free since 2002, polio virus has been detected in the waste water of at least one European country every year from 2015 through 2023. In recent months the rate of detection has sky-rocketed; from September through December 2024 polio virus was found in the waste water of 14 European cities in 5 countries. If you are a regular reader here you will have already surmised that the virus present persistently there is not wild type (or natural polio) but the circulating vaccine derived mutant polio cVDPV2. Genetic analysis shows that this circulating vaccine derived polio in Europe is most closely related to a strain of vaccine polio isolated in Nigeria—but that it has been circulating for at least a year before its detection in Europe. That sort of timing is deduced from the genetic distance between the strains, and a very predictable mutation rate. What shows up in Europe shows up in the US, and unvaccinated people, and those with compromised immune systems, will be susceptible to paralytic disease caused by this mutant virus. I’m always amazed that I never hear hard core anti-vaxxers mention this issue—they spew endless non-scientific nonsense, but never mention this very real vaccine problem. Perhaps I just don’t spend enough time listening to their channel, but it does seem like low hanging fruit. I doubt that any of that ilk are likely to be reading my blog to get new ideas, but in any event I never shy away from inconvenient facts. The Law of Unintended Consequences is predictable and sometime brutal.

The last item today involves things you would rather not have in your food. I have covered the issue of toxic food badatives, and the glimmer of hope that a perhaps a sufficient movement may be in place to force the food industry into submission. That of course covers chemicals which are intentionally added to our food, and not the insecticides, herbicides, phosphate compounds, heavy metals, or the polybrominated flame retardants discussed in my last post. There are other noxious things I personally would prefer to skip but seem to be unavoidable, at least in trace amounts, in our highly processed food supply. I am referring to the low levels of rat and mouse droppings, insect parts, and rodent parts found in industrially prepared food. Did you know there is DAL (defect action level) for acceptable rodent hairs in your pasta? 4.5 hairs/ 225 grams is the level the FDA says is ok, and you certainly won’t notice that. Moving on to a higher level, the European Union’s food regulatory body just announced that from now on pasta manufactured or sold in the EU may contain up to 4% mealworms. I always dismissed the claims that Bill Gates and the World Economic Forum want us to eat bugs, but now I’m curious to see Bill’s recipe book, and I won’t be ordering macaroni in Europe—or buying it at home.

The old Chinese proverb, “May you not live in interesting times”, has never been truer, and we seem to be stuck in a cycle of interesting times. The world won’t end no matter what either political party does or says. On the other hand the US is 36 trillion dollars in debt, with the debt increasing by 2 trillion a year, and projected to continue steadily increasing. When this Ponzi scheme, which both political parties are architects of finally implodes, you will see truly interesting times with chaos on a level hard to imagine. In the mean time, enjoy the weekend, try some meditation— but don’t order the pasta special. The like button at the top is radioactive so please don’t touch.