Avian Flu Is Now A Mammal Thing, And We Are Mammals

COVID’s late summer surge

This week a consistently reliable journalist covering the Pandemic, Zeynep Tufecki, has drawn attention to the critically important issue of Avian Influenza H1N5 infecting mammalian species with close contact to humans, and the potential for incubating the next pandemic virus. The mink farm risk is something I have discussed in the past, [Who Is Watching The Mink House?] and the infection of domestic cats in Poland more recently, but it’s reassuring to see someone with much greater bandwidth than me drawing attention to the threat. Some further information is now available, from what seems a perhaps perfunctory investigation in Poland, showing that the infected cats were located all over the country, and in addition to having no contact, some of the cats were indoor pets with no possible interaction with wild birds. The logical conclusion drawn by Polish investigators is that the cats were infected from contaminated food. Unsurprisingly, the affected cats all were infected by an H1N5 variant possessing two mutations which are known to facilitate the virus’ ability to infect mammals. See Tufecki’s NYT article for more details. Despite Kim Kardashian having all her fur coats remade in faux copies, the fur industry is still a powerful force in multiple countries, with support in the US from both Conservatives and Liberals (the same is true in Europe, and it all depends on who gives you money to remain in power). Mink are susceptible to both Human and Avian influenza strains, with the very plausible dual infection leading to a reassortment of genomes, so that Avian flu acquires the ability to spread readily among humans. Denmark placed a pause on their mink farm industry when it became clear that novel COVID mutants were evolving in the animals and jumping back to humans. The Danish government is now relaxing that ban on these farms as COVID is seen as less of a risk—but what about H1N5, or the next pandemic Avian Influenza? Anyone surprised that a very small but well moneyed monopoly is dictating illogical public policy on an issue with profound implications for human health and safety?

Let’s turn to the US COVID scene, where for several weeks the media has been telling you that a COVID upswing is underway, usually with the subtext that it is insignificant compared to prior periods in the Pandemic….and you just need to get your fall booster shot. It looks like the rates of increase in Hospitalizations and Deaths have both accelerated in the last two weeks, and here is the most recent CDC data.

For near term perspective on these numbers, hospitalizations were at a low of 6000/week in June, and deaths (which we can only estimate at this point given the new CDC reporting paradigm) currently show a similar near tripling since then. Projections suggest that within 1-2 weeks we will be seeing hospitalizations of 20,000/week, which will be half of the 40,000 seen during the spring surge. Whether there a point at which this upswing will be labeled “very significant”, is anybody’s guess. The following CDC Nowcast charts show first, the growth of EG.5 and the closely related FL.1.5.1 which now comprise 34% of the COVID sequences in the US. Following that is a chart where I have made it easier to see the rapid evaporation of the new fall booster targeted XBB.1.5 variant, something I predicted months ago under the deja vu category. Once again, for the third year, we will be getting vaccinated with booster that precisely targets a virtually extinct viral clade—but enough of the good news.

There is no reason to suspect that the new fall booster will have any unexpected side effects. Conversely there is no evidence that it won’t, since it has not been tested on human subjects. It is the first mRNA vaccine not to be based, at least in part, on the original Wuhan strain. The reasoning justifying it’s likely safety follows the path of the annual Flu vaccine, where small changes and 70 plus years of experience are considered sufficient to justify release of the new vaccine every year without human testing. That path obviously avoids the fork in the road leading to the Swine Flu debacle where the vaccine, distributed for an Influenza epidemic which never materialized, unexpectedly caused a much higher incidence of serious neurologic complications than any flu shot before or since. It seems a puzzling bit of timing that the CDC has cancelled their COVID V-Safe vaccine safety monitoring program with the new vaccine formulation on the horizon, and our time limited experience with these shots. The CDC is of course maintaining the general VAERS side effect reporting system—which has been criticized repeatedly for it’s passive nature, cumbersome use and under reporting of serious events. As you probably remember the V-Safe was a user friendly, consumer reporting App based system; not dependent on busy physicians to enter data or make judgements about the significance of reported symptoms.

The prevailing ethos regarding COVID vaccination has dramatically changed with the Joint Commission on Hospital Accreditation announcing that they will no longer require hospital compliance with COVID vaccination as a requirement for accreditation. Along the same lines, it was almost a year ago in October 2022 that a Federal Court in NY determined that the Mayor’s order firing city sanitation workers for refusing COVID vaccination was illegal, and forcing their reinstatement with back pay. Now, as reported by Becker’s Hospital Review, a Federal Judge in Buffalo has ruled that a nurse terminated from Roswell Park Hospital for refusing COVID vaccination must be reinstated, with negotiated back pay and all benefits. The Judge’s ruling leaves no doubt about how the pendulum of legal thought has swung. Some of the ruling apparently was based on the fact that the plaintiff’s termination occurred after a point in time when it was manifestly clear that vaccinated people could easily be infected, and just as easily transmit the virus.

"Ms. Cooper is an unfortunate victim in the wake of excesses exhibited by governors, administrators, legislatures, and yes, even the judiciary," state Supreme Court Justice Emilio Colaiacovo wrote in his decision. "All too frequently did critical thinking and the exercise of personal liberties expire at the altar of false righteousness, fear and authority."

I have generally avoided reporting on long COVID. It is covered ad nauseam in the press, and in general there has been little of true value in terms of fundamental understanding translatable to actionable treatment. Indeed Eric Topol has suggested that a billion dollars of NIH research money allocated to studying Long COVID has been WASTED, (his term not mine) on endless repetitive studies collecting data on frequency of symptoms, post hoc observational studies of patients who received this or that treatment during the acute illness, and few to no randomized controlled trials of potential interventions. “I don’t think they have contributed anything, except more confusion”. There is a very long list now of observations of various epiphenomena (alterations in various cytokines, hormones, inflammatory molecules and neurologic parameters) associated with Long COVID, which do not prove causation or add to our mechanistic understanding of the condition. It’s pretty well proven that patients with severe COVID have a higher incidence of PASC (Post Acute Sequela of COVID), even though people with extremely mild acute disease can be affected, and that vaccination lowers your risk, likely as a result of decreasing disease severity. This past week a report was published in the journal Cell which may provide very important clues into understanding exactly how the virus produces such long lasting effects on the immune system. Using novel techniques to amplify circulating stem cells, (SC’s) these scientists have shown that severe COVID produces what are called epigenetic changes in the cells. These are lasting changes not in the DNA, but in structures closely associated with it, which control how genes are expressed. The interesting finding is that these changes are passed down to daughter cells as the SC’s divide, and push these cells in the direction of developing into a type of white blood cell called monocytes with a distinctly inflammatory phenotype. Below is a quote from an NIH (sponsor of the study) summary of the findings.

In these rare stem cells—the parents of immune-system cells—taken from people recovering from COVID-19, the scientists identified changes in the instructions for which genes got turned on or off. These changes were passed down to daughter cells, leading them to boost production of immune cells called monocytes. In the monocytes from people recovering from severe COVID-19, the changes in gene expression led the cells to pump out greater amounts of molecules called inflammatory cytokines than monocytes from people who were healthy or had non-COVID-19 illnesses. The researchers observed these changes as much as a year after the participants came down with COVID-19.

These results seem important to me and if you want to delve deeper into the original paper here is a link: https://www.biorxiv.org/content/10.1101/2022.02.09.479588v1

Enjoy the Labor Day weekend and the final days of summer. Disinformation is a fact of human existence, it is nothing unique to our time, and no particular group has a monopoly on it. A wide array of people, both in positions of authority and not, will try and influence your decision making for all kinds of reasons. Sometimes the message will be in your personal best interest—most of the time it won’t be. Be skeptical when things seem to contradict your common sense. Remember, a person calling themself a fact checker doesn’t mean they are any more qualified to convey scientific Truth to you than I am to fix you car. One man’s disinformation is another man’s scientific paradigm—if you don’t believe me ask Galileo, Copernicus or Einstein. If I was Winston Churchill, I would advise you to forward this to your friends—if you have any. Comments are most welcome, as is pounding the like button.