Infection Control, Emergency Management, Safety, and General Thoughts

There is enough to cover with two topics this week. There wasn’t much new on H5N1 other than it is showing up in more places and continued resistance by big agriculture to allow public health to conduct surveillance monitoring. That seems to be an analogy to the “Goodbye Data” section related to COVID this week.

Contents:

• Goodbye Data
• Antibiotic Resistance and COVID

Goodbye Data

Two major sources of COVID data went dark this week. First, Biobot Analytics stopped their public reporting of wastewater data. Wastewater has been a useful early tool to detect increasing rates of COVID in a community.

Worse, the CDC had pulled the plug on mandatory reporting of COVID data by hospitals on May 1st. I simply had thought that the consequences of this would be having a smaller sample size from which to draw inferences. I had been using two large data tables as important sources for the visualizations on this site.

Last June, the CDC had dropped the reporting requirements for suspected cases. I had developed a methodology to still visualize data adjusted for these changes and had thought that I could use the same approach for when some hospitals stopped reporting. The data from the CDC lags the reporting dates by two weeks, so this current weekend was when I expected to see just how that was starting to impact data. May 1st was on a Wed, so there would have been full reporting for the first half of the week and then voluntary for the last.

Unfortunately, that’s not how things played out. Instead, CDC just stopped updating the data tables altogether. This was unnecessary because many sites continued to report. I still continued to report daily for my hospital, even on weekends and did so this morning (Saturday). I can see what hospitals are reporting in my region of the state I’m currently in and saw that hospitals that represent 84% of beds in the region are still reporting. This makes me think that the CDC is still getting a lot of data but is not making it available under political pressure. Sometimes I honestly wonder if this site put enough pressure on the CDC or embarrassed them enough to drive the change. I know that many had tweeted out some of my tweets using it to @cdcdirector and @cdcgov.

I have been doing MORE to make this data readily understandable by the public which is part of the reason I created this site since nobody had been doing so. I hoped that a university might do something as well, but it didn’t happen. Early on we knew the need for data for making public health decisions.

On the CDC’s data authority web page, they even discuss the need for quality data at the federal level.

In the MMWR, they even titled an article “Summary of Guidance for Minimizing the Impact of COVID-19 on Individual Persons, Communities, and Health Care Systems — United States, August 2022.” The article tells people to know their risk. How are they supposed to do that with no data available? They even provided an infographic showing their four recommendations. I had been using this data all the way down to the metro area level to help people understand their local risk and not just that of their state.

In the article, they state “Persons can use information about the current level of COVID-19 impact on their community to decide which prevention behaviors to use and when (at all times or at specific times), based on their own risk for severe illness and that of members of their household, their risk tolerance, and setting-specific factors.”

Unfortunately, this is pretty much impossible to do now. In May 2022, the CDC dropped their “Community Levels” tool, which really had been efficient at minimizing COVID compared to their prior tool, but at least it was something. Even so, this data lagged quite a bit because of the 7-10 days it takes to develop symptoms after an infection. Forbes stated it nicely. “Relying on hospitalizations and deaths to determine what to do can be sort of like saying that you are going to wait until you’re fired or the company is bankrupt before determining whether you need to improve your job performance. Or waiting until the divorce papers arrived before saying, ‘Hmm, maybe I should start doing the dishes and not do all that that cheating stuff?’ Hospitalizations tend to occur about one to two weeks after people have gotten infected.”

On September 9, 2021 President Biden stated “But what makes it incredibly more frustrating is that we have the tools to combat COVID-19, and a distinct minority of Americans –supported by a distinct minority of elected officials — are keeping us from turning the corner.  These pandemic politics, as I refer to, are making people sick, causing unvaccinated people to die.” One of the biggest tools is gone. Maybe it’s time for the Democratic party to look in the mirror and do some reflection and fix this.

True, things would have been far worse under a Republican administration, and there are many studies supporting this, leaving us three bad options for president. One who minimized the pandemic from the beginning setting the stage to make it political, one who is a science denying quack infested by a brain worm, and the current one who is following the minimizing lead of the prior in the support of politics. From a public health standpoint, we are screwed.

This is incredibly bad timing with the emergence of the FLiRT strains, not that any time is good IN THE MIDDLE OF A PANDEMIC.

SHAME ON YOU CDC

Antibiotic Resistance and COVID

A massive (n=892,312) global study and metanalysis of 173 studies on antibiotic resistance was published this week. What was particularly alarming is the high prevalence of resistant organisms among COVID patients.

Part of my role in healthcare is related to antibiotic stewardship and ensuring that patients with any of these above categories of resistant organisms are properly isolated to prevent spread. It makes me wonder if we should be asking patients on admission if they have a COVID history. If they do, I wonder if we should be doing surveillance cultures given these high rates to ensure that they are placed in contact precautions.

Antibiotics are useful when indicated. Unfortunately, many of the antivax/ivermectin grifters include antibiotics in their protocols. Antibiotics do as much for viruses as hydroxychloroquine and ivermectin – absolutely nothing. They are beneficial if there is a secondary bacterial infection, but widespread use of them pushes us closer to the post-antibiotic era.

One of the organizations pushing these protocols is the Front Line COVID-19 Critical Care Alliance (FLCCC). Their protocol BEGINS with ivermectin and hydroxychloroquine. Both have been shown to be useless for COVID, but they are making a lot of money of people by selling this stuff. I’ve previously written a rebuttal to one of the websites that is often used to push ivermectin. What is written in this screenshot is simply unsubstantiated garbage used for grifting patients.

DON’T DO THIS:

If patients don’t improve within three days, then they suggest adding antibiotics.

Their website is designed to make it look like that their protocols are a widely used. That’s simply not the case. Further, this blind use of antibiotics contributes to the antibiotic resistance problem leading to the post-antibiotic era. To put that phrase into context, “Imagine a world where routine surgery or chemotherapy is considered too dangerous because there are no drugs to prevent or treat bacterial infections.“

Imagine living in a world where tending to your rose bushes causes a small scratch to your skin or a small scrape to a knuckle like I had yesterday could become fatal if an infection invades.

The last time I spoke on antibiotic resistance was about 10 years ago. I’m going to provide a few slides from that presentation many of which contain references if interested. I would also recommend the book reviewed here if this topic interests you.

I also want to give a shout out to @ejustin46 (who reviews more primary sources than I think possible in a day and is worth following on Twitter) for this summary on resistance and COVID from a year ago.

COVID: Early Warnings about the FLiRT variants.

There is an early indication that KP.2 is causing trouble in the UK. Here is positivity over the pandemic using PCR for the area.

The US is just slightly behind the UK in the rise of dominance of it.

As a general thumb rule, I’ve noticed that hospitalizations tend to start rising rapidly when a variant reaches about the 40% mark of all variants in a country, so it will be interesting to watch what happens when the UK crosses that threshold. Currently the downward trend in COVID hospitalizations seems to have hit a plateau, suggesting that this estimate may prove to be correct again.

The forecast for KP.2 in the US also suggests that we are going to be following that trajectory.

One of the problems with the new variants is a distinct growth advantage over JN.1. That will be the case for each variant to become dominant. Almost by definition, it has to have a spread advantage over those before it in order for it to gain dominance.

The advantage of KP.2 and KP.3 has been worked out by the Murrell Group in comparing to the JN.1 variant.

Some preliminary data suggests that these variants may also be more immune evasive, but fortunately less infectious. However, the lower number of COVID hospitalizations in the US during the past year compared to the rest of the pandemic suggests a lower number of infections, which may be due to prior infection or vaccination.

We know that immunity from both infection and from vaccination wanes over time. Given the low uptake of the most recent booster and the large proportions of those who were infected who don’t build antibodies, we have a large proportion of the population in the US that might be considered to be immune naive, especially in the context of a more immune evasive variant.

I would still advocate for a booster if you can get one because data with influenza suggests even when there is not a good match, there is still some protection provided from vaccine. However, all of this also emphasizes the need for good respiratory protection with a respirator as well as improved ventilation.

Of course, it doesn’t help that Republican lawmakers are trying to criminalize mask use even for medical purposes. It’s no surprise though given that they have been the instruments of disease and death for some time.

It also doesn’t help that the CDC seems to be sweeping COVID under the rug with the lifting of the healthcare reporting requirements on May 1 as well as removing the link to those data sets right on the front page of the healthdata.gov website. It used to say “COVID-19 Datasets” in the area indicated by the red arrow. I estimate that next weekend we will start to see the drop in reporting in the data, although since it happened midweek, it will be the following weekend when the scale of this change becomes most apparent.

Contents:

• COVID
  • HHS Reporting
  • Positivity in the UK
  • New “Truths” Section
  • Studies Added
• H5N1
  • Wastewater
  • Cattle Workers

COVID

HHS Reporting

The big change this week is that HHS no longer requires COVID reporting from hospitals. This is very concerning based on what happened when they stopped requiring the reporting of suspected COVID admissions last June. Here’s how that influenced the data in a number of major cities. The dotted line represents the reports received. There is a very clear drop in the admission numbers at that time.

Atlanta

Boston

Chicago

Cincinatti

Cleveland

Dallas

Indianapolis

Houston

Las Vegas

Little Rock

New York

It’s also suspicious that this change had been made when we were not in a surge, just like now. That made it much easier to let this slip by, such as can be seen in Denver.

Positivity in the UK

The FLiRT variants, KP.2 and KP.3, are descendants of JN.1 and are becoming dominant in the UK. The rise in positivity in the country is alarming, suggesting very rapid spread. This is at a time of year when people are heading outside more often in the northern hemisphere and we would expect a decrease in spread. The big question will be how sick it makes people.

This rapid spread is also supported in a preprint. “The R_e [effective reproduction number] of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide.”

New “Truths” Section

It dawned on me that not only should I organize material about myths, but also make it easy to find truths based on primary sources. The first one in this section is Vaccines reduce the risk of hospitalization and death. There is a lot here to build out.

Studies Added

• Severe neurological manifestation associated with COVID-19 in children during the Omicron variant-predominant period
• COVID-19 Vaccination and Incidence of Pediatric SARS-CoV-2 Infection and Hospitalization
• COVID-19-Associated Hospitalizations Among Vaccinated and Unvaccinated Adults 18 Years or Older in 13 US States, January 2021 to April 2022

H5N1

Wastewater

I had written about influenza A surging in wastewater at a treatment plant in Amarillo, TX on April 22. It was odd that CNN did a story about it on April 30. As a follow up, here’s the influenza wastewater curves from across the country, with that site highlighted. It’s good that it has come back down, but I still suspect that it means that H5N1 has entered beef cattle.

Cattle Workers

We also learned more about the dairy worker in Texas that had been infected with H5N1. A neuroscientist pointed out that this is likely a very neurotropic (affinity toward nerve tissue) virus based on the condition of the eyes of the dairy worker.

Also in Texas, “The first calls that Dr. Barb Petersen received in early March were from dairy owners worried about crows, pigeons and other birds dying on their Texas farms. Then came word that barn cats — half of them on one farm — had died suddenly…

…At the same time, on almost every farm with sick animals, Petersen said she saw sick people, too.

‘We were actively checking on humans,’ Petersen said. ‘I had people who never missed work, miss work.'”

Contents

COVID
Hospital Reporting
Subsequent Pandemics
CO₂ Monitoring
H5N1

COVID

Hospital Reporting

The big surprise this week was learning that hospitals will no longer be required to report COVID data on May 1 and any reporting will be voluntary.

It’s very easy to see what happened in June of last year when the reporting requirement of suspected COVID cases was lifted. The red and black dotted lines are the drops in the number of facilities reporting suspected cases. It’s quite apparent how this impacted the apparent COVID admission numbers on the stratified area chart right below.

I had built a formula to adjust for that and use it to look at the respective waves over time at the state level. For example, here is New York without the adjustment.

Here is the same New York data, with the correction formula. You can see that the most recent wave looks lower than the last wave before the change, but with the adjustment, it is obviously higher.

I’ve been working on an even more refined way of doing this over the weekend to use different coefficient formulas based on reporting with each age strata instead of applying the same one across all. I’m hoping that experimenting with this will make it easier to adjust for when hospital reporting disappears in the data come mid-May due to the two-week lag from the CDC.

I really find this puzzling given that just over a week ago, the CDC director stated “Data is essential to public health…”

Subsequent Pandemics

The other thing that has been on my mind this week is what will become massive numbers of people with chronic diseases in the future. A learned of a paper earlier this year titled “Predicted risk of heart failure pandemic due to persistent SARS-CoV-2 infection using a three-dimensional cardiac model,” which point this in the forefront of my mind. Others are clearly seeing the writing on the wall about the future as well. Even worse is how we are going to be losing healthcare workers as the demand for healthcare services increases.

CO₂ Monitoring

On the prevention side, there was a really good paper correlating CO₂ concentrations to COVID risk. The authors stated “We model the likelihood of COVID-19 transmission on the ambient concentration of CO₂, concluding that even this moderate increase in CO₂ concentration results in a significant increase in overall risk. These observations confirm the critical importance of ventilation and maintaining low CO₂ concentrations in indoor environments for mitigating disease transmission.” That gives pretty good support for why people have CO₂ monitors like this one.

H5N1

While the response of the US to H5N1 seems eerily similar to the lack of response at the start of the COVID pandemic, other countries are being more proactive. Colombia was the first to restrict the import of US beef. Of course, industry organizations went directly into self-protection mode when a spokesperson for the U.S. Meat Export Federation stated “The restrictions Colombia has imposed on U.S. beef as a result of the recent highly pathogenic avian influenza (HPAI) findings in lactating dairy cows have no scientific basis.“

The big problem is that we just don’t know the scale and ramifications of the problem as of yet. Until we do, I have to side with Colombia on this one. They can certainly source beef from other countries. Brazil exports almost double of what the US does annually. I think Colombia just being cautious. If I were making the decisions in another country, I’d look at the US response to COVID and think twice about any assurances of safety and safe practices from US sources.

This caught my attention today. I’m hoping it’s nothing, but it’s worth looking into more closely.

This is influenza A in wastewater at two sites that are monitored in the Amarillo, Texas area. I’ve expanded it to include the entire influenza season. What grabbed me was the sharp climb at the River Road facility (the red line).

It also might help to put that in context of influenza A across all monitored sites in the US over the same time period.

I also pulled up Biobot Analytics for their influenza A data. What is interesting is that the southern region of the US is the only place that influenza A is increasing.

From FluView, we can see a clear decline in influenza A across the US in public health labs.

This is the data from clinical labs from across the US, showing the same pattern.

This view is of the clinical lab data in Texas alone, which should make it clear that it’s been declining there overall as well, even more steeply than in the US overall.

I knew that the Texas panhandle was a major cattle area in the country, so my thinking went to H5N1, although we have only seen it in dairy cattle, not beef. This article paints a picture of the beef industry in that area.

I also wonder what the recent wildfires did as far as mixing of herds and some of the decisions by ranchers as they faced losing their livelihoods.

Another interesting view is influenza A from Amarillo Public Health over the past four years. I couldn’t find any data for Moore County where the wastewater treatment plant in question is, but I would be surprised if these trends were very different there, which also suggests that perhaps that the anomaly could be from cattle.

H5N1 is a strain of influenza A. It’s impossible to know at this time if this is what is driving this increase, but vigilance is warranted. Hopefully this is simply all a coincidence or just a statistical anomaly. I watch for early signals to monitor.

Interestingly enough, CNN picked up this story just over a week later on 4/30.

Contents:
H5N1
COVID Topics:
Group A Strep
Psitticosis
Disability

H5N1

H5N1 continues to be a growing problem. Thus far, we have seen “Bird-to-cow, cow-to-cow and cow-to-bird transmission have also been registered during these current outbreaks, which suggest that the virus may have found other routes of transition than we previously understood” according to Wenqing Zhang of the WHO.

We have known about the risks of H5N1 for a very long time. CDC guidance from 2013 stated “Work with HPAI H5N1 virus should be conducted, at a minimum, at biosafety level 3 (BSL-3), with specific enhancements to protect workers, the public, animal health, and animal products.”

One interesting publication by the CDC this week sends a bit of a warning.

The question then becomes one of if dairy products are safe. Per the USDA Animal and Plant Health Inspection Service, “We know that the virus is shed in milk at high concentrations; therefore, anything that comes in contact with unpasteurized milk, spilled milk, etc. may spread the virus. Biosecurity is always extremely important, including movement of humans, other animals, vehicles, and other objects (like milking equipment) or materials that may physically carry virus.” In other words, raw milk is dangerous as are fomites that come in contact with it.

Raw milk products should never be consumed because of the disease risk they pose. It is unclear if pasteurization will make dairy products safe, although influenza viruses tend to be destroyed by pasteurization. I really hope that’s the case, because this is from an expert in the field I trust.

A major warning bell should sound if there are cases of H5N1 in humans who are not connected to agriculture.

Another interesting thing to think about is the impact of infected waterfowl on marine life. While H5N1 is not known to infect fish and invertebrates, they can become transiently colonized. I think this could pose a problem in shallow oyster beds and for those who enjoy raw oysters, among other marine foods. If seafood is part of your diet, you might want to read this thread that links to a number of studies.

While not a food animal, it is also interesting that H5N1 has been detected in a marine mammal for the first time, in this case, bottlenose dolphins in Florida.

COVID

Group A Strep

There was a very interesting tweet this week about invasive Group A streptococcus (GAS) in a hospital in New Brunswick. It dovetails very well with the immune system damage from COVID. When GAS is invasive, it can cause necrotizing fasciitis, or what is sometimes more commonly called flesh eating disease.

I was curious if I could find more info from the area due to the alleged public health response and sure enough, I found a story on two deaths including a picture of the hospital, confirming that this account is likely true.

Psitticosis

In a similar vein that could be related to COVID immune damage, psitticosis, or parrot fever, is erupting both in South America and Europe.

From ProMED: “In the past 30 days there appears to have been an increase in severe atypical pneumonia requiring critical care in Buenos Aires [Argentina]. The affected individuals are mostly young people without major risk factors. Bilateral consolidative infiltrates are seen on chest CT scans with patients often requiring mechanical ventilation and pronation. Informally, 20 of the 60 cases collected presented evidence of psittacosis with 10 positive by PCR. Many of the affected patients have no apparent history of contact with birds.”

For perspective, Argentina was hit by COVID roughly as badly as the US, which was one of the worst performers during the pandemic. Case number became pretty useless after the original omicron wave in 2022.

It also appears to be showing up in Europe in unusual numbers. This is an excellent thread with linked citations.

Disability

One of the things that has made COVID so difficult is that people think that COVID is just an acute illness, with some exceptions among people with long COVID. This is particularly true among those who minimize it and think that death is the only real adverse outcome. The truth is that COVID sets people up for a number of diseases in the future.

The Lancet published a study this week titled Global incidence, prevalence, years lived with disability (YLDs), disability-adjusted life-years (DALYs), and healthy life expectancy (HALE) for 371 diseases and injuries in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021.

“In 2020 and 2021, global health outcomes, as measured by age-standardised DALY rates, worsened for the first time in three decades. From 1990 to 2019, GBD analyses showed consistent and rather encouraging improvements in overall health outcomes at the population level. During this period, achievements by the global health community included reductions in vaccine-preventable deaths and improvements in under-5 mortality rates, contributing to the trend of people living longer. However, as a global epidemiological transition occurs wherein the greatest share of disease burden shifts from communicable diseases to non-communicable diseases, populations are living longer but in poorer health. GBD 2021 reports a new global trend: the global number of DALYs and age-standardised DALY rates increased in both 2020 and 2021.”

It really comes down to those who continue to play the roulette wheel with COVID are going to be facing a considerably reduced quality of life and shortened lifespan. That is the problem with COVID. Most of the impact of the pandemic is going to show up years in the future, which is why there is so much temporal discounting.

For example, in January, Murata et al. published “The human iPS cell-based cardiac tissue model established in the present study is the first report to experimentally demonstrate SARS-CoV-2 persistent infection of the human heart exhibiting functional deterioration caused by the opportunistic intracellular reactivation of viral infection. We experimentally demonstrated that cardiac tissues under persistent infections with SARS-CoV-2 are at high risk of cardiac dysfunction with additional hypoxic stress. In other words, the explosive increase in the number of virus-infected patients due to the COVID-19 pandemic may have led to an enormous increase in the number of patients at potential risk for future heart failure.”

The healthcare system cannot handle the burden of the diseases that are currently in the pipeline as a result of COVID.

This week will be a very short set of thoughts because I had been preparing to travel yesterday and finished settling in today at my home for the next three months.

CDC

Dr. Mandy Cohen, the director of the CDC, made two interesting posts on Twitter.

Where she states “Protecting health is a team sport,” the linked article in NEJM is paywalled. So much for real time data sharing.

Further, two sets of COVID data appear not to have been updated this week on https://healthdata.gov/, which is where I pull much of the data I visualize on this site. I pointed this out earlier this week in a Tweet where I linked this screenshot.

I started pulling the data to do the updates on the metropolitan section here and saw that nothing was changing in about the first 40-50 metropolitan areas. I’ve concluded that while SOME of the data has been updated at CDC, the COVID admission data has not been, which is already a lagging indicator of activity by two weeks.

I and others have been doing our best to provide data, but it’s hard when what should be a quality source of frequently updated raw data keeps shutting down the tap to just a trickle.

Psychology and H5N1

Currently there are about two dozen dairy cattle herds that have been infected in eight states. The number is likely much higher than that since testing is voluntary. It is also safe to assume that beef cattle are getting infected as well. As this spreads in farm animals, the risk of a human pandemic climb.

Systematic Densitization

One type of cognitive behavioral therapy is systematic desensitization therapy. It’s often used to treat phobias, anxiety disorder, and PTSD. The idea behind it is to reduce stress, anxiety, and fear of a stimulus by using relaxation techniques, working through fear on paper, and using VR or the actual stimulus to reduce that fear in a safe setting.

Some have argued that as a society we have become desensitized to violence through real events and the media, including fiction.

Now that we have experienced a pandemic for over four years, it seems reasonable to think that we are getting desensitized to the waves of disease and death. Many people are acting as if the pandemic is over, and many are even saying that it is, when the evidence shows that it clearly is not.

That poses a significant problem if H5N1 becomes a human pandemic. At the start of COVID, the majority of the population took it seriously. Now, it’s very uncommon to see anyone wearing any type of mask, much less a respirator. That kind of lackadaisical approach is not going to go well should another pandemic begin soon.

Temporal Discounting

That kind of systemic desensitization also plays into what is known as temporal discounting. It is simply the nature of humans to do something for a reward in the present as opposed to taking a bigger reward in the future because we are impatient as a species. As an example, we see this in corporate settings at times, when executive decisions are made that could hurt the company in the long term but will placate investors in the short term.

In the infectious disease setting, this means that people are more likely to take risks when they think that the costs to them are too far off into the future to be considered. This is exactly what is happening with a number of people related to COVID. They argue that deaths have gone down but are completely ignoring the long-term impacts of an infection, that may not show up for many years. The public does not seem to understand the occult damage of a COVID infection.

Even seasonal influenza does this kind of damage at a lower level, but people only look at the acute illness. The risk of an acute myocardial infarction goes up after having influenza.

Pluralistic Ignorance

This is a particularly interesting concept in psychology. It is part of the reason why people don’t step up to help someone who needs first aid. There is an assumption that there must be someone there who is more qualified in a crowd, so nobody responds. It also leads to think that larger proportions of the population share a majority opinion than actually do.

The problem is enhanced on two fronts. First, there are all of the physicians who are making false claims about the pandemic. People tend to gravitate towards those who speak what they want to hear, even if it isn’t the truth. There are many examples of this throughout the pandemic. Twitter has made this worse by allowing some of those who are spreading lies and misinformation to post again, and those posts tend to go viral in their circles.

Worse though is the lack of action by the CDC. One good example of this is when they changed the colors on the Community Risk Map for the US, That action led many who don’t dig into the data or just trust it blindly to think that the risk had dropped considerably. The lack of clear messaging that this is a respiratory virus that is airborne and that people should be wearing respirators in shared indoor spaces also leads people to assume that maybe things aren’t that bad.

It goes back to the idea of “Someone must know more about this than me.” When people stop wearing respiratory protection, those who may have been on the fence figure that maybe things have gotten better and I’ve just been overreacting. It has become somewhat of a positive feedback loop. If H5N1 comes into play, that is going to be a very hard trajectory to change.

Contents:
H5N1 and Food Chains
COVID and Workplace Fatalities

H5N1 and Food Chains

There has been a lot lately related to H5N1. It’s VERY concerning that it has shown up in more mammal species because that means the virus is more adapted to the mammalian respiratory tract, but also because of the impacts of the virus on both poultry and cattle. The CDC has a page about the history of H5N1 since 2020.

There is a LOT to unpack in this story. First, most people don’t know the dark side of the egg industry. Chickens are bred either to be layers or broilers for eating. Male layers obviously can’t lay eggs and aren’t profitable as a human food source. What gets done to them might disturb a lot of people. This includes gassing them to death with carbon dioxide, manually breaking their necks, or running them through a macerator. The video is rather graphic, so skip it if you would be bothered by it.

What happens to the ground up chicks and eggshells? It varies by country and laws, but in general, they become a component of pet food, large animal food, or organic fertilizer.

Even if chicks aren’t used in this way and are part of the layer or broiler populations, they still enter the animal food chain. The urine, feces, spilled chicken food, and feathers are used as food for cattle.

Something similar happens with butchered pigs and cattle. The portions that aren’t used for human consumption go through a rendering process. One of the products of rendering is bone meal. It is used in human dietary supplements, as an organic fertilizer, and as animal feed.

Another common product from rendering is meat meal. It is often combined with bone meal for use in the production of pet and livestock foods. In relation to H5N1, there are obviously some concerns about the safety of this practice, such as an example of 38 cat deaths in a South Korean animal shelter linked to pet food.

Some of the above has been banned in other countries, but the agriculture industry has a very strong lobbying presence in the US.

Many diseases can be transmitted through livestock feeding practices. One that eventually impacted humans was a disease in sheep called scrapie, which got its name for the characteristic behavior of inflicted sheep which would rub their sides against objects, leading to bald patches where wool would normally be.

Scrapie is a transmissible spongiform encephalopathy, or what is commonly called mad cow disease, caused by infectious proteins called prions. The proper name in cows is bovine spongiform encephalopathy (BSE) and in humans, Creutzfeld-Jakob disease (CJD). It eventually became apparent that BSE was likely the result of rendering the brains of sheep to become cattle feed.

Mad cow disease was identified in Britain in 1986. In the early 90s, a health advisory board in Britain proclaimed that cattle were a “dead-end host.” Eventually that assessment was proven wrong, and the first death related to BSE transmitted to humans occurred in 1995. It was called new variant CJD (nvCJD or vCJD were both used).

Oddly enough, the same “dead end host” language had been used about cattle in relation to H5N1. The first cases of H5N1 showed up in cattle just over two weeks ago, but by April 1, that “dead end host” assumption was proven wrong with a cattle to human transmission.

As an aside, if the story of prion diseases through food interests you, I highly recommend this excellent book by Richard Rhodes.

We are already seeing cracks (pun intended) in the egg supply chain. Realistically, this will likely result in the culling of over 2 million chickens.

The simple take away is that we are stepping into uncharted waters in relationship between the food supply and H5N1. I would really urge people to take emergency preparedness seriously. I generally point people to https://www.do1thing.com/ because of their approach of ongoing preparedness.

COVID and Workplace Fatalities

Most of my week has been consumed with H5N1, but I had an idea about where to look for more data suggesting impacts from COVID in industry. I realized that fatal work injuries might tell something of a story about risks of death in the workplace from brain fog and other neurological injury from COVID. In the last two years, the rate of workplace deaths either matched or exceeded the prior highest rate since the start of this data set in 2012.

Contents:
H5N1 in Dairy Cattle
Group A Strep in Japan
Transportation Incidents
Dengue in the Americas
COVID in the US

I’ve decided to write a weekly summary of my thoughts on publications and news sources around COVID and other public health/public policy interests during each week. Some of these might seem familiar to those who follow me on social media.

H5N1 in Dairy Cattle

One of the biggest news items of the year so far started on March 20th, with the announcement that a goat had died of H5N1 avian influenza in Minnesota. This is the first death from this virus among ruminants in the US. I posted my concerns on social media about the impacts on the food supply should something like this take hold in other ruminants.

We learned on Monday that H5N1 had been detected in dairy cattle in two different states. The Texas Department of Agriculture had recognized sickness had been occurring, but like we have seen repeatedly among organizations, took a minimizing stance related to this news.

It was detected in herds in both Idaho and Michigan as well, strongly suggesting that this is a widespread problem that is already underway. This coincides with the start of the annual northward migration of waterfowl.

This is concerning for many reasons. First, given that we have seen it in ruminants in multiple states, this implies that this strain of H5N1 is already widespread. Most likely, it is in waterfowl flocks spreading it across North America. I suspect that the fecal-oral transmission is the most likely cause. Waterfowl land in water sources and defecate where ruminants later use for drinking. This means that containing spread is almost impossible.

Second, influenza viruses undergo genetic shift and drift quite regularly. This is part of the reason we need new human influenza boosters each year. While the current strain of the virus infecting ruminants appears to only cause illness for 7-10 days, it is also likely that this virus will mutate. That could make things better, or perhaps much worse, which could have devastating impacts on food supplies.

The most concerning thing though has to do with waterfowl migration across continents.

My biggest concern is those with migration routes including NW Canada and Alaska. That is because it shares space with waterfowl from SE Asia. Introducing this strain into waterfowl from that region increases the risk to humans considerably.

SE Asia has the densest human, waterfowl, and pig populations in the world. The problem lies in introducing this virus into pig populations in that area. The reason is that pigs are more unique in that their physiology is much more similar to humans than other animals. In addition, they can be easily infected by both human and avian influenza strains.

Influenza is a promiscuous virus. It will incorporate genetic sequences into its genome from the environment and is a very sloppy replicator, which introduces mutations readily. This also means that a pig can act as a petri dish to mix the genes from a human virus that makes influenza readily transmissible among humans and mix it with the genes of an avian strain that could make the virus much more deadly to humans as well. In 2013, H5N1 was repeatedly entering human populations and had a 60% fatality rate.

Dairy products that are pasteurized should be safe for human consumption and would be low risk. However, unpasteurized milk products are high risk for both this and other diseases:

• Unpasteurized milk or cream
• Soft cheeses, such as Brie and Camembert, and Mexican-style soft cheeses such as Queso Fresco, Panela, Asadero, and Queso Blanco made from unpasteurized milk
• Yogurt made from unpasteurized milk
• Pudding made from unpasteurized milk
• Ice cream or frozen yogurt made from unpasteurized milk

Problems with Possible COVID Links

Group A Strep in Japan

Group A strep is responsible for strep throat which can normally be easily treated with antibiotics. If it spreads systemically through a bloodstream infection, it can cause streptococcal toxic shock syndrome (STSS), which can cause organ failure and leads to about a 30% mortality rate, hence the need to treat strep throat early.

There has been a massive surge of STSS in Japan in Q1 2024 (941 cases so far this year compared to 894 for the entire year of 2019). This is very unusual and could be a result of some of the immune system damage from COVID infections.

Transportation Incidents

There have been a LOT of airline incidents related to maintenance and manufacturing this year that have received plenty of media attention, as well as some that haven’t.

In addition, there was also the container ship that hit the Francis Scott Key bridge in Baltimore.

Obviously, we don’t know with any certainty if any of these are related to COVID. However, we do know about brain fog and other neurological issues that arise after a COVID infection. Even the Aircraft Owners and Pilots Association has spoken to the brain fog risk.

Let’s use motor vehicle accidents (MVAs) as a proxy for commercial incidents. We know that infections can increase MVA risks. For example, “The result…suggests that subjects with latent toxoplasmosis had a 2.65 (C.I.95= 1.76–4.01) times higher risk of a traffic accident than the toxoplasmosis-negative subjects.”

Motor vehicle deaths were climbing quickly starting in 2020.

One thing that had gotten my attention was a study using the Rey–Osterrieth complex figure (ROCF) test.

In the study, “We observed significant cognitive impairment only in the ROCF, a drawing task test used to assess visuospatial abilities, executive functions and memory. The deficits observed in the ROCF could not be explained by socio-demographic factors, ophthalmologic deficits or psychiatric symptoms, suggesting cognitive deficit secondary to SARS-CoV-2 infection. Other factors which may influence performance, such as motor coordination, spatial neglect, visual attention, semantic knowledge, intelligence and executive functions were not likely to explain the observed difficulties, since we did not find any significant differences in other non-verbal (Trail Making Test and Five Points Test) and verbal tests (verbal fluency, digit span) also related to these processes.

Visuoconstructive deficits are usually defined as an atypical difficulty in using visual and spatial information to guide complex behaviors like drawing, assembling objects or organizing multiple pieces of a more sophisticated stimuli. In drawing a complex figure, as in the ROCFT, the patient must organize visual and spatial information in a planned manner to execute the drawing per se, a processes that demand several more specific cognitive abilities related to perceiving, processing, storing and recalling visuospatial information, both regarding shape and position, as well the planning and execution of the drawing per se.”

People that have visuospatial deficits could have difficulties estimating speeds, directions, and other variables that are important in operating transportation, especially in circumstances where quick action is required. This is why I have concerns about public and commercial transportation as well as shipping.

It’s not just an issue in the US either. Other countries have a similar trend in the aggregate. What is particularly interesting though is how much the US contributes to the aggregate numbers. It’s not surprising given that we already have a distracted driving problem here as well as unmitigated COVID. I worry that these kinds of problems are only going to become more prevalent.

Could there be problems with both manufacturing and maintenance because of the pandemic? Perhaps…

Dengue in the Americas

Dengue cases are surging across both continents. It is a vector borne disease spread by Aedes aegypti or Aedes albopictus mosquitoes. It is also known as breakbone fever due to the severity of muscle spasms and joint pain, dandy fever, or seven-day fever because of the usual duration of symptoms.

There have been 549 cases this year in Puerto Rico so far, compared to a total number of 1,283 in 2023. During the first six months of 2023, there were 5,492,755 passengers out of the capitol, San Juan. The range for the incubation period of Dengue is 3-10 days, which suggests that there could be a number of arrivals in the US that are not yet symptomatic.

Puerto Rico has issued a public health emergency.

COVID in the US

This is weekly US COVID admissions. The dotted lines that drop in June last year is due to the requirement for reporting suspected admissions, so after that time, this data is only representing about 1/3 of the actual numbers.

This means that there are about 45,000 COVID admissions/week up to 3/17. About 1% of COVID cases need hospitalization, suggesting around 450,000 cases/week. However, this is also a gross undercount. This image shows the percentage of patients being screened from a sample of hospitals. Note the caveat on the chart, but we can then assume that the figures are closer to double that.

It also suggests that there are about 900,000 new cases/week based on hospital data alone. However, with better treatments including drugs like Paxlovid in play, the 1% hospitalization rate is likely a bit of an overestimate compared to the past.

I’ll ballpark that this means that there are about 150,000-200,000 new cases/day in the US. I’m old enough to remember when there was a big push to use NPIs because these numbers seemed insane. Now the country seems to give a big collective shrug. That doesn’t end well, especially for those who have gotten repeat infections.

I have this in the Myths section, but you can go directly to the article here.