Monthly Archives: April 2024

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.