An Odd Time for Influenza A

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.

2024-Week 15

Contents:
H5N1
COVID Topics:
Group A Strep
Psitticosis
Disability

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.

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.

2024-Week 14

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.

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.

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.

2024-Week 13

Contents:
H5N1 and Food Chains
COVID and Workplace Fatalities

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.

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.

2024-Week 12

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.

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.

https://pacificbirds.org/birds-migration/the-flyways/

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

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.

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 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.

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.

Myth: We Don’t Know the Long-Term Effects of the Vaccine

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

Is COVID Driving a Surge in Mycoplasma pneumoniae Pneumonia in Children?

Image from Mycoplasma pneumoniae and Its Role as a Human Pathogen. (Waites and Talkington, 2004).

There have been many reports of unusually high case counts of pneumonia in children and some of this appears to be related to Mycoplasma pneumoniae. Some are calling this white lung syndrome. h/t to @celestial_bean_ for this list of different locations.

The review article Infection with and Carriage of Mycoplasma pneumoniae in Children provides an excellent background on this problem (Meyer Sauter et al., 2016).

An eight-year study beginning in the 1960s in Seattle found carriage rates that varied between endemic (2%) and epidemic (35%) periods (Foy et al., 1979). One study found that 21% of asymptomatic children carried M. pneumoniae in their upper respiratory tract at a single study site (Spuesens et al, 2013). In a separate study, 24% of children with pharyngitis were found to have M. pneumoniae on testing as well (Esposito et al., 2014).

A 2023 study of children with recurrent respiratory tract infections found that 68% carried M. pneumoniae (Koenen et al., 2023). Why is this rate doubled of that a few years ago? Could COVID be a driving factor?

This organism is more likely to cause severe disease in an immunocompromised host (Yacoub et al., 2016). One problem is that colonization may not drive a mucosal antibody response (de Groot et al., 2022). I have a number of studies linked on this page indicating immune system damage from COVID.

Think of the immune system as a chemical defense system against pneumonia. Another defense system is mechanical. “Mucociliary clearance (MCC) is the primary innate defense mechanism of the lung. The functional components are the protective mucous layer, the airway surface liquid layer, and the cilia on the surface of ciliated cells. The cilia are specialized organelles that beat in metachronal waves to propel pathogens and inhaled particles trapped in the mucous layer out of the airways.” (Bustamante-Marin and Ostrowski, 2016).

In a hamster model, “SARS-CoV-2 infection is followed by a severe loss of cilia.” (Schreiner et al., 2022). Part of the mechanism of spread to other cells in the respiratory epithelium has been described and illustrated (Su et al., 2023).

“The step-by-step model of SARS-CoV-2 penetrating the mucus barrier and infecting human nasal epithelium. Air-liquid interface culture of primary human nasal epithelial cells to form nasal epithelial organoids composed of ciliated, goblet, and basal cells. Firstly, small amount of virus penetrates the peri-ciliary layer, along the cilia, after binding to ACE2 on cilia. Activation of various kinases such as PAK1/4 and phosphorylation of several actins such as EZR occur in the infected ciliated cells immediately. The microvilli then form dome-shaped alienated structures and high degree of extension. Cytoplasmic vesicle-encapsulated viral progeny pass through the PCL layer along alienated microvilli and exit at the mucus layer. Mucus flow, which depends on ciliary movement, assists the spread of viral progeny to other surrounding cells.”

The mechanism of the loss of cilia has also been described (Fonseca and Chakrabarti, 2022).

SARS-CoV-2 ORF10 impairs ciliogenesis by enhancing the activity of the E3 ligase CUL2ZYG11B. (A) The CUL2ZYB11B RING E3 ligase complex contributes to cellular protein degradation via ubiquitination. (B) Upon SARS-CoV-2 infection, the viral protein ORF10 binds the E3 adapter ZYG11B, increasing the ubiquitination activity of the complex, and inducing the proteasomal degradation of ciliary proteins, including IFT46. (C) ORF10 overexpression in serum-starved NIH3T3 and MRC-5 cells blocks primary cilium biogenesis and maintenance. (D) The lentiviral transfer of ORF10 is sufficient to induce cilia loss in human ACE2 knock-in mice and in primary human nasal epithelial cells, highlighting the role of this viral protein in SARS-CoV-2-mediated cilia disruption.”

This damage can clearly be seen in both transmission and scanning electron microscopy.

This damage has been seen with other coronaviruses. “Transmission electron micrograph of nasal epithelium before and after coronavirus inoculation. a) Transmission electron micrograph day 0. This shows normal tissue with an intact well-ciliated surface and minimal disruption. b) Transmission electron micrograph day 3. This shows abnormal tissue with severely disrupted cell surface. Marked loss of cilia is seen. Internal scale bars=2.9 µm.” (Chilvers et al., 2001).
A Scanning electron microscopy (SEM) image of a massively infected cell at 2 dpi (left) with a lack of cilia and an accumulation of viral particles at the surface of membrane ruffles (enlarged in right panel). B SEM image of an infected cell at 2 dpi with few remaining cilia (left) and scattered viral particles (vp) at the plasma membrane (right). C, D SEM images of infected cells at 2 dpi showing cilia abnormalities, including shortened misshapen cilia (D left, enlarged in middle panels) and crescent-shaped proximal axonemes (E). E SEM image of pleiomorphic SARS-CoV-2 viral particles.” (Robinot et al., 2021)

The authors also showed the impact of infection on the ability of the cilia to sweep away low density 30 µm-sized polystyrene microbeads. The first video is of mock-infected cells where “beads deposited on mock-treated epithelia moved generally in the same direction, consistent with coordinated beating of the underlying cilia.”

“In contrast, beads deposited on infected epithelia were mostly immobile or showed randomly-oriented limited movements, indicating an impairment of the mucociliary clearance function.”

It’s clear that both immune system dysfunction and respiratory epithelial damage could be contributing to the M. pneumoniae problem in the pediatric population. The question then becomes one of why this seems to be surging now. Could it be that a new variant is driving this? The answer seems that this seems to be a distinct possibility. “Omicron variants dramatically accelerate spread via the ciliary transport/microvilli reprogramming pathway, which explains the increase in its attack rate compared to previous variants.” (Wu et al., 2022).

What variants do the impacted countries have in common currently? 23F (EG.5) and its sublineages (HV.1 is one of them).

https://covariants.org/per-country?region=World

This variant is also dominant in Ohio…

https://covariants.org/per-country?region=United+States

…as well as Massachusetts.

https://covariants.org/per-country?region=United+States

However, the HV.1 sublineage seems to be what is becoming dominant in the US which correlates with the M. pneumoniae cases. It’s interesting that the EG.5 is dominant in the world.

Of course, this could all be correlation with the variants. It’s possible that there is ascertainment bias and that much of the pneumonia in pediatric populations is a combination of COVID, RSV, influenza, and M. pneuomoniae which are all on the rise. Even more concerning is the possibility that this is a new virus. The rapid rise in cases would certainly suggest that. It’s also worth learning about the concepts of sufficient and necessary causes in epidemiology if one has that level of interest in this topic.

Mainly though, I hope to impress on people that COVID not only is a causal pathway for a number of chronic diseases, but I think I’ve made a case that it is also causal for infectious diseases as well, with a special focus here on respiratory ones. We need to be doing far more to protect children.

Myth: VAERS Proves Massive Injury and Death from COVID Vaccines

Tackled another myth today. You can read the entire piece here. Robert F. Kennedy Jr. and Steve Kirsch are singled out.

An Important Preprint

This preprint study has some stunning findings. The short version is that even among those who had COVID but no symptoms, there is tissue damage.

When cells die, their contents are released into the surrounding tissue. Parts of the DNA of the cell are also released and can be detected in the bloodstream. That’s what is meant by cell-free DNA (cfDNA). Epigenetic liquid biopsies study the cfDNA and can determine the type of cells that it came from, based on characteristic molecular structures. The authors state “Patients with severe COVID-19 had a massive elevation of circulating cell-free DNA (cfDNA) levels, which originated in lung epithelial cells, cardiomyocytes, vascular endothelial cells and erythroblasts, suggesting increased cell death or turnover in these tissues.”

Cardiomyocytes are the muscle cells of the heart that contract to provide the heartbeat. When a large area of these become damaged, it is called a myocardial infarction, or commonly called a heart attack. This is normally due to either fatty plaques forming in the blood vessels that feed the heart or a clot that enters one of them. Keep that in mind for the part on vascular endothelial cell damage.

Endothelial cells line the inside of tissue. Epithelial cells line the outer surface. Damaged lung epithelium means that the cells that take up oxygen in the air sacs of the lungs (alveoli) which gets diffused into the bloodstream and carbon dioxide to flow into the alveoli no longer function. Erythroblasts are the cells that become red blood cells when mature. The damage to these just these two cell types means that other tissues will be supplied less oxygen, but that is just part of the widespread damage.

The damage to the vascular endothelium is really one of the most critical things to understand about COVID. It is the layer of cells lining blood vessels.

Capillaries become small enough that they only allow for a single red blood cell to pass at a time, as illustrated video.

That is the problem with endothelial damage. When that occurs, capillaries can be occluded, which would lead to reduced (or no) oxygen flow to the tissue supplied by the capillary. These blockages are what are referred to as microthrombi.

An important finding of this study is “Patients with severe COVID-19 have a higher concentration of cfDNA, originating in affected tissues.” When endothelial damage occurs and microthrombi form on a large scale, such as in severe COVID, it leads to acute organ damage and potentially organ failure.

The damage of clot formation is evident in a stroke. (The other common type of stroke, where a blood vessel ruptures, is called a hemorrhagic stroke). When a clot causes a stroke, it’s called an ischemic stroke, because the clot deprives the downstream brain tissue of oxygen, as illustrated in this animation.

There was an autopsy study of patients who had died of COVID. “151 autopsies were included, and 91 cases presented microthrombi in the lung (73%), heart (11.2%), kidney (24%), and liver (16.3%). The age range was between 27 and 96 years.” Clearly the COVID microthrombi risk is real across many organs.

Endothelial damage is not only dangerous due to clot formation, but also because the endothelial cells are responsible for the transfer of oxygen from red blood cells into the surrounding tissue, which can also lead to that tissue being starved of oxygen and potential death of those cells, which is called ischemia.

The preprint also refers to erythropoiesis, which is simply the production of new red blood cells. Why would this increase? Because the body recognizes that parts of it are starving for oxygen.

There is more to the study, but this is the basic biology that is important to understand in how COVID causes damage.

I suspect that part of the reason that COVID seems less damaging in younger or healthier populations is that they can more easily handle some tissue damage since the surrounding unaffected tissue can take on some of the load of the damaged tissue. However, as that unaffected tissue ages, it won’t work quite as efficiently as when it was young and healthy, and the impacts of the COVID infection will start manifesting themselves as a number of chronic diseases. The fact that we are seeing many of these in such a short time is extremely concerning. It suggests that we will see massive amounts of chronic diseases among people who had COVID infections in the future. You can find information on some of these broken down by organ system on this page. Click the link of the system to see some of the studies.

My Nod to Gary Larson