Pathogen Update: 1-28-2025 Forecast Edition

New Forecast and Masking Study, H5N1 updates

Hey, daddies, how did I get here? Read more in And now for something completely different …

I found a pandemic essay very much aligned with my thoughts and sentiments. This is an excellent read, folks. You can read it here. Thank you,

Cat Herding Science Nerd

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MAPS

MAPS USA Ensemble (N=20) Forecast 1-6-2025 to 5-6-2025 with Masking Results

This is the first forecast done with a newly added compartment used for immunity profiles from natural immunity with/without prior vaccination. This was implemented by dividing the re(C)overed compartment into two compartments: C-hybrid with natural immunity plus vaccination and C-natural with only infections. Based on a recent paper the protection imparted by these C-compartments was implemented in MAPS as a Gompertz curve function, with the values shown in the table and graphs below. The differences in the pre/post-Omicron curves are rather stark. This is expected as variants have continued to increase their Immune Escape (IE). As I have stated previously, the model parameters, including waning periods, are adjusted based on data quantifying IE and the ACE2 binding affinity for each variant, removing my guesswork. I hope to write this up in a journal paper soon.

The most important table values are highlighted in yellow. The C-natural protection starts at 80.77 and decreases to 37 after 266 days. The hybrid protection begins at 86.38 and drops to 46.5 after 183 days.

We will see how it works out, but historical runs indicate better agreement than the prior version of the model. The figure below shows the +/- 95% CIs (thick black lines), the ensemble mean (thick red line), and other ensemble members within the bounds. If this is verified, it would be an unprecedented early spring wave. This modeling period would produce 91.3 New Daily Infections (NDIs) with between 4.6 and 20.3 possible Long Covid outcomes. The resultant deaths could be over 15,000.

From start to end, the last holiday wave was fairly linearly increasing at 20.3K-NDIs/day. The current forecasted spring wave is linearly increasing at 16.7K-NDIs/day. It takes longer but starts at a much smaller minimum. The holiday wave was also enhanced due to increased travel and interactions.

Here is the current US makeup of the variants, with two new updates posted by the CDC. LP.8.1 has continued growing, with XEC.4 as a newly quantified variant. The current model forecast includes all of the top variants in the latest analysis for a total of twelve. We can see that XEC is slowly declining, and LP.8.1 is increasing by 50% over the two-week period. The MC.* variants have stagnated, and XEK/XEC.4 indicates a slight growth.

Studies have helped considerably in setting the model IE/ACE2 values for many variants and NextStrain was also examined. These can be found here and here.

The forecast numbers, resultant LC and fatal outcomes, and damage to immune systems should be extremely concerning. So, what could be done to mitigate this? Based on the current forecast, this is the perfect time to look at a new masking study. In this version of the masking study series, the effects of masking compliance were integrated into MAPS with compliance set to 0, 2.5, 5, 25, 50, and 75 percent values. In the forecast above, the masking is set to 2.5% percent of the population, and the masking is assumed completely randomized, and the mask protection (N95’s) was 78%. The results are displayed in the graph below.

The red line is the current forecast (2.5% compliance) and is bounded above with no masking and below with 5% masking. These subtle changes can result in an appreciable reduction; this is a non-linear characteristic of masking. What differs from previous masking studies published here is that the 25% compliance results in no early spring surge, while the previous studies required around 50% to attain this result. What has changed? It is the implementation of the new compartment model algorithm, the main feature being the minimum protection imparted after the waning period. The values were 37 and 46.5 for the infection-only and hybrid compartments. Combining this minimum protection with 25% mask compliance surely puts the overall protection near the magic 50% value. Above 50%, the virus will decline as Reff goes below 1. In the 25% case, the newer infections (remember, the model knows about past infections going back to May 2024) present early in the simulation period have lost some of the protective value, and the NDIs begin to increase. At 50 and 75% compliance, the cases are nearly shut down.

When I first posted this on X late last night, some suggested I was dreaming if I thought we could get to 1 in 4 masking (25%). Let us digress. It was in July of 2021 that B.1.617.2, known as Delta, began an alarming rise at a time when folks thought we were in the clear and had largely quit masking. The history is shown in the graph below.

Slowly, the masks came back on, and the country reached a maximum by September. This is shown graphically below and comes from a study I have previously published in this substack. Look at some of those numbers, with Virginia almost reaching 80%! The population-weighted national average was nearly 57%. I believe we can see a 25% masking rate in the future as we educate the population about how serious “living with an infectious airborne neurotropic vascular disease, sans masks” (well stated @AndrewHewat). I ask you to share this information among your social circles.

Andrew’s tweet:

I will inform you about the dire situation due to the new administration’s freeze on vital health-related data, including wastewater data. This could be one of the last forecasts with our wastewater initialization procedure, which is grim.

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H5N1 update

The situation in the United States is getting very serious, and worldwide for that matter. As you have likely noticed, the price of eggs has risen dramatically due to the culling of domestic birds across the country. USDA data shows the estimated population of farmed birds is roughly 855 million. The most recent USDA-APHIS numbers show 148 million birds have been culled, representing 17.3% of the total population. This situation has not been quickly rectified since bringing back viable birds takes roughly 1 year and is expensive. It is also in further decline because the infections continue to spread alarmingly. Here is a graph that shows how this has progressed over the last 3 years. It shows the percentage of the total flock that has been culled.

To put that in perspective, over the last three years, we have lost an average of 4.8 percent of our domestic birds annually. Domestic production is further being hampered as migrant farm workers are not reporting to work over fear of the virus but of ICE activities. Looking at just one aspect of the HPAI, you should be very worried about our food supply. This ongoing outbreak will clearly affect your pocketbooks.

The situation in cattle, particularly dairy cattle, is also becoming very grim. Here is the USDA-APHIS map showing the number of herds impacted by HPAI. California has the bulk of the herds infected, followed by California. Because of the nature of the virus, this has not impacted the beef cattle. To put some numbers on this, there are 28,000 registered dairy herds in the US, with an average herd size of 377 cows, representing a total of 10.5 million animals. The percentage of herds infected is about 3.4%. Remember this is the Bird Flu infecting mammals. To further raise your concern, since the early 2000s, the number of herds has been reduced by more than 50%. Despite this reduction, the number of animals in production has actually increased. What should concern you is the number of herd reductions represents more of big Ag overtaking small farms and an increased density of animals on the farm, which benefits the pathogens spread in numbers of animals infected. As I just mentioned, this is another assault on our food supply.

One more thing that concerns me is the human component of the spread of H5N1. It appears the virus is a mutation in infected humans, and one of the two mutations needed to go human to human through an airborne pathway has already been detected in infected individuals. If these two mutations are achieved, it could spell disaster for humans due to the high infection fatality rates. Two more mutations can enhance the replication of the virus within the host. Thus, increasing viral load and one another can enhance its viability in sustaining itself in the air. When those last two happen, and some indicators suggest it accelerates its changes due to reassortment, all hell will break loose. What are the indicators I see? First, an H5N9 case was detected in Merced County, CA ducks. Previously, this farm had culled 119,000 birds in December, but it appears a possible reassortment might have occurred between H5N1 and an H*N9 virus. The second is the human case in the UK, which was shown to be from the D2.1 genotype, not the D1.1 genotype seen in human cases in the US. The final concern comes from a paper that flew under the radar for most of the time since I saw it last November. This had extensive genome sequencing done on a human case from an exposed dairy compared to the dairy cattle at the Texas farm. A total of 9 distinct mutations in the human case were documented in this study.

Folks, we are on the precipice of another pandemic. It is not a question of if; it is a question of when. I speculate it will spread efficiently from human to human within the next two years. Due to a combination of factors, I would not be surprised if it passed the first hurdles to go human to human by this coming fall.

Dog help us.

And now for something completely different …

The key points from this study are shown below. I have written to much tonight.

"This work will help to address a number of limitations in stem cell and regenerative medicine research," says Li.

"The unique characteristics of imprinting genes have led scientists to believe that they are a fundamental barrier to unisexual reproduction in mammals," says co-corresponding author Qi Zhou, also of CAS.

"Even when constructing bi-maternal or bi-paternal embryos artificially, they fail to develop properly, and they stall at some point during development due to these genes."

"Further modifications to the imprinting genes could potentially facilitate the generation of healthy bi-paternal mice capable of producing viable gametes and lead to new therapeutic strategies for imprinting-related diseases," says co-corresponding author Zhi-Kun Li of CAS.

Mouse with two fathers survives to adulthood, marking scientific milestone

Adult bi-paternal offspring generated through direct modification of imprinted genes in mammals

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Stay safe, and do kind acts for others and most of yourself. Thank you for reading.

Joe

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Miscellaneous items you might like follow below.

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Here is a kick ass at home test, nearly equivalent to a PCR test.

SARS-CoV-2 is a vascular virus, not just a respiratory virus. To make it simpler for folks call it a whole-body virus. No organ is spared. It infects our entire body and creates reservoirs throughout and should be thought of as a Long Covid virus and will exploit pre-existing risk factors.

Interviews Dr. Michael Hoerger, Dr. David Joffe, Emmanuel Justin, and Dr. Yaneer Bar-Yam.

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Check out this article. I love it. It’s an easy read but stimulates the brain in many ways.

Viruses Finally Reveal Their Complex Social Life - Quanta Magazine

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Where do viruses hide in the human body? | The BMJ

Understanding immunity and viruses through the John Snow Project

Variant tracking at the CDC

Infections at WHN (updated!)

The neuroinvasiveness, neurotropism, and neurovirulence of SARS-CoV-2: Trends in Neurosciences (cell.com)

Indoor Air