Pathogen Update: 4-23-2024
Going, going, gone. Our trust in public health institutions that is.
Mrs. Olson has just did a triple flip in her grave. Read more in And now for something completely different …
Last newsletter I left off by describing a multitude of pathogens (and I forgot to mention the outbreak of Parrot flu in Europe, no I am not kidding) raising a ruckus. In particular, I focused in on the lack of transparency in our institutions concerning H5N1. Well, there has been a wee bit of headway. The USDA has released 239 genome sequences from the recent cattle outbreak (genetic sequences released).
Today, the APHIS National Veterinary Services Laboratories made available 239 genetic sequences from the U.S. H5N1 clade 2.3.4.4b influenza virus recently found in samples associated with the ongoing highly pathogenic avian influenza (HPAI) outbreak in poultry and wild birds, and the recent H5N1 event in dairy cattle. APHIS routinely publishes influenza genetic sequence data on GISAID (the Global Initiative on Sharing Avian Influenza Data); however, in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and development to benefit the U.S. dairy industry, APHIS is also rapidly sharing raw sequence data to the National Institute of Health’s National Library of Medicine, National Center for Biotechnology Information. Sequences posted are from cattle, cats, chickens, skunk, racoon, grackle, blackbird, and goose. APHIS will continue making additional raw genetic sequences available on a rolling basis at Home - SRA - NCBI (nih.gov); use the search term “WGS of H5N1”.
Dippity do da day! Oh, thank you purveyors of knowledge, you are so generous. Bullshit!
If you are on X here is a must follow.
As much as it hurts me to say it, my mind is telling me less than 3 years until the human-to-human change is complete. The R-value will be around the Wildtype strain of COVID and the way our society rolls it will have free reign until people realize 1 out of 2 infections will prove fatal. Yes, you read that correctly, 50%! Oh, and the WHO has found the virus in raw milk. Supposedly our pasteurized milk is safe. Ultra-high temperature (UHT) pasteurization 140C (284F) supposedly will do the trick but my question is whether they are doing it long enough (currently 2-5 seconds is used to keep from breaking down all the proteins in milk). And not all grocery milk uses UHT. 75C for 15 seconds for example.
I should mention we have a barely stocked supply of vaccines. However, which comes first, the chicken or the egg-based vaccine? Folks, our institutions have failed us miserably. I could go into the geopolitical and economics of this, but I might put you into a permanent sleep.
The Covid Wire
will return next Newsletter.
MAPS
MAPS is still trying to gain my complete trust. I do not feel comfortable releasing the latest forecasts yet. I have a few more hurdles for it to pass the smell test. Currently, it is indicating a slight rise in new daily cases into June followed by a leveling off into August. Towards the end of the mini-ensemble, it begins to tick up by September.
I am also going to include measles in my future forecasts and am currently working on an avian flu module for several mammals. That will not be ready for a couple of months though. Also, I have resumed working on the county initialization. What is the delay you might ask. In a nutshell, try calibrating several thousand counties with sketchy calibration data.
So let us ride on the back of the dear Dr. Hoerger. It appears to agree somewhat with what I am seeing with the “new” MAPS, indicating an increase until mid-May then it levels off. Still over a half million new cases a day at that point. Good grief how long are we going to let this scourge run amok! 20,000,000 long Covid cases to date. And you will see below all the symptoms and points of attack. There is evidence that it is causing a lapse in the tight regulation of retroviruses through the interaction with transposable elements. Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection Folks, viral persistence will be oft repeated in conjunction with each other. We cannot clear this damn thing out. Extreme cases have been documented that indicate upwards of 60 different variants in the same host. This is freaking grim, particularly be our health institutions remain reactive with an ability to communicate information that we should all have access to.
The Covid Xfeed
I am not sure what I would do without Justin’s tireless updates. I think him and Vipin could be part of a vampire nest. When the hell do they sleep?
Graphically this is an extraordinary presentation. Emotionally it takes a toll as you realize the vastness of COVID’s tentacles in reaching all parts of the human body.
Emmanuel
𝗖𝗢𝗩𝗜𝗗 𝗜𝗡𝗙𝗘𝗖𝗧𝗜𝗢𝗡 & 𝗟𝗢𝗡𝗚 𝗖𝗢𝗩𝗜𝗗
𝗪𝗵𝗶𝗰𝗵 𝗼𝗿𝗴𝗮𝗻𝘀, 𝘀𝘆𝘀𝘁𝗲𝗺𝘀 𝗮𝗿𝗲 𝗶𝗺𝗽𝗮𝗰𝘁𝗲𝗱 ? 𝗪𝗵𝗶𝗰𝗵 𝘀𝘆𝗺𝗽𝘁𝗼𝗺𝘀 ?
The pathophysiology of infection and PASC is complex and multifactorial, involving direct organ damage from virus infection ..
2) ...immune system dysregulation, autoimmune responses, microthrombosis, and persistent viral proteins/inflammation.
Multiple functions and organs are commonly impacted include lungs (pulmonary fibrosis, vascular dysfunction), heart (myocarditis, microvascular damage),
3) ...brain (neuroinflammation, autonomic dysfunction), gut (microbiome changes), kidneys, blood (hypercoagulability), and skin.
In these tables, there are the systems affected, the number of patients, their characteristics, symptoms and so many reference studies.
4) We have decided in this thread to summarize partially, these 2 tables with affected systems, nb of studies, nb of patients and symptoms, to visualise to what extent COVID-19 can impact our body.
5) 𝙍𝙀𝙎𝙋𝙄𝙍𝘼𝙏𝙊𝙍𝙔 𝙎𝙔𝙎𝙏𝙀𝙈
12 studies, more than 3.000 patients, follow-up 3-12 months, symptoms :
▶️ 42% of survivors had mild pulmonary function abnormalities
▶️ 25.4% of the patients, mostly demonstrated diffusion reductions in DLCO
...
6)
▶️ Diminished TLC and diffusion capacity in 23 and 36 participants
▶️ Impaired DLCO in 33 (36%) and VA in 24 (26%) participants
▶️ Abnormal pulmonary function in 43 (75.4%) patients
▶️ Pulmonary diffusion abnormality in 22-56% of participants
...
7) 𝘾𝙄𝙍𝘾𝙐𝙇𝘼𝙏𝙊𝙍𝙔 𝙎𝙔𝙎𝙏𝙀𝙈
7 studies, more than 2.000 patients, follow-up 17-97 days, symptoms :
▶️ Cardiovascular-related symptoms (70, 13%), resting heart rate increase 60 (11.2%)
▶️ Chest pain (21.7%)
▶️ Abnormal CMR (78), including raised myocardial native T1 (73)
8)
▶️ Abnormal echocardiogram 667 (55%), new myocardial infarction in 36 (3%). ▶️ Abnormal CMR (60.4%). Either pericarditis and/or myocarditis (30.9%): isolated pericarditis (5.8%), myopericarditis (7.9%),
▶️ Cardiovascular pathology (12%), myocarditis (8%)
...
9) 𝙉𝙀𝙍𝙑𝙊𝙐𝙎 𝙎𝙔𝙎𝙏𝙀𝙈 𝙖𝙣𝙙 𝙋𝙎𝙔𝘾𝙃𝙄𝘼𝙏𝙍𝙄𝘾 𝘿𝙄𝙎𝙊𝙍𝘿𝙀𝙍𝙎
8 studies, more than 100.000 patients, follow-up 15 days-6 months, symptoms :
▶️ Smell and taste loss was reported in 68% (40/59)
▶️ Fatigue (40), "brain fog" (29), and changes in cognition (25)
10) ▶️ Headache (97, 74.6%), severe headache (24), anosmia/ageusia (54.6% vs. 18.2% in headache)
▶️ Late onset of Guillain-Barré syndrome
▶️ 28% PTSD, 31% depression, 42% anxiety, 20% OC symptoms, and 40% insomnia
▶️ Psychiatric illness (18.1%), mood disorder (9.9%)
...
11) There is of course much more information in this fascinating study that we highly recommend.
If you want to read the entire article it might take half a day. This baby is packed with information. One notable omission was vision. I know there is not a lot of work in that arena, but I have seen and heard in chat rooms from long haulers, about vision issues.
As I just stated, the man is tireless. Check this gem out. Another excellent presentation by the article’s authors and Justin.
Emmanuel
𝗣𝗢𝗦𝗧-𝗖𝗢𝗩𝗜𝗗 𝗣𝗔𝗜𝗡 𝗦𝗬𝗠𝗣𝗧𝗢𝗠𝗦
journals.lww.com/painrpts/fullt…
Investigating the fluctuating nature of post-COVID pain... : PAIN Reportspandemic were scheduled for a telephone interview at 8.4 (T1), 13.2 (T2), and 18.3 (T3) months in average after hospitalization for collecting data about post-COVID pain. Patients were asked for abou…https://journals.lww.com/painrpts/fulltext/2024/06000/investigating_the_fluctuating_nature_of_post_covid.10.aspx
2) The study investigated the fluctuating nature and trajectory of post-COVID pain in previously hospitalized COVID-19 survivors over 18 months using Sankey plots and exponential bar plots.
3) The prevalence of post-COVID pain was 41.07% at 6 months, 34.29% at 12 months, and 28.47% at 18 months. Sankey plots showed a fluctuating pattern, with some patients developing delayed-onset pain.
4) Exponential bar plots visualized a decreasing trend in post-COVID pain prevalence over time, though some pain may last up to 5 years.
Common locations were lower extremity and widespread pain. Around 45-50% of patients reported new-onset post-COVID pain.
5) Risk factors for long-term post-COVID pain included female sex, pre-existing musculoskeletal pain, headache as onset symptom, longer hospital stay, and having pain at 6 months.
6) The study identified fluctuating patterns of new-onset, delayed-onset, and persistent post-COVID pain using visualization methods. Post-COVID pain may be underestimated and deserves more focused study.
Thanks for reading 🙏
Are you in sensory overload yet? This beauty will surely take you over the top!
Emmanuel
𝗧𝗵𝗲𝗿𝗮𝗽𝗲𝘂𝘁𝗶𝗰 𝘁𝗮𝗿𝗴𝗲𝘁𝘀 𝗳𝗼𝗿 𝗖𝗢𝗩𝗜𝗗-19
2 𝘸𝘰𝘯𝘥𝘦𝘳𝘧𝘶𝘭 𝘴𝘵𝘶𝘥𝘪𝘦𝘴 𝘸𝘪𝘵𝘩 𝘨𝘳𝘦𝘢𝘵 𝘷𝘪𝘴𝘶𝘢𝘭𝘪𝘴𝘢𝘵𝘪𝘰𝘯𝘴, 𝘧𝘰𝘳 𝘢 𝘱𝘰𝘴𝘪𝘵𝘪𝘷𝘦 𝘰𝘶𝘵𝘭𝘰𝘰𝘬 🤗
2)"Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies"
Current treatment strategies for COVID-19 can be classified into "target virus" and "target host" categories. Repurposing existing drugs, emerging drugs .. nature.com/articles/s4139…
Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies - Signal Transduction and Targeted Therapyhttps://www.nature.com/articles/s41392-021-00733-x
3) ...and promising potential targets fall under these categories.
For the host, ACE2 receptor, TMPRSS2 protease, inflammatory cytokines and their pathways, CD147, and HMGB1 are potential therapeutic targets based on their roles in viral entry/pathogenesis/excessive inflammation.
4) Future directions include focusing on more promising targets, strengthening multi-disciplinary cooperation, addressing gaps between preclinical/clinical research, and monitoring viral mutations. A combination of antiviral and immunomodulatory therapies may be most effective.
5) For vaccines ...
6) "Therapeutic strategies for COVID-19: progress and lessons learned"
nature.com/articles/s4157…
Therapeutic strategies for COVID-19: progress and lessons learned - Nature Reviews Drug DiscoverySince the COVID-19 pandemic began, many potential therapeutics that target SARS-CoV-2 and/or human proteins to control viral infection have been investigated, with a few receiving authorization by reg…https://www.nature.com/articles/s41573-023-00672-y
7) Potential therapeutic targets include viral proteins like spike, protease, RNA polymerase, and host proteins involved in viral entry/ immunopathology. Various agents have shown anti-SARS-CoV-2 activity in preclinical/clinical studies, but most require further development.
8) Treatment strategies aim to administer antiviral drugs early to outpatients, while immunomodulators may benefit severely ill inpatients. Treating long COVID remains challenging due to its unclear mechanisms. Development of pan-coronavirus therapies is another priority area.
9) Overall, while progress has been made, more convenient and broadly effective antiviral therapies are still needed to effectively tackle COVID-19 and future coronavirus outbreaks, including those targeting key viral proteins and able to counter emerging variants.
10) Thanks for reading 🙏 and have a wonderful sunday 🤗
And now for something completely different …
OK fellow humans, we can just have a feeding tube, catheter, and colonoscopy bag and lay on are assess all day and watch AI-generated movies through our VR goggles. AI will make everything peachy. Give me a break, this gives me a caffeine crash.
An artisan roastery based in the Finnish capital has introduced a coffee blend that has been developed by artificial intelligence in a trial in which it's hoped that technology can ease the workload in a sector that traditionally prides itself on manual work.
It is only apt that the Helsinki-based Kaffa Roastery's "AI-conic" blend was launched this week in Finland, a Nordic nation of 5.6 million that consumes the most coffee in the world at 12 kilograms per capita annually, according to the International Coffee Organization.
The blend—an AI-picked mixture with four types of beans dominated by Brazil's velvety Fazenda Pinhal—is the end result of a joint project by Kaffa, Finland's third-biggest coffee roastery, and local AI consultancy Elev.
…
OK, send me a bag …
In addition to coming up with its chosen mixture of beans from Brazil, Colombia, Ethiopia and Guatemala, AI created the coffee package label and a detailed taste description saying "AI-conic" is "a well balanced blend of sweetness and ripe fruit."
Hampf acknowledged he was surprised that AI "somewhat weirdly" chose to make the blend out of four different type of coffee beans, rather than the usual two or three which allows distinction in taste between flavors from different origins.
After the first test roasting and blind testing, Kaffa's coffee experts agreed, however, that the tech-assisted blend was perfect, and there was no need for human adjustments.
According to Elev's spokesman Antti Merilehto "AI-conic is a tangible example of how AI can introduce new perspectives to seasoned professionals" while offering coffee lovers new taste experiences.
A coffee roastery in Finland has launched an AI-generated blend. The results were surprising
There is so much going on right now I left out some goodies that we will get to next time.
Stay safe and help those who need it most.
take care,
Joe
*A special note: this is a free newsletter. I spend 4 hours a day just reading and another couple of hours putting together this newsletter. Donations out of kindness are deeply appreciated. All donations go toward the purchase of another server that will allow my modeling work to go global with a small percentage toward climate causes. You can go to my substack homepage if you wish to donate.
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)
Deja vu ...
Yep, it all makes me feel nuts!