Michael
@mrmickme2
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FAFO warrior and martyr.
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Pretty sure I just located the intermediate host that initiated H5N1 transmission amongst Dairy Cows in the US. It appears that it was a Canadian Goose. The sequence from New Mexico in mid-Feb is pretty clear in relation to cattle divergence on the tree below.
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It appears that a new pandemic is unfolding. Lots of uncertainty ahead.
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If the WHO is so suddenly concerned about the global proliferation of a supposedly novel or fitness enhanced existing Mpox clade, then why are they not recommending the immediate closure of international borders to contain its spread?
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There are extraordinary outbreaks of flu taking place throughout Asia right now in Thailand, India, Taiwan and so on. in the middle of summer. Because the WHO has suddenly chosen to focus on Mpox, all attention is diverted to that right now. Something off about the whole thing.
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This is just insane. Now more severe spike phenotypes showing up and growing like S:T1273I Higher viral loads, more syncytial spread leading to organ damage. Just more virulent and transmissible variants showing up because they can.
BREAKING: U.S. Records Historic 1.3 Million COVID-19 Infections Per Day
As of August 19, 2024, the United States has hit a new milestone in the COVID-19 pandemic, with daily infections surging to 1.3 million.
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If Mpox has in fact significantly lowered its replication fidelity, which appears to be the case, all bets are off about how it evolves from here. Allowing it to spread freely will be absolutely catastrophic, and that is not hyperbole.
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Heads up. Numerous reports like this of an aggresive Influenza-A spreading very quickly throughout Thailand right now. Many experiencing moderate to severe symptoms and doctors talking of vaccines being ineffective at stopping bad outcomes.
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People need to zoom the F out and stop obsessing over H5N1 levels in milk. There is a much much bigger shitstorm incoming.
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From what I can tell everything points to a massive H5N1,H3N2 and H1N1 convergence taking place.
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Unidentified Flu A going crazy over the north-east US. This time last year there were virtually no traces in sewage surveillance and now it's hitting levels not seen since March/April.
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A year ago someone suggesting cows would be infected with bird flu would have been met with skepticism if not downright ridicule. A month ago someone suggesting that Mpox would mutate uncontrollably would of been met with the same response. These situations can turn on a dime.
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Why is Cov suddenly substituting K for R at 679 in the spike? Something extra sinister going on with this virus right now.
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Starting to think that bird flu and human flu are mixing a little bit too easily at the moment. Something is really off about this. Some kind of genetic leap has triggered this whole clusterfuck of a situation.
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If there is still any doubt about how infectious Cov is getting, have a look at the short baseline duration between March and May. This virus is moving further and further away from even achieving reasonably limited herd immunity. Just relentless immune escape. Disastrous stuff.
UK COVID-19 deaths are up 20% in the past week, with rising cases, increasing hospitalizations, and a positivity rate of 15.9%.
UKHSA Data
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There have literally been hundreds and possibly thousands of posts from Thailand on here saying the exact same thing over the last couple of weeks. I'd take their word for it.
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Mystery solved. The massively saltated branch leading to both the Kenya and Uganda sequences had a weird G191388A mutation in OPG148 which regulates DNA polymerase processing, which in turn controls fidelity of DNA replication. This is totally f'd up stuff. Not meant to happen.
The only conclusion one can reach from seeing stuff like this is that Mpox by some extraordinarily rare fluke underwent a huge leap that has seemingly helped it to optimize its replication and immune evasion machinery. Also, this thing bypassing error checking is just incredible.
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More really bad Mpox news. Clade B.1 "the mild one" is showing apparent selective pressure in various key proteins responsible for stuff like double-strand break repair, suggesting that it could be having a much easier time for engaging in stuff like homologous recombination.
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I do often wonder about how many people got very ill, including lifelong sequela or died by throwing caution to the wind because they believed misinformation like this that claimed that vaccines will magically prevent them from being infected. This is really a tragedy.
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More weird stuff. India's been going through a bad H1N1 outbreak in the last couple of months and just uploaded an early sequence collected from Pune. It has a transversion nuc 29T in the HA N-term only seen in a couple of US sequences and abundant in US H5N1 cattle sequences.
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The Chinese are well aware of what’s coming and are trying to be as prepared as possible for it. They are first stop on the East Asian-Australasian Flyway that would see many millions of migratory waterbirds disseminating potentially numerous influenza A strains.
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Reminder that Mpox is a relatively slow spreading and stable dsDNA virus with a high fidelity rate, unlike a lot of the other stuff that’s getting around right now. Unless they can show a sudden shift in transmission mode its pandemic potential is pretty limited.
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The dude just tested positive and is hopeful of a return to competition. Pretty much sums up the current mentality.
🚨 Paris Olympics update: Adam Peaty has tested positive for Covid-19, a day after missing out on gold. Team GB confirms he tested positive Monday morning but remains hopeful for a return to competition in Paris.
#Olympics2024Paris
#TeamGB
#AdamPeaty
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If you have a look at Mpox protein OPG148 which regulates the DNA polymerase processivity it has been super stable since sequence collection started in 85 which makes this rogue branch which included mutation G126389A all the more puzzling. There was only this one blip in Dec23.
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If you have a close look at what H5N1, H1N1 and H3N2 are up to you’ll find they are converging on mutations that positively impact fusion with their host cells. I suspect this is happening by reassortment from the samples I’ve seen so far. I guess that will be confirmed soon.
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Gotta say that there is definitely some weird stuff going on with Mpox for there to be at least 2 very significant structural disruptions in an incredibly conserved protein responsible for DNA polymerase processing, all within several months of each other, across 2 clades.
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Wtf! Check out the insane divergence (.0158) in this very recent H3N2 sample from New York. Could be an inbound airport sequence? Carrying multiple H5N1 AA mutations in HA1 and prob others. I've counted at least 2: 50E and 267E and there are likely many more
@RickABright
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US completely Covfuckd right now. Which variant comes next will have its work cut out for it when it meets hundreds of millions of recently convalescent hosts. I’m sure the virus will rise to the challenge.
US: COVID-19 Wastewater Data
Data up to August 9th 2024
CDC
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Strikes me as a little bit odd that Colorado has a huge sudden surge of Flu A amidst the outbreak amongst the poultry cullers yet only seeing moderate H5 levels in their wastewater. What is that saying?
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The only conclusion one can reach from seeing stuff like this is that Mpox by some extraordinarily rare fluke underwent a huge leap that has seemingly helped it to optimize its replication and immune evasion machinery. Also, this thing bypassing error checking is just incredible.
1/2 Was just perusing the recent Mpox sequences collected in Uganda around a month ago. This one has 2 particularly odd T>G transversions with T14910G in the Ankyrin repeat which is known for interfering with IFN activation during early protein synthesis.
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Poxviruses are pretty unique—they replicate in the cytoplasm and have their own machinery, so they mutate less than most viruses. This means they’re usually stable targets for vaccines … until something unexpected happens and they aren’t.
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Many are expecting a sudden global pandemic to emerge from Avian Flu, but this overlooks a more likely scenario: its phenotypes gradually infiltrating regular seasonal flus. This could result in far more insidious outcomes, including increased pathogenicity/immune evasion.
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As the southern migration accelerates, almost every part of the world right now is in the process of being seeded with this virus, either as H5N1 or recombo or reassortment of one. Multiple avian flu outbreaks taking place over Asia, Europe at this time. People about to find out.
🚨🇫🇷 Suspected HPAI outbreak in French poultry farm reported
📍 Combourg, Ille-et-Vilaine
🐦 500 mixed poultry (indoor/outdoor) affected
🚧 10km temporary regulated zone
▶️ Poultry movement currently restricted
If confirmed, first case of 2024-2025 season
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Could be a total coincidence but it is curious timing in that Pneumonia has started trending over the last 10 days in Finland. Particularly, in the province that Helsinki is located in exactly around the time that the southern migration is expected to kick off. Is it connected?
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Watch the situation in India very closely. They're experiencing a large H1N1 oubtreak that's concurrent with global HPAI spread. The risk of co-infection has never been greater. The risk of this quickly picking up fitness-enhancing mutations has never been greater.
@doctorsaluja
I know that India is no stranger to massive H1N1 outbreaks but this one appears to be quite significant and widespread. The context around global HPAI spread makes it even more concerning in my opinion.
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Hearing stories like this is alarming in the context of H5 circulating in greater intensity throughout the planet. The risk of more pathogenic seasonal flu strains as a result of this is something that could hit us very hard and unexpectedly.
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This is very concerning.
⚠️ BREAKING
New H3N2v Flu Outbreak Hits Colorado and Michigan 🇺🇲
The Colorado Department of Public Health and Environment has reported a new case of H3N2v flu, involving a person under 18 who attended an agricultural event before showing symptoms.
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China completely Covfckd right now. Meanwhile, western economists scratching their heads as to why their economy is completely in the toilet these days.
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CCP news outlets are reporting that XDV.1 is mostly leading to bad outcomes in the elderly, yet the sequencing metadata has the 0-10 age bracket massively overrepresented compared to other variants. Starting to suspect that they may not be all that forthcoming with the facts😜
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The rest of the world would be wise to take note of what’s happening over there and pay less attention to the privileged libertarian trolls on here and on other media platforms who are downplaying the impacts of a diabolical virus that is causing immense human suffering.
🚨Mpox surge in DR Congo: hospital overwhelmed with patients as virus vaccine demand rises.
An ever-growing number of patients have been flocking to a Goma hospital in eastern Democratic Republic of Congo.
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@mrmickme2
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This H5N1 sequence in a chicken from a few weeks ago has the 139S mutation in the critical HA protein, previously seen only in a skunk in February in New Mexico (clade 2.3.4.4b) circa Feb. This mutation can enhance binding affinity to human receptors.
@RickABright
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Significant rise in non-subtyped Flu A showing up over the last 7 days in Bangor Maine watershed. Just around where infected birds would be crossing over into US surveillance points. Doesn't appear to be specifically H5N1 which could confirm substantial recombination at play.
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Not looking good.
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🚨This H3N2 sample taken by what looks like US CDC surveillance contains Q327K in HA1 which is adjacent to its monobasic cleavage site. K adds a very powerful AA mutation to H3N2 in this area. I really hope this isn't a precursor to it somehow acquiring a polybasic cleavage site.
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This virus can now potentially spiral out of control and evolve fitness-enhancing mutations that we haven't seen before.
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It shows. The stuff coming out of there is next level Cov. By letting it spread so easily we’ve given it the tools and it sure knows how to use them. Happening everywhere, just that countries like Canada have superior detection in place so we can observe FAFO closer to real time.
Canada: About 1 in 54 people infected with Covid
Many states now flashing red.
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Given that this sequence was collected over a month ago and probably only picked up weeks after these mutes emerged, could this mean it’s already made its way in to multiple countries with poor surveillance standards and is currently seeding throughout various communities?
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Only question I have these days is WTF are southbound migratory birds carrying back with them from arctic and subarctic regions? I expect that we are gonna be seeing lots of insane disease spread over coming days and weeks.
US - California & Oregon: "Klamath Basin wildlife refuges battle suspected botulism and bird flu outbreak" Pacific Flyway migration area h/t Commonground
#H5N1
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Thai media reporting a large flu outbreak over the last several weeks in certain provinces. Watch this space in the context of what the sequencing data appears to be indicating.
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According to local media the man who introduced the infection in to the household was just deported from the US. I really hope they have solid infection control processed in immigration detention facilities.
Honduras 🇭🇳 reports five suspected cases of the more infectious and deadly Mpox clade one.
All cases are from the same family, according to Health Minister Carla Paredes.
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India is clearly concerned enough to start screening arrivals coming into its most densely populated city. Good start but still another half measure.
⚠️ BREAKING:
Thermal Screening Begins at Pune 🇮🇳 Airport Amid Rising Monkeypox Concerns
In response to the global monkeypox threat, Pune Airport has implemented thermal screenings for all international arrivals, according to Hindustan Times.
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Indicative of a significant drop in replication fidelity in a dsDNA virus like Mpox, driving rapid evolution, leading to new variants, vaccine escape etc. Unpredictable times ahead.
BREAKING: 1,200 new Mpox cases of the latest variant were recorded in Africa this past week. This constitutes more than 6% of all cases in Africa this year, occurring within just one week.
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Looks like XDV.1 has skyrocketed over there in the last several weeks. Anecdotally, sounds like people are getting hit quite hard by it compared to prior waves.
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Watching the North-East US like a Red-tailed Hawk. Things about to get lit y'all.
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Keeping an eye on Trends in lieu of actual epi data. Concerning stuff in parts of Canada, where this would be expected to show up right about now. Influenza-like illness searches have taken off in the past 10 days. Adds more mystery to the non-subtyped Flu A showing up in sewage.
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Southbend Indiana now seeing environmental contamination of unspecified Flu A subtypes in contrast to zero readings this time last year. Right under the Mississippi Flyway and close to wetlands, which makes it an attractive stopover for disease-carrying birds to rest and eat.
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Shame that we don’t have a global health body that’s proactive rather than reactive. Too busy virtue signalling and pushing half brained vaccine solutions based on conjecture instead of going in to high risk countries, collecting sequences and mitigating transmission events.
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Not now Dengue, not now.
Sri Lanka - "Dengue Cases Surge: 2,373 New Cases in 18 Days" h/t Shiloh
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Already multiple farms showing outbreaks in Western Europe along flyways. Likely a lot more farms already impacted but not yet detected.
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When people say that Cov no longer packs the acute punch it once did, it finds ways to dramatically increase its viral load, simply because it can. This leads to lots and lots of very sick people that will have unpredictable short and long term outcomes.
@ACEGIK1476
One highly concerning mutation that’s been growing over there in Kp.3s is N:G204P made up of 2 transversed nucleotides. It was big in Alpha around mid early to mid 2021. Right in the middle of the N protein domain that impacts replication and disease.
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Very interesting finding that could potentially indicate a possible reassortment event taking place amongst h3n2, h1n1 and h5n1. Seasonal H3n2 clade 2a.3a.1 has apparently acquired HA1 54R in this cluster below seen in South America, Netherlands and also in California.
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Good thing that ships aren’t synonymous with spread of disease. Phew.
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@ReidMueller5
Has been going on for weeks now. Hell only knows what billions of birds have reassorted/recombined over that time. Follow the flyways. Most don’t peak until Oct/Nov. P2P spread obviously far less documented and predictable.
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Great article that sums up how bad the bureaucracy is at handling H5N1 spread on farms - although at this point I don't think the situation can really be controlled anymore. Too many hosts, too much global spread of this thing.
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Enormous Flu outbreaks taking place across many regions over the world and yet only 1 sequence of H3N2 gets dropped for the entirety of the epiweek.
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@UseBy2022
Highly unlikely on its own but it can co-infect mallards which can recombine it with ones that can like H3N2 and H1N1 via template switch. And that’s the real risk i.e Hong Kong 1968
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Can see that the infamous fusion enhancing L452R spike mute from Delta has shown up in some recent Kp.3 samples. So much Cov infection means more pressure for this stuff to show up and to see what it can get away with. Pretty bad on the back of P681R in FCS and Kp immune evasion.
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Yeah. It’s definitely attenuating 🙄 shout out to that chart whisperer and others on here claiming it’s all under control and predictable blah blah blah.
JUST IN: U.S. reports more than 1,000 new COVID deaths this week, highest since March
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Cov and a bunch of other viruses and bacteria replicate in the cytoplasm. Think about burden that this places on chaperones after Cov hijacks host cell machinery with ever growing replicative efficiency. Any surprise that more viral an and bacterial proteins are now misfolding?
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Wouldn’t trust them. To give you some perspective, US flu levels according to wastewater readings are around 15x greater than this time last year and jumped 2 fold in the first week of Aug. And the proper migration season doesn’t even start until later this month.
🆕 Updated joint FAO, WHO and WOAH assessment of recent H5N1 events in animals and people
▶️ Global public health risk: Low
▶️ Risk for occupationally exposed people: Low to moderate
▶️ Additional human infections likely, but minor global impact
@FAO
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These birds are a menace. I’m pretty sure they’re responsible for getting the cows sick with bird flu and have much more in store for us. They poo like 30 times a day, which contaminates enormous areas. They spread dangerous bacteria across rivers and are just trouble.
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Good idea. Let's apply much more immune pressure without reducing infectious pressure. Worked out so well for us with Cov. What could go wrong with a chaotic flu virus that's acting much more chaotically than usual?
A new mRNA vaccine is being tested on cows and dairy workers in an attempt to deal with the global bird flu outbreak.
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This is a process by which a virus gives the vaxx and relax crowd the middle finger for believing that a single vaccine dose and no accompanying behavioral adaption will make everything alright. At least viruses aren't that stubborn and ignorant.
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Why did this 🤡 copy my post and present it as his own? Jokes on him because I accidentally copied and pasted the wrong Nucleotide
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H5N6 could be a dark horse of the H5 subtypes. Significant evolution obvious between the sample taken in May of this year compared to a year earlier. The sample taken from the 41yo that died several days after testing positive containing the rare and dangerous Q131R in the RBD.
The July 2024 sample shows more changes in the HA protein, suggesting ongoing evolution to enhance binding affinity, immune evasion, and fusion efficiency. The E142- gap in this sample could be particularly significant, possibly with altering Ag recognition.
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While everyone is focused on American cows this virus is circulating throughout all parts of the world and coming in to contact with flu types to are very well adapted at infecting humans.
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1/2 Was just perusing the recent Mpox sequences collected in Uganda around a month ago. This one has 2 particularly odd T>G transversions with T14910G in the Ankyrin repeat which is known for interfering with IFN activation during early protein synthesis.
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Comforting to see Spanish Flu trending over the last 10 days in areas where shit tons of birds known for carrying HPAI are passing through as we speak. This one could be the best pandemic ever.
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Talk of vaccinating against HPAI reminds me a lot of our false assumptions about Cov. Thinking that we’re targeting a homogenous set of Antigens rather than a quasi species swam of variants with a tapestry of mixed and matched mutations evolved via massive selective pressure.
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Some apparently chronically infected individual has spawned this heavily saltated HV.1 lineage (XBB.1.9 derivative) in France. Will be interesting to see how it performs at the upcoming Olympics.
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Sounds under control.
"Greece's hospitals overwhelmed as nearly every household reports at least one Covid patient, says hospital professor".
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Things are getting progressively worse. This has already exceeded the huge 2019 outbreak and they’re in summer. Doctors highly concerned as over 1200 people have been hospitalised so far.
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These evolved flu types are clearly not fluffing around. They are highly pathogenic and can severely sicken or kill anyone, anywhere.
🇮🇳🚨6 deaths, 42 cases: Swine flu on rise, Bilaspur worst hit.
The deceased include a 41-year-old resident of Manendragarh and a 37-year-old resident of Rajnandgaon.
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Would strongly suggest examining this recent cattle sequence from Iowa. This in large part tells us about how much trouble we're in.
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This 2010 study on more pathogenic seasonal viruses like H3N2 due to genetic reassortment with H5N1 couldn’t be any more pertinent at a time like this.
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KP.3.2.3 lineage is rising aggresively, which is driven by a rare and what seems like an incredibly powerful Orf3a:S40P mutation in the TRAF3-binding motif that regulates activation of the early antiviral response. This delays activation of type 1 IFN allowing much more virus in.
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Another couple of H3N2 samples from Virgina taken around a week ago. Also appears to be collected via inbound airport surveillance. Enormous genetic diversity particularly in HA1/2 and NA region with numerous AA mutes in key regions matching H5N1 root.
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I mean what could possibly go wrong with seeing more and more waterfowl infected with H5N1 …
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@HealthcareGlob1
My expectation is that it will be worse than Cov. Flu has virtually no proofreading mechanism. It will split off in to many many different strains and if it gains significant fitness advantage such as a polybasic cleavage site it will be even more virulent and unstoppable.
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@DavidJoffe64
Okay I take back what I said earlier, I'm pretty freaked out by Mpox right now.
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The chickens are coming home to roost and then getting infected with H5N1.
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Please be specific when referring to detected MPox cases. For the sake of accuracy important to distinguish between endemic clade B.1 vs clade 1.
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I knew that things were bad when I personally reached out to the birds for comment and they simply tweeted back “you’re fucked”
UPDATE: For the first time during this Summer Covid wave, ILI (influenza like illness) activity EXCEEDS 2022 year over year as reported in this week's CDC report.
ILI activity for the week ending Aug 3 in 2024 is 112% worse than 2019.
For the week ending Aug 10 it is 100%
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Wondering what the Cov PANGO lineage tracking nerds on here will be doing based on recent Mpox developments. If they decide to focus on that too, these guys might never see the light of day again, given the Mpox genome is roughly
6.5x larger and is getting quite volatile.
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Find it a bit rich that WHO now declares an Mpox emergency whilst ignoring its apparent growth in fitness throughout Africa over the last 12 months. There has been almost no interest on their part to compel them to provide for more genetic sequences. Useless as tits on a bull.
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