What should be a higher priority for society, preventing pigs from becoming sick or preventing human illness? Personally, I place a higher value on preventing human illness. I think most would agree. Why, then, are pig barns much better ventilated than schools? 1/40
An airborne virus has killed 900,000 Americans & left countless others with long Covid & its attendant long-term—maybe permanent—mental & physical afflictions. We know ventilation & filtration of indoor air prevents illness. 2/40
The manifold benefits of improved ventilation are well documented & uncontroversial. @Don_Milton has been publishing studies for over 20 years showing improved ventilation reduces respiratory illnesses & absences, though his findings were largely ignored. 3/40
Yet we’ve done almost nothing to improve ventilation & filtration in schools, workplaces, restaurants, & other buildings. @CDCgov gives lip service to ventilation but has issued no minimum ventilation requirements & offers no specific guidance. 4/40 cnn.com/2021/02/25/hea…
On the other hand, great cost & effort is put into ventilating & filtering the air in pig barns to prevent disease outbreaks. Let us compare the ventilation & filtration of pig barns with buildings inhabited with human beings. 5/40
First, note that airborne spread of porcine reproductive & respiratory syndrome (PRRS) was readily accepted based on circumstantial evidence & lab studies. French farms even installed HEPA filtration systems in pig barns despite “no hard data to support” their use. 6/40
Contrast this with the stubborn, year-long denial or airborne Covid spread by WHO & CDC, despite abundant evidence. The precautionary principle is obeyed when pigs’ health is at stake but not when mere human health is at risk. 7/40
Incredibly, droplet dogma still reigns supreme in some places. E.g. @math_rachel is still fighting against appallingly ignorant public officials & nonsensical guidelines in Australia. Some officials haven’t gotten the memo: #COVIDisAirborne 8/40
Many careful, controlled studies of ventilation & filtration in livestock facilities have been carried out, and the cumulative evidence compiled leaves little doubt of their effectiveness at preventing disease in farm animals. One of many examples: 9/40
In contrast, before Covid, research on ventilation/filtration & disease in human buildings was quite sparse. @linseymarr, @Don_Milton, Julian Tang, Yuguo Li, & a few others were lone voices in the wilderness, shouting into a void, ignored by CDC & WHO. 10/40
For buildings that humans inhabit, enforced minimum ventilation requirements are almost nonexistent. The HVAC in a school or nursing home can be completely non-functional, creating a superspreader environment, with no legal consequences. 11/40
This is not hypothetical. Here is one documented instance in which all 226 residents in a Canadian nursing home contracted Covid, resulting in over 70 deaths. The cause? A non-functioning ventilation system. And this was a less transmissible, pre-Alpha SARS-CoV-2 variant. 12/40
The same private company owned another nursing home in which 96% of residents and 116 employees got Covid, leading to the death of 66 residents. I think we can surmise that the ventilation in this facility was also very poor. 13/40 ici.radio-canada.ca/nouvelle/17027…
Why were the ventilation systems in these nursing homes not audited? Because such auditing is simply not done—not in nursing homes, schools, workplaces, or restaurants. Ventilation/filtration recommendations exist, but not enforced standards. They’re essentially voluntary. 14/40
What about pig barns? While there are no legal requirements, the ventilation/filtration systems at these facilities are assiduously checked *every day* by a worker whose *sole duty* is to inspect and maintain the ventilation equipment. 15/40 nationalhogfarmer.com/animal-health/…
No aspect of the system is left unchecked. “Look for any gaps or openings that would allow dirty air in... make sure chutes collapse properly, creating a good seal.” “Cracked fan housings or a broken shroud” are checked for and “weep holes plugged w/a rubber stopper.” 16/40
But daily inspection is only the start. In addition, at least once a month, a system filtration technician (SFT) audits the ventilation system, coaching the on-site manager. Another monthly audit is performed by the herd veterinarian, who guides the SFT. 17/40
In contrast, human buildings such as nursing homes are virtually never audited, even during a pandemic. It apparently requires a court order for such an audit to occur. 18/40
Are HVAC systems in human-occupied buildings well maintained? HVAC expert Jeffrey Siegel (@IAQinGWN): “The best HVAC in the world performs poorly when it’s not well maintained, and the usual standard is ‘not well maintained.’” 19/40
The same article describes an HVAC unit installed upside-down in a large store, making it impossible to change the filter, meaning, “The air inside the store would be that much crummier.” It was “like 1000 other HVAC mistakes Siegel has seen...” 20/40 wired.com/story/the-next…
“...dampers supposed to admit outside air into a building rusted open or shut, badly installed filters letting air pass around their edges, forced-air fans running 18% of the time. In theory, HVAC heats & air-conditions. In practice, it doesn’t always ventilate or filter.” 21/40
What sort of air filters are used for pig barns? First, a mesh net catches larger objects in the air, such as feathers. Then the air goes through a MERV 8 “prefilter.” This prefilter is of a higher grade than the filters used in many schools, which are MERV 7. 22/40
After passing through the MERV 8 prefilter, air entering pig barns is filtered by MERV 15 air filters—similar to the filters used in hospitals. Very few schools, workplaces, nursing homes, or restaurants use anything above MERV 11. MERV 15 is unheard of. 23/40
Does such high-quality ventilation and filtration of pig barns reduce disease outbreaks? Of course it does, as the extensive literature on livestock-facility ventilation & filtration attests. 24/40 researchgate.net/publication/22…
However, there is a potential problem: What if some of the dirty air from the human-occupied office building on a farm were to leak into the pig barn? Perish the thought! To allow pigs to breathe the same filthy air breathed by humans would be unthinkable. 25/40
Therefore, pig farms are designed so that none of the filthy air from the farm’s human office is allowed to contaminate the pristine, highly filtered air of the pig barn. “If there is dirty air in the office [narrator: “There is”], it will stay in the office.” 26/40
The notion of providing pig-quality air to the office is considered so absurd it doesn’t merit consideration. After all, if the health of the workers on a farm is improved, this doesn’t affect profits. A sick pig, on the other hand, hurts the bottom line. Priorities. 27/40
One article on the ventilation & filtration of pig barns notes a peculiar “side benefit” of improving the pigs’ air: human workers notice the better air & seem healthier for it. How much healthier? No one knows, as such trivial topics as worker health are not researched. 28/40
Why is the air quality in human buildings so poor? Why haven’t greater efforts been made to improve IAQ, the enormous benefits of which are well known & uncontroversial? After all, we regulate water and food safety. Why not indoor air? From @ShellyMBoulder: 29/40
The WHO recommends schools & other buildings have at least 6 air changes per hour (ACH). A typical school HVAC provides ≤1 ACH. 30/40
IAQ experts recommend CO2 levels be <800 ppm (or <700 ppm in a pandemic), but CO2 levels regularly reach much higher levels in schools. I’ve occasionally registered levels near 3000 ppm but others report >4000 ppm readings. 31/40
What about hotels? I stayed in a room at the Disney Caribbean Resort Hotel with my brother. CO2 reached well over 3000 ppm each night. I did a CO2 decay study & found that the room got 0.11 air changes per hour. Not good. 32/40
It’s long past time to greatly improve ventilation & filtration by imposing serious, enforced IAQ standards in nursing homes, schools, workplaces, & other public spaces. Many aerosol & IAQ experts have been calling for this for a long time... 33/40 science.org/doi/10.1126/sc…
The vast majority of people would be much better off if IAQ were improve through better ventilation & filtration.
We spend the majority of our lives indoors. Proper filtration & ventilation would enormously improve the air we breathe. 36/40
When we think of air pollution, we usually think of lung damage. But polluted air damages all organs of the body. With cleaner air, brain function would improve, heart attacks & strokes would fall, & illness would be reduced. It works for pigs. It can work for humans. 37/40
Air pollution is possibly the single largest health problem in the world. It causes the loss of more years of life than alcohol & narcotics, unsafe water, HIV, malaria, & war/terrorism combined. Cleaning the air we breathe is essential. 38/40
However, the pecuniary interests of the 1%—landlords, real estate magnates, business owners, & capitalists in general—might not be so well served. Installing better ventilation systems & filters might put a dent in their investment returns—an unthinkable notion. 39/40
To sum it up, improving IAQ in human buildings merely improves the health & well-being of humans—a minor consideration—while improving air quality in pig barns improves profits, a sacred objective & the chief aim of life under capitalism. 40/40
Fantastic review on chronic SARS-CoV-2 infections by virological superstars Richard Neher & Alex Sigal in Nature Microbiology. I’ll do a short overview, outline a couple minor quibbles, & defend the honor of ORF9b w/some stats & 3 striking sequences from the past week.
1/64
First, let me say that this is well-written, extremely readable, and accessible to non-experts, so you should go read the full paper yourself, if you can find a way to access it. (Just realized it’s paywalled, ugh.) 2/64nature.com/articles/s4157…
Neher & Sigal focus on the 2 most important aspects of SARS-CoV-2 persistence: its relationship to Long Covid (including increased risk of adverse health events) & its vital importance to the evolution of SARS-CoV-2 variants. I’ll focus on the evolutionary aspects.
3/64
In SARS-2 evolution, amino acid (AA) mutations get the lion’s share of attention—& rightfully so, as noncoding & synonymous nucleotide muts—which cause no AA change‚ are mostly inconsequential. But there are many exceptions, including a possible new one I find intriguing. 1/30
I’ll discuss four categories of such “silent” mutations, two of which might be involved in the recent growth of one synonymous mutation.
Maybe the single most remarkable example of convergent evolution in SARS-CoV-2 involves noncoding mutations: the multitude of muts in major variants that have pulverized the nucleocapsid (N) Kozak sequence.
I wrote about this below & a few other 🧵s 3/
@SolidEvidence There was yet another paper this week describing someone chronically infected, with serious symptoms, but who repeatedly tested negative for everything with nasopharyngeal swabs. On bronchoalveolar lavage (BAL), they were Covid-positive. 1/ ijidonline.com/article/S1201-…
@SolidEvidence BAL is very rarely performed, yet there must be dozens of documented cases now where NP-swab PRC-negative patients who were very ill tested positive by BAL. This has to be way more common than we realize.
If we had a similar GI test, I imagine we'd find something similar. 2/
@SolidEvidence Importantly, the patient was treated and improved, likely clearing the virus for good. Many, maybe most, chronic infections could be treated and cleared. But they have to know they're infected for that to happen. 3/
Read full 🧵for explanation, but the short story is that the best apparent escape mutations all interact w/something else—like a nearby spike protomer or other important AA—making mutations there prohibitively costly.
In short, the virus has mutated itself into a corner. 2/6
It's very hard to effectively mutate out such a local fitness peak via stepwise mutation in circulation since multiple simultaneous muts might be required to reach a higher fitness peak. 3/6
It's an interesting thought. I think the evidence is strong that all new, divergent variants have derived from chronic infections. The first wave of such variants—Alpha, Beta, Gamma—IMO involved chronic infections lasting probably ~5-7 months. It's controversial to say.... 1/15
…that Delta originated in a chronic infection, but I think the evidence that it did is strong. One characteristic of chronic-infection branches is a high rate of non-synonymous nucleotide (nuc) substitutions (subs)—i.e. ones that result in an amino acid (AA) change. 2/15
For example, if 80% of nuc subs in coding regions cause an AA change, that’s a very high nonsynonymous rate. The branch leading to Delta has 17 AA changes—from just *15* nuc subs! That’s over 100%. How is this possible? 3/15
I'd add that XEC's had no noticeable impact on cases & isn't likely to going forward barring a serious change, which we've not seen since S:Q493E & the glycan-adding S:S31-/S:T22N appeared months ago. Next major change seems likely to take the form of an entirely new variant. 1/4
I've been in lockstep with @SolidEvidence and @JPWeiland on this front. Despite the sensational early growth advantages XEC appeared to have, it never seemed likely to me ever to have a noticeable real-world impact. 2/4
In fact, XEC resembles BA.5.2 + ORF1b:T1050N, which had a similar growth advantage in summer 2022. That one, however, never had a sexy name like "XEC" that was distinct from other major contemporary variants so it passed unnoticed. Names matter. 3/4