COVID-19
Pathology
This paper from France (2024-08-02) reported that they found SARS-CoV-2 in semen. They got positive tests from 11% of subjects who’d had mild COVID-19 infections. In one man’s semen, they were able to find replication-competent virus (i.e. it wasn’t just virus RNA fragments) after 90 days!
Transmission
This preprint from USA (2024-07-31) (also mentioned below) reports that when they were testing cows for H5N1, they also found one cow who tested positive for COVID-19.
Protect your pets! This paper from USA (2024-07-18) reports that a lot of pets got COVID-19 from their guardians. They found that 33% of dogs and 27% of cats who lived with people who got COVID-19 tested positive for COVID-19 antibodies in their blood.
Vaccines
This paper from England (2024-07-31) reports that COVID-19 vaccines are good for your cardiovascular system. In a large electronic records study of practically everybody in England, they looked at who had cardiovascular events in two groups:
- people who had gotten vaccinations vs.
- people who were not vaccinated and pre-pandemic people.
They found that the risk of cardiovascular events (e.g. pulmonary embolism, stroke, cardiac arrests, lower limb deep venous thrombosis, etc.) went down after a vaccination. There is an increased risk of vaccine-induced thrombotic thrombocytopenia from AstraZeneca and a slightly increased risk of myocarditis from AZ, Pfizer, and Moderna, but the risks of everything else went down.
It looked to me like they bundled all of the unvaccinated people — pre- and post-2020 — into one big group, which meant I couldn’t figure out if vaccines made cardiovascular events lower than pre-pandemic, i.e. if you had been able to time travel back to 2019 and give people COVID-19 vaccinations, would their risk of a cardiovascular event go down? Is it something about the vaccine itself, or just that it keeps you from getting the increased risk of CV events from COVID-19? I don’t know, sorry.
For boosters, the data is a bit more clear: each additional shot dropped the CV risk compared to people who got only one shot. This held for at least 24 weeks, and the protection increased over time. In general, the mRNAs helped more than AZ, and Moderna helped more than Pfizer (although there were big error bars on Moderna because not that many people in England got Moderna).
The effect was not small. As an example, the rate of CV events after three shots of Pfizer was ~40 events per 100,000 person-years, while the rate was ~200 events per 100,000 person-years for unvaccinated people (pre- and post-2019) — a 5x difference!
The abstract of this paper from USA (2024-07-28) is really dry and it wasn’t clear to me why it was important (especially since the body of the paper is paywalled), but this podcast/transcript with the principal investigator helped me understand why: it gives hope for mucousal vaccines.
There are these things called germinal centres (GCs) which are sort of like dojos for the immune system: GCs are where the various immune cells learn how to fight a specific pathogen. This study took nasal swabs and nasopharyngeal swabs (the kind that they do for PCR tests, the ones which feel like they are poking your brain) and found GCs in the nasopharyngeal swabs. This was a surprised, because nobody knew that GCs lived in the tonsils (which the study verified got touched by the nasopharyngeal swabs). Everybody thought GCs were just in the lymph nodes. (Tonsils are secondary lymphatic tissue.)
They found a lot of immune cells, not just the germinal centres. This is not a surprise but also really good news. You WANT the immune system to be close to where you need them: the principal investigator (PI) explicitly said on the podcast that cells made elsewhere in the body might take three days to get to the upper airways — which is a lot slower than you’d like for infections. (I have the impression from the podcast that the immune cells tend to hang around where they were trained, which is why the news about finding GCs is such good news.)
They had a lot of participants with a wide range in ages, and found that the number of germinal centres dropped with age, but even so, the researchers still found them in about 75% of people. One of the things that the PI pointed out in the podcast was that it kind of doesn’t matter how many germinal cells you have if you get vaccinated: “the whole point of the vaccine is you get to generate the immune response on your own time.” Furthermore, there’s an exponential process in the training (because cells divide in two?), so it only takes a sixty year-old like three days longer to generate as many targeted immune cells as a twenty year-old. Three days is forever when you are learning from an infection, but almost no time when you are learning from a vaccination.
The study also found that mucosal SARS-CoV-2 B-cell immunity could last for quite a long time. The B-cells which recognize SARS-CoV-2 Receptor Binding Domain (part of the spike) cells diminished slowly, and the B-cells which recognize the nucleocapsid (part of the “ball” part of SARS-CoV-2 virions, and a part which changes much more slowly than the spike!) diminished even more slowly:
They also mentioned that vaccinated subjects didn’t have a lot of T cell memory for SARS-CoV-2 in the upper airway, but infected-but-not-vaxxed subjects did. That suggests that local exposure does give you the memory but an intramuscular vax does not.
Finally, the techniques that they demonstrated in this paper could be used to help guide the development of mucosal vaccines. With intramuscular vaccines, you jab someone, wait two weeks, and count antibodies in the blood. Easy. For mucosal, however, they haven’t had good ways of measuring the immune response in the nose before, but this study really shows how to do that.
This paper (2024-07-31) reports that a mucosal vaccine does better at stopping transmission than a conventional intramuscular vaccine does. They vaccinated two groups of hamsters, one intramuscularlly (with Pfizer) and one nasally (with iNCOVACC, which is currently authorized in India). They then infected a third group of hamsters, then let them fraternize with the other groups. 86% of the nasally vaxxed hamsters got a breakthrough infection, while 94% of the intramuscularly vaxxed hamsters did. Nice, but not a huge difference.
The next thing, though, was they took those breakthrough-infection-mice and let them fraternize with a fourth group of hamsters. About half of the hamsters which fraternized with the intermuscularlly vaxxed breakthrough group got sick, but none of the hamsters which hung out with the nasally vaxxed breakthrough group got sick.
If we can’t get a vax which prevents breakthrough infections, a vax which prevents followon transmission is the next best thing.
Variants
This paper (2024-07-29) reports that some Omicron subvariants are as antigenically distinct from each other as COVID Classic is from the Omicron BA.1 variant.
(NB: This analysis was done in test tubes using blood from hamsters. Using hamster blood instead of human blood is probably a good proxy for human responses, but I am not aware of any research saying that “yes it is” or “no it isn’t”, and I don’t know enough about the biochemistry to be able to say “yes” or “no” based on my own knowledge/training.)
Long COVID
Good news! This paper (2024-07-12) reports they have characterized a pathway that leads to mitochondria damage in Long COVID patients, and they know how to block that chain! They found that SARS-CoV-2 causes reactive oxygen species formation in the brain, which kicks off a cascade of things (which the paper documents carefully) that leads to mitochondria dysfunction. However, JAK inhibitors are already known to block one of the steps. They are kind of nasty drugs, but they are something.
COVID-Related Excess Deaths and Sickness
This paper from UK (2024-07-31) reports that people still have reduced cognitive abilities two to three years after hospitalization for COVID-19. They found that such participants were about .71 standard deviations below the mean that they would be expected to have the basis of their sociodemographic characteristics across all cognitive domains tested. Not only that, but their symptoms got worse over time, not better. 🙁
Slightly more than a quarter of all the participants changed jobs over the course of the study, with most citing poor health as the reason for the change. 😬
This paper from Korea (2024-07-29) reports that the chance of a sudden hearing loss in young adults with no prior hearing loss is more than three times higher if they had a COVID-19 infection than if they did not.
This paper found that people who had COVID-19 infections were 15% more likely to get shingles than people who did not get COVID-19. If they were hospitalized with COVID-19, that raised their risk to 21%.
This paper from Korea (2024-08-02) reports that COVID-19 is bad for you if you’ve had prior heart failure. For people who had prior heart failure and COVID-19, their risk of death from any cause within 30 days of a COVID-19 infection was 2.19 times that of people who did not have COVID-19 infections. Their risk of all-cause mortality was almost as high from 30 days to one year (2.04x higher than people with prior heart failure and no COVID-19 infection) .
This report from USA (2024-07-31) found that traffic deaths were 17% higher than expected based on pre-pandemic modelling, despite traffic levels returning to near pre-pandemic levels.
Mitigation Measures
This web page (not peer-reviewed, but probably still good) (2024-07-30) reports that you can reuse your mask multiple times. They wore masks in Delhi — which is highly polluted — and found that the masks were basically just as good at the end of 30 days as they were out of the box:
Recommended Reading
Vax nerds, Hilda Bastian has another vax update out!
H5N1
Transmission
This preprint from USA (2024-07-31) reports that there has been more H5N1 spread in humans than we knew about.
- While they did not find any H5N1 in nasal swabs from 17 dairy workers at two farms which had outbreaks, they did find H5N1 antibodies from 14.3% of the fourteen workers who volunteered blood samples (and who reported getting sick).
- There was a cafeteria worker who worked near to a barn but not in a barn who had H5N1 antibodies in her blood. It is likely that she caught it on the farm. (The alternatives are that she caught it from a wild bird off the farm or that she had a false positive from some other influenza/A antibodies.) That means either that there is significant airborne transmission or that there is human-to-human transmission. I don’t like either of those possibilities.
This article (2024-08-01) reports that the US Animal and Plant Inspection Service has added three more species to its list of mammals confirmed infected with H5N1: deer mouse, prairie vole, and desert cottontail.
The US Animal and Plant Inspection Service HPAI Confirmed Cases in Livestock dashboard says that the current totals are 178 herds in 13 states are confirmed to be infected with H5N1.
This paper from Japan (2024-05-04) reports that they found H5N1 virus in blowflies, which feed on dead or decaying animal flesh. They have not proved that blowflies spread H5N1, but it seems likely. (Oh great.)