2024-11-03 General

Vaccines

⭐ This preprint from USA (2024-10-12) is about an influenza vaccine study, but it relevant to both COVID-19 and bird flu so I’m putting it at the top.

In this study, the researchers used what they call “prime and spike” strategy for influenza where “prime” is an intramuscular injection and “spike” is a nasal vaccine. This is similar to a study the same lab did a few years back (2022-10-27) but for COVID-19. The 2022 study showed really good results in mice.

The influenza study also showed good results. In that study, no mice died from a normally-lethal dose of influenza when they were protected by three doses of a combination of injected mRNA influenza vaccine and intranasal hemagglutinin (HA) from an H1N1 strain. (Hemagglutinin is the “key” which lets the virus get into the cell, similar to the spike protein of COVID-19, and the H of the HxNx influenza naming scheme.) Either two doses of the mRNA and then one HA or one dose of the mRNA and then two doses of HA protected all the mice completely. One mRNA and two HA gave a near-sterilizing immunity and reduced viral shedding.

They also gave the 2 mRNA+1 HA or 1 mRNA+2HA vaccinated mice a dose of a different H1N1 strain, and the mice were “robustly protected” against that strain as well.

Three doses of mRNA protected the mice almost as well as 2 mRNA+1 HA or 1 mRNA+2HA, but having at least one HA dose made the mice shed a LOT less virus, which means they were almost certainly a lot less contagious.

COVID-19

Health Care System

This paper from USA and Canada (2024-10-31) reported on the effects of supply-chain issues on the availability of drugs in both Canada and USA. They found that, when there was a supply chain issue, Canada was 47% less likely to have a shortage of the drug than USA.

Long COVID

⭐ This paper from Vancouver (2024-10-15) reports that the risk of Long COVID-like symptoms among vaccinated school staff was:

  • 21% for people with zero infections (as determined by careful serology);
  • 30% for people after their first infection;
  • 33% for people who had their first infection before the start of the study period who did not get infected during the study period (which I think approximates “one infection”);
  • 43% for people who had their first infection before the start of the study period who did get infected during the study period (which I think approximates “two infections”).

If you are asking, “How can so many people without COVID-19 get Long COVID? Is it psychosomatic?” Note that these were Long COVID-like symptoms. Long COVID has a long list of potential symptoms, so it’s hard to distinguish Long COVID from other things. Look at the difference between how many report symptoms with and without COVID-19.

This report by the Institut national de santé publique du Québec (2024-10-30) reports that their health care workers have a lot of Long COVID.

  • The cumulative risk of Long COVID increases with the number of infections increasing: 13% for one, 23% for two, and 37% for three infections.
  • A quarter of the people with Long COVID have severe symptoms.

This paper from Germany (2024-10-10) reports that people with Long COVID have impaired fat oxidation capacity (which I believe means “ability to extract energy from fat”, and which might be a marker of mitochondrial impairment).

⭐ This paper (2024-10-21) looked at a very large number of people hospitalized for COVID-19 in 17 countries, and found that a lot more people in high-income countries had Long COVID than people in low/middle-income countries. Maybe rich people carry more fat, and that matters? Maybe low/middle-income countries are more likely to be tropical or sub-tropical and have more windows open, so they were infected with lower doses?

This paper from USA (2024-10-28) reports that children who were overweight got Long COVID more often. Children who were obese were 25.4% more likely to get Long COVID; children who were severely obese were 42.1% more likely to get Long COVID.

This news is made even more depressing by this paper from USA (2024-10-25), which reports children gained weight during the pandemic. The proportion of children who were overweight or obese was going up by 1.4% per year in the year before the pandemic, and by 4.9% per year during the first year and a half of the pandemic.

Vaccines

Reminder: I don’t usually talk here about results from vaccine studies in lab animals because there are so many of them and because of the extremely long lead time to get from lab rats to humans. However, I will tell you that there is a lot of improvement that will be made to COVID-19 vaccines in the next five years.

⭐ This press release (2024-10-15) reports that a company called Empatica got a bunch of money from the US Government to study using wearable tech (e.g. smartwatches) to gather data for vaccine trials. There have been previous wearable tech studies that have shown that smartwatches can pretty accurately tell if you’re sick; this study leverages that to see if they can run randomized clinical test for vaccines without requiring that study participants come to a physical location on a regular basis. This would make it easier to get a wider sample of people less able to travel: the rural, the infirm, the poor, etc.

⭐ This paper (2024-10-18) reports that ARCT-154 — which has been approved in Japan under the brand name Kostaive — has much better durability than Pfizer:

ARCT-154 is a self-amplifying RNA (saRNA) vaccine, meaning that when it instructs the host cell to make spike protein, it also tells the host cell to make a copy of itself. The advantages are that you need a MUCH smaller dose of the active ingredient than conventional mRNA vax, and that it sticks around for longer, giving a better immune response.

However, this also makes it scarier to people. This article (2024-10-07) reports that there is a lot of scaremongering in Japan about the vaccine. In particular, misinformation is running wild that people who get the ARCT-154 vaccine will shed viral particles. This is completely horseshit: there is no virus in the vaccine, just spike protein. (You know who does shed viral particles? People with COVID-19!) This article also mentions that the saRNA vax only keeps going for about eight days.

As a programmer, I was hyperaware of the dangers of infinite loops, so I tried to figure out what makes the saRNA stop, and the best I found was an offhand comment in this article (2024-02-02): “And just like mRNA, saRNA degrades quickly in the body. It lasts longer than mRNA, but it doesn’t amplify forever.”

This paper from Dubai (2024-10-29) reports that Paxlovid reduces the risk of Long COVID by 58%.

Transmission

⭐ This paper from Vancouver (2024-10-15) reports that a COVID-19 infection drops the risk of reinfection in vaccinated school staff in the next year by 50%.

⭐ This blog post from USA (2024-11-01) had an interesting graph, showing that COVID-19 waves in the US keep getting worse over time, not better:

If you think that the amount of testing is also going down over time (which I do), then the waves are actually getting quite a bit worse.

Pathology

⭐ This paper from China (2024-10-24) reports that many people hospitalized for COVID-19 had decreases in bone marrow density. They were careful to say that they did not know if COVID-19 caused problems with bone marrow density or if conditions that cause bone marrow density made people more susceptible to COVID-19. (They also did not have a control group of people hospitalized for similar lengths of time who did not have COVID-19.)

⭐ This paper from UK (2024-10-17) reports that 64% of all pediatric hospitalizations for COVID-19 in England are for infants under 1 year old. This fraction has increased over time: during Delta, only 30% of pediatric COVID-19 admissions were for infants. I apologize that the graph below is kind of small, but you can see the 14-day rolling average number of infants hospitalized with COVID-19 over time as an orange line, and other ages in other colours, and you will see that the gap between the orange line and all the others gets wider over time.

The authors believe the higher proportion of infants among pediatric hospital admissions is due to, basically, all the older kids have had COVID-19 by now, while the infants are still terminologically naive with respect to COVID-19.

⭐ This paper from Austria (2023-10-14) found that people had lower immune function even at ten months after a COVID-19 infection. This mass media article from Germany (2024-10-24, in German) talks about that paper and brings in other information.

Testing

Local company Vitacore (who you might know as a manufacturer of facemasks) says in this press release (2024-10-18) that they have developed a PCR-quality rapid test that gives results in three minutes. !!

Treatments

⭐ This study from USA (2023-05-16) was intended to see how rapamycin use affected various age biomarkers. They discovered, however, that patients who happened to get a COVID-19 infection while they were taking rapamycin had much milder cases, and none of them got Long COVID.

I think they used red (not grey) for severe cases.

This article (2024-10-30) reports that a study of rapamycin use in Long COVID patients is about to start, yay! (The principal investigators are highly respected in the Long COVID field, so I have a good feeling about this.)

I wonder, even if they determine that rapamycin prevents 100% of Long COVID, if it will be easy to get the drug — especially in the US. It does have some significant possible side effects, debilitating Long COVID is relatively rare, medical systems don’t really care about illnesses that are not debilitating, and a lot of people (including doctors!) don’t really believe that Long COVID is a real/dangerous thing. On the other hand, this article (2019-07-19) says that some people think it’s a wonder anti-aging drug, so there are a lot of studies of rapamycin going on.

Recommended Reading

One of my favourite recurring blog posts is out with a vaccine roundup! I have excerpted what I think the most interesting ones were, above in the Vaccines section, but if you are a real vax nerd, look there for more details.

This page has a neat visualization of excess deaths in Australia for the past five years. Yes, it’s Australia and their seasons are reversed and they had much stricter mitigation measures for a long time, but it really shows how COVID is not over. 🙁

You can also look at a visualization for Canada (slow); here’s a shitty screengrab of it below. April 2020 is at the top, April 2024 is at the bottom; each dot is one excess death. I think the top dark band is probably the eastern care homes — BC didn’t see very many deaths in the first half of 2020. The darkish bit at the beginning of 2021 was Alpha; the September 2021 bit was Delta, and the quite dark bit at the beginning of 2022 was Omicron. The dark patches from August to December in 2023 and 2024 are just the consequences of no mitigation measures.

H5N1

Transmission

⭐ This article from USA (2024-10-28) found that virus taken from an infected human dairy worker was fatal to mice and ferrets. Also, infected ferrets passed the infection to other ferrets. This isn’t actually that surprising, given that bird flu has killed lots of mammals before. (This old article (2023-03-19) says that eight skunks died of bird flu in Vancouver, for example.)

⭐ This article (2024-10-30) reports that they found bird flu in a pig in Oregon. The pig was one of five pigs (and associated other livestock) kept in a backyard (i.e. non-commercial) lot; they euthanized all the pigs and are checking the other four as well.

Epidemiologists have been worried about H5N1 getting into pigs because pigs act as a good mixing bowl: they can catch both bird flu and human flu, then blender them up to make new viruses which we humans wouldn’t have immunity against.

⭐ Unfortunately, there is another mammal which can catch both bird and pig flu and act as a mixing bowl. Furthermore, that mammal can’t just be culled easily. I’m talking, of course, about humans. This article (2024-10-29) reports that the bird flu case count in Washington State is up to six confirmed now. This page (2024-11-01) from the Washington State Department of Health says that there are an additional three more probable cases in Washington.

This press release (2024-10-30) reports that eight herds of dairy cattle in Utah have tested positive for H5N1.

This article (2024-10-29) reports that the US now has 388 infected herds, with 186 of them in California.

This article (2024-10-28) talks about how the upcoming flu season is going to make dealing with H5N1 is about to get a lot harder.

  • The cooler weather might make H5N1 easier to spread, meaning more cases to track.
  • People with flu-like symptoms will might be less likely to get tested because having the flu is something kind of “normal” to have in the winter
  • Testing labs will be busier.
  • There might be “reassortment events”, where someone gets infected with bird flu and normal human flu and those two swap pieces of their code. Many reassortment events will make crosses that are no worse than their parents, or even less viable. However, given enough time, a bug is likely to evolve which is even nastier than H5N1.

Testing

Well, it’s about damn time. This article (2024-10-30) reports that the US Department of Agriculture is going to start doing testing of milk in bulk across the US. They didn’t put it exactly this way, but the sudden appearance of almost 200 infected herds in California was a bit of a “come to Jesus” moment.

Mpox

Mpox is still spreading in Africa, as this article (2024-10-31) reports. That article also reports that Rwanda has reached 100% of its vaccination target, whatever that means.

This press release from the UK government (2024-10-30) says that they have found their first case of mpox clade 1b. (That’s the more serious one.)