COVID-19

The blog has been on hiatus for three weeks and I am feeling overwhelmed. I hope to put out several General postings this week to chip away at the backlog.

Personal Story

The reason for the hiatus was that I went on vacation to the East Coast of the US for three weeks. This was the first vacation and plane flight since the start of the pandemic, and I wasn’t sure how it would go. Could I avoid COVID-19 on a long trip? I can’t know for sure — I’ve only been back for three full days, so Spouse and I could conceivably be presymptomatic (or asymptomatic), but so far so good.

I could say, “but I was verrry careful”, but I have learned that when people say, “I’ve been very careful!”, what they mean “I have been very good about following the protocols that I have decided are good enough to bring me to a risk level that I am comfortable with” — and different people have radically different levels of risk that they are comfortable with and some very different ideas about what measures are effective. Therefore, I will tell you in some detail what measures we took.

Spouse and I both got vaccinated with Novavax XBB 1.5 three weeks before we got on a plane.
We picked a time of year when the weather would be compatible with eating outside. We had actually first scheduled the trip for March/April (to coincide with the solar eclipse), but I ended up vetoing it because dining outside in March would be difficult.
We picked a time of year when I thought that COVID-19 levels would be low. As it turned out, the bottom of the lull was in April, but I tried.
We bought an air purifier, a bunch of masks, a box of RATs, and about eight NAATs with us. (Why the RATs? Because they are cheap. If a RAT tells you that you have COVID-19, you don’t need to use one of the expensive NAATs. If the RAT tells you that you do not have COVID-19, you still need to take the NAAT.)
We bought Business Class seats to reduce the likelihood that someone next to us would be coughing on us. (That also gave us higher baggage limits, which made it more possible to bring an air purifier.)
We went to some trouble (thank you, Spouse!) in selecting hotels.
- For the first hotel, where we stayed for a week, we chose a hotel that had an attached restaurant and a courtyard where we could take the food. (It turned out that they wouldn’t serve in the courtyard, but they would pack meals “to-go” which we could eat in the courtyard. We did that for breakfast almost every day.
- For the second hotel, where we stayed for two weeks, we chose a hotel with a kitchenette, so we could cook our own meals. They also had an included breakfast buffet. We never did cook our own meals, but the counter/sink/fridge/cutlery/dishes/breakfast table turned out to be very useful. We also made heavy use of the breakfast buffet — we’d go down, pack up the breakfast “to-go”, and eat in our room. We got pizza to go three times (there was a by-the-slice hole-in-the-wall a half a block from the hotel) and ate it in our room, but all the other times, we ended up eating dinner out. (We usually did not have a formal lunch.)
Before we left, we did a DIY fit test on a bunch of different masks, using a nebulizer to blow saccharine at a masked person and seeing if we could smell anything. Spouse’s FloMask passed with flying colours. I, on the other hand, had a lot harder time finding a mask that did a really good job. (I guess I have a funny-shaped face.) I found two headband N95s which took a while before I smelled the saccharine, but the only mask where I never smelled the saccharine was a Readimask single-use stick-on mask. (NB: I reuse my non-stick-on N95s for a while. I don’t think they “go bad”.) Unfortunately, the headband N95s which worked for me makes my skin itch slightly and the headband actually hurts after a few hours.
- I also had bought some sip valves for straws. I did not test one in a Readimask because that would have meant wasting another Readimask and the Readimasks are a bit pricey. Spouse did test a SIP valve in an earloop facemask (which did not do as well as his FloMask, even without the sip valve) and the sip valve did not seem to degrade it much.
Airport security was a bit of a challenge, because we had to drop our masks three times per flight: once at Security, once to get on the plane, and once at Immigration. That is much easier to do with a non-stick-on mask, but I think the absolute most dangerous point in airplanes is the boarding and deboarding period (because you’re stuck in a enclosed space with very high population density and no ventilation).
- On the outbound flight, I wore my headband mask through security, then found a somewhat less crowded spot (we had a CO2 meter with us) and put on the Readimask with a sip valve, not realizing I’d have to drop the mask when boarding. I stuck the Readimask back on, and that seemed to work, but it’s not something I want to trust.
- Coming home, I wore the headband mask to the gate, where I asked the supervisor if she could verify my identity, I go away and put on the Readimask, then she verify me when it came time to board. She said she couldn’t do that because of laws and procedures, but what she could do was verify me, then let me on to the ramp and have me wait there. Sounded great to me, but after she checked me, she just walked away… so I guess she was letting me go elsewhere to put on my Readimask? It turned out she had meant for her colleague to let me through, but I missed that, and in the boarding crush they just let me through. (Ooops, my bad?) Then at immigration, I took off the Readimask and left it off.
On the first plane flight, when we got to altitude (i.e. once the HVAC system had been on for a while, pushing any recirulated air through HEPA filters), the CO2 reading was ~1200ppm, which is a little high. (Outside usually ranges between 450 and 500ppm.) However, the particle count was at a staggeringly low 0.1 PM2.5. That was the lowest I have ever seen our particle count read. Spouse pointed out that HEPA filters remove particles but not CO2. We both ate at least some of our meals, though I was still a chickenshit and did my best to reseal my Readimask between bites.
On the second plane flight, I was planning on not eating or drinking, but eventually caved. I ate some nuts and inhaled a can of soda very fast, then restuck my mask on as best I could. How well did it seal? I don’t know. It felt like it was sealed, it puffed in and out when I breathed, but I had not done a fit test after resticking.
We took a taxi probably about an hour to our hotel when we landed, and that was probably a bad idea. The taxi driver agreed to wear a mask (which we had to provide because he didn’t have one), but the CO2 level in the taxi reached 3600ppm, the highest I’ve ever seen it. I think at some point we cracked the window, but we were on the freeway and it was hot outside/AC inside so that was suboptimal.
Once we got outside the airport, we never ever ever ever EVER went unmasked in an indoor space with other people, which included dining. We either ate in restaurants’ outdoor dining areas (mostly sidewalks), took the food to someplace outside, or ate in our hotel room.
I wore different masks depending upon what level of risk I thought there was.
- Outdoors, I almost never wore a mask. (This included standing in line for an hour outside waiting for an Event.) This maybe was overly risky, but I think outdoor transmission is rare, especially in or near sunshine.
- If the exposure was brief (like taking the elevator down to the street), I would wear my earloop N95 mask — most comfortable, easiest to take on and off, but least protective.
- If the exposure was for a medium duration with lots of people (like taking the subway for 30 minutes) and I wasn’t going to be masking later, I would wear a headband N95.
- If the exposure was for a long time (like going to a museum or show), I wore a Readimask. I sometimes put it on before the Event, e.g. on the subway on our way to the Event.
We did eat (outside, obviously) five times with a total of seven different people. Those dinners frequently lasted past sundown (when there was less UV).
We used a nitric oxide nasal spray before setting out to do high-risk things. (NB: I frequently forgot, and once the Readimask goes on, I didn’t want to take it off to spritz. Spouse was much better at remembering.)
Every day that we did a high-risk thing, we did a nasal irrigation before going to bed.
There were a few times when I woke up with a little sore throat and panicked; I did multiple nasal irrigations per day on those days. (The first time, I did a RAT and a NAAT, both of which were negative.) The sore throats went away quickly, so I think it was just sleeping with my mouth open in an air-conditioned room or something like that…. but it is possible that I did catch a glancing blow from some pathogen.
Spouse sang (masked) in a concert (and three rehearsals). Spouse has been singing (masked) for about two years with a Vancouver chorus, and amazingly does not appear to have caught COVID-19 yet. (Yay for how well his FloMask fits Spouse!)
We did a lot of outdoor activities, probably a higher percentage than most vacationers do at urban locations, and used ebikes for a lot of our transportation. (Ebikes are fun!!) Still, we took the subway four or five times, taxis three times, and longish trains twice.
We kept the DO NOT DISTURB sign on the door of our hotel for essentially the whole time. We stayed for two weeks at our second hotel, and did have them clean one day at the midpoint, but we didn’t return to the room until pretty late that day (and we ran the air purifier for good measure). I did pop into the room briefly to change my clothes that day, but I kept a mask on while changing.

Bottom line: we spent quite a bit more money in order to lower our COVID-19 risk; we got vaccinated close to the departure time; we were fanatical about masking; we did a small number of risky things; we appear to have not caught COVID-19.

Could we have done things more safely? Absolutely, including above all not going. We treated outdoors as magic, we did eat/drink on planes, I forgot the nasal spray occasionally, I used an imperfect mask sometimes, we went to large indoor events, we shared vehicles, we could have rented a more private space (e.g. AirBnB), the list is pretty long.

Did we need to do all the things we did do? Did we need to spend all that extra money? Who knows! Maybe getting vaccinated three weeks before the trip was all we needed to do. Maybe we just got lucky — maybe what we did would not have been enough if we had been around more contagious people. It is really frustrating operating in such a low-information environment. My only comfort is knowing that we know almost infinitely more than they did like 300 years ago!

COVID-Related Excess Deaths and Sickness

I don’t usually say who wrote papers because unless you are an academic in this area, you won’t care and you’ll forget. (And if you are an academic in this area, you aren’t reading this blog!) But I think it’s worth saying that Bloomberg News funded a study on post-COVID excess sickness! This article (2024-06-14) reports that the study found that yes, people really are getting sick a lot more often post-pandemic. People in the US took 42% more sick days and the average time off was 15% higher in 2023 than 2019.

This article says that some of the increased sickness could have been due to lockdowns:

If a bunch of people don’t catch X for two years like they normally would because of the mitigation measures for COVID-19, then when social interactions go up again, they won’t have antibodies to X, so a lot of people will catch X. However, the lockdowns are long over, so the catch-up infections should be over by now. (And the idea that immunity is like a muscle that needs exercise is wrong: it’s more like a reservoir that gets used up.)
It was harder to vaccinate kids plus a whole lot more anti-vax sentiment popped up, so vaccination rates are lower.
Some people explain excess mortality by saying that frail people who would have died a few years ago from random pathogens (but who didn’t because of mitigation measures) are finally dying now.

Interestingly, the article doesn’t mention the possibility that COVID-19 makes you more susceptible to diseases.

This paper from (2024-05-30) (by some really credible folks!) found that in a three-year followup period, non-hospitalized people who had COVID-19 were at a higher risk of death for the first year than non-COVID-19 patients, but not after that. In hospitalized patients, the risk of death was still 29% higher ~~after the first year~~ in the third year than for people who had not had COVID-19.

No, I don’t understand how the cumulative excess death can go *down*. Maybe they made some adjustment?

This study from Russia (2024-06-05) found that patients who were hospitalized with COVID-19 between June 1, 2021, and August 31, 2021, many had persistent symptoms for at least three months:

59% had smell/taste disorders
36.7% had severe shortness of breath;
15.8% had palpitations and other cardiovascular issues;
13.2% had headaches;
11.7% had joint pain;
9.8% had muscle pain;
and more than 5% had hair problems.

By 60 days, symptoms improved by 5-10%; by 90 days, symptoms improved by 25-35%.

Long COVID

This paper (same as one above) from USA (2024-05-30) found that over three years, some people did recover from Long COVID:

DALYs are Disability-Adjusted Life-Years

This preprint from Netherlands (2024-05-31) reports that Long COVID is transmissible! They found that if you inject mice with purified IgG taken from Long COVID patients, the mice have statistically significant differences in behaviour. What’s more, they found three clusters of blood chemistry in the Long COVID patients, and the mice acted slightly differently depending on which cluster the Long COVID humans were in. (Alas, the mice can’t really be asked how they feel.) One group exhibited sensory hypersensitivity; another group moved around less (but did not lose coordination).

IMHO, looking at the paper, it didn’t look like the behavioural differences were huuuuge: it’s not like the mouse behaviour fell off a cliff or anything. However, finding that Long COVID is transmissible by gammaglobulin antibodies is huge: it gives an area to focus on and it gives an animal model to work with.

This study from USA (2024-06-06) found that US Marines (i.e. very physically fit people!) who were PCR positive in Spring-Fall 2020 had long-term negative impacts from COVID-19. 25% got Long COVID:

41.6% had taste/small disorders;
37.6% had shortness of breath;
22.8% had a cough.

Compared to a historical group of Marines, Long COVID Marines scored lower on their running times one year after they finished training.

So if you have friends who say, “I don’t need to worry, I am fit and work out”, tell them about this study. Exercise does help the immune system, but it’s not a get-out-of-jail-free card.

This paper from India (2024-06-10) found that 57.7% of people with symptoms lasting more than four weeks had not recovered after a year.

This paper from USA (2024-05-31) found that men with Long COVID were more likely to get impotent than men who had COVID-19 infections without Long COVID. However, having been hospitalized or prescribed vasopressors did not raise the risk of erectile dysfunction.

Transmission

This paper from Taiwan (2024-05-22) shows that viruses live longer in air with higher CO2 levels (as did another recent paper).

This paper from USA (2024-05-28) found that masks work. They looked at a sample of airline flights which enforced masking and some that did not. For flights without enforced masking, every hour increase in flight duration (between Jan 2020 and April 2021) cased a 1.53x risk of catching COVID. Airline flights with enforced masking had zero transmission.

I don’t normally report on stuff happening in other countries, but COVID-19 is spiking in multiple places around the world. This article (2024-05-30) says that cases have quadrupled in Spain in the past month; this article (2024-05-31) that South Australian hospitals have suspended all elective surgeries; this article (2024-05-27) says that New Zealand is in its worst wave in seventeen months.

<rant>Note again that COVID-19 is not seasonal! It’s winter in Australia and New Zealand and summer in Spain. What is really important is how much immunity people have, which changes as immunity from the infection or inoculation wanes and as new strains appear.</rant>

Vaccines

This preprint (2024-06-14) and this paper (2024-05-01) both found that an instranasal vaccine reduced onward transmission of COVID-19 in hamsters.

I think this is important! One problem with the current vaccines is that they don’t reduce onward transmission. I don’t completely understand why a previous infection doesn’t also reduce onward transmission of the next infection (since infections almost always come in through mucous membranes), but I have seen no evidence that the virus less contagious less than it used to be in a population that has basically all had at least one infection.

In both cases, they vaccinated hamsters with one intramuscular (IM) vax and one intranasal (IN) vax, waited four weeks, deliberately infected those vaccinated hamsters and unvaccinated controls, then put the infected (“donor”) hamsters near uninfected (“acceptor”) hamsters. In both studies, the vast majority of acceptor hamsters got sick from unvaccinated donor hamsters, while none of them got sick from IM/IN vaccinated donor hamsters:

In one of the studies, they also vaccinated some hamsters with two intramuscular vaccines (IM/IM). Two-thirds of the acceptor hamsters paired with IM/IM donor hamsters got sick.

In another part of the second study, they deliberately infected IM/IM, IM/IN, and unvaccinated mice with COVID-19 a year after vaccination. All of the unvaccinated mice died, half of the IM/IM mice died, and none of the IM/IN mice died.

This paper (2024-05-23) reports that a viral vectored intranasal vaccine (using the Newcastle virus as its base) protects hamsters and mice from Delta and Omicron for at least six months.

This paper from USA (2024-05-22) found the tuberculosis vaccine can help protect some people against COVID-19 better than some COVID-19 vaccines.. For people who have Type 1 diabetes, an mRNA COVID vaccine doesn’t protect them from COVID-19 at all, but vaccinating them with five or six doses of the Tokyo strain of the TB vaccine (called the BCG vaccine) gave them a 52.1% lower risk of Omicron infection.

Other studies had found that BCG vaccination did not help, but those studies used different strains, and/or gave only one dose, and/or did not screen the control group for prior BCG vaccination or TB cases, and/or didn’t do follow-up for long enough.

Interestingly, the BCG vaccine didn’t help right away — its effects accumulated over about two years. It also didn’t help against pre-Omicron strains; I don’t know if that’s because the vaccines didn’t have enough time to work, because of the strains being different, or because Omicron hit the control group much harder.

The BCG vaccine also gave some protection against other pathogens, e.g. sinus infections, urinary tract infections, common cold coronaviruses, and “flu-like symptoms” (which I think means ‘common colds’).

The paper did not look at vaccine effectiveness waning over time.

This paper from USA (2024-06-11) found that yes, the more reactions to a vaccine you have, the better immunity you get from it. For example, each 1 °C increase in skin temperature after dose 2 corresponded to 3.1x higher neutralizing antibodies six months later. Headaches, chills, tiredness, and “feeling unwell” also corresponded to higher neutralizing antibodies later.

This press release from Moderna (2024-06-10) says that their combo flu/COVID-19 vax is better than standard care for both influenza and COVID-19. In a phase 3 trial, they found:

For the the over-65 cohort, their new combo vax was 6-15% more effective (depending on the strain) than Fluzone HD and 60% more effective than Spikevax against XBB 1.15. (Note: they didn’t say in the press release which Spikevax; it might have been the COVID Classic Spikevax.)
For the 50-64 y/o cohort, it was 21-41% more effective against influenza and 30% more effective against Omicron.

Pathology

This paper from Spain (2024-02-20) looked at infants born to mothers who had and had not had COVID-19 during pregnancy. They found that infants whose mothers had COVID-19 (especially in the third trimester), were “less responsive to cuddliness”, described as “the ability to ‘let themselves go’ in the arms of an adult and relax in a comforting position”. The babies also did statistically significantly worse in the “pull-to-sit” maneuver. Unfortunately, I don’t know how big the effect was — they gave “F” values for the magnitude of the effect, and I don’t understand how to interpret F-scores in that context.

Treatments

This paper from USA (2024-06-07) found that a fifteen-day course of Paxlovid didn’t help Long COVID patients a statistically significant amount at 10 weeks after the start of treatment. 🙁

Mitigation Measures

This review article (2024-05-22) says that:

COVID is airborne.
Yes, when worn properly and consistently, masks do reduce transmission.
Yes, respirators (e.g. N95) are way better than cloth masks or baggy blues.
Mask mandates are, overall, helpful.
Wearing or not wearing a mask has social signifiers, showing membership in a group.
While masks are generally not harmful, there are certain subgroups who need exemptions.
Some people (especially deaf people) are disadvantaged by other people wearing masks.

H5N1

Transmission

This report from US CDC (2024-06-12) found that H5N1 is pretty deadly to ferrets, and that ferret-to-ferret spread is pretty easy. Three of three ferrets who were placed in cages with three ferrets deliberately infected with the human H5N1 (A/Texas/37/2024, to be exact) got sick; all six ferrets died. One of three ferrets placed in a neighbouring cage got sick, meaning that it can spread through the air but not super-well.

It’s H5N2, not H5N1, but this article (2024-06-05) reports that a medically fragile man in Mexico died from H5N2. (H5N2 is a bird flu but not the one infecting dairy herds right now. Yeah, this means that I have to figure out another way to talk about bird-maybe cow-flu than as H5N1.)

According to the US FDA’s Highly Pathogenic Avian Influenza (HPAI) Detections in Livestock page, they have found ~~101~~ 96 infected daily cattle herds in twelve states by now.

This press release from USDA (2024-05-28) reports that they found bird flu in an alpaca in Idaho.

This article from USA (2024-05-22) reports that a second dairy worker — this time from Michigan — had mild conjunctivitis, tested positive for H5N1, and has since recovered. Authorities say there does not appear to have been any human-to-human spread.

This article from USA (2024-05-30) reports that a third dairy worker — again from Michigan, but from a different farm — tested positive for H5N1. This time, the dairy worker had respiratory symptoms (and was given antivirals and is recovering).

This article reports that the third case’s H5N1 had a mutation that makes H5N1 better adapted to infect mammals. Not good.

This preprint from Argentina (2024-06-01) reports on mass die-off among seals from H5N1, and found that there were a lot of mutations in that strain that made it spread more easily in mammals. (Yes, that’s ominous for us human mammals.) Furthermore, it looks like that strain jumped *back* into birds (which is even more ominous for us humans that live in different countries we can’t keep wild birds out of).

Testing

This preprint from Canada (2024-05-28) reports that a group of Canadian scientists across Canada has made their own testing network to test retail milk for H5N1. So far, they have tested 18 milk samples and have not found any H5N1 yet.

This article (2024-06-13) reports that the US Department of Agriculture plans to roll out a pilot program for testing for H5N1 in dairy cattle “soon”.

COVID-19

Personal Story

COVID-Related Excess Deaths and Sickness

Long COVID

Transmission

Vaccines

Pathology

Treatments

Mitigation Measures

Recommended Reading

H5N1

Transmission

Testing

Recommended Reading

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