COVID Transmissions for 8-23-2021
Transmission and the vaccinated
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 643 days since the first documented human case of COVID-19. In the 7th century, Frankish Merovingian kings had become so irrelevant that the “mayor of the palace” in kingdoms like Austrasia (part of modern France), were the real source of authority. The maior domus, known today as the majordomo, might even be assassinated by rivals to bring about a regime change, as happened to the unfortunate Otto, mayor of the palace of Austrasia, in 643.
Today I want to talk about rising vaccination rates in the US, but also about whether vaccinated people with symptomatic COVID-19 are a real transmission risk. There is new data, but I’m not sure we can walk away with very satisfying answers just yet.
Bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
Vaccination in the US is picking up
I wish it hadn’t taken a new surge in the virus for this to happen, but US vaccination rates are climbing again. Over the weekend, the US hit its third consecutive day of 1,000,000+ doses administered, or so I heard, and the 7-day moving average for vaccinations is up 26% from 3 weeks ago, according to CNN: https://www.cnn.com/2021/07/31/us/us-vaccination-rates-rising-southern-states/index.html
Some of this may be people who are going out early for their booster vaccinations, but I don’t think that would explain the entire trend. The surge in the virus is making people realize that vaccination is not something to be put off. I wish they had realized this sooner, but you work with the reality that you have. If you know people who are on the fence, please encourage them to be part of the trend. It’s time to get vaccinated. It’s past time, frankly.
New preprint suggests that the vaccinated do not shed as much Delta variant SARS-CoV-2 as the unvaccinated
A preprint is making the rounds that purports to show that the vaccinated are less infectious during breakthrough Delta variant infections than unvaccinated people are. This can be read here: https://www.medrxiv.org/content/10.1101/2021.08.20.21262158v1
If you’ll recall, we all went back to masking, regardless of vaccination status—you did go back to masking, right?—because the CDC had evidence that unvaccinated people with symptomatic cases and vaccinated people with symptomatic cases had similar levels of virus RNA in their testing samples. The concern here was that if the RNA amounts were the same, then perhaps vaccinated people would be as likely to transmit COVID-19 as unvaccinated people—if sick. This appeared to apply only to Delta variant infections.
The issue, as I mentioned at the time, is that we don’t know for certain that the amount of RNA in a vaccinated person actually correlates with real infectious virus. A virus is a naturally occurring and naturally evolved nanomachine that is made up of proteins, fats, water, and nucleic acids. The RNA is only one part of that nanomachine, and the virus needs all of its machinery in order to function—there is a lot more to a virus particle than just RNA, but RNA is what most tests look for.
The immune system is very good at obliterating virus particles in the body, but it does not necessarily obliterate all the RNA that was in those particles. In fact it often spits out such pathogen building blocks in mucus, to flush them from the body. So detecting RNA might not mean a person who is vaccinated is actually infectious.
Still, without clear data saying anything about this, the RNA load figures were really concerning and it was worth masking back up. However, this paper wishes to enter the conversation and tell us whether RNA load correlates with actual recovery of infectious virus particles.
The paper has one data figure, which attempts to demonstrate the following three facts:
People with vaccine breakthrough cases see increased RNA load for several days after symptom onset
These people may demonstrate RNA loads that are similar to what unvaccinated people have
These RNA loads are potentially misleading, because consistently, the correlation between RNA load compared with ability to recover amounts of actual infectious virus is lower in the vaccinated cohort than the unvaccinated
Unfortunately, I think this paper has a lot of problems. What the authors are trying to do is meaningful, and I think they actually made an effort to establish their limitations, but they do not convince me that we can safely rely on vaccinated breakthrough cases to be definitively less infectious. For one thing, their control group is a historical control from before vaccination, involving a group infected with non-Delta variant virus. So it becomes very complicated to interpret what we are looking at here given that their “vaccinated” group is infected with “primarily Delta.”
Their key figure panel—figure 1C—demonstrates a lag in the ratio of RNA load to probability of being able to culture virus, between the unvaccinated historical cases vs the vaccinated “primarily Delta” cases. The vaccinated ones show a slightly lower ratio of probability of culture-positivity compared with RNA load.
What does this mean? RNA load in vaccinated patients does not correlate with actual infectiousness the same way that it does in the unvaccinated. That is as far as I would take it. At high levels of RNA load, the unvaccinated and the vaccinated cases look somewhat indistinguishable. At middling levels, however, there is only a 50-80% chance that infectious virus could be recovered from the vaccinated breakthrough cases by comparison with the unvaccinated cases, where the chance ranged from about 70-90+% over the same range of RNA loads. There is a difference here, but I do not know that it is a difference that we should be using in public health decision-making.
Also, what really strikes me as a flaw here is that there was no effort to quantify the recovered infectious virus from vaccinated vs unvaccinated people. Instead we are just shown a probability of positive recovery, which is a binary value, compared with a measurement of RNA, which is a continuous number. Don’t love that.
These critiques make it hard for me to look at this paper and sound the all-clear, saying that vaccinated people may feel sick but they’re unlikely to spread COVID-19. In fact, the data here give me the contrary view to that, indicating that a person with a symptomatic breakthrough case may very well be able to transmit COVID-19 to others.
However, that doesn’t mean the paper is useless. The results do suggest to me that the ability to recover virus from vaccinated patients with breakthrough is reduced relative to the ability to recover it from the unvaccinated. This suggests that vaccinated people, even if sick, are at least less infectious…provided that the dynamics of Delta in the unvaccinated are similar to the dynamics of the different variants that had actually infected the control group here. I could envision a universe where Delta is extremely contagious, but only at very high RNA loads…but it also happens to produce these very high RNA loads frequently. A situation like that could yield a curve like what we see for the vaccinated patients in this dataset. The lower viral loads, with their reported lower probability of infectious virus, might represent stages in the course of infection that are after the immune system has gotten control over the pathogen.
I recognize this is probably a bit confusing. My point is to demonstrate that there are a lot of unknowns that are not directly examined in this very short paper. That having been said, this is the first paper I’ve seen that tries to tackle this topic, and I applaud the authors for attempting it. More work needs to be done, though.
Right now, I feel confident that a vaccinated person with symptoms can potentially transmit COVID-19 to others. I feel somewhat confident that they are less likely to do this than an unvaccinated person. However, I cannot put a number on that and I still think that universal masking is scientifically and epidemiologically prudent. Also, if you feel sick with any new or unusual symptoms that might be consistent with COVID-19, you need to get tested for COVID-19. This is whether or not you are vaccinated.
I will continue to monitor this topic area and report back as I learn more.
What am I doing to cope with the pandemic? This:
Cooking: Elote & more
It’s been a while since I’ve done food here. Partly, I feel like the recipes started as an effort to help people through the isolation of lockdowns, and give ideas for using the foods you might have stocked up on, but I hear people like them, so I’m not planning to stop until I hear otherwise. But they certainly have slowed down a bit.
What you’re about to see is not a picture of elote, the Mexican street corn that I made this weekend. I didn’t take a photo of that, because I made it on Shabbat, when I don’t take photos. However, it was interesting to make, because I discovered partway through, my corn already grilled on Friday, that the crema I’d purchased to use as a base for the elote sauce had developed a nice thick layer of mold while unopened a week before its sell-by date. Great. Unable to purchase more, I had to think relatively quickly.
The solution? Cream cheese. Normally I would have just used sour cream, but I didn’t have any of that. I did have cream cheese, though! And Since it was my only cultured milk option, I tried it out.
Normally, elote sauce will take ground chipotle pepper, chopped cilantro, lime zest, lime juice, crumbled cotija cheese, mayonnaise, and crema—also called “Mexican sour cream.” This makes for a thick coating that you can use on grilled corn, and it’s delicious. It’s not exactly health food, but it’s delicious. Surprisingly, cream cheese worked great as a substitute. It just took a little more mixing than I might have expected.
Anyway, having made this over the weekend, but not actually having a lot of corn to put it on, I’ve been trying to get creative with it for the rest of the weekend. Turns out it makes a great dip for tortilla chips (OK, not actually surprising in the least), but it also is great as a dressing for chopped cucumbers, which is what you’re about to see.
My wife is super into cucumbers lately, a product of pregnancy eating patterns and the fact that they have a lot of water in them. I’ve been trying to find good ways to use them, and it turns out that tossing them with elote sauce is pretty perfect. I comnbined this with some purple rice and salmon filets cooked with chile-lime and Old Bay spicing, and got the following:
This turned out great. There’s a lot of stuff that can serve multiple purposes, which I’m sure we’re all well aware of as quarantine veterans at this point.
Reader Nanette Sulik left the following comment about a personal family situation, which mentions an interesting air filtration technology (as well as some other particulars):
Molekule makes a combination HEPA/PETA filter setup in various sizes that is FDA approved for hospital use. The PETA filter kills bacteria and virus particles.
I have purchased 2 for the rooms my 96 yo father is in as he has several caregivers coming in and I am not certain of their safety levels. Because of his age, medical history, and degree of frailty, I am not convinced that the J&j vaccine has even mounted enough immune response for him to be fully protected.
I am considering getting him a booster as well since even mild disease might place him in jeopardy. Even flu vaccines have higher doses to boost immunity in the elderly population.
I’m debating if I should get the booster as well since I not only care for him at home but work in the hospital environment, nit for my own benefit but to further protect him. At the same time, I want everyone to have access to vaccines. I struggle with this.
This sounds like a tough situation. 96 years old is a high-risk age group, and immunity definitely wanes with age in general. Taking extra precautions sounds prudent to me. The air filter technology being used here is neat, as I mentioned in my reply:
Sounds like a good setup. I think what Molekule uses is actually a "PECO" filter, though, which stands for photo electrochemical oxidation. It's a combination filter-sanitizer. The filter standard itself is not readily disclosed on the Molekule site, which is somewhat frustrating, but they claim it is at-minimum better than HEPA, and their publicly-available data suggest that that is so. Unfortunately standards for consumer products data reporting are not usually as high as for drugs, but their technology is pretty cool. The filter is just the first step. The second step is the use of light to mobilize chemicals within the filter to create hydroxyl free radicals, which are very harsh and reactive. These then apparently begin the work of destroying particulates deposited on the filter.
The cool thing about this is that instead of just filtering the air, this thing then goes ahead and sanitizes its own filter, which probably helps with disposal of more persistent things like bacteria, which don't necessarily perish shortly after being caught in a filter. For a virus like SARS-CoV-2, I would expect HEPA to be enough since the filters do not need to be changed daily, but this would qualify as more than enough. More than enough isn't bad :)
Re:boosters...I agree, it's a difficult situation. I'm going get one if told to get one, but until then...I'll wait, happily.
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Always,
JS
You don't take photos on Shabbat, but you do cook? Or did you start the dish before sundown?