COVID Transmissions for 4-6-2021
CDC data shows that vaccination can reduce risk of infection
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 505 days since the first documented human case of COVID-19. “505” is the title of a somewhat ponderous Arctic Monkeys song, from their album Favourite Worst Nightmare, that has long been kind of puzzling to me. It’s about a relationship that has a lot of tension in it, and potentially about a reunion that might not go well.
The song:
It reminds me a little bit of the journey we’re going on with the pandemic—success is around the corner, but there’s a lot of tension over whether we’ll be responsible enough to actually get there.
Today, one big headline on CDC data regarding the ability of vaccinated people to become infected with—and thus spread—SARS-CoV-2.
As usual, bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
CDC data on vaccines preventing infection
Last week, a paper ran in Morbidity and Mortality Weekly Report that described data on the prevention of infection with SARS-CoV-2 in people who had received COVID-19 vaccination with mRNA vaccines: https://www.cdc.gov/mmwr/volumes/70/wr/mm7013e3.htm
To give the topline results, 4,000 healthcare personnel were tested weekly for SARS-CoV-2 infection. Those who were fully vaccinated were 90% less likely to test positive for infection than those who were not. This is how the paper states the conclusions; it isn’t exactly what the work did, though.
We have covered studies like this before; one of them, the SIREN trial in the UK, I discussed at length in a previous issue. The main issue I want to carry forward from that is that while being negative at regularized testing points is a great thing, it doesn’t actually mean that the patients are protected from infection. It means they are protected from infections that last long enough to be picked up on weekly testing. It’s possible they still get infected, but it only lasts for a day or two. Even if that’s happening here it’s still great news, though, because a short, abortive infection probably limits any ability to transmit disease to a substantial extent.
Now, to explain my comment about how the paper’s conclusions don’t exactly reflect the work. This study portrays itself as studying vaccinated vs unvaccinated patients. However, 75% of the subjects in this study got at least one dose of a vaccine during the study period. It seems that instead of comparing the 75% of vaccinated subjects with the 25% unvaccinated (which would not have been random samples, so I’m glad they didn’t), the authors chose to compare data collected before subjects were vaccinated with data collected after subjects were vaccinated. So they compared the chance of becoming infected on an unvaccinated “person-day”1 compared with the chance of becoming infected on a vaccinated person-day. The chance of testing positive for SARS-CoV-2 infection was 90% lower for vaccinated person-days than for unvaccinated person-days.
What this means is that, largely, they compared not vaccinated people with unvaccinated people—not exactly—but rather time that subjects spent unvaccinated with time that subjects spent vaccinated. In 75% of cases, this means the unvaccinated condition included patients who later became vaccinated. That means we are comparing information that was collected at very different points in time, and there are inherent biases that come into play in such situations. As you may recall, in the fall, the US had a remarkably strong COVID-19 surge. Vaccines became widely available to healthcare workers as this surge was cresting, and most would not have become fully vaccinated until it began to subside.
This may have impacted the results in this case, though I am not sure to what degree. Healthcare workers continue to be exposed to COVID-19 on a daily basis, even as the epidemic in the US waxes and wanes.
Still, I am encouraged by these results because they do indicate to me with near certainty that the mRNA vaccines can prevent the spread of COVID-19, by limiting the potential for vaccinated people to be infected. I’m just not sure how much confidence I have in the exact numbers. Still, it looks very good, and taken together with other data from places like Israel, leaves me confident that we can use vaccination to genuinely control the pandemic.
The paper itself is a good read, though, and pretty accessible. Take a look at it.
What am I doing to cope with the pandemic? This:
Cooking: the wonders of a good rice cooker
I think a lot of Americans who cook might read the above line and think, “Wait, rice is easy, you put it in a pot and you cook it.”
I too used to think this way. I had a cheap rice cooker for convenience, and it worked very well for 10 years. In fact it still works, but its lining pan is falling apart, so I decided to replace it.
I went this time and got an expensive (ish, I went for a cheaper model) Japanese rice cooker. It has all kinds of fancy features, like something called “synchro-cooking,” which is intended to cook both a food recipe, and rice, simultaneously so that they both get finished at the same time.
What’s really good about this device is that it uses both heat and pressure to cook rice. Rice is an exceptional food, and one that has many subtleties that go unappreciated. The cooking process for it seems simple, but really it is a complex use of water and heat to soften the starchy matrix of the seed. Pressure, which can change the temperature dynamics within a cooking vessel, offers advantages for control of the cooking process.
Anyway, I’ve used this new machine for the first time this week and it’s frankly fantastic. It takes a lot of the guesswork out of cooking a large amount of rice at once—for example, did I stir it frequently enough? This machine makes it possible not to care about that.
It isn’t perfect for every rice cooking technique—it’s designed to cook rice the way that Japanese cooks make it, in a minimal amount of water that leads to a clumped mass of rice, ideal for consumption with chopsticks. Other cultures boil rice in an excess of water, then strain off that excess, which tends to yield easily-separated grains.
Anyway, I love my new rice cooker, and if you eat a lot of rice but don’t have a high-end tool for cooking it, I recommend you do some research and invest in one.
Reader Molly weighed in on the question of some people having been offered the option to receive two different vaccines, while others have not been offered even one:
I’d like to respond to the questions about getting a second vaccine. Not to sound indignant, but I haven’t been able to get one vaccine. People line up for extra doses. Why should an already vaccinated person get a second vaccine? I’m fine with waiting my turn, but it seems unfair that someone could get multiple vaccines while others wait for one.
I think this is a comment that goes to show how important health equity is. I don’t know how to define fair, exactly. But here’s what I said:
I can't comment on the relative fairness of the situation. Vaccine is variably available in many different places, and health inequity is a problem around the globe. Here in the US we've long had access to medicines that cost tens of cents, but are unavailable in Africa where the diseases they treat kill thousands of children. I would never say we should get used to these types of inequities, but I will say that this vaccine thing is yet another manifestation of how healthcare is rarely regarded as a human right.
I hope that very soon everyone has complete, fair, and equal access to every vaccine they could want.
Carl Fink writes in about a story that broke yesterday regarding variants of concern in India:
Quote from India's Ministry of Health and Family Welfare's press release: "The analysis of samples from Maharashtra has revealed that compared to December 2020, there has been an increase in the fraction of samples with the E484Q and L452R mutations. Such mutations confer immune escape and increased infectivity. These mutations have been found in about 15-20% of samples and do not match any previously catalogued VOCs. These have been categorized as VOCs but require the same epidemiological and public health response of “increased testing, comprehensive tracking of close contacts, prompt isolation of positive cases & contacts as well as treatment as per National Treatment Protocol” by the States/UTs."
https://pib.gov.in/PressReleasePage.aspx?PRID=1707177
Virologist, please assist: are those known mutations, e. g. from P.1? How concerning is this?
I’ll start off by saying that I don’t think any single mutation is the one that will cause some scary new virus to emerge. That never how it works. Scary new things emerge by combinations of mutations that accumulate over time. For example, nature did not take a tree-dwelling monkey, give it a single mutation, and end up with the terrifying Homo sapiens species. Scary things take time to emerge. Here are my thoughts on these specific mutations:
E484K is a well-known antibody escape mutation that is found in many different variants of concern. L452R is one that I have heard about but that I consider less well-characterized. It is predicted to have effects on virus binding to the ACE2 receptor, as well as potential neutralizing antibody escape.
This overall fits with the pattern of certain amino acid changes being favored that may lead to escape of neutralizing antibodies. So far I don't see anything that has compromised vaccine efficacy meaningfully, though, so I'm not concerned about currently-circulating variants. What I am concerned about is their potential descendants. The longer the pandemic burns on, the more likely it is for new variants to emerge that combine various mutations and genuinely compromise vaccine efficacy.
We need to get this pandemic under control as soon as possible.
You might have some questions or comments! Send them in. As several folks have figured out, you can also email me if you have a comment that you don’t want to share with the whole group.
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No corrections since last issue.
See you all next time.
Always,
JS
You may be thinking “person-day”? Isn’t that just a “day”? Person-day here combines individual subjects with the duration of time the existed within a condition (in this case, being unvaccinated or vaccinated). A set of patients may have very different unvaccinated periods of time on-study. To normalize this, we count the number of patients and the number of days they were unvaccinated, and multiply persons by days. We get a number in person-days, which represent individual risk units of the number of individual susceptible subjects across the time they were susceptible. Exposure is risk (in this case, captured by the persons) times time (in this case, days).