COVID Transmissions for 11-4-2020
Good morning! It has been 353 days since the first documented human case of COVID-19.
Yesterday was the end of the Presidential contest in the US, and as of this writing, it is not clear who won. I do not know if it will become clear by the time this message is scheduled to go out, but I encourage everyone to try to stay positive nonetheless.
The headlines section today is actually an in-depth on one item that is very cool, so I gave it a lot of attention.
As usual, bolded terms are linked to the running newsletter glossary.
Keep the newsletter growing by sharing it! I love talking about science and explaining important concepts in human health, but I rely on all of you to grow the audience for this:
Now, let’s talk COVID.
New York serosurvey results in Nature
I’ve written about this before, but Florian Krammer’s lab keeps hitting them out of the park this week, with the publication of New York City serosurvey (antibody prevalence) numbers in Nature magazine, building on his other recent publication in Science.
You can look at this paper here: https://www.nature.com/articles/s41586-020-2912-6
This work is super interesting because it looks at data from 10,000 plasma samples out of Mount Sinai hospital from February to July. That’s a huge volume of data from a huge span of time, and it can teach us a lot.
I’d like to share Florian’s tweet on the subject:
To go point by point:
This is the best estimate we have of infection-fatality rate (IFR); IFR is the percentage of people who die compared to the overall population infected. This is different from case-fatality rate (CFR), which looks at cases of COVID-19, because not everyone who gets infected with SARS-CoV-2 gets sick with COVID-19. As a result of this, IFR should be lower than CFR, and IFR is already quite high at 0.97%. While this number may look small, if 1 in every 100 people you knew died suddenly, you’d notice. This is quite different from the IFR expected from seasonal influenza, which is under 0.5%.
The first official detection of the virus in NYC was March 1st; this serosurvey detects antibodies in patients from February, specifically mid-February. This generally tracks with my understanding of the detection apparatus in the US at the time; due to commonplace asymptomatic infections and the incubation period for the emergence of symptoms, I've long felt that our delay time was about two weeks. The presence of antibodies in samples from two weeks earlier than the first “official” case detection essentially confirms this, though there are some reasons for uncertainty. Specifically, it takes some days for antibodies to be detectable; mid-February is an estimate. It might have been earlier.
This one is a little harder to explain. Here, Florian is saying that the percentage of antibody-positive patients (seroprevalence) and the typical amount of antibodies in such patients (titer) remained stable across the length of time that the study was performed. This suggests that antibody waning did not have a substantial effect in this large patient sample. People keep antibodies against SARS-CoV-2 for a good long while, it appears.
There’s a lot of interesting work here. This is a great paper.
Something that’s very cool is that the patients are separated by the “urgent care group” vs the “routine care group”; specifically, they separated patients by how serious their condition was when they presented for care. We see an interesting effect in the seroprevalence in the patient base when we look at this separation:
Image is two panels of a figure from this paper; the top represents the “urgent care group”, and shows a huge, exponential spike in March followed by cresting of the curve around 60% in April, with prevalence then falling gradually to around 20-25% in May in this urgent care group. The routine care group shows a very different pattern, where the rise in prevalence is striking, but delayed relative to the urgent care group, starting in late March and then rising through April. It then gets pretty stable around 20% without much variation.The difference between these groups is reflective not of changes in patients that were followed over time, but rather reflects changes in the types of patients presenting for antibody tests. The urgent care group spikes because a lot of COVID-19 patients were swamping NYC hospitals during the period of that spike. The routine care population represents the overall NYC population a lot better over time and doesn’t spike the same way.
The question that one might have here, then, is: why does the “urgent care” group fall? Well, it falls because the NYC outbreak was controlled. As it is controlled, the patients presenting for urgent care are presenting for COVID-19 less and less frequently and more commonly for other things. In light of that, the urgent care group starts to approach the routine care group because it is not selecting for as many COVID-19 patients. This confirms to me that New York really did start to get COVID-19 under control in May and then approached pretty stable control in June. That validates the Governor’s decision to begin reopening procedures in June.
There’s a wealth of information in this paper and I would be happy to take questions on it, or even do a full walkthrough of it at a later date. Let me know!
What am I doing to cope with the pandemic? This:
Sheet pan cooking
All this being at home means more cooking at home—which is good when restaurants mean being unmasked around strangers for a long period of time, but bad when the home cooking means a need to meal plan and deal with cooking all the time.
Enter the humble sheet pan, which can cook a ton of stuff at once. Yes, yes, if you’re like me and you cook at home all the time, you use sheet pans for everything. You may even use sheet pans for things that I don’t, because I’m no baker. If you’re not one of those folks, you may not realize how easy it is to cook with a sheet pan. You may be getting very sick of ordering delivery or making pasta. This section today is for you.
It works like this:
1) preheat oven to cooking temperature
2) cover the sheet pan with aluminum foil to make it easier to clean later
3) put your food on the pan, season it (in the pictures you’re about to see, the food is sweet potatoes and chicken thighs, the chicken thighs being seasoned with a mixture of adobo seasoning, chipotle chili powder, smoked paprika, and sumac)
4) put it in the oven until it’s cooked (Yes, this can be tricky, but you can use the Internet or an oven thermometer or both to help understand when your food will be safely done)
This is what I made last night:
Image is of a plate with a cooked chicken thighs and two sweet potatoes. They are cooked and edible (very edible, in fact, if I may say so myself).This is how it started:
Image is a picture of raw chicken and sweet potatoes on an aluminum-covered sheet pan.This required approximately zero thinking. That is good when the pandemic and the news are making it hard to think about anything else. If cooking during this whole thing is driving you nuts, try it out.
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Thanks for reading, everyone!
See you all next time.
Always,
JS