COVID Transmissions for 7-16-2020

We join our program already in progress…

Greetings from an undisclosed location in my apartment.

It has been 242 days since the first documented human case of COVID-19, and for some reason, I have chosen now to start this newsletter. Perhaps it’s a subconscious Douglas Adams reference.

COVID-19 is something that many of us have already followed and read about obsessively, so I am going to be diving in to the information stream like the confusing cold open to a third-season TV drama. The beginning of each issue of this newsletter is going to focus on “new news” in the story of the pandemic; later on in each newsletter I will include discussions and explainers on more basic topics in case anyone needs to backfill. Please do give me feedback on structure and topics included; I want to make this as useful to you as possible.

Housekeeping note: in each edition of this thing, I am going to bold certain words. There will be a glossary at the end of the newsletter explaining those words.

I’d also like to keep growing this newsletter, so if you like what you see—or what you might see in the future—remember that this button exists:

Now, let’s talk about COVID.

---

In the headlines

Moderna vaccine:

Image is the Moderna corporate logo.

This made big headlines recently for the publication of early results from the trial in The New England Journal of Medicine (NEJM), full paper found here: https://www.nejm.org/doi/full/10.1056/NEJMoa2022483

A more approachable summary can be found at STAT news: https://www.statnews.com/2020/07/14/moderna-covid19-vaccine-first-data-show-spurs-immune-response/

These results’ main takeaway is that the 100-μg dosage for the vaccine is what will go forward into Phase 3 clinical trials, which are planned to include 30,000 patients.

I am impressed with the amount of neutralizing antibody response found in these results. However, we still do not know if neutralizing antibodies are what protects you against the virus. We are still looking for correlates of protection.

I am also reassured (though not surprised) that the safety profile looks tolerable. Most of what is listed in the NEJM paper are things that you expect from most vaccines—redness at the site of injection, irritation, chills. These are things that happen with a lot of injected vaccines and medicines and are easily managed.

The bad news for the Moderna vaccine is that their Phase 3 trial date has been delayed, but it seems only by a matter of days or weeks. STAT news has that story: https://www.statnews.com/2020/07/02/trial-of-moderna-covid-19-vaccine-delayed-investigators-say-but-july-start-still-possible/

Protests:

Image is a pre-pandemic photo I took at a BLM march in NYC; a crowd of people is facing away from the camera in a nighttime urban scene. At the center of the photo, a Black man carries a sign reading "ENOUGH." I just happen to like the picture.

The Economist has a nice post looking at the effect of protests on COVID-19 transmission and number of hours that people were remaining at home; like other work on this, they determine that the protests did not have a substantial effect, and even that they probably resulted in more people staying home than before they began. The article is paywalled, but you can see the figure: https://www.economist.com/graphic-detail/2020/06/30/black-lives-matter-protests-did-not-cause-an-uptick-in-covid-19-cases

Masks:

Image is me, in the mask I generally wear, which was made by Joe Biden's presidential campaign. When it comes to masks, please wear a mask no matter who you’re planning to vote for.

The CDC keeps issuing guidance that everyone in the US should all be wearing masks, and has a nice press release highlighting two things:

• More people are adhering to mask recommendations

• Masks really work! This one is the hair salon case study

The press release is found here: https://www.cdc.gov/media/releases/2020/p0714-americans-to-wear-masks.html

Recently the Journal of the American Medical Association (JAMA) did an interview with CDC Director Robert Redfield, where he claimed that if everyone in the US wore masks, the outbreak here could be brought under control in just 4-6 weeks. You can see the whole interview here:

Mentioned in this interview is this paper about masking in a healthcare setting: https://jamanetwork.com/journals/jama/fullarticle/2768533

If there is interest, I can comment on this paper in depth in a future issue.

They also make reference to Dr. Redfield’s recent JAMA editorial about masks: https://jamanetwork.com/journals/jama/fullarticle/2768532

---

Pandemic life

This section is going to be about how I’m personally staying sane in this thing.

Reading

Image is a book; the cover of Jeff Vandermeer's Annihilation, carrying the title of the book as well as a design of plants and insects intertwined with the letters.

I just finished Jeff Vandermeer’s Annihilation. It felt like a less-annoying House of Leaves, with a strong dose of the things I liked in Hyperion. I didn’t like that the main character is called a “biologist” when she is clearly an ecologist, but that’s a ridiculous nitpick! A good read if you like dark themes.

Find it here: https://bookshop.org/books/annihilation-9780374104092/9780374104092?aid=45

Listening

Image is the logo for This Week in Virology (TWiV).

I’ve trying to catch up on a massive backlog of the TWiV podcast, because I need to get current again. I was a past guest and cannot recommend this podcast enough. You can find it at https://www.microbe.tv/twiv/

Cooking

Last week’s CSA delivery brought us a head of escarole, and early on in the pandemic I had stockpiled tactically significant amounts of cannellini beans. Inspired by this recipe: https://www.foodandwine.com/recipes/tuscan-white-bean-and-escarole-soup-tuna, I made a dish that’s somewhere between a soup and a chowder, to be best delivered on toast. You can achieve this by cooking the beans a bit longer, letting them break down a bit and thicken the soup. It works better if you use dried beans instead of canned, but this takes longer. For the bread, instead of the toaster, I went for pan-toasting some Bread Alone sourdough in olive oil. This had a very nice, rustic feel.

---

In-depth

In future editions, I’d like to cover certain topics in greater depth. I’ll do these by request. Please comment on the discussion thread for this edition about what you’d like to see here. Topic selection will prioritize paying subscribers first, but suggestions from free subscribers are also welcome.

---

Join the conversation

Since this is the first issue, I need feedback on what you want to see, how frequently you want to see it, and what is most likely to make you tell your friends about this newsletter. Tell me things. I will possibly listen to your advice.

Also, please feel free to discuss the content of the podcast—start a conversation, tell us what you think. But please, be respectful of other commenters. I will remove comments and discussions that I think are harmful, without warning.

---

Glossary

Correlate of protection: Let’s break this one down. “Protection” is something that we determine by epidemiology. We look at a population, and if we see less infection in that population than some comparator population, we call that population “protected” to some degree. But we know that protection is the result of immune responses. This is where we get into “correlates.” This will not surprise anyone who has immunology training, but we are really, really confused about how immunity actually works. Science has discovered some incredibly complex systems available to us that protect us against pathogens; they are so complex that for every pathogen, it requires a large amount of research to figure out which system is actually the one protecting us the most. What we typically do is find evidence of an immune response (eg, antibodies, cells that react specifically to the infection, etc.) that we know is commonly and significantly associated with people in protected populations. In other words, we figure out who is protected and then we figure out what immune responses exist in people who are protected—these immune responses correlate with protection, and accordingly are named “correlates of protection.” These can be hard to figure out—right now we do not know the correlates of protection for COVID-19. However, it’s worth noting that we also don’t know the correlates of protection for pertussis, a disease against which we have a very nice vaccine.

Neutralizing antibody: Not every antibody is effective at hindering viruses. There are a lot of reasons for this, but mostly they relate to the fact that viruses replicate themselves very efficiently and saturate the area with their copies. This means that immune responses that involve cells eating every infectious particle are often too slow to be effective. For this reason, people are often interested in antibodies that “neutralize” the virus. Neutralization refers to stopping the targeted pathogen from being able to be infectious or pathogenic; it renders it inert. Antibodies can target any part of the virus, but not all parts of the virus are involved in actually infecting cells, so only antibodies that target key antigens involved in the infection process will be “neutralizing.” There are experimental systems that can be used to assess whether or not antibodies are neutralizing or not. If there is interest (please comment), I can go into more depth on this in a future issue of the newsletter.

---

Mistakes

I am human and fallible. This newsletter will contain mistakes. When you find them, tell me about them so that I can fix them. I do not have any pride regarding my mistakes, and both invite and encourage you to correct me. I would rather this newsletter be correct than protect my ego. In the future, this section will notify on corrections.

See you all next time.

Always,

JS