Saturday, January 02, 2021

Weekend Reading: Dark Days Ahead Edition

I've had a nice holiday break, and am now coming to terms with the fact that it is basically over. I go back to work on Monday. I needed a little more time. One thing I learned from 2020 is that I really need a proper 2 week vacation each year. I wasn't able to get one this year, and I think that was a mistake. I'll do better in 2021. 

Anyway, the break I did have was good and so I'll be happy with that. We had glorious weather here in San Diego. I didn't get as much time on creative endeavors as I would have liked, but I got two beach walks and a rollerblade outing and I crossed a couple of things off my long term to do list that remove some irritants from my daily life (I cleaned my desk and I moved my recipes from a spiral notebook that was falling apart to recipe binders). And there is still this weekend....

On to the links.

The big local news is that we have found four cases of the B.1.1.7 variant of COVID-19. Since the four cases are spread across the county, none had contact with each other, and the three they've fully interviewed so far have no history of travel outside the county, I think it is safe to assume the variant has been circulating in our community for awhile. 

I think the variant has probably made it to many places in the US. For the most part, we aren't sequencing enough samples to have a good picture of what the US cases look like on a genomic level. 

Between this new variant and the slower than ideal rollout of vaccines here in the US, it has been a tough couple of weeks in coronavirus news. I really wish we had the new team in the White House now, because I think this moment could really benefit from better messaging from the top. I'll say what I think of our situation right now (with all the usual "I am not an expert" caveats) with evidence linked in as possible, and then I'll share some additional things that have informed my opinion.

All of the evidence so far is that the B.1.1.7 variant is not more dangerous to any single individual who catches it, but that it is more dangerous to the community as a whole because it is more transmissible. The early studies indicate it raises the reproduction rate by ~0.4 - 0.7. You can read the preprint of this study.

These are epidemiological studies, and we don't yet have answers about the mechanism by which the reproduction rate is raised. Two theories I have seen are that the mutation in the spike protein makes it easier for the virus to get into cells and that the variant accumulates a higher viral load in the upper respiratory tract. These are just theories, though. Since we don't yet know the mechanism by which the variant is easier to transmit, we can't have specific advice on how to protect ourselves from this variant. However, we do know in general how to protect ourselves from COVID-19: Wear a mask, avoid groups, don't be indoors with people from outside our household, have good hand hygiene, etc., etc. 

Ian Mackay (one of the experts I follow on Twitter) created an infographic showing a Swiss cheese model of COVID-19 avoidance. That infographic has spread far and wide (he wrote about it on his blog), and I think it is a particularly useful way to think about how to protect yourself from the variant COVID-19, so I'll embed a tweet that shows the graphic: 

Clearly, what was working for some people isn't sufficient against this variant - hence the higher reproductive rate. Therefore, I think the thing to do is to take a look at your practices and think about where you can further reduce risk. Can you make some of the holes in the Swiss cheese smaller? Before Christmas, I shared the rules my little family of four have been living by. Given the high case load in San Diego and the evidence that we have the B.1.1.7 variant here, we've decided to decrease our risk by being even more careful about seeing friends. We aren't yet sure what that will mean. Our old rule was we could occasionally see friends outdoors as long as we wore masks or were ~6 feet apart. We're going to halt seeing people outside our family for a little bit while we figure out the new rules. We will figure out new rules and see friends, though, because we think the grown ups in our family are at least 6 months from getting a vaccine and who knows when there will even be a vaccine for kids? So again, we need to find some set of rules that minimize risk that we can sustain for many months.

Speaking of vaccines... wow, what a mess. The rollout is not going as well as we'd like. I think the pace will pick up as we leave the holiday period and as the local officials who have had managing vaccinations dumped on them on top of all the other extra work brought by the pandemic figure out how to manage. This undoubtedly could have been better coordinated and it is infuriating that it was not. However, I don't think the slow rollout is a reason to change the overall plan. We have a problem with getting actual vaccinations coordinated and done. Let's fix that problem. I don't see how delaying the second dose helps fix the actual problem at all. Basically, I agree with this:

Delaying the second shot would address a supply problem, but our vaccination rate is not currently limited by supply. Let's solve the problem we actually have.

I also found this point compelling. We aren't going to outrun an exponential curve by vaccinating faster. We need to double down on our non-pharmaceutical interventions!

Finally, this long thread from Carl Bergstrom matches my thinking on why I don't think we should change our plan, even though I have zero experience with cold-weather mountaineering!

I know everyone is frustrated that people aren't avoiding crowds and wearing their masks, and so they are looking for a way to work around that. I don't think there is one. I think our energy would be better spent fixing the vaccine rollout problems and working on improving compliance with the non-pharmaceutical interventions we know work. Can we come up with a "wear your mask" campaign that would reach some of the people who won't wear them now? Can we help stores and other indoor places where people need to be improve their ventilation?  And so on.

However, it doesn't really matter what I think about our vaccine strategies. I will control what I can control (my own behavior and my family's activities) and hope for the best on the rest.

Also: more vaccines may be coming soon, which further argues for investing our effort in figuring out how to get vaccinations done as quickly as possible. The J&J trial is expecting to provide results by the end of the month. The US study on the Oxford/AstraZeneca vaccine will perhaps help sort out the confusing set of information we have about that vaccine. Novavax has fully enrolled their phase 3 trial. And there are more.... Derek Lowe has an excellent round up of where we are at.

And here's a good thread summarizing what we know about the B.1.1.7 variant so far:

Of course, the highest levels of the US government aren't focused on vaccines and handling the new variant at all. They are focused on a futile but deeply disturbing attempt to overturn the results of the November Presidential election. 

I saw this tweet this morning and I am honestly stunned. We have a big problem.

I am glad some Republicans have started speaking out against this nonsense, but honestly I fear they may be too late to really help.

I recommend this interview Chris Hayes did with Brandy Zadrozny and Ben Collins, two NBC reporters who cover QAnon. It is from before the election, but remains very relevant. 

Enough of that. Here are some things that made me happy:

David Roberts on why he is a progressive.

All the tweets about health care workers getting their vaccines! Too many to share. Here's one particularly moving picture:

Some beautiful art:

Patrick Dexter's Twitter feed. Here's Auld Lang Syne:

These pictures:

And this photo:

This quote (click through to read the full thread):

The Blue Forest in Belgium went on my "things I want to see" list.

The guy who got the deer off the ice:

Service dogs, learning how to listen to a live performance:

This dog, living his best life:

Here's some bunnies to end on:

Happy New Year, everyone! Have a good weekend, and stay safe.


  1. Anonymous6:41 PM

    Thank you. Hope you share your new rules for your family with the variant clearly here and a long wait for vaccine eligibility to arrive. I am absolutely team double mask and extreme care. But also solo and retired so isolation is easier if not 100% ... groceries.....

    1. I will share once we settle on them! I think we're currently leaning towards shorter outdoor meet ups, with no eating (so we can stay masked the entire time). But we may take a complete pause for a few weeks to hopefully let things stabilize here. What was safe at 200 cases per day may not be safe at our current level (over 4000 cases today).

      For groceries: We get most of our groceries delivered on the principle that getting our specific items isn't worth the risk. Exceptions are a Trader Joes run about once per month (my husband wants their cereal and NZ cheddar cheese) and me picking up my prescriptions plus a few things at the drugstore ~once per month. The drug store will do curbside, though, so I may move to that unless there's something else I really need. I have also found that Target's order pick up here is well-organized. They have a tent outside so I don't even have to go into the store. (Or I could get their app and then they'll do drive up pick up.)

      Basically, we have prioritized maintaining some contact with friends (particularly for the kids) as the thing worth a little risk. I personally think outdoor and masked, particularly if in a place with a breeze, is probably very low risk. I think 30 minutes talking to a masked friend outdoors (particularly if that friend is also being careful) is much lower risk than 30 minutes in a grocery store.

  2. Socal Dendrite8:45 PM

    It's crazy here (LA County) right now. My son has a mole that is probably nothing but the pediatrician said in our teleappointment that we should get it checked out in person... but it feels risky to do that right now (but also risky not to). Ugh. I'm especially interested in the J&J trial results since husband and I are both enrolled in phase 3 (but I strongly suspect we both got placebo).


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