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:
A new version with colour & division inspiration from @uq_news and strict mouse design oversight by @kat_arden (ver3.0).— ɪᴀɴ ᴍ. ᴍᴀᴄᴋᴀʏ, ᴘʜᴅ 🦠🤧🧬🥼🦟🧻 (@MackayIM) October 24, 2020
It reorganises slices into personal & shared responsibilities (think of this in terms of all the slices rather than any single layer being most important) pic.twitter.com/nNwLWZTWOL
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:
So we're not good at getting shots into people at scale.— Eric Topol (@EricTopol) January 1, 2021
So instead of fixing that problem (a strategy with incontrovertible data for high efficacy and safety)
Let's double the number of people to get shots without any data (beyond 3-4 weeks) to support it.
That's so logical.🤦♂️
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!
Best case with that plan is you double the slope of a linear function (vaccinated fraction) racing against an exponential function (virus spread). The exponential function will win.— Nicholas Bauer, PhD 👨🔬🔬 (@BioTurboNick) January 1, 2021
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!
Why do I have this reaction? I've been trying to put my finger on it all day.— Carl T. Bergstrom (@CT_Bergstrom) January 2, 2021
There are a lot of reasons, but at the core of them has to do with the way that going off plan compounds risk.
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:
We’re in a new year and we have also entered a new phase of this pandemic. So I thought I’d start off the new year with a quick catch-up thread on the UK variant B.1.1.7 and where we are at in this pandemic.— Kai Kupferschmidt (@kakape) January 2, 2021
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.
Source confirms this list and says it will include nearly a dozen Republican senators joining Hawley in rejecting the results. They're seeking an independent commission on voter fraud, per the source. https://t.co/5gwbmBTJxw— Maggie Haberman (@maggieNYT) January 2, 2021
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:
All the tweets about health care workers getting their vaccines! Too many to share. Here's one particularly moving picture:
Nurse Elena Betti reacts after receiving the Pfizer-BioNTech COVID-19 vaccine at the Careggi hospital in Florence, Italy. More photos of the day: https://t.co/JHNdi4zsrg 📷 Jennifer Lorenzini pic.twitter.com/QdXsdM6xsw— Reuters Pictures (@reuterspictures) December 28, 2020
Some beautiful art:
Patrick Dexter's Twitter feed. Here's Auld Lang Syne:
You can watch Auld Lang Syne in full here: https://t.co/Cs9WtYgKpM Happy New Year!— Patrick Dexter (@patrickdextervc) December 31, 2020
I went to photograph ducks tonight, but found something even more magical. pic.twitter.com/nnWHbPuY5i— Carl T. Bergstrom (@CT_Bergstrom) December 23, 2020
And this photo:
Well here is my #1 photo of the year click for full screen. The reason I chose this photo was it exudes Sask. and our amazing skies. I feel as we go into a new year that if we can just stay the course and stay on track good things are sure to come in #2021 #HappyNewYear2021 pic.twitter.com/J1wNHnTN90— Craig Boehm (@Skstormchaser) January 1, 2021
This quote (click through to read the full thread):
From the historian Tony Judt before he died of ALS in 2010: “Something is profoundly wrong with the way we live today. For thirty years we have made a virtue out of the pursuit of material self-interest..." 1/— Gregg Gonsalves (@gregggonsalves) December 30, 2020
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:
I’ve watched this 10 times at least. Hope it brings all who need it some laughter! pic.twitter.com/8pvSiHfKWr— Dr. Adriane Lam (@ForamWhisperer) December 25, 2020
Here's some bunnies to end on:
Happy New Year, everyone! Have a good weekend, and stay safe.