I support making boosters broadly available for those 18 and older. Even if breakthrough cases are generally mild in younger age groups, there is significant societal benefit to reducing circulation. 1/6 nytimes.com/2021/11/16/us/…
Currently Washington State is seeing almost 30% of cases as breakthrough cases (doh.wa.gov/Portals/1/Docu…). 2/6
Here, I think of @alexismadrigal's piece on the implications of a positive COVID test (theatlantic.com/health/archive…). It's crazy to me that we're saying to healthy younger individuals they must isolate for 10 days after a positive test, but that they're not eligible for a booster. 3/6
We should have consistency in how we're thinking of public health interventions. Either we're promoting interventions to reduce circulation or we're only thinking about disease as endpoint. 4/6
All this has been complicated by vaccine availability. Given constrained supply it makes sense to prioritize the vulnerable, but we should be clear that that's the decision being made, not that boosters are not necessary because protection against severe disease is robust. 5/6
Anyway it seems the ship is now sailing, which is welcome news. And of course, can we invest the resources to please address vaccine equity? This @OurWorldInData map remains depressing (ourworldindata.org/covid-vaccinat…). 6/6
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The evolution of SARS-CoV-2 in the past year has been remarkable with Delta increasing transmissibility by perhaps 2.2X over "non-variant" viruses. 1/14
We should expect this evolution to slow as SARS-CoV-2 continues to adapt to the human host, but when should we expect this? Here, I propose that we've already seen slowing between 2020 and today. 2/14
One very important concept here that I keep coming back to in thinking about evolution is @GreatDismal's quote that "the future is already here. It's just not evenly distributed yet". 3/14
I've meaning to write a "COVID endgame" thread for a while and I apologize this is somewhat delayed compared to media interviews like science.org/content/articl… and statnews.com/2021/09/20/win… and to recent seminars like . 1/17
Here, I've been trying to think about what COVID will look like in its endemic state, ie once the (more or less entire) population has immunity to the virus, blunting transmission and disease relative to the pandemic state. 2/17
I expect endemicity to be achieved at different times throughout the world due to inequities in vaccine distribution and I expect this to be a soft transition rather than a sudden flip of a switch. 3/17
I realize this is rather late to the party, but I wanted to provide a look at the prospects of Mu variant virus. I believe we can conclude that Mu appears more transmissible than all circulating variants except for Delta, but Delta is substantially fitter than Mu. 1/9
If we look within Colombia, we see Mu becoming predominant around May 2021, outcompeting other endogenous South American variants Gamma and Lambda. However, recent sequencing suggests that Delta is successfully invading on this Mu background (nextstrain.org/ncov/gisaid/so…). 2/9
In neighboring Ecuador, we see a heterogeneous mix of Alpha, Gamma, Iota, Lambda and Mu by June 2021. Delta has been successfully displacing most of this diversity since July 2021, while Mu has remained relatively stable (nextstrain.org/ncov/gisaid/so…). 3/9
I'm honored and completely overwhelmed by the recognition from @macfound and @HHMINEWS. Flexible funding with a multi-year commitment is the professional scientist's dream and I'm incredibly grateful for this opportunity. 1/4
For me, like others in the field, responding to the pandemic has been a ceaseless and exhausting endeavor. But I'm immensely proud of what the teams at @nextstrain, @fredhutch and the @seattleflustudy, as well as the larger scientific community, have accomplished. 2/4
That said, it's difficult for me to sort out my feelings about these awards, as they are so intertwined with the pandemic. It feels perhaps uncomfortable to be professionally rewarded for doing something that felt like a moral imperative. 3/4
New (not yet peer-reviewed) work by Katie Kistler and @huddlej in the lab assessing adaptive evolution in SARS-CoV-2 across the viral genome. 1/12 biorxiv.org/content/10.110…
We measure adaptive evolution by correlating mutations in different regions of the genome with growth of clade frequency. For this, we use a viral phylogeny of ~10k genomes sampled equitably through space and time across the pandemic (nextstrain.org/groups/blab/nc…). 2/12
If mutations to a region result in fitter viruses, clades bearing these mutations should expand more rapidly. We find that the S1 domain of spike accumulates protein-coding (nonsynonymous) changes rapidly and that clades with more S1 mutations tend to grow in frequency. 3/12
It looks like we're about at the peak of the Delta SARS-CoV-2 wave in the US (figure based on @CDCGov data). A thread on current circulation patterns and the impact of Delta. 1/14
This inflection point in case loads at the country-level is due to decline in some states (such as FL and LA) and growth in others (such as OH and WV). Figure shows cases per 100k population on a log axis to emphasis state-level growth and decline. 2/14
Using previously described method to split cases by variant frequency (
), we see a striking pattern in which most states have a moderate spring wave comprised of a mix of Alpha and other variants, but show a large Delta wave in the summer. 3/14