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
So many scientists, public health officials, health care workers, journalists and others have worked themselves bare during the pandemic. Though there’s still a long road in front of us, I’m confident that our collective effort will ultimately get COVID under control. 4/4
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New (not yet peer-reviewed) work by Katie Kistler and @huddlej in the lab assessing adaptive evolution in SARS-CoV-2 across the viral genome. 1/12 biorxiv.org/content/10.110…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
I'm not an immunologist, but I've been trying to read into the literature on waning immunity to SARS-CoV-2 and to understand the recent NIH, CDC, FDA booster recommendation (hhs.gov/about/news/202…). I'll share some takeaways here. 1/14
Previous studies in other viruses found that the potency and the concentration of circulating antibodies in an individual is often predictive of their protection to infection or illness after exposure. 2/14
This potency + concentration is commonly quantified as the titer required to neutralize 50% of viral plaques in a lab assay. These assays are run by diluting sera from an individual and seeing what dilution causes loss of neutralization. 3/14
How big of a wave of #COVID19 do we expect in the US from the Delta variant? Here I describe a simple approach to this question and attempt a rough back-of-the-envelop estimate. 1/16
First off, epidemic size is determined by two primary factors: 1. Efficiency of onward transmission from an index case, commonly quantified as R0 2. Size of susceptible pool
2/16
Given a specified R0, we can calculate final epidemic size in a simple SIR model with the following equation where Z is final epidemic size. For initial R0 of 1.1, an epidemic is expected to infect 18% of the susceptible population. 3/16
Jesse Bloom's preprint has, of course, caused quite a stir. I wanted to try to explain a bit about the "rooting issue" discussed in the manuscript and also provide some hopefully clarifying phylogenetic trees. 1/15
For this post, I've made a @nextstrain "build" targeted at SARS-CoV-2 genomes from Dec 2019 through Jan 2020, totaling 549 viruses. All code is here: github.com/blab/ncov-earl… and should be reproducible using a download of @GISAID data. 2/15
There is genetic diversity within these very early samples with much of it arising from a split in early transmission chains into lineage A and lineage B viruses (lineage B as in B.1.1.7). Lineage A and lineage B viruses are separated by mutations at sites 8782 and 28144. 3/15
An update on genomic surveillance in the US and spread of the Delta variant (PANGO lineage B.1.617.2, Nextstrain clade 21A). At this point, 95% of viruses circulating in the US are "variant" viruses that have been designated as "Variant of Concern" or "Variant of Interest". 1/12
This update mirrors how I was looking at the rise of P.1 across the US in May. 2/12
Here, we can look at frequencies of different variant lineages through time and across states where it's clear that variant viruses and in particular B.1.617.2 viruses are continuing to increase in frequency. 3/12