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Bio: Scientist @fredhutch, studying viruses, evolution and immunity. Collection of #COVID19 threads here: bedford.io/misc/twitter/
Location: Seattle, WA
I’ve been using 4x for recent weeks. However, given spectrum of disease and asymptomatics I’m not sure fraction detected gets much higher than this even with further increases in testing capacity.
Yep. Given range of disease severity getting a mild infection tested and finding out it’s COVID should prompt responsible individuals to self-isolate and thereby slow spread. Testing is one of the only direct interventions against transmission we have with this disease.
I expect SARS-CoV-2 to eventually settle down as a seasonal coronavirus but not until 2021/2022 season at the earliest. Open question on whether it will attenuate much with time. My guess would be that it won’t and we’ll just have to reduce circulation through vaccine.
Yep. For H1N1 “swine flu” in 2009 we counted continually from initial cases in Feb/March through the initial pandemic of 2009 and early 2010. Went back to regular “seasonal” counting in 2010/2011 season.
That “10% of the population” number comes from influenza serology which should catch asymptomatic and pauci-symptomatic infections.
This is Mathematica’s network viz via force-directed layout. There’s a convenient “community clustering” option that pulls nodes within a defined cluster closer together.
Although cases in the US are trending upwards across the board, incidence is still quite different state-to-state. I’d be more strict than I am right now if I lived in Wisconsin or North Dakota where per-capital incidence is high. 2/2
Data from state DOHs that I’m familiar suggests that a large fraction of transmission is from social settings and workplaces. I get take out regularly. I don’t eat indoors at restaurants. 1/2
Given 50 points in the plot, I think best way to look at particular states is probably just directly at rt.live.
We don't test for flu to nearly the same degree and instead in Jan 2020 we detected about 20k confirmed cases of flu per *week* in the US at the peak (cdc.gov/flu/weekly/ind…). 3/2
We're detecting ~1/4 infections as a case with COVID. So, if we were testing for flu like we do COVID, I'd expect around 60k confirmed cases detected per day averaged across the flu season. 2/2
Good question. It varies season-to-season, but the general expectation is that seasonal flu will infect 10% of the population each winter season. Very roughly this is 33 million people in 20 weeks or about 235k infections per day on average. 1/2
I expect both to play a role in countering the current surge, but I won't hazard a guess at this moment as to when this occurs and what we eventually suffer in terms of daily case load. 10/10
I've written previously about the dynamic relationship between COVID-19 cases, deaths and societal response (twitter.com/trvrb/status/1…) as well as the effects of relatively small levels of population immunity in the presence of mitigation (twitter.com/trvrb/status/1…). 9/10
This indicates that the current surge has no evidence yet of cresting. It's exponential "velocity" is the same or greater than two weeks ago; we've not yet seen signs of deceleration. 8/10
Notably, 49/50 states are currently estimated to have Rt > 1 and in 40/50 cases Rt is estimated to be larger on Oct 28 than on Oct 14. 7/10 pic.twitter.com/T5twdqNcys
Broadly, Rt varied widely across states in May-Aug corresponding to differing societal behavior and state-level "reopening" policies, but during Sep and Oct states have largely equilibrated in terms of Rt. 6/10 pic.twitter.com/5LKZKbYb7y
Exponential doubling of COVID-19 is proportional to the instantaneous reproductive number Rt at a particular point in time. If Rt is greater than 1 then the epidemic is growing, if less than 1 it's shrinking. In the following I plot Rt estimates from rt.live. 5/10
If we look across states and plot confirmed cases on a log scale we can see a steady linear-on-a-log-scale trend in the past 4-8 weeks across most states. This pattern is indicative of exponential growth. 4/10 pic.twitter.com/bFLTQlk02N
Confirmed cases have continued to tick up across the US, though with the Midwest and Mountain West contributing to most of the recent increase. Data from @COVID19Tracking. 3/10 pic.twitter.com/9fN41JBbaz
Please consider this somewhat of a follow up to the thread two weeks ago on circulation patterns across states. 2/10
twitter.com/trvrb/status/1…
I know that everyone has been (justifiably) distracted by other things, but the #COVID19 epidemic in the US is looking pretty dire with 125,552 confirmed cases reported Friday by @COVID19Tracking. 1/10
twitter.com/COVID19Trackin…
Follow up #2: We've had another pass at sequencing WH2. This time we got a complete genome with 5574X coverage. We find that WH1 and WH2 are completely identical across the full genome. This does not change any conclusions from the manuscript, but increases certainty. pic.twitter.com/tGSeyTTeXh
Definitely. The folks in the lab are taking another run at it. Hopefully have results shortly.
Good question. There are a larger number of possible cases of reinfection based on 2+ PCR positives. In many cases both samples can’t be sequenced. So gold standard evidence is only available for a fraction. But this larger number of 2+ PCR positives is small in absolute terms.
It was Brian Morgenstern washingtonpost.com/health/2020/10…. (Sorry, I should have been more clear, or provided a link)
washingtonpost.com/health/2020/10…
Depends on the setup the lab is using but generally between $35 and $120.
It’s part of the toolkit for epidemiological investigation. See for example eurosurveillance.org/content/10.280… or cdc.gov/mmwr/volumes/6…. On a larger scale, we’ve learned a lot about geographic patterns of epidemic spread within and between countries (cdc.gov/mmwr/volumes/6…).
eurosurveillance.org/content/10.280…
I’ve been public about the need for better data systems and recording of exposure setting (mobile.twitter.com/trvrb/status/1…). “Protest-associated” exposure would fall in here as well. To my knowledge, the data to address this question (including protests, bars, …) isn’t being collected.
mobile.twitter.com/trvrb/status/1…
Thanks for the catch. We’ll correct this typo.
Follow up #1: The @medrxivpreprint preprint is now up at medrxiv.org/content/10.110….
My understanding is that NIH / NSF want to prevent people from circumventing the application page limits by including links to supporting materials, etc... Still, I find it very strange as well.
There's still a lot of backfill happening in GISAID and this may change, but yeah. I was surprised as well.
Good question, but I'll defer to @lea_starita for the answer. We've relied on amplicon sequencing for the Bedford Lab sequencing work, but the much larger-scale efforts at BBI have been hybrid capture. I believe there's a "no amplicons in the sequencing lab" policy.
I believe it would be inappropriate to sit on results of such obvious public interest and so moved forward with releasing the technical report today. 10/10
Regarding timing, we've worked hard this month to seek IRB approvals, enroll individuals, collect swabs and sequence these specimens, with the second sequencing run finishing yesterday morning. 9/10
I wanted to show that this could be done and to use science to shed light on something dismissed as "unknowable". 8/10
The lack of genetic sequencing of the White House COVID-19 cluster is just one more example of scientific / technological solutions not being implemented. 7/10
This program never launched and was never really attempted. 6/10
More generally, we could have had a national program to conduct case-based interventions with targeted testing, contact tracing and isolation. I wrote about this as "the Apollo program of our times" over seven months ago on March 18. 5/10
twitter.com/trvrb/status/1…