Another update on #COVID19 circulation in the US. With today's report we're seeing an average of ~172k daily cases reported compared to ~157k a week ago, and we're seeing ~1650 daily deaths reported compared to ~1200 a week ago. 1/10
Although this is still a staggering amount of cases and growing daily, the rate of growth at the US level appears to be (at least temporarily) slowing. Here, I've plotted data from @COVID19Tracking, showing daily cases in the US on a log scale alongside 7-day moving average. 2/10
Throughout October we saw steady exponential growth of the US epidemic (indicated by linear-on-a-log-scale dynamics and shown in the graph as the dashed straight line). Early November outpaced this steady growth but has recently slowed. 3/10
We can get a sense of this with the ratio of cases at a particular day relative to cases a week before. This ratio climbed throughout October indicating an accelerating rate of growth. However, it's been declining so far in November indicating a decelerating rate of growth. 4/10
If we look at estimates of Rt through time via rt.live we can see this trend where Rt of incident infections on Nov 15 is estimated to be lower in 42 states than it was on Nov 1. However, in 38 states, Rt is still estimated to be greater than 1. 5/10
Here, I'm plotting state-level trends to show cases per capita as bubble size and Rt as bubble color. The midwest and the mountain west have generally the highest per capita case loads, but the hardest hit states including the Dakotas have begun to subside slightly. 6/10
Although Rt is generally moving in a good direction, I don't know how rapidly societal measures can bring Rt below 1 across the US. 7/10
Deaths continue to increase reflecting case loads from ~3 weeks previous. The forecast using a 1.8% case fatality rate and a 22-day lag is still fitting the data well and has predicted the current 7-day average of ~1650 daily deaths (though with a slight under-projection). 8/10
This method projects that the huge ongoing case loads will translate to an average of over 2500 deaths per day in just two weeks, even assuming no further increases in circulation. 9/10
Reporting of cases and deaths will likely be down over Thanksgiving weekend. We'll have to wait until the week of the 30th to have a good sense of where things are headed. 10/10
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When I ran these simple lagged case fatality rate (CFR) calculations last week I was surprised and troubled at how big the predicted numbers of deaths in the coming weeks were. Since then #COVID19 daily case counts have continued to rise. 1/10
@alexismadrigal and @whet describe in much better detail the simple logic behind this calculation here: theatlantic.com/science/archiv… and they do a thorough job investigating assumptions of the method. 2/10
Ryan Tibshirani with the Carnegie Mellon Delphi Research Group very helpfully did an independent replication of the method here: htmlpreview.github.io/?https://githu…. 3/10
One small note about these trials. It's often assumed that vaccines are only a proxy for immune response to natural infection. However, there's nothing that prevents vaccines from inducing better, more durable protection than natural infection. 3/8
The #COVID19 epidemic is rapidly growing throughout the US. What happens now? Here I try to make some predictions, but mostly try to explain how I think about the epidemic. 1/14
The US just reported ~170,000 cases in a day. However, there hasn't been a sudden increase in transmission. This is the same exponential growth process going on for weeks now. Rt has ticked up from a US average of ~1 in August to ~1.15. Data from rt.live. 2/14
This increase in Rt can be ascribed to seasonality of the virus. Seasonality of respiratory pathogens is (incredibly) not well understood but is thought to be due to a combination of indoor crowding and increased stability of viral particles in drier winter air. 3/14
A brief update on our work with the sequencing of the White House #COVID19 outbreak. Since posting on Nov 1, groups from all over the US have shared an additional 2798 #SARSCOV2 viral genomes via @gisaid and additional connections have emerged. 1/9
This sequencing has revealed additional viruses circulating in Virginia and collected between Aug and Oct that fall alongside the WH lineage, as well as three viruses from Michigan collected in Oct that are closely related to sequences from the White House outbreak. 2/9
These three viruses from Michigan possess 1 differentiating mutation and the two White House-associated viruses also possess 1 differentiating mutation. A molecular clock analysis places their common ancestor in Aug or Sep. Interactive figure at nextstrain.org/community/blab…. 3/9
After posting about sharply rising #COVID19 cases Friday, there were multiple replies to the effect of "but deaths aren't going up". As should be obvious to most at this point, (reported) deaths lag (reported) cases. This thread investigates. 1/8
There is a lag between when a case is diagnosed and when the individual may succumb to their disease and there is a further lag between date of death and when the death is reported. 2/8
Here, I compare state-level data from @COVID19Tracking for cases and deaths and find that a 22-day lag maximizes state-level correlations. 3/8
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
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