Trevor Bedford Profile picture
Nov 11, 2020 8 tweets 3 min read Read on X
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 Image
This can be seen across states where the solid lines show reported cases by date of report and dashed lines show reported deaths lagged by 22 days. You can see some detailed correspondences, especially in states experiencing the summer surge like Florida, Arizona and Texas. 4/8 Image
Given this 22-day lag we can compute a lag-adjusted case fatality rate (CFR) by dividing reported deaths at day t by reported cases at day t - 22. This declines from ~6% in April, averaging 1.8% after August. 5/8 Image
Looking backwards, this lag-adjusted CFR means that 991 deaths in the US today (with 7-day smoothing) should be compared against 57,206 cases reported Oct 19 (with 7-day smoothing). In this case, 991/57206 = 1.7% is consistent with this overall lag-adjusted CFR. 6/8
Or looking forwards, this lag-adjusted CFR suggests that 118,976 reported cases today (with 7-day smoothing) will translate to ~2150 deaths reported in 22 days on Dec 2. 7/8
I expect the US to be reporting over 2000 deaths per day in 3 weeks time. Importantly, this doesn't assume any further increases in circulation and is essentially "baked into" currently reported cases and represents conditions that take time to resolve and to be reported. 8/8

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More from @trvrb

Dec 5, 2022
Currently, the US is reporting about 54k daily cases of COVID-19 (16 per 100k per capita) and the UK is reporting about 4k (6 per 100k). This seems comfortingly low compared to even this summer's BA.5 wave and let alone last winter's BA.1 wave. Figure from @OurWorldInData. 1/16
However, at this point, nearly all infections will be in individuals with prior immunity from vaccination or infection and this combined with a roll back in testing makes it unclear how to interpret current case counts compared to previous time periods. 2/16
We're interested in the case detection rate or the ratio of underlying new infections compared to reported cases. Throughout much of 2020 and 2021, I had a working estimate of 1 infection in ~3.5 getting reported as a case. 3/16
Read 16 tweets
Aug 16, 2022
Largely through partial immune escape, lineage BA.5 viruses resulted in sizable epidemics throughout much of the world. However, in most countries these epidemics are now beginning to wind down. What do we expect after BA.5? 1/10
Lineage BA.2.75 (aka 'Centaurus') has been high on watch lists due to sustained increase in frequency in India combined with the presence of multiple mutations to spike protein. We now have enough sampled BA.2.75 viruses from outside India to make some initial conclusions. 2/10
If we look at frequency data we see sustained logistic growth of BA.2.75 in India, Japan, Singapore and the US. Critically, in India it is clearly displacing BA.5. 3/10
Read 10 tweets
Aug 3, 2022
Based on the experience in winter 2020/2021, seasonal influence on SARS-CoV-2 transmission is quite clear, but much of the Northern Hemisphere is currently experiencing large summer epidemics driven the spread of evolved BA.5 viruses. 1/11
It's necessarily fraught to try to make predictions of seasonal circulation patterns going forwards, but we can gain some intuition from simple epidemiological models. 2/11
In particular, we can use an SIRS system in which individuals go from Susceptible to Infected to Recovered, and then return to the Susceptible class due to immune waning / antigenic drift of the virus. 3/11
Read 12 tweets
Jul 20, 2022
There seems to be a worry that telling people we've exited the "pandemic phase" will lead to further reduced precautions. As always however, I think it's best not to conduct messaging for intended behavioral effect and just try to make scientifically accurate statements. 1/5
Given vaccination and infection, the US and global population now has widespread immunity to SARS-CoV-2 and deaths per-infection are about 10 times lower than they were pre-immunity in 2020 with a ballpark IFR of 0.05% (though this will vary by immunity and age demographics). 2/5
You can see this reduction in mortality rate in looking at projections of deaths from lagged-cases keyed to early case fatality rate. 3/5
Read 5 tweets
Jun 27, 2022
The @US_FDA VRBPAC committee will be meeting tomorrow to discuss variant-specific COVID-19 vaccines (fda.gov/advisory-commi…). Based on present observations, I would argue that the most important metric to optimize are titers against BA.4/BA.5 viruses. 1/10
We've seen repeated replacement of SARS-CoV-2 variants during 2022, first of Delta by Omicron BA.1 and then by sub-lineages of Omicron, with BA.2 replacing BA.1 and now with BA.4/BA.5 replacing BA.2. 2/10
Viruses have been evolving to be higher fitness through both increases in intrinsic transmissibility (seen in BA.2 vs BA.1) as well as escape from existing population immunity (seen in Omicron vs Delta as well as BA.4/BA.5 vs BA.2). 3/10
Read 10 tweets
Jun 3, 2022
Global monkeypox confirmed and suspected cases compiled by @globaldothealth show initial rapid increase as case-based surveillance comes online, followed by slower continued growth. 1/10
This is data from github.com/globaldothealt… and has had a 7-day smoothing applied and all y-axes are shown on a log scale. 2/10
If we focus on the last 11 days, we can see steady exponential growth in global cases with a ~7.7 day doubling. 3/10
Read 11 tweets

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