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Trevor Bedford Profile picture
@trvrb
Nov 7, 2020 • 10 tweets • 4 min read • Read on X
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
Please consider this somewhat of a follow up to the thread two weeks ago on circulation patterns across states. 2/10
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 Image
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 Image
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
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 Image
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 Image
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
I've written previously about the dynamic relationship between COVID-19 cases, deaths and societal response () as well as the effects of relatively small levels of population immunity in the presence of mitigation (). 9/10
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

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More from @trvrb

Trevor Bedford Profile picture
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
Trevor Bedford Profile picture
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
Trevor Bedford Profile picture
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
Trevor Bedford Profile picture
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
Trevor Bedford Profile picture
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
Trevor Bedford Profile picture
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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