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Natalie E. Dean, PhD Profile picture
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17 Feb, 7 tweets, 4 min read
THINK LIKE AN EPIDEMIOLOGIST: Lately I have been asked why we are seeing a dramatic turnaround in cases in the US. Is it vaccines? Herd immunity? An artifact due to a drop in testing? Behavior change? Weather?? A few tweets about how I step through this question. 1/6 Image
To start, I look to see whether the drop is an artifact. While testing has dropped somewhat, it's not enough to explain the rapid drop in cases. A drop in testing would also not explain the drop in hospitalizations that is consistent across regions. 2/6
covidtracking.com/data/charts ImageImage
I then consider the similarity of the drop across locations, looking by subregion and by state. The similar patterns seen are relevant because different places have different vaccination coverage, levels of acquired immunity, and weather. Why the turnaround at a similar time? 3/6 ImageImage
I also note the dramatic speed of the drop. Weather has not changed much over the last few weeks. Vaccination coverage is quickly increasing (and is targeted!), but we have not achieved broad coverage yet. And the turnaround started a few weeks ago. 4/6
covid.cdc.gov/covid-data-tra… Image
It reminds me a bit of the quick summer turnaround in Florida. The timing of the slowdown was similar across areas in Florida, which to me signaled that herd immunity was not the major driver. That plus the resurgence we have seen in FL this winter. 5/6
covid.cdc.gov/covid-data-tra… Image
Taken together, I think the most likely explanation is a mix of policy and individual-level behavior change, as people react to what they see in the news and in their communities, but helped along by acquired immunity due to widespread infection plus targeted vaccination. 6/6
Addendum. A few folks have mentioned the holidays, which I didn't touch upon in the thread, but are relevant as they temporarily expanded our social networks. For what it's worth, the thread is just as much about the thought process as the answers. Add your own insights below!

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More from @nataliexdean

Natalie E. Dean, PhD Profile picture
15 Feb
How do we measure how well the flu vaccine works every year? We use an observational study called the "test negative design." A few tweets on how it works, and why it will be a big part of ongoing COVID-19 vaccine evaluation. 1/8

Figure source: Fukushima et al. (2017) Vaccine
In the test negative design, individuals with disease symptoms seek healthcare and testing. If they test positive, they are TEST POSITIVE CASES. If they test negative (and their symptoms are caused by something else), they are TEST NEGATIVE CONTROLS. 2/8
We can then look back and see how many of the test positive cases were vaccinated, and how many of the test negative controls were unvaccinated. Where the vaccine works well, there won't be many vaccinated people testing positive. 3/8
Read 8 tweets
Natalie E. Dean, PhD Profile picture
8 Feb
Warning - some in-the-weeds tweets about vaccine efficacy trials, new strains, and decision making under uncertainty. I offer more questions than answers, but hopefully it can generate some discussion...
1/6
For COVID vaccine studies, we can imagine two goals:
(1) We aim to measure efficacy precisely (minimize uncertainty, regardless of the true efficacy), or
(2) We simplify our goal and try to measure if the vaccine is doing well enough - is efficacy above our success threshold? 2/6
This is relevant for discussions about how well vaccines are performing against different variants. For those who are already vaccinated, we want to know how well the vaccine works against a new strain. What is the efficacy, even if it is lower? This is like the first goal. 3/6
Read 6 tweets
Natalie E. Dean, PhD Profile picture
3 Feb
Oxford/AZ reports overall reduction in PCR positivity of 54.1%, but only 2% "vaccine efficacy against asymptomatic infection."

Confused?

Allow me to explain with crudely drawn pictures why the overall findings are still quite positive. 1/8
Let's start by imagining the base case (no vaccine). SARS-CoV-2 infections fall into a range of categories: severe, moderate, mild, or asymptomatic.
(Categories not perfectly to scale for all of this, don't @ me). 2/8
Vaccines protect against disease in two major ways.
- They can prevent infection entirely.
- Or they may not prevent infection, but they prep your immune system so that you don't develop symptoms. Usually it is some combination of the two. 3/8
Read 9 tweets
Natalie E. Dean, PhD Profile picture
29 Jan
With Novavax results, a welcome addition of another efficacious vaccine. The more, the merrier. Though the observed lower efficacy in South Africa is discouraging (and exactly how much lower is hard to tell given uncertainty), I’m glad we have these data in hand. 1/5
Well-conducted placebo controlled trials can give us the clearest read on how these vaccines are working against different variants. It was fortuitous to have these two trials in the UK and South Africa that we can compare in this way. We want to know what we’re dealing with. 2/5
Fortunately the vaccine is working well against the UK variant. But as we see in South Africa (and in laboratory studies with other vaccines), we cannot assume that vaccines are equally effective against all variants. We will need to continually monitor their effectiveness. 3/5
Read 5 tweets
Natalie E. Dean, PhD Profile picture
13 Jan
A few tweets on a topic that keeps coming up in discussion. There are many different types of vaccine efficacy - efficacy against infection, against transmission, against disease, and against severe disease - and these can vary for a single vaccine. How are they related? 1/5
Efficacy against infection will by necessity be lowest, because if a vaccine protects you from infection, it also protects you from transmitting to others and getting symptoms. We have a little data on this from Moderna and Oxford, but will get more from antibody testing. 2/5
Even if a vaccine does not prevent infection, it could make you less infectious by reducing viral load, reducing duration of infectiousness, or by preventing symptoms like coughing/sneezing. This effect is hard to measure without contact tracing or cluster randomized studies. 3/5
Read 5 tweets
Natalie E. Dean, PhD Profile picture
29 Dec 20
Our group's household secondary attack rate meta-analysis has gained traction, but not for the reasons I'd hoped for. We did not conclude "no asymptomatic or pre-symptomatic spread" of SARS-CoV-2. A short explanation of what we did observe. 1/7
jamanetwork.com/journals/jaman…
Using only the household studies included in our main analysis, we conducted a sub-analysis breaking out index cases designated as symptomatic versus asymptomatic/pre-symptomatic. We observe lower transmission from this latter group, though there was much less data. 2/7
Since we are relying upon other studies in the literature, we were unable to separate out fully asymptomatic index cases (never develop symptoms) from pre-symptomatic index cases. But others have tackled this problem directly. Their conclusions below. 3/7
medrxiv.org/content/10.110…
Read 7 tweets

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