Youyang Gu Profile picture
11 Dec, 15 tweets, 5 min read
By many accounts, the US will have 100 million vaccine doses by February.

I estimated yesterday that we need ~100 million people to gain immunity via vaccination to reach herd immunity.

So *theoretically*, we can reach herd immunity by March if we vaccinate the right people.
This involves allocating the initial (limited) supply of vaccines based on two main criteria:

1) Each individual receives only one dose instead of two.
2) We prioritize individuals who have not had a prior infection.

This would be temporary, until supply catches up.
There is some evidence, though inconclusive, that even one dose of the vaccine can have reasonable efficacy (potentially >80%).

With the existing approach, my model estimates that by the time the US reaches herd immunity in summer 2021, we would've distributed ~300M doses.

That's an "efficiency" of 100M / 300M = 33%

If we follow the two criteria from above, I believe we can double the efficiency to 70%.
Here's my thread from yesterday that links to all the assumptions I made to model vaccine rollout:



Under the existing approach, I expect the US to reach herd immunity by June/July 2021.
Reaching herd immunity two or three months sooner will have profound benefits throughout society, ranging from fewer cases & deaths to faster economic recovery.

What is the downside? I can't think of many that are on the same scale.
Of course, I'm not necessarily advocating for this approach. More studies would need to be carried out first. But I do feel like this is not being talked about enough.

@michaelmina_lab and @zeynep have also raised this issue (I recommend the thread).

There are those that believe this approach would be a disaster:



The reasoning hinges on a set of untested assumptions. My response would be: why are we not testing these assumptions? The stakes are about as high as you can get.
This approach does not mean every individual can only receive one dose ever.

I imagine individuals can receive a second dose when supply is no longer the bottleneck.

Since I'm not an expert, I'm not too familiar with the downsides of taking a second dose months after the first.
If this approach proves viable, the question would be: would you be willing to hold off on taking a second dose of the vaccine if we can get a much sooner "back to normal"?

My guess is that most people would say "yes".
Former CDC Director @DrTomFrieden and @EricTopol have also advocated for the idea of deferring vaccination for people with prior infection, especially those that are low-risk.

This is fundamentally going to be a trade-off. But we make tradeoffs all the time.

Notable examples:

- Keeping the economy open vs implementing restrictions to curb spread
- Making the general public wait so we can vaccinate high-risk individuals first
Realistically, this approach is unlikely to be executed in the US.

But the world is not just the US. There are still 7+ billion people that need to be vaccinated.

Furthermore, as scientists, we are always trying to figure out how we can do better the next time around.
Anyways, I'm curious to hear people's thoughts. I'm sure I missed a lot of finer details in the proposed approach.

But that shouldn't change the main question, which is: "when it comes to vaccine distribution, is it worth sacrificing effectiveness for perfection?"
I hope to see a bigger push by the public health community to recommend deferring vaccinations for individuals who have had a prior COVID-19 infection.

It needs to be emphasized that reinfection is very, very rare.

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More from @youyanggu

14 Dec
Many people are unaware that the COVID-19 vaccine has significantly more side effects than the flu vaccine. I hope to see more honest discussions regarding this.

Props to @Cat_Ho for her realistic, data-centric reporting of this issue. It's much needed.

sfchronicle.com/health/article… Image
Some notable numbers from the vaccine trial participants after the 2nd dose (age 16-55):

- 16% developed a fever vs 0% for the placebo
- 59%/52% had fatigue/headache vs 23/24% for placebo
- 45% took pain medication vs 13% for placebo

Those age 55+ have a slightly lower rate.
In comparison, roughly 1% of flu shot participants report a fever (16x lower), and ~20% report fatigue/headache (2x lower).

On top of that, COVID-19 vaccine participants have to go through this twice. Though the side effects are milder after dose #1.

Read 12 tweets
10 Dec
I launched a new page that shows the path to US COVID-19 herd immunity: covid19-projections.com/path-to-herd-i…

It's built on the assumption that herd immunity will be achieved via vaccination and natural infection.

Tl;dr version: I estimate a "return to normal" by June/July 2021.
The underlying methodology is a simple model that simultaneously simulates daily vaccinations and new infections through 2022.

By May/June 2021, I estimate vaccinations to exceed 1 million people per day as they become available to the general public.
By mid-summer 2021, I estimate roughly 1/2 of the population have been vaccinated & 1/3 of the population have been infected.

After accounting for overlap/loss of immunity, this amounts to ~60% of the population possessing immunity to the virus, sufficient for herd immunity.
Read 8 tweets
9 Dec
The COVIDhub Ensemble model that combines all the models did not perform well over the past 2 months.

This is due to the fact that the majority of model submissions did not properly forecast this current wave.

Roughly half of all models failed to beat the baseline. ImageImage
This is a known issue with pandemic modeling. For most scenarios, it's beneficial for models to make forecasts close to the status quo (since that's usually true).

This means the they're accurate a majority of the time, but they will miss large spikes such as this current wave.
On the flip side, if a model predicts a large spike and is wrong, it will be heavily penalized by most evaluation metrics. This can happen even if the spike does happen but is a few weeks early/late.

That's the dilemma a lot of modelers face, including myself earlier this year.
Read 7 tweets
3 Dec
I posted the methodology for the new covid19-projections.com nowcasting model:

covid19-projections.com/estimating-tru…

I'm going to do a layman summary here, and hopefully receive some feedback from #epitwitter. Image
I've adjusted the methodology that I posted back in August based on new data and research:



Disclaimer: with that said, this is still a simple heuristic and hence is not perfect. There are more advanced methods (e.g. see covidestim.org).
The basic idea is this: for each day, we try to estimate the ratio of true infections to reported cases that day.

We call this the prevalence ratio, and we model this ratio as a function of the day and positivity rate: Image
Read 16 tweets
1 Dec
I deployed some new features to covid19-projections.com over the past week. Here's a brief summary:

1) Maps over time - you can now view how the pandemic progresses over time for the US, on both a state and county level: covid19-projections.com/maps-infection…
2) Plots of confirmed cases and deaths for every state and county in the US (in addition to estimates of true infections).

Example: covid19-projections.com/infections/us Image
3) Methodology writeup: covid19-projections.com/estimating-tru…. Will write a more detailed Tweet soon.

4) Daily county-level estimates: github.com/youyanggu/covi…. Due to storage constraints I moved it to a separate repository.
Read 5 tweets
24 Nov
Last week, Illinois reported 15,415 cases in a single day, more than Florida ever did in a single day. This is despite Illinois' population being 40% lower.

Many of you probably did not know the dire situation in Illinois. That's because no mainstream media chose to report it.
Here is how the media chose to report Illinois now (left) vs Florida in July (right).

Unfortunately, no national news outlet is covering the situation in Illinois.
No other state has ever averaged 12,000 cases a day for a whole week. Not even Florida (1.7x pop), California (3x pop), and Texas (2.3x pop).

For deaths per capita, Illinois also exceeded the peak deaths in Florida twice, once in May and once again now. So why is this not news?
Read 6 tweets

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