One term I worry that we (as a public health community) have mis-messaged during the pandemic:

"herd immunity threshold"

A non-technical thread on why this is not "% of the population that needs to be vaccinated for us to return to life as normal while eradicating COVID-19"...
Disclaimer to the experts: This is for a non-expert audience.

Let's start with the virus that's currently circulating, and estimate roughly that - with no vaccine, no immunity, and "life as normal" - this person would infect ~5 other people before recovering (or dying).
Next, let's take a situation similar to the USA. Out of these 5 possible people infected, 2 might be vaccinated; 1 out of the remaining 3 might be someone who's already have had COVID; and 1 of the remaining 2 might be prevented by current behaviors (masks, distancing, etc).
This would lead to, on average, each person with COVID-19 infecting 1 other person. Meaning the epidemic will be *stable* (and decline very slowly as more people get infected).

This is the "herd immunity threshold". Note that case counts are falling ever-so-slightly. Not zero.
A key thing to note - while we may be at this stable level even now in places like the USA, case counts can easily rise again ("above the herd immunity threshold") if we relax behaviors such as distancing & mask-wearing too quickly.
The same thing can (and will) happen gradually over time as the virus mutates to become more infectious (for example, if the average person with COVID-19 would infect 6 people rather than 5, in the absence of any immunity and "life as normal").
On the flip side, if we vaccinate people faster, we reduce the number of cases (and deaths) faster.

It's not about getting to a threshold where the epidemic is stable, it's about how fast we can get the epidemic under control - meaning going *beyond* the herd immunity threshold.
Once again - we should be focusing on the *number of cases* (and how fast that number is falling), not on whether we are above or below a specific threshold.

Asking "have we reached the herd immunity threshold" is similar to asking "are cases going up or down right now"?
It's also important to remember that we are talking about "the average contacts of people with COVID-19 today," not "the average person".

Even though 40% of the population might be vaccinated, for example, this doesn't mean that 40% of current COVID-19 contacts are vaccinated.
As a result, simple calculations of "XX% of people must be vaccinated to reach herd immunity" may be over-optimistic (e.g., if the average COVID-19 contact is less likely to be vaccinated or distancing) or pessimistic (if they are more likely to have been infected already).
Take-home messages:
1) Focus on the case count, not on reaching a threshold.
2) The more people who are vaccinated, the better.
3) Activities like wearing masks & minimizing large indoor gatherings still have an important effect.
4) Progress is always slow, but it is being made!

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More from @davidwdowdy

7 Mar
The B117 variant is now the dominant strain of SARS-CoV-2 in the UK, Ireland, Israel, Denmark. Likely also Portugal, Belgium, France, Italy, Norway.

Yet for the most part, these are not the countries where COVID-10 cases are rising (see below). What gives?
One explanation is that B117's transmission is being offset by restrictions, population immunity, etc. And that those countries w high B117 (UK, Ireland, Portugal) have locked down most. There is likely some truth to this - but not too much correlation w stringency index (below).
But it's also worth considering B117 and non-B117 COVID as separate epidemics. For example, look at Danish data below - it's tempting to think of B117 (red) as "replacing" non-B117 (grey). But that's not what's actually happening...
Read 8 tweets
9 Feb
In the past week, COVID cases have fallen in the majority of countries across the globe (see below for weekly change). But not all countries are locked down.

A thread on what might be - and what probably isn't - happening.
1. Lockdowns/restrictions have almost certainly had a major effect in countries that instituted them. Look at the peaked curves in the UK and South Africa - natural processes are generally smoother. But it's notable that current declines are even sharper than w the 1st lockdowns.
2. If this were just due to seasonality, one might expect similar behavior as with flu. But historically, flu rates in the US generally do not start to fall until March (see non-red lines below). Seasons likely contributed to the Oct rise, but likely not the Jan decline.
Read 15 tweets
31 Jan
Many are interpreting data from Denmark as strong evidence of increased transmissibility of B117.

With the caveat that I believe this prevailing hypothesis to be credible, if not likely...

A thread on how Danish data can be explained w/o invoking increase in transmissibility.
First, Denmark should be applauded for their rigorous genomic surveillance. Other countries should follow their example!

The data, in brief, show an increase in the percentage of sequenced cases that are B117, from 0.2% in early December to (prelim) 12% in mid-Jan.
This was, however, occurring in the context of a dramatic fall in cases throughout the country, likely reflecting the effects of a country-wide lockdown. Image
Read 15 tweets
27 Jan
A counterpoint to the alarm bells that are sounding over novel SARS-CoV-2 variants.

Is it possible that we are misinterpreting differences in human behavior as differences in the biological fitness of viral variants?

A thread to explain this hypothesis...
1. Infectious disease transmission is heterogeneous (overdispersed), largely due to human behavior.

Large "superspreading events", differences in behavior, and/or people who have many contacts generate an outsized number of transmission events.
2. This makes it easy for viral variants - even those with no inherent transmission advantage - to take over a population.

Imagine an infected person attending a large indoor gathering with hundreds of people. That viral strain will expand - because of behavior, not biology.
Read 19 tweets
22 Dec 20
What do trainees want from their mentors?

Turns out, it's not so different from what people want in any other relationship.

A top 10 list based on some recent discussions (and not-so-occasional missteps on my part):
1. Time
Time is everyone's most valuable resource - there's nothing that conveys support to a trainee more than meeting regularly, face-to-face.

Arguably the most important thing a mentor can do to support a trainee is maintain a weekly check-in, even if only for 30 minutes.
2. Attention
Trainees want a mentor who will engage with them, not one who is so "important" to have many other engagements.

Spend face-to-face meetings talking with your trainees, not checking email, responding to texts, etc. (Admittedly not my strength in the zoom era...)
Read 11 tweets
18 Oct 20
After some conversations with a trainee, I've recognized at least 7 "academic phenotypes" based on underlying core professional goals.

A thread, aimed primarily at junior researchers learning to navigate the academic world.

Take-home: know your phenotype, know your superiors'.
Phenotype -> core goal:

Politician -> power
Performer -> fame/pubs
Pragmatist -> things that work
Inquirer -> knowledge/insight
Idealist -> a better world
Epicurean -> pleasure/time off
Humanist -> relationship

We are all each of these to some extent. But more some than others.
Step 1: Recognize your (actual & ideal) phenotype by asking yourself which goals you would sacrifice for others.

Ex.: would you delay promotion to achieve an ideal?

Be honest w yourself about which phenotypes you (a) are, (b) want to be.

(PS All phenotypes prioritize family.)
Read 9 tweets

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