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.
3. The slide above also shows that people have changed their behavior, substantially. Flu rates across the globe have been down. Human behavior is likely contributing to lower transmission rates than we would otherwise see (and may also have caused a rise over the holidays).
4. As a side note, we should stop invoking "low temps". In Europe, the lowest COVID mortality rates have been in Norway and Finland - compare to warmer Spain, or more-open Sweden. This is again about human behavior (crowding indoors, etc), not degrees C.
5. It's tempting to claim herd immunity. In Western countries w roughly similar age structures & good vital registration, SARS-CoV-2 seroprevalence is roughly proportional to cumulative COVID mortality. In August, seroprevalence in the US was under 10%. bit.ly/3q9kp6Q
6. Since that time, cumulative COVID mortality in the US has roughly tripled. Meaning that a reasonable estimate of SARS-CoV-2 seroprevalence in the US is now ~30%. Add in 12 vaccine doses per 100 people, subtract some waning immunity...maybe 35% of the population is immune.
7. Another observation is that cumulative COVID mortality per million is remarkably similar in most of Europe and much of the Americas. Meaning that in these places (which account for most confirmed COVID cases), ~30% population immunity is probably reasonable.
8. So, back to the original question - if we're seeing across-the-board declines in COVID cases, and it's not seasonal, not classical herd immunity, and not sufficiently high vaccination rates, what is it? (Other than lockdowns, which as above are definitely having an effect.)
9. I think the most logical explanation is one proposed initially by @mgmgomes1 and others - namely that we are seeing the effects of population immunity with heterogeneous mixing + strong behavioral effects.
10. Take a(n overly) simple example. Assume 60% of a population has zero respiratory contacts, while the other 40% lives life as normal. If 75% of that high-mixing group has immunity (e.g., 30% population seroprevalence), you could easily see herd effects.
11. It's worth noting that this ~30% level is very similar to what was proposed as a "herd immunity threshold" under these conditions. We just hadn't gotten there - until now.

(I'm leaving "herd immunity" in quotes, because it doesn't mean most people are immune - see below.)
12. If this is true, there are two important reminders.

First, what we are doing to limit viral spread is working - and must be continued (to some extent) in the short term. If we were to rapidly go back to "life as normal", we would see yet another wave of spread.
13. Second, even though we may be seeing "herd" effects, it doesn't mean that most of the population is immune. People are still very susceptible to (dying from) this virus. Around the world, 13,000 people are dying every day - that's one confirmed death every 9 seconds.
In summary, I think the most logical explanation for falling COVID cases is: strong ongoing behavioral limitations + heterogeneous mixing + rising population immunity.

If true, there is reason for long-term optimism...but we can't let our guard down in the short term.

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More from @davidwdowdy

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
16 Oct 20
This may be controversial, but here's a thread on 5 problems I see with the #JohnSnowMemorandum.

I agree with the concept, but am worried about the message it sends.

I sympathize w/ those who have signed, submit this in the spirit of scientific debate.
First, I am no fan of surrender (aka "herd immunity") strategy articulated in #GreatBarringtonDeclaration. "Those...not vulnerable should immediately be allowed to resume life as normal" suggests vulnerable & non-vulnerable can be (a) identified & (b) kept apart. Both fallacies.
Second, full disclosure, I have a personal stake - an immediate family member has been in the hospital for months, with no visitation due to COVID restrictions. My pandemic life is not OK.

But with those caveats, here are my concerns.
Read 11 tweets
28 Sep 20
After sitting in study section last week reviewing proposals for K-series career development awards, thought I'd list my top 5 reasons why such proposals fail. (Not linked to any one submission.)

Junior scientists who might be interested in applying - avoid these pitfalls!!
1. The primary mentor(s) never read the proposal in detail.

Many applications have clear holes in logic that no mentor would let through.

Give your mentors enough time to review your proposal, and steer away from mentors who will not spend the time to offer you comments.
2. The candidate is not quite ready.

Reviewers like to see upward trajectory and (if K22/K99) near-independence.

Be strategic about when you apply. Not a bad idea to put in an initial submission before major papers come out, so you look like a "rising star" on resubmission.
Read 7 tweets

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