March 12, 2020
The feeling is different since my last post. Before yesterday, the most challenging aspects of the local epidemic were the innumerable pieces of uncertainty. I have been fielding a lot of very reasonable questions from friends and family. I am always hoping for soft balls: “can my 85 year-old dad with COPD go on a cruise? (No)” or “Can I still pet my dog? (Yes)” but never seem to get them. The reality was that most questions fell in a grey zone. I had no idea what to tell healthy people when they asked me if it is ok to eat out or to plan a family trip in mid-May. These are ultimately questions about personal risk which have no numerical estimate. I can provide an answer that sounds confident, but this would just be dishonest. It was a bit distressing.
In my personal life, these same questions were difficult. I ruminated for 20 minutes about whether to send our son to school (he had the sniffles). Last week, I cancelled a trip east to present exciting new data in Boston at CROI and regretted this decision immediately after I made it. Soccer practice for the kids? I had no idea what to do.
Uncertainty is no longer the issue. CROI was cancelled and that seems like a year ago: 70 people were infected at a different conference in Boston that same week. Famous people are getting infected. It is now abundantly clear that the next few weeks are going to be historically challenging in our city, and I suspect in many other places in the US. So look out for each other, protect the vulnerable and be safe. If you are on the fence about attending a crowded event, or traveling, just don’t do it. ---------------------------------
There is a simple analogy to captures some of the theory underlying outbreak epidemiology. Think of forest fires (the other apocalyptic scourge on the West coast). There are 3 components that matter.
The first I would call sparks: these are the rare events which initiate but do not maintain the fire. Big fires produce more sparks which can float in the air and seed new fires elsewhere. This epidemic started in Wuhan which sent off lots of sparks to other places, mostly contingent upon travel patterns of airplanes and trains.
The second component is conditions on the ground when the spark ignites a small fire. This is R0, or the basic reproductive number. If the spark hits in a moist environment where a fire cannot take, R0<1 and the fire burns out spontaneously. If it is dry and susceptible, then R0>1 and the fire takes off. If R0~1, then a smoldering pattern may emerge. The higher the R0 the faster the fire and the greater % of land that gets burned. (The other determinant of speed in an epidemic is generation time or time from infected to infecting, which is ~5 days for SARSCoV2.) R0 depends on lots of things like population density, mode of transmission, the given pathogen, and contact networks. In the case of SARS-CoV-2, public health readiness (ability to quickly identify cases and contacts, test broadly and quarantine) is a key determinant of R0.
The third component is the fire department: once you have a fire that is out of control, how quickly can you get the effect reproductive number (Reff) which is a real time measure of R0 to <1. In our current situation in Western Washington, the fire is out of control and contact tracing is no longer a sustainable option. Our only option to get Reff<1 at this point is mass social distancing (prolonged school closures, work from home etc…). In the future, a widely implemented vaccine could theoretically achieve this as well. If an outbreak is left to its own devices, then eventually Reff will go < 1 based on herd immunity.
With this framework, the different trajectories of outbreaks in different countries can be understood somewhat. Please keep in mind that these are vast overgeneralizations and not meant as judgmental towards a given country, but rather as a way to understand why things may be so different in some country or region versus others:
Wuhan: 1) one very unfortunate spark, 2) complete lack of readiness to immediately contain the outbreak augmented by lies and the Chernobyl effect, 3) extraordinary fire department
Taiwan / Hong Kong / secondary cities in China / Singapore: 1) hundreds of sparks, 2) conditions for a widespread fire limited based on aggressive contact tracing and quarantine, 3) very effective fire department so far for small fires
Korea: 1) hundreds of sparks, 2) conditions for a widespread fire existed within several pockets of society, 3) extraordinary fire department effort so far leading to a tangible deceleration of the epidemic: https://twitter.com/HannahNamMD/status/1237618148125409281
Iran / Italy: 1) few sparks but only one is required unfortunately, 2) complete lack of readiness to immediately contain the outbreak, 3) fire department arrival way too late
US: 1) moderate number of sparks, 2) lack of readiness to immediately contain the outbreak (related to lack of tests & CDC’s initial policy to not test widely), 3) fire department -> too soon to tell but promising.
If one uses this analogy to judge Trump’s policy of stopping incoming flights from Europe, then the absurdity is obvious. Stopping an inflow of sparks into an already raging fire will achieve nothing and have obvious harmful secondary effects.
The executive branch clearly ignored expert opinion in this case which is a disgrace. This continues a string of otherworldly incompetence that would never be accepted in most workplaces: many lives that will be lost because of this: https://www.theatlantic.com/…/trump-ensuring-worst…/607867/…
Some reading in no particular order:
The situation in Italy is horrifying. Physicians are being forced to make decisions about ventilators based on actuarial data and not clinical need. This is unimaginable https://www.newsweek.com/young-unafraid-coronavirus-pandemi…
Iran looks to be in even worse shape. Of everything I have read, this article stunned me the most: https://www.theatlantic.com/…/irans-coronavirus-pro…/607663/
The concept of flatten the curve is widely disseminated now, which is a good thing. Explained here: https://www.statnews.com/…/03/11/flattening-curve-coronavi…/
I can’t help but notice that the tropics have been spared from the worst so far. Africa, Indonesia, the Philippines, Vietnam, India & others. There have been a couple of pre-print articles showing no apparent dependency on viral spread within China based on humidity or temperature. However, this paper is interesting & has pretty figures showing a band of infection at a fairly narrow latitude in Figs 1 & 2. Please understand that this is not a proper epi paper, just descriptive data. They do not consider the myriad variables other than climate that might limit spread to these countries. I also would not be surprised if major outbreaks were to take hold eventually in some or many of these countries. That said, it will be interesting and critically important to see whether this trend holds: https://poseidon01.ssrn.com/delivery.php…
A cool paper from 2008 showing how people mix according to age structure in Europe. Figure 3 shows something obvious but important, that kids tend to mix other kids and parents. The elderly mix with people their own age but have less contact with other ages. The high mixing among children puts them at highest risk of contracting an infection (Figure 4): they then seed other age cohorts explains why keeping kids separated is a necessary social distancing measure: https://journals.plos.org/plosmedicine/article…
Mode of spread. I am perplexed by this outbreak in Boston at a Biogen conference. 70 cases at a conference sounds less like respiratory spread than another mode (water supply, fecal / oral). Key details are lacking but this outbreak needs to be studied in depth to understand whether super-spreader events are possible with this virus and if so, how: https://www.cnn.com/…/coronavirus-massachusetts-…/index.html
A surreal story about early testing for SARS-CoV-2 in Seattle. Must read: https://www.nytimes.com/…/…/coronavirus-testing-delays.html…
Very thought provoking article on whether & how SARS-CoV-2 will change our politics: https://www.nytimes.com/…/opini…/coronavirus-socialism.html…
Drive through testing for UW / FHCRC personnel. Proud of my colleagues at UW / FHCRC who made this happen. I wish it were available to the whole population but this is a great start: https://www.seattletimes.com/…/uw-medicine-and-seattle-ca…/…
And on the topic of humans being idiots. I never liked smurfs. Nice color. Cool name. Bad cartoon: https://www.washingtonpost.com/…/11/smurf-coronavirus-fra…/…