Covid-19 Came to the U.S. later than we thought

Research into the spread of Covid-19 continues, with an important new preprint by Michael Woroby et al up today (tl;dr see the writeup in Stat News).  The standard narrative about the arrival of Covid-19 in the U.S. is that a patient arrived in Seattle, WA from Wuhan on January 15^th.  He felt ill, and aware of CDC messaging about a new virus circulating in Hubei, sought medical help.  On Jan. 19, he became the first confirmed case of Covid in the U.S. Then, a few weeks later on Feb. 24, another patient turned up with what appeared to be community spread.  Containment had failed.  Per Woroby:

“On February 29th, 2020, a SARS-CoV-2 genome was reported from a second Washington State patient, ‘WA2’, whose virus had been sampled on February 24th as part of a community surveillance study of respiratory viruses. The report’s authors calculated a high probability that WA2 was a direct descendent of WA1 [the first patient, from January], coming to the surprising conclusion that there had by that point already been six weeks of cryptic circulation of the virus in Washington State. The finding, described in a lengthy Twitter thread on February 29th, fundamentally altered the picture of the SARS-CoV-2 situation in the US, and seemed to show how the power of genomic epidemiology could be harnessed to uncover hidden epidemic dynamics and inform policy making in real time” (3, internal citations omitted). 

Then there was more genetic sequencing, and it turned up a strange anomaly: the cases that appeared to stem from WA2 had mutated from WA1 in two places, and there was neither evidence of a transitional virus strain between them or of other infections in Washington whose genetic sequencing matched WA1.  Woroby et al then ran a computer simulation – 1000 times! – of the epidemic, seeding it with WA1.  The result was a surprise: “when we seeded the Washington outbreak simulations with WA1 on January 15th, 2020, we failed to observe a single simulated epidemic that has the characteristics of the real phylogeny” (7).  In other words, the narrative about the early spread in Washington is almost certainly wrong.  Patient WA1 was not the source, and the virus was not spreading covertly for weeks before emerging again in WA2.  Rather, the spread around WA1 was contained, and WA2 represented a new infection, and was either the source of the actual epidemic, or near it.  Specifically, the virus arrived a second time from Hubei, around Feb. 13 (95% probability between 2/7 and 2/19) (9).

This means that the virus arrived a month later than previously expected.  They detail some of the implications:

“This timing is approximately four weeks later than had been proposed, implying: (a) archived ‘self-swab’ samples may have retrospectively detected the virus within as little as a week of its arrival, (b) the Washington State outbreak may have been smaller than estimated based on the earlier inferences, and (c) the individual who introduced the founding virus likely arrived in the US after the initiation of the ‘Suspension of Entry’ of non-US residents from China on February 2nd, 2020 but during the period when an estimated 40,000 US residents were repatriated from China, with screening described as cursory or lax. These passengers were directed to a short list of airports including Los Angeles, San Francisco, New York, Chicago, Newark, Detroit and Seattle. So, although our reconstructions incorporating unsampled lineages do not account for travel restrictions, the remaining influx likely provided ample opportunity for a second introduction to Washington State.  It is also possible that the virus entered via nearby Vancouver, British Columbia, which is closely linked to both China and Washington State” (9, internal citations omitted).

So the one thing Trump says he did almost provably did nothing to stop the spread.  It was lazy and capricious and probably racist.  Also, the excuse that Covid was already here and so how could we have prevented it from spreading… is horse shit.

Woroby et al do similar work on the European spread, concluding that it did not go from Bavaria to Italy, but was likely introduced independently into Italy from Hubei (arriving in New York from Italy around Feb. 20).  This matters because it provides evidence that the European strains running rampant in New York are not a more transmissible mutation of the one in China.

The discussion section is genuinely depressing.  It emphasizes that early containment efforts in Washington (around WA1) and Bavaria were successful.  Further:

“By delaying COVID-19 outbreaks by even a few weeks in the US and Europe, the public health response to the WA1 case in Washington State, and a particularly impressive response in Germany to a substantial outbreak, bought crucial time for their own cities, as well as other countries and cities, to prepare for the virus when it finally did arrive” (12).

The study does not answer all the questions one might have on the early origins of the pandemic.  For example, French researchers identified a case of probable community transmission from a flu sample taken in late December, so there is clearly more to be said about the European case at least.

These details cannot obscure that today saw the 100,000^th U.S. death from Covid-19.  A study done at Columbia a week ago concluded that if the U.S. had locked down two weeks earlier, over half of those lives could have been saved.  There is no excuse for the endless dithering and malignant incompetence that cost so many Americans their lives so far.  None.