Arguably Wrong

  • Overdispersion decreases variant fixation rates

    February 15, 2021 by

    My first post on this blog was about fixation of a new beneficial mutation. I presented Haldane’s original 1927 result showing that with some reasonable assumptions, the likelihood that a new mutation with a small selective advantage fixed in the population was approximately . That derivation assumed a Poisson-distributed number of descendants. We’ll show some… Read more

  • Watching for SARS-CoV2 hypermutability

    February 15, 2021 by

    One of my perennial concerns in this pandemic has been that the SARS-CoV2 virus would evolve a hypermutability phenotype, mutate rapidly, and become much more difficult to control. I’m going to briefly cover 1) why this would be bad 2) why this would be possible and, in a rare bit of optimism 3) why I… Read more

  • Revisiting viral selection

    July 14, 2020 by

    This preproof from Nathan Grubaugh (Yale, PhD in microbiology, 2016), Bill Hanage (Harvard, PhD in epidemiology), and Angela Rasmussen (Columbia, PhD in microbiology, 2009) came across my desk. It’s about the spike protein variant that, as Bette Korber at Los Alamos demonstrated, has become the dominant strain of the coronavirus in the last couple of… Read more

  • Effective Local Response to SARS-CoV-2

    May 11, 2020 by

    I think it’s become fairly apparent that effective federal and even state responses to this pandemic are not going to happen in the short term. I had a discussion over at Greg’s blog where I pointed out that effective local responses are still perfectly possible in most places. So let’s take a brief look about… Read more

  • Likely selection for D614G S

    May 2, 2020 by

    There’s some foolishness going around about this recent preprint from Los Alamos.   They’ve spotted several mutations in collected SARS2 sequences from around the world that look as though they may be under positive selection.  We’re going to look into one in particular, a D614G mutation in the spike protein.  This mutation looks as though it’s increasing… Read more

  • IHME projections are absurdly optimistic

    April 2, 2020 by

    The state-specific projections from IHME have been widely disseminated and used for federal, state, and hospital planning. For example, here’s an interview with one of the UW professors on the project describing how their projections are being used by the feds. They have done yeoman’s work in collecting appropriate data, but their actual model has… Read more

  • Updated Epidemiological Modeling

    March 27, 2020 by

    The previous model I built was a toy model: the simplest possible dynamics that would give you a feel for what’s going on, and parameter selection that was educated guesswork. There was sufficient interest in it, though, that I decided it would be worth building a more sophisticated and hopefully accurate model. State dynamics and… Read more

  • Epidemiological modeling – costs of controls

    March 12, 2020 by

    One point that’s come up a couple of times is the expense of imposing serious infection controls. China probably lost hundreds of billions of dollars on controlling the outbreak in Wuhan. Let’s try to make a guess of how much it would cost us, and use that to figure out what the best path forward… Read more

  • Epidemiological modeling

    March 10, 2020 by

    A basic SIR model for the epidemic. Total population 327 million, with a single initiating infection. 12 day course of disease, initial R0 of 3.5 (as per the stats from China that Steve linked.) Assume 5% of cases are critical, 2% of those critical cases die with ICU care, 5% with general hospital care, and… Read more

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