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NathanGrubaugh's profile
Nathan Grubaugh
Nathan Grubaugh
Nathan Grubaugh
@NathanGrubaugh

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Nathan Grubaugh

@NathanGrubaugh

Associate Professor @YaleSPH. Studies 🦟🦠 transmission, evolution, and emergence. PI of @covidCT. Will sequence for 🍺 (and funding).

New Haven, CT
grubaughlab.com
Joined September 2015

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    Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

    12/14 Yale SGTF update We can now track daily TaqPath tests from Yale New Haven Hospital, and of the pos tests with ORF target < 30 CT, report the fraction likely Omicron (SGTF) and Delta (non-SGTF). From tests on Dec 13, *23/214 (9.7%)* had a SGTF Explanation & caveats in 🧵pic.twitter.com/OM6zrNRMOm

    12:12 PM - 14 Dec 2021
    • 39 Retweets
    • 122 Likes
    • ✪ بهـاء جاسـم || Baha Jassim Masked Socialist Cat mitchelltsai DeepVard ClemoMozart Brian Staples Mike Honey 💉💉💉 Betty Scarpino The Premonition Feed
    4 replies 39 retweets 122 likes
      1. New conversation
      2. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Our data represent a fraction of the samples tested by YNHH, and the catchment is primarily New Haven and Fairfield Counties. So they don’t represent all of Connecticut. I’ve heard from others tracking SGTFs elsewhere in the state that they are not seeing a high % yet. (2/11)

        1 reply 2 retweets 19 likes
        Show this thread
      3. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Not all non-SGTFs are Delta and not all SGTFs are Omicron (see BA.2). But of the 184 sequences on GISAID from the US collected after 11/25 with the spike 69/70 del that causes SGTF: 163 (89%) = Omicron (BA.1) 15 (8%) = Delta (most AY.44 & AY.103) 6 (3%) = B.1.637 (3/11)

        2 replies 6 retweets 27 likes
        Show this thread
      4. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        We haven’t sequenced all of our SGTFs, but so far they’ve all turned out to be Omicron. Some probably wont be though. Also, our daily denominators (100-200 +samples w/ CTs <30) are fairly small and individual data points can be noisy. (4/11)

        1 reply 3 retweets 18 likes
        Show this thread
      5. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        I expect that Omicron frequencies are very different by location, and what we are seeing in parts of Connecticut is probably behind the growth in NYC and other big cities, but probably ahead of many other parts of the country not as connected to major travel/urban hubs. (5/11)

        1 reply 5 retweets 24 likes
        Show this thread
      6. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Nathan Grubaugh Retweeted Pavitra Roychoudhury

        Interestingly, our trends are similar to what @pavitrarc reported from @UWVirology - <1% through early December then a rapid increase starting around Dec 6th. (6/11)https://twitter.com/pavitrarc/status/1470447735585214464 …

        Nathan Grubaugh added,

        Pavitra Roychoudhury @pavitrarc
        At @UWVirology, we continue to screen positive specimens using SGTF. Confirmation by sequencing usually lags by a few days, but we expect the majority of these SGTFs to be Omicron. If so, definitely seeing a rapid rise similar to reports from South Africa, UK, Denmark, etc. https://twitter.com/pavitrarc/status/1467310081939177476 … pic.twitter.com/1d7Rheqoe6
        Show this thread
        1 reply 8 retweets 28 likes
        Show this thread
      7. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        The rapid rise in Omicron that we are seeing here should not be surprising considering what we saw in South Africa. (7/11) https://outbreak.info/location-reports?loc=ZAF …pic.twitter.com/S7XFxJBb4E

        3 replies 8 retweets 23 likes
        Show this thread
      8. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Nathan Grubaugh Retweeted Mads Albertsen

        And the trends that we are seeing with the YNHH Connecticut data are similar to the SGTF % from Denmark. It looks like we are about 1 week behind their rates, which seems about right. (8/11)https://twitter.com/MadsAlbertsen85/status/1470766064539783191?s=20 …

        Nathan Grubaugh added,

        Mads Albertsen @MadsAlbertsen85
        #Omicron update from Denmark. 16.7% of cases were Omicron on Dec 11th. It is becoming very difficult to compare raw numbers without accounting for co-founding effects. 1/5 pic.twitter.com/4sgqe5UoXf
        Show this thread
        1 reply 7 retweets 23 likes
        Show this thread
      9. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Keeping the caveats above in mind, I expect SGTFs (mostly Omicron) from the YNHH testing catchment area (mostly New Haven & Fairfield Counties, CT) to surpass 50% within 1-2 weeks. That’s *if* the current growth rate at 0.26/day (0.1-0.3) remains the same. (9/11)pic.twitter.com/hA57dB9Scd

        2 replies 18 retweets 49 likes
        Show this thread
      10. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        Nathan Grubaugh Retweeted Richard Neher

        The rapid doubling time of ~3.8 days estimated from the YNHH SGTF data above is consistent with early estimates from Europe, but this may decrease as explained by @richardneher. (10/11)https://twitter.com/richardneher/status/1470484564942462997 …

        Nathan Grubaugh added,

        Richard Neher @richardneher
        Many countries have reported very rapid growth of Omicron with doubling times of 2-4 days and an almost perfect exponential increase. Now we see discussions of decreasing growth rates. This is expected for several reasons and doesn't mean early growth was overestimated. [1/3]
        Show this thread
        2 replies 3 retweets 20 likes
        Show this thread
      11. Nathan Grubaugh‏ @NathanGrubaugh 14 Dec 2021

        I am hoping that by presenting these early findings that individuals and public health agencies will start to take more precautions. Lets not put more stress on our already over-stressed healthcare system when this should be a time to enjoy our friends and family. (11/11)

        8 replies 12 retweets 49 likes
        Show this thread
      12. End of conversation

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