Sam Scarpino @svscarpino
Scientist. Director @Experiential_AI, Faculty @Northeastern, @sfiscience, @uvmcomplexity; Cofounder @globaldothealth. Now @ https://t.co/aAQzm0G0mf scarpino.github.io Boston, MA Joined February 2014-
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Important update on metadata of H5N1 in cattle (and back to birds): Thanks to the extraordinary detective skills of @flodebarre, we are pleased to be able to share this table containing locations and dates for several H5N1 cases in cattle and birds: github.com/andersen-lab/a…
I learned from @svscarpino today that budget for weather surveillance and forecasting is 10 to a 100 fold higher than health surveillance. + super interesting stuff about permutation entropy and crowding as a kind of epidemic threshold.
Reminder: If you would like to analyze bovine H5N1 influenza A virus consensus sequences from SRA data shared by @USDA_APHIS , @xrayfoo has assembled them and we have shared them here. Please repost (if willing). github.com/andersen-lab/a…
OK, I think we're close to decisive evidence that US bovine H5N1 had a single origin from birds, and that when related viruses from birds *have* been found, they are jumps from cattle back into birds. Grackles, blackbirds, chickens all show mammalian adaptation like PB2 M631L.
So, *preliminary* molecular clock analyses indicate that the time of the most recent common ancestor (TMRCA) of the US cattle flu clade was late December. TMRCA of that clade and the closest relatives in birds, mid-December. If single intro, likely between those rough dates.
The point of pasteurization is to inactivate pathogens. This is *exactly* what we'd expect if cows are infected w/ #H5N1, but milk was safe after treatment. We need more tests, but, given the long history of safety after pasteurization, sowing panic isn't good public health.
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@svscarpino @jamesian @MOUGK @jkbren Your timeline is wonderful and will be a valuable resource, so I wanted to help boost it. #AvianInfluenza #BirdFlu
Fellow #science #journalists here is resource on many details of #H5N1 unfolding epidemic Thanks to @svscarpino +@MOUGK + @jkbren #IDtwitter
@jamesian @svscarpino @MOUGK @jkbren And as promised, @svscarpino, I linked to your terrific timeline in today's post: forbes.com/sites/judyston…
The virus-laden milk appears safe, but the prevalence of the virus in milk indicates widespread cow infections and thus concerning level of opportunity for mutation.
FDA announces no infectious #H5N1 was found in PCR positive milk. They used the “gold standard” egg inoculation tests that many have been waiting for. Together with NIAID grantee studies and past publications, it’s pretty conclusive the milk is safe. fda.gov/food/alerts-ad…
@jkbren @svscarpino @breakfast_dogs @MOUGK Really? You're able to make this amazing timeline with Google slides??? 👏🎉 How do you keep everything so well aligned?
@svscarpino @breakfast_dogs @MOUGK and… google slides 😂
Printed this ongoing timeline for kid educational purposes. Probably won't stick it up like a conspiracy wall..
@svscarpino @jkbren @MOUGK this is brilliant, thank you so much for building and making it available
Good news, but expected.
FDA announces no infectious #H5N1 was found in PCR positive milk. They used the “gold standard” egg inoculation tests that many have been waiting for. Together with NIAID grantee studies and past publications, it’s pretty conclusive the milk is safe. fda.gov/food/alerts-ad…
@svscarpino Noted, thanks! I see the genome reference from 4/16. Perhaps give them their own color if reports continue to come in?
@svscarpino Any way to know sample volumes/replicate numbers tested from PCR positive samples?
While it's highly likely that pasteurization inactivates H5N1 in milk (no reason to think otherwise), it would be helpful to see a preprint on top of a press release. Lots of people have lost trust in institutions in the last several years, so words alone may not suffice.
FDA announces no infectious #H5N1 was found in PCR positive milk. They used the “gold standard” egg inoculation tests that many have been waiting for. Together with NIAID grantee studies and past publications, it’s pretty conclusive the milk is safe. fda.gov/food/alerts-ad…
Very Important Thread by @svscarpino on Thread Reader App threadreaderapp.com/thread/1783926… Please share, retweet, bookmark, and donate to their Git hub if you can. #H5N1 #H5N1Resource @DebHolloway @sasswashere @MeetJess @noxygen
I was just talking about how things are progressing faster than I can keep up. This is great.
Glad to see these independent efforts...
@svscarpino @jkbren @MOUGK thank you so much for this
@svscarpino @jkbren @MOUGK Thanks to all the team involved
@svscarpino @beansprouts_mom @jkbren @MOUGK Fantastic work all, cheers!