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Sam Scarpino Profile picture
Sam Scarpino
@svscarpino
Scientist. Director @Experiential_AI, Faculty @Northeastern, @sfiscience, @uvmcomplexity; Cofounder @globaldothealth. Now @ https://t.co/aAQzm0G0mf
3 subscribers
Oct 15 • 9 tweets • 4 min read
1/ We're seeing a concerning rise in H5 wastewater positivity in Turlock CA.

Unlike previous H5 signals, @WastewaterSCAN is showing an exponential rise in H5 (and flu A) concentration that has persisted for almost a month! Figure shows an exponential rise in flu A concentration in wastewater over the past month. The inset shows H5 positive samples. Data from WastewaterSCAN. Location is Trulock CA. 2/ For those following #H5N1 in CA, there have been positive farms there since late Aug.

@globaldothealth we're working w/ @ThinkGlobalHlth and @CFR_org to maintain a timeline of key events. This tracking allows us to better piece together signals. thinkglobalhealth.org/article/timeli…Timeline showing the first announced positive farms in CA on Aug 30th.
May 6 • 13 tweets • 4 min read
1/ New #H5N1 pre-print ⬆️ the threat level for the ongoing outbreak in dairy cows.

Researchers found that cow mammary glands contain the same kind of mixed flu receptors seen in pigs.

This mix of receptors is why scientists call pigs "evolutionary labs for flu host switching". Graphical abstract showing the three cell surface receptors used by influenza in humans, chickens, and ducks. The figure then shows where sampling occurred in cows (brains, trachea, mammary glands), and the distribution of cell receptors in the various organs. 2/ One of the key changes required for avian flu to transmit effectively in humans involves flu's hemagglutinin (HA) host cell receptor preference.

tl;dr The cell surface receptor influenza uses in birds is subtly different from the one in the human upper-respiratory tract. Cartoon from Chauhan & Gordon illustrates influenza's replication cycle. A red arrow indicates where the HA glycoprotein is binding to the host cell receptor triggering uptake into the host cell.
Apr 24 • 6 tweets • 2 min read
1/ I've seen many comments along the lines of, "We have no evidence that pasteurization inactivates #H5N1."

We actually have quite a bit of evidence to suggest pasteurization will work and the presence of viral RNA is compatible w/ that evidence.

Why am I not panicked? A🧵 2/ Milk is pasteurized by heating it briefly to ~72 C (161F). This inactivates pathogens, but does filter the milk. As a result, there can be degraded genomic material from pathogens following pasteurization. PCR, as was done by the FDA, can detect these degraded genomes.
Apr 1 • 10 tweets • 3 min read
1/ A human case of #H5N1 was just reported and is linked to the ongoing outbreak in US dairy cattle.

How concerned should we be?

It's good news that the patient is experiencing eye symptoms and had direct exposure to infected cattle.

Why? 🧵 2/ As you may know, avian influenza doesn't readily infect humans (and doesn't transmit well from human-to-human) in part because of subtle differences in key cell surface receptors. journals.asm.org/doi/full/10.11…
May 17, 2023 • 9 tweets • 4 min read
1/ What's the global state of wastewater surveillance?

On behalf of authors from >20 countries & all continents, A Keshaviah, @megan_b_diamond, M Wade, & me survey capacity & what's needed going forward. @RockefellerFdn @MathematicaNow @NUBouve @LancetGH thelancet.com/journals/langl… 2/ Following a convening of @RockefellerFdn's Global Wastewater Action Group, we partnered w/ @MathematicaNow and surveyed representatives of wastewater monitoring programs in 43 countries (16 LMICs, 27 HICs) spanning six continents (when I said "all" I didn't count Antartica). Figure: Population coverage...
Jan 31, 2023 • 4 tweets • 2 min read
1/ Data from @WastewaterSCAN shows that rates of SARS-CoV-2, RSV, and influenza have dropped precipitously from their winter peaks!

We still have a ways to go, but things are clearly headed in the right direction. US national wastewater surveillance data from the wastewater 2/ Although for SARS-CoV-2 we've been hovering at peak levels for over a month and we need to see at least another month of continuously falling prevalence before we're back to more "baseline" levels. US national wastewater surveillance data from the wastewater
Jan 6, 2023 • 11 tweets • 4 min read
1/ For those concerned about #XBB15 and hospitalizations, I think the evidence is more mixed than many are admitting.

While it's true hospitalizations are up in states like MA where XBB.1.5 is common, they are up across the entire US, even in states w/ little-to-no #XBB15! Data from NY Times shows that hospitalizations are up 14% ac 2/ If we plot daily XBB.1.5 prevalence at the state-level vs new adult hospitalizations for #COVID19, you can see there are some states (each color is a state) with weakly positive relationships, but this the signal isn't very strong. Figures shows a scatter plot of XBB.1.5 prevalence on a log-
Jan 4, 2023 • 21 tweets • 9 min read
1/ From COVID to cancer, molecular networks change & are changed by myriad stressors. But how might these networks evolve?

The answer is related to Google and social networks!

Work w/ @chiahungyang, out in The Royal Society Interface, explains how. royalsocietypublishing.org/doi/10.1098/rs… 2/ Our work builds from a network-science-based approach to modeling gene networks, called the Pathway Framework, which Chia-Hung developed during his @NUnetsi dissertation. You can read more about that model here:
Dec 30, 2022 • 31 tweets • 9 min read
1/ What's going on w/ #COVID19 in China? A 🧵 on what I'm seeing:

1 - The math says Zero Covid can't work against these new variants.

2 - The new genomes don't suggest a novel variant is to blame.

3 - I don't think Chineses gov. was caught off-guard.

Read on for the details. 2/ "The math says Zero Covid can't work against these new variants."

The OG Wuhan strain of SARS-CoV-2 could be contained w/ test-trace-isolate. We know this because *many* countries ran successful Zero Covid campaigns, e.g., South Korea, Vietnam, Japan, China, New Zealand, etc.
Nov 28, 2022 • 5 tweets • 4 min read
Excited to announce that I've rejoined @Northeastern full-time as their Director of AI + Life Sciences in the Institute for Experiential AI. I'm honored to work with @usamaf and the @Experiential_AI team to help make the century of biology a reality! 1/5 news.northeastern.edu/2022/11/28/ai-… I am deeply proud of what we accomplished @RockefellerFdn and the direction things are headed @PPI_Insights!

To all my friends and colleagues, thank you for an incredible experience and your tireless commitment to making opportunity universal and sustainable! 2/5
Nov 28, 2022 • 16 tweets • 2 min read
1/ I'm not worried about outdoor Omicron transmission and you shouldn't be either.

Even if the study from the Chinese CDC is correct (which is hard to answer because no data were provided), 39 secondary infections will happen from <5% of index cases.

A short thread to unpack. 2/ First, there's been no wide-spread evidence for large-scale outdoor Omicron transmission. This includes countries with surveillance as good or better than what's done in China, e.g., South Korea, Japan, South Africa, etc..
Nov 15, 2022 • 7 tweets • 3 min read
1/ I'm growing increasingly worried about #Ebola in Uganda.

Over the past few days, cases have been reported in previously unaffected districts, rates have started increasing, & the MoH sit reps were plagued w/ errors.

All signs point toward a deteriorating situation. 2/ Over the past week, confirmed Ebola cases have been reported in the Masaka and Jinja districts. This is the first time EVD cases have been reported in these districts. who.int/emergencies/di…
Oct 17, 2022 • 12 tweets • 6 min read
1/ The XBB and BQ.1.1 variants are driving #COVID19 surges in many countries.

Using our @RockefellerFdn variant tracker, we’re able to gain more insight into what’s happening globally. A thread on what we’re seeing*. 2/ *As you may have noticed, our @ppi_insights twitter account is down (we're working on that), so the information I'm sharing is about a week old. I will tweet out updated data tomorrow.
Oct 7, 2022 • 6 tweets • 6 min read
The science team @PPI_Insights has a new model for tracking #COVID19 variants.

tl;dr - we're worried about BQ.1.1 & expecting a surge in the coming months.

@TRyanGregory @HelenBranswell @EricTopol @firefoxx66 @angie_rasmussen @cmyeaton @g0ingmad @sciencecohen @jessicamalaty 1/6 Unlike BA.4.6 and BA.2.75.2, we are seeing signs of growth in #COVID19 cases where BQ.1.1 is also growing in prevalence. 2/6
Apr 15, 2022 • 19 tweets • 7 min read
1/ It may sound crude, but, did you know that last year's Noble Prize in physics was awarded for using the "ask your friends if they're sick" method to study complex systems? 🤯🤯🤯

And, that asking your friends is provably the optimal strategy for assessing infection risk. A 🧵 2/ In 1985, Giorgio Parisi [2021 co-Nobel Laureate in Physics] and colleagues published a new method for studying spin glasses*.

Now called the "cavity method," it's closely related to Judea Pearl's "belief propagation." Abstract for Judea Pearl's ...Abstract for Mezard et al. ...
Apr 3, 2022 • 15 tweets • 9 min read
1/ You've probably heard that some key #COVID19 data systems are scaling back. But what does that mean for our ability to respond?

As I told @carlzimmer, "right as things get hard, we’re dialing back the data systems." 🧵 nytimes.com/2022/04/02/hea… 2/ Back in 2020, #COVID19 was pretty straightforward.

Yes, behavior, social networks, etc. were changing rapidly, but there was no immunity & only one variant.

@MOUGK, @EvolveDotZoo, et al. & I showed how to model this using data from @globaldothealth.
Jan 13, 2022 • 25 tweets • 13 min read
How fast will #Omicron drop after peaking? Turns out, it's not so obvious. A thread on the shape of epidemics. 1/25 You might think that if an epidemic curve goes up quickly, then it will come down quickly. We (@LHDnets, @all_are, & me) did too. And, it can! For example, replacing sick workers can drive accelerating disease spread and decline. 2/25 nature.com/articles/nphys…
Jan 12, 2022 • 6 tweets • 5 min read
Last week I told the @BostonGlobe models showed a #COVID19 peak in 1-2 weeks (i.e. later this week or next). The data are consistent with a peak happening now, but, the Globe picked a different forecast for their headline. 🤦‍♂️ 1/6 bostonglobe.com/2022/01/12/nat… Wastewater data are peaking in Boston. However, as @davidlazer mentions we’re still *way* above record highs & hospitalizations will continue rising after cases peak. So things will get worse healthcare-wise. Masking & testing are vital now. #wastebeforecase @BiobotAnalytics 2/6
Dec 19, 2021 • 15 tweets • 8 min read
I told @Brabbott42 in the @WSJ that the US is facing a "perfect storm" of #COVID19 test demand. But what does that mean? @RickABright @PPI_Insights @RockefellerFdn @uche_blackstock @HelenBranswell wsj.com/articles/covid… 🧵 1/15 When it comes to testing, there are 6 kinds of people we need to consider:

1.) The worried well

2.) The worried ill

3.) Those with #SARSCoV2.

4.) Those exposed to SARS-CoV-2.

5.) Those who need a test for work/school/travel.

6.) Those who need a test for the holidays. 2/15
Aug 26, 2021 • 6 tweets • 2 min read
"Acute infections in vaccinated and unvaccinated people feature similar proliferation and peak Ct, but vaccinated individuals cleared the infection more quickly. [BUT] Viral concentrations do not fully explain the differences in infectiousness..." 1/6 medrxiv.org/content/10.110… New pre-print from the labs of @yhgrad & @NathanGrubaugh using data from the NBA, confirms that peak viral load is similar between vaccinated/unvaccinated cases, but clearance is faster in vaccinated. 2/6
Jul 19, 2021 • 4 tweets • 3 min read
I'm honored and humbled to announce that I'm #MeetingThisMoment by joining the @RockefellerFdn as the Managing Director of Pathogen Surveillance. I'll be working w/ @RickABright & the incredible PPI team to build an equitable, ethical surveillance program. rockefellerfoundation.org/blog/rapid-gro… I'm staying on @Northeastern as an affiliate assistant professor & would not be in a position to take on this incredible responsibility w/out the support from so many amazing individuals at NEU, especially Prof. Vespignani (@alexvespi) and the wonderful members of @NUnetsi.