Sam Scarpino Profile picture
Sep 22, 2020 13 tweets 6 min read Read on X
Tomorrow I'm speaking @yale_eeb on "Network Theory and COVID-19." My goal is to pull a thread across the 10+ papers we've written on the topic & convince you that #COVID19 became a pandemic because the world does not understand complex systems. h/t to my host @big_data_kane. 1/13 Image
First, building from foundational work in math. epi. and network science, we showed how super-spreading creates havoc for pandemic risk predictions and then derive a method for correcting the predictions. 2/13
Second, how de-coupling the risk of infection from transmission breaks the friendship paradox, which most (non-mass-action) herd immunity thresholds rely on & can mean that backwards case investigation is more important than forward contact tracing. 3/13
Third, accounting for stochasticity changes the way we should think about super-spreading events and #COVID19 interventions. 4/13
Forth, that real-time mobility data during one of the largest human population disruptions in history--i.e., the cordon sanitaire of Wuhan, China--revealed the complex epidemiological dynamics of #COVID19. 5/13
Fifth, the way in which human behavior and policy interventions (or lack thereof) interacted to shape mobility patterns and physical distancing during lockdowns. 6/13
Sixth, why visits to places like churches and parks reveal the epidemiological risks associated with heterogeneous policies regarding non-pharmaceutical interventions. 7/13
Seventh, using data from >300k US survey responses to show how mask wearing affects COVID-19 transmission (pre-print and formal tweets coming soon). 8/13
Eighth, why, now, more than ever, understanding the non-SEIR dynamics of #COVID19 and the *potential* role of environmental transmission is critical. 9/13
Ninth, that classic ecological theory on crowding predicts the intensity & duration of #COVID19 epidemics and that hierarchical structure in mobility and social networks may be a critical driver of this pandemic (as predicted by network scientists). medrxiv.org/content/10.110… 10/13
Lastly, how an international consortium has compiled, what Steven Johnson in The New York Times Magazine, describes as what "may well be the single most accurate portrait of the virus’s [#COVID19's] spread through the human population in existence." 11/13
I'm excited & also nervous. Nervous because the work we've done stands on the shoulders of so many giants (including one my PhD advisors @meyerslab, which is where the title comes from) & it may take an hour just to acknowledge collaborators/funders. 12/13 ncbi.nlm.nih.gov/pmc/articles/P…
And excited because so many of us are convinced that the work of complex systems and network scientists matters more than ever. I can't wait to tell the world why and it starts tomorrow @Yale. 13/13

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More from @svscarpino

Oct 15
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.
3/ I'm concerned about the H5 wastewater signal because it lags far behind the uptick in farms and is better correlated with the rapid rise in human infections. thinkglobalhealth.org/article/timeli…Timeline shows the rise in reported H5N1 human infections beginning in late Sept/early Oct.
Read 9 tweets
May 6
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.
3/ While changes in HA binding are only one of many required, they are thought to be key in governing influenza host range.

journals.asm.org/doi/full/10.11…
Read 13 tweets
Apr 24
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.
3/ Numerous peer-reviewed studies have found that pasteurization will inactivate influenza A virus, including #H5N1. ncbi.nlm.nih.gov/pmc/articles/P…
Read 6 tweets
Apr 1
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…
3/ However, our eyes actually contain the bird-flu-friendly confirmation of the cell surface receptor. This is why eye inflammation is often a symptom of avian influenza infection in humans. thelancet.com/journals/lanin…
Read 10 tweets
May 17, 2023
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...
3/ In high-income countries, composite sampling at centralized treatment plants was most common, whereas grab sampling from surface waters, open drains, and pit latrines was more typical in low-income and middle-income countries.
Read 9 tweets
Jan 31, 2023
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
3/ And note how *LONG* the RSV outbreak has been in the US.

We've been above 25% of the peak height for >3 months! US national wastewater surveillance data from the wastewater
Read 4 tweets

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