Transcript of Currents 099: Samuel Scarpino on Preparing for the Next Pandemic

The following is a rough transcript which has not been revised by The Jim Rutt Show or Samuel Scarpino. Please check with us before using any quotations from this transcript. Thank you.

Jim: Today’s guest is Sam Scarpino. Sam is the director of AI and Life Sciences at the Institute for Experiential AI at Northeastern University, and he’s a professor of the Practice in Health and Computer Sciences. He also holds appointments in the Institute for Experiential AI and the Network Science, Global Resilience, and Roux Institutes. Previously, he was the vice president of pathogen surveillance at the Rockefeller Foundation, and chief strategy officer at Dharma Platform, a social impact technology startup.

In 2020, Scarpino co-founded a data sciences initiative called, which was backed by Google and the Rockefeller Foundation. He’s also an external professor at the Santa Fe Institute, and an external faculty member of the Vermont Complex System Center. Welcome back, Sam.

Sam: Thanks so much for having me back, Jim.

Jim: Yeah, this will be great. I think I met you back in the days when you were a postdoc at SFI, is that right?

Sam: That’s right, yeah. I was an Omidyar postdoctoral fellow, starting in 2012.

Jim: Yeah, I was there in 2012. I left at the end of 2012 basically. Thought I was still back and forth, but I was still there at the time. Sam and I had a wonderful chat, people have told me how useful it was back on December 15th, 2021, Currents 047, kind of right in the second phase of the pandemic when Omicron was coming on. And we really did talk about all kinds of things, from epidemiology, to surveillance to some things that you were very excited at the time, which was sewage surveillance, as I recall.

Sam: That’s right.

Jim: And lots of other things. But now, time has marched on. We have lots of data, one of the great found experiments in biomedical history, the Covid epidemic. And so, today’s topic is what have we learned, and what can we apply, or what anti-patterns can we try to learn how to ignore for the next pandemic?

Sam: No, I think it’s a great time to reflect on that, because we’ve certainly learned a lot over the past few years around what works and what doesn’t. And also, I think have seen areas where we need to take a much harder look at whether we’ve actually implemented anything we’ve learned during the pandemic that might help us in the future.

Jim: Yeah, it really is an interesting time here. I went on the covid.cdc/covid-data-tracker this morning to update my knowledge, and it says so far there’s been 1.13 million deaths in the United States, 6.18 million hospitalizations. And I looked at other data, some of the Johns Hopkins data, which unfortunately they stopped updating in March, 2023, things for fatality rates and things of that sort. So, it’s quite interesting, because part of the found experiment is comparing the cross-national experiences. What is your takeaway from looking at the data cross-nationally? Because we’ve had, again found experiment, countries like Sweden did one thing, New Zealand did another, US and UK. I was surprised actually, US and UK, I was looking at whether having a national health program the UK does, one of the best in the world, made any difference. And the answer is it didn’t. They had almost identical death rates and fatality rates, et cetera. What’s your takeaway from the international aspects of the found experiment?

Sam: Well, just to briefly mention the US-UK difference in terms of national healthcare, and it’s not my direct area of research, but it would be useful to look at some of the federal programs that went into effect during the earliest parts of the pandemic that did provide more access to healthcare for individuals, and whether that was helpful or not in terms of the federal expenditure around providing increased access to healthcare during the pandemic. And certainly around insurance reimbursements, even for tests and those kinds of things that were made a lot easier. But I think what we’ve learned internationally, the playbook that we saw actually work to keep schools and businesses open but deaths low are what happened in many countries in Southeast Asia, and places like New Zealand and Australia, which is very effective, test, trace, isolate early on. And then, border screening, rapid response, epidemiological task forces, and then a quick switch over to vaccination and reopening.

And that’s, of course, one place where we saw China not do as well, which was holding on to that zero-Covid strategy without the vaccination coverage of one of the high-quality mRNA vaccines for far too long. Which had probably an economic impact that we don’t fully understand, but certainly had a loss of life impact. And if we contrast that with the US, the UK, a lot of other countries in Europe, we incurred these major economic costs in terms of what we called lockdowns, although they weren’t really comparable to other lockdowns in the US, we had lots of school closures, et cetera. And certainly it saved a lot of lives, but not at the levels that we saw in other countries that I think ultimately actually had less societal disruption than we did in the US and the UK.

Jim: Yeah, it’s interesting. Because I remember as it was going down, my wife who’s a biologist and thinks about such things, her and I are having conversations, and we were saying, “God, we’re kind of doing it in a half-assed fashion. It’s not strong enough to actually stop anything, but it’s just strong enough to disrupt the economy, put kids back a year in school.” I just was reading in the newspaper yesterday that the loss in reading scores, particularly amongst marginalized groups, are terrible. And no recovery yet, or almost unmeasurable recovery.

So, countries like the United States and UK kind of came out in this middle zone where we took on large costs, but it’s not clear it had much effect. The one effect it did have, at least it’s my view, I’d love to get your view on it, is it did spread the peaks out a bit. It may not have reduced the total number of cases much, but at least they didn’t all hit in May, June and July of 2020, which would’ve truly swamped the healthcare systems. Is that a fair analysis? Or did our sort of half-assed approach to lockdown actually accomplish anything on the area under the curve?

Sam: Well, it probably accomplished something in terms of the area under the curve, but in terms of how big that something is, it was not very much. I remember it was The Economist, I think, that had their social misery index that they were publishing for different countries, and it was meant to be an amalgamation of all the different ways in which our lives were being disrupted. And you contrast New Zealand and the US, and New Zealand would have these very short bouts of really intense disruption that were far more disruptive than anything we had in the US over any period of time, but then long, long periods of essentially normal life. Whereas in the US, we were kind of stuck at this persistent level of misery, really until we got through the Omicron wave in 2021, before we started to get, for the most part, things returning not to normal, but something that looked a little bit more like day-to-day life before the pandemic.

You’re right about what happened in 2020, early on. By the time we realized what was going on in the US, we were so far behind, we didn’t have much of a choice. If you remember, and I think culturally we’ve probably already forgotten about a lot of this, that there were refrigerator trucks with bodies in them in parts of the US, and there wasn’t much we could do aside from go into those lockdowns to try to prevent the hospitals from being overwhelmed. I think the take-home message is that when things happen like that, when we have these lockdowns, and the school closures, et cetera, that represents the failure of public health to control the spread. And if we’re successful with test, trace, isolate, we’ll probably talk about wastewater surveillance later, it actually keeps things open, it keeps life more normal, but also prevents the hospitals from being overwhelmed.

Jim: Yeah, that’s the one thing you can certainly say that the semi-lockdowns did. Now, the other huge missed opportunity, though it’s also at a giant cost, and I’d love to get your thoughts on this, particularly with respect to a potential future pandemic that might be a lot worse, because I like to remind people, as pandemics go, while this one was highly, highly contagious, its kill rate wasn’t all that bad. Maybe it was four tenths of a percent, something like that, half a percent. Compared to SARS, which was maybe 15%, MERS, which was 35, 40%, weaponized Soviet smallpox, that would probably be 50%. And smallpox is probably about as contagious as the early, pre-Omicron versions of COVID-19 were.

So, when I’m thinking about the future, I’m thinking about what would we do if we had one that was as, let’s say, contagious as COVID-19, but as deadly as SARS? It kills 15% of the people, so instead of losing a million Americans, we lost 50 million Americans. That would be a very, very different thing. And it seems to me the thing that we missed, and part of it was politics, part of it was not readiness, part of it was just plain difficulty, was we didn’t seal the borders. You talk about New Zealand, a small island with only a couple ways in, right? United States, we have land borders, we have many air borders, we have water borders, we got all kinds of things. And if we were really in a serious, deadly, kill 50 million Americans type pandemic, don’t we need to be able to shut the borders rock solid on two days’ notice, something like that? Is there anything else that would actually work in the event of a global, truly scary pandemic?

Sam: Well, I think the biggest challenge, the results on border closures are pretty mixed. And the reason that they’re mixed is not because they don’t work if you do them correctly, it’s just that, typically, by the time you decide to close the borders and get them closed, it’s already too late. And then, that also assumes that you can really close the borders, right? Again, we never know exactly what will happen if this pandemic that you’re talking about ends up occurring. I’m sure there’s going to be another pandemic, whether it’s the big one or whether it’s another one that’s still quite severe, like another SARS-CoV-2-like pandemic. But I didn’t think before SARS-2 that I would ever see the kinds of interventions in the US that we saw in March and April, 2020. I just never thought we’d see mask wearing in the US like we see in other countries. And obviously, there was eventually societal pushback against that.

And so, I don’t think we can know what will happen if there’s a 15, 20, 30% fatal pathogen that’s clearly spreading with epidemic potential. But what I do know is, almost certainly, by the time we figure out that there is a pathogen spreading that is killing 15% of the people, it’s spreading fast enough to cause a pandemic, it will be too late in the US to rely on border closure alone. We will have to also be able to stop the transmission with test, trace, isolate inside of the country, because we will already have enough cases to cause an epidemic throughout the US by the time we get this figured out. That’s basically what happened in 2020, by the time we figured it out, there were already so many cases in the US that it was too late.

Jim: Yeah, where was it, New York and Seattle I think were two big early hotbeds. Now, interesting about trace and isolate, my home state of Virginia attempted to do trace and isolate, but it was completely incompetent. Anyone who got a case did get a call from the state health department, but it would always be a few days later, and, “Oh, yeah,” and then just some soft advice on what you should do for personal isolation, et cetera. What should a country be ready to do? Do you have any ideas from, again, international examples, or just thinking from first principles, on what the United States ought to be ready to do in the event of the big one?

Sam: Yeah. Well, it’s something I’ve been thinking about quite a lot, going back to my time at the Rockefeller Foundation, is kind of what can we really do early on? And we have domestic examples of this working. So, there were a number of colleges and universities, Northeastern University was one of them, who used test, trace, isolate to keep the university open and safe all the way up until Omicron. And so, Northeastern University had in-person classes, in-person work, no transmission events on campus all the way up through Omicron. And what they were doing is not rocket science, it’s just following basic epidemiological principles, which is the virus takes, back then it was around four days in between when somebody would become exposed and when they would infect the next person, we were testing everybody on campus every three days. That’s inside the transmission window.

Someone would test positive, maybe they got infected off campus, they got infected returning, so anyone returning to campus had to have, I think two or three negative tests in a row before they could come out of quarantine in their dorm rooms. And it worked. And it worked in a lot of settings around the US. And we saw this work in other countries, that’s ultimately what China did, and their case numbers were much more serious than ours were initially, in terms of how it had spread throughout the country. They of course put in incredible measures that we wouldn’t really be able to do in the US. So, I think in order for test, trace, isolate to work, you have to test everybody frequently enough that you’re inside the transmission cycle. And this was one of the biggest failures, assume there’s going to be asymptomatic or minimally symptomatic transmission, and so you have to test people who aren’t symptomatic. So, everybody in Northeastern University was getting tested, whether or not you had symptoms, whether or not you had a known exposure.

Jim: Yeah, interesting. Now, when you think about this from the coming big one, one of the things that it obviously begs is, do we have the capacity to develop the tests fast enough?

Sam: I think that we do if we’re thoughtful and creative about it. So, do we have the capacity to develop the tests fast enough, get them certified? Yes. The CDC, they had problems in terms of delivering the tests out to people, but they had a test that worked and was approved in, what, February I think? Which would’ve been early enough probably. The problem was the distribution out of the CDC, and then our ability to actually scale up testing. So, I think it’s a supply side problem, not a development problem.

Jim: Do you know if we have invested in standby surge capacity to be able to manufacture and distribute these tests very rapidly should the big one occur?

Sam: Sort of. So actually, I spoke about this at the National Academies of Sciences, Medicine, and Engineering about six weeks ago now. They had just a workshop on the future of laboratory surveillance in the US. And the panel I was on, they asked us to opine on what are real opportunities today that we could leverage. And the real opportunity today around PCR testing, around diagnostic testing, universities all over the US built CLIA-certified, meaning that they can run clinical diagnostics in compliance with the FDA, CLIA-certified labs for mass PCR testing. These are sitting all over the US at universities. The beautiful thing about colleges and universities is that they’re in the big cities, but they’re also in the rural areas as well.

And if we had some federal investment to sustain this infrastructure that’s already built, it would be ready to scale as soon as the next one came along. So, we’re actually at this interesting juncture where we have the infrastructure, it was built during the pandemic at these universities, we have the know-how, we have the certifications that take time to get. What we need to do is invest in maintenance of this, and then we will actually have the ability for the CDC to quickly develop and validate a PCR test, distribute it out to the universities who can then massively scale. The private labs will catch up, but that’s just not their business model. There have to be enough cases before the private labs will be able to retool and get up to speed. And again, we need the private labs also to be doing other things as well, and so investing in this strategic resource around these university labs is, I think, a path forward.

Jim: Interesting. At the time of Covid, I was on the board of advisors for the Fralin Medical Institute at Virginia Tech, and they just jumped into it with both feet and created a massive scale lab. And I think they developed their own test and got it approved by the CDC very quickly, and were, I think, the second-biggest operator of tests for a while in the State of Virginia. Now, but I have no clue what they have done with all that capacity that they built, because they basically just threw money at the problem and built the capacity.

But as you say, it’s not their business, they don’t have a business model to preserve that, they’re currently not doing any testing. Has that equipment been sold, given away or not? And of course, as you know about universities, there’s nothing more dreadful than fights about space at a university, right? So, somebody’s got the forks out to get that space back, if they haven’t already reclaimed it. So, that’s really interesting, that somebody at levels of authority that control purse strings ought to be incentivizing the preservation of this capacity.

Sam: I think so. There’s no other way to prevent a pandemic of a novel pathogen. For influenza, and we’ve done sort of a lousy job of this, we’ve done some effort, but we can stockpile vaccines, we can stockpile antivirals, maybe they’ll work, maybe they won’t. But yes, we probably should have a pan-betacoronavirus vaccine that’s developed and staged. We’re still going to need to use mass testing in order to prevent the pandemic. In fact, we saw this kind of fail again with mpox, which formally we were calling monkeypox.

Jim: [inaudible 00:21:28]. Oh, I was going to say, “What’s mpox?” Oh, monkeypox? Okay.

Sam: Yeah, so still really can’t get tests for mpox. It’s like it was for the early days of SARS-CoV-2, and it’s just sort of inexcusable that we don’t have the ability to really rapidly scale up testing, because that’s the first line of defense. And it has to work, otherwise there really isn’t much else we’re going to be able to do to prevent the pandemic. We’re going to be back in the lockdowns again, or we’re going to have a huge amount of death. And for a 15% fatal infection… We were pretty close, I think, to some major societal breakdowns in 2020. And if the SARS-CoV-2 had been a little bit worse, again, as you understand, it’s not like it’s going to be a little bit more of a problem, it’s going to be a non-linear problem on the societal side of things. And so, we really have to be able to stop a pandemic from spreading. And it has to happen very early, and it has to rely on mass testing.

Jim: Yep, indeed. And I think that is the one thing that listeners should take away. This was a big warning shot, but it was just the warning shot. There’s so many worse scenarios. The other one, interestingly, from a societal impact perspective, Covid mostly killed old farts like me, unlike the Spanish flu of 1918, which principally killed people in their prime, people from 20 to 45, as I understand, was the core dead zone for the Spanish flu in 1918.

And so, if you had something that was killing 15% of the people, and instead of being very heavily skewed to the 80s and above, it was people in their prime, oh my God, the social impact would be orders of magnitude greater than it was. So, we should consider ourselves lucky that we’ve been warned, but if we don’t take the appropriate lessons, and take the preparations that we should, of the sort Sam’s talk talking about, which we’ll talk about later, it’ll be a gigantic missed opportunity. Who is supposed to be coordinating readiness for the next one?

Sam: Well, I know that we have an office of pandemic preparedness in the US that’s doing some inter-agency coordination. I think that’s the real challenge, is that there are a whole bunch of big federal agencies that need to be involved in pandemic preparedness. However, quite often, most of the actual authority rests at the very local level. Of even with county judges are the ones that have some of the necessary authority to actually enact measures. And so, the coordination problem is one of the really big challenges in the US. It’s one of the special parts about our government and our country, that we have measures of autonomy between local, state, and federal, that we have a number of federal agencies that are dedicated to different aspects of infectious disease preparedness and response. That has pluses. The minuses are on the coordinating side of things.

I think the one place where we probably should have more support and coordination is actually on the side of the public. And I remember when I was growing up, it was kind of right in the transition between smoking being ubiquitous in restaurants and the end of indoor smoking in most restaurants. And there was this sort of interstitial period where restaurants were investing an enormous amount of money in air handling and ventilation so that they could have a smoking and a non-smoking section, and the non-smoking section wouldn’t go home and have to air their clothes out afterwards because it smelled like cigarette or cigar smoke.

And if we were investing in indoor ventilation, it would make it a lot easier to stop another pandemic, but it also would just make it a lot less likely that people would get sick with anything. And so, there would be this immediate benefit in terms of our health. And so, one of the ways that we can kind of force the government to coordinate is through public action and holding elected officials accountable for strategic federal investment in ventilation plans, for strategic federal coordination around testing infrastructure, around pandemic response, et cetera.

Jim: Interesting. And ventilation’s interesting, I actually have it on my list further down in my topics. Let’s hop to it now. One of the things that stands out from the statistics is that the tropical zone countries mostly, with a few exceptions, had relatively low rates of infection. Now, I don’t know how good their data was, but could that be from the fact that, you go to a place like Costa Rica, I’ve been to Costa Rica a number of times, houses are open, it doesn’t freeze, right? Japan also had a singularly low rate, about a sixth of the US and the UK. And apparently they’ve invested heavily in ventilation in their office buildings-

Jim: And apparently they’ve invested heavily in ventilation in their office buildings for historical reasons. They built them too tightly originally, and they’ve retrofitted them. And Japanese houses, again, aren’t built nearly as tight as US houses and Canadian houses and Australian houses are. Do you think that the geographic data supports the power of ventilation as a prophylactic for something like COVID-19?

Sam: I haven’t seen a rigorous analysis published, but I bet it has been done. So that’s a gap that I’m going to try to fill after this in terms of doing some Google Scholar or Web of Science searching. But the evidence certainly that you have pointed to really suggests that it has had a big effect. There’s something that sticks in my mind early on in the pandemic. I think this was in 2020, in the summer. Movie theaters in Japan had a stoplight in front of each theater, and the stoplight was indicating the CO2 concentration, basically how well-ventilated the movie theater was. And it was sort of green, yellow, red, and you could pick your poison, so to speak, in terms of which movie you wanted to see based on how the ventilation was working.

I have a distinct event that I remember when I was visiting colleagues in India. We were having an indoor work session. It was hot and humid outside, so we had the windows closed with the air conditioning, but we had a CO2 sensor sitting on the table, the round table that we were all sitting. And we’d watch the thing sort of creep up. And when it got too high, we’d open the windows up and clear the air out. And I mean, that’s not the perfect way of doing it.

And you see it in the US also in terms of timing of different waves. When things were getting hit in the southern part of the US, their summer is actually probably when ventilation is worse because it’s so hot and muggy and people that can afford it have air conditioning and the windows closed. Whereas up in Boston and the Northeast, that’s when the windows are open, and it’s the reverse. So the evidence is definitely there. I should know if someone has published a rigorous analysis. I imagine that they probably have. Somebody listening to this is rolling their eyes that I don’t know the name of the paper off the top of my head, but I’m sure someone has done it.

Jim: If someone knows the paper, send it to and we’ll put a link up on the episode page. Now, let’s revisit something we talked about last time, which are clever passive surveillance systems like sewage systems or actually last November’s Santa Fe Institute Business Network Colloquium, there was a woman there that presented about her company that had an air monitoring system that you could hook into the air system in an office building and detect not just COVID, but lots of other stuff as well. Where’s the world at now, and what’s your thinking about that as part of the package?

Sam: So I think it’s essential, in part because you can’t have always on clinical surveillance for a broad array of pathogens, especially unknown, unknown threats. It’s just too expensive and too invasive. You can have that with wastewater surveillance. Just imagine a scenario, where we’d had wastewater surveillance globally, and I mean, probably we would’ve not have even had the pandemic because it would’ve gotten stopped in China and Southeast Asia, but we certainly would’ve seen it in Northern Italy. We certainly would’ve seen it on the East Coast of the US. And we would’ve been able to deploy resources that might have included things like targeted border closures fast enough to actually stop the pandemic from spreading. But in addition, that’s also how you do things like keep the schools open. So for example, one of the things we funded while I was at the Rockefeller Foundation were a lot of kind of very targeted case studies around how you deploy wastewater surveillance for maximum societal benefit.

And my favorite example, there was a school in Oklahoma, and they were running multi-pathogen wastewater surveillance. So it’s straightforward to not just look for SARS-CoV-2, but RSV and norovirus and cholera and typhoid. It doesn’t have to be something that’s transmitted through feces. SARS-CoV-2 really isn’t. Anything that’s in the blood, in the body, is going to get shed out in the urine, in the feces. They had a cluster of sick kids in the school. They looked at the wastewater. No SARS-CoV-2. They see norovirus. They go in, they bleach down the desks, the kids are back in school the next day, and the school stays open. So there are sort of peacetime applications of wastewater surveillance that keep schools open, et cetera.

On the air handling side, there are international airlines that pilot-tested this during the pandemic, no pun intended, but they would have air handling devices on long-haul international flights that could actually run the PCR testing over the course of a nine-hour flight. The plane would touch down, and they would know if somebody had been breathing out SARS-CoV-2 on that flight. And that does a couple of things. One, that helped get through kind of immigration and quarantine processes faster in some countries if they had this as a part of the plane.

It also gives confidence to the business travelers, and that affects the bottom line of the airline industry because business travelers typically are, by far, their biggest margin. And they’re also fickle. I mean, probably a lot of people listening to this have been business travelers, and it’s not really a big deal if I cancel a flight because I’m not on the hook to pay for it. We’ll have the remote meeting now, or I’ll push it off another month until it’s safe to travel. And so anything the airlines can do to give confidence back to the business travelers is going to directly affect their bottom line revenue.

In addition, we’re not going to have a pandemic unless it spreads through the airports. It’s just basically impossible. And having the kind of airport surveillance that we’re starting to see get deployed, the CDC and the US is investing in this, that will tell us early enough to act if we have both air handling and wastewater surveillance in the airport. So the short answer to your question, Jim, is I don’t see how we do this without wastewater and air handling. The exciting part is during the pandemic, we just published about this in Atlantic Global Health, is everybody knows about wastewater now. Everybody understands it. The public health officials understand it. It’s low cost, easy to implement. The public is familiar with it. Decision-makers are used to working with data coming from wastewater surveillance. All the pieces are in place. Just a little bit of investment in coordination, and we’re off to the races there.

Jim: Yeah, due to the ability for you to see, do the public authorities, have they come to that conclusion? Are they moving forward with investment and deployment? But we have, I must say, rather incompetent governance in the United States. It just seems again and again and again. So just because we know what the right thing to do is doesn’t mean we will do it.

Sam: So I think the answer in the US is actually pretty positive.

Jim: Good.

Sam: So the federal government has dedicated funding through Health and Human Services for wastewater surveillance. The CDC has a wastewater surveillance group now that is coordinating nationally. We have some private funders who are supporting wide scale multi-pathogen surveillance. The CDC and the federal government are supporting airport-based surveillance for COVID and other pathogens. I think what’s probably needed now, more international coordination coming from the WHO and other funders, support for scaling up from the World Bank and organizations like that, because what we have seen, and we’ve seen this all over the globe, is that governments will invest in sustaining wastewater surveillance. This happened. A bunch of projects that the Rockefeller Foundation funded as proof of concept are now budget line items in states around the US, in places all over the globe.

Bangalore, India, for example, has one of the more sophisticated wastewater surveillance systems on the planet that’s supported by the City of Bangalore, as well as the state and probably with also some federal dollars. So the other really interesting thing about wastewater is the sustainability models have also been kind of proven out, that if you invest in the proof of concept, you provide some seed funding for implementation and scale, the governments are following behind. So I think just need more coordination and probably also a little bit more imagination around how we might be able to use the data, the kinds of pathogens we could screen for, et cetera.

Jim: Cool. Now, when I’m thinking about this, suppose there’s a new pandemic virus. Let’s say it’s a virus. We can’t screen for it unless we know we’re looking for it. Is that correct? So how does the value chain go from an initial clinical discovery, there’s a novel virus that’s causing a problem, seems to be spreading locally very rapidly, to doing the presumably DNA sequencing, I don’t know what the measure is, and then getting that information out to the people that build the reagents and the tests in the sewage monitoring system? How does that information chain work, and does it work fast enough?

Sam: Yeah, so in terms of novel pathogen threats, the challenges you pointed out in the wastewater is that much of the screening that happens involves PCR testing, which is very similar to not rapid tests, but very similar to the clinical nasal swab test that a lot of us had during the pandemic. And if you’re going to do PCR testing, for the most part, you have to know exactly what you’re looking for to run the test. So that, of course, is a problem if you think it’s novel. Now, SARS-CoV-2 sure was novel in the sense that we’d never encountered SARS-CoV-2 before. However, we have been concerned about the family of beta coronaviruses that include SARS-1 and MERS, et cetera, for a long time. And so we can build PCR tests that look for coronaviruses in the family that includes SARS and MERS, but are non-specific enough that they would pick up coronaviruses that we had never seen in that specific form before.

So I think there’s a list of kind of mostly known threats that we could be building against right now. So for example, why don’t we have pan-betacoronavirus PCR tests? We could build that. We could have them staged. We could be ready ahead of time. Even if the tests weren’t great, doing something fast in public health is always better than doing nothing and waiting for something better to come along. I mean, that’s true probably for …. We were talking a little bit about first mover advantage in AI before the podcast started. I mean, in general, doing something fast first is a good strategy because if you’re going to wait around and try to be the best, you have to be way, way better because you’ve missed out on this window of opportunity. For truly unknown pathogens, something that isn’t similar to anything we’ve ever seen before, there actually are some approaches for doing this in the wastewater. And this is one of the things we’re working on at the Institute for Experiential AI at Northeastern. And this is bringing AI to the problem of wastewater surveillance.

So another way of doing wastewater surveillance is instead of doing PCR testing, you can basically sequence short snippets of bacteria, virus, fungus, other pathogen genomes that are circulating around the wastewater. And you can do this in a non-specific way. So it just sequences kind of everything that’s in the milieu of the wastewater. And so you generate a huge number of what we would call these short read non-specific sequences. And in the drinking water community, individuals like Professor Ameet Pinto, who’s at Georgia Tech, they look for shifts in the microbial community as evidence that there’s some kind of contaminant present. So there’s something. We don’t know what it is. In the case of drinking water, it could be a heavy metal. That heavy metal is going to affect the bacterial communities that are present, and they basically use the bacteria as sensors for some kind of unknown threat. And we can take that and leverage it for screening for novel pathogen threats.

Now, the problem is you’re searching for a needle or a pathogen on a needle inside of a haystack of needles, that kind of thing. And this is the sort of pattern recognition problem that AI systems are quite good at. There’s a lot of stuff that AI is still struggling with, but one of the things that it’s pretty good at right now is pattern recognition and searching for needles in haystacks. And so this is what we’re bringing now to the wastewater surveillance space through artificial intelligence is trying to push forward into being able to screen for kind of truly unknown, unknown pathogen threats.

Jim: Yeah, you’re right, because that is exactly what current deep-learning style, deep-learning-reinforcement-learning style AI is particularly good for, right, looking for anomalies in large data sets. Yeah. Now, you mentioned a general coronavirus screening. Doesn’t that run into the problem that there are already some endemic coronaviruses of the sorts that cause common colds and what have you? So there’s already ubiquitous coronavirus signal out there.

Sam: That’s right. So the challenge would be to try to design a test that didn’t pick up the common cold-causing coronaviruses, but did pick up other kinds of coronavirus. Again, I think for the listeners, the key take-home message is that anything we do very early on, even if it doesn’t work that well, is going to have a huge benefit in terms of our ability to control the virus or the bacteria or whatever it is.

So if we go back to the Mpox example, we have a vaccine that blocks about probably 30% of transmission for Mpox, and that doesn’t sound great, but it turns out that that’s actually enough. When cases are rare, there’s a lot of effective randomness on infectious disease transmission. It’s a social network property. It’s boom-bust. You probably heard of the 80-20 rule, right, where typically, for a lot of these infectious diseases, 80% of the infections come from 20% of the people. And so a vaccine that’s only sort of okay can be hugely effective early on. A test that is only sort of okay and has cross reactivity with coronaviruses, et cetera, can be hugely effective early on at screening.

And so I think what is sort of required is a switch in how a lot of public health officials, especially in the US, think about the response. Right? So the standard public health response is like, we need a test with really rock-solid sensitivity and specificity. We need vaccines that prevent 95% of disease and block 80% of transmission. And yes, we do need that when the shit has already hit the fan, so to speak. But if we have stuff that kind of works early on, that can actually be more than enough to prevent a small number of cases from growing into a large number of cases.

Jim: Yeah, exactly. And of course, how do you educate things like politicians to the mathematics of network epidemiology? That’s a problem, right? Presumably, there are people in the bureaucracy who you can educate on the mathematics of network epidemiology.

Sam: So we’re actually thinking about that at Northeastern University and at the CDC and the WHO. There are efforts, right? So the WHO has a hub for outbreak analytics now out of Berlin, and part of the mission of that hub is to generate analyses, but part of that mission is also to educate individuals across the global health space around how you interpret models, how you use AI with human-in-the-loop, how you think about complex data sets, how you think about complex systems. And the CDC now also has their Center for Forecasting and Outbreak Analytics with a similar focus. At Northeastern, our angle on artificial intelligence is both human-in-the-loop, that’s what the word experiential means in the title, but also training the next generation of decision-makers, whether that’s business leaders or political leaders, who won’t have to actually open up a terminal in code, but who will be asked to make decisions, in whole or in part, based on models that include artificial intelligence or machine learning.

I do think there’s another problem, which is …. I’m going to say something that’s probably going to upset a lot of people, but I’m just going to go for it, which is we tend to put medical doctors in charge of public health agencies. And medical doctors are great. They save a lot of lives. They know how to do things that I will never know how to do, and they have the ability to make life or death decisions that I will probably never have the ability to do. They are not typically trained to think about population level problems, complex systems and modeling, et cetera. And so I think what we need are either training programs for medical doctors that are being put in charge of public health agencies about how to think about complex systems, how to think about non-linear dynamics and modeling, or we need to be elevating the kinds of people that have that background.

I mean, we want these people also to have masters in public health and public health and government experience, but we need to be putting people in charge of organizations and in charge of decision-making that actually have the skill sets to function in our modern sort of heavily algorithm-driven complex society.

Jim: Yep, or maybe more realistic are the trusted advisors of and that let’s say you do still have a physician running CDC. There is a well-recognized and well-respected function there that is completely up-to-date on non-linear dynamics and network epidemiology, and they are trusted so that they are used as principal advisors for these kinds of decisions. That may actually be easier to achieve than to change the traditions of staffing.

Sam: Probably, although I think part of the problem is that a lot of the, and again, I don’t want this to turn into a physician bashing, I don’t mean it to be that way, but some of the physicians that I’ve had exposure to that run these agencies have a deep skepticism of a lot of these approaches. And you can’t change that quickly. And so they come in with the skepticism. I think a shining example of where that’s different, the State of Maine did an incredible job during the pandemic of keeping people safe, protecting the population, also getting tourism restarted in a safe way. And Dr. Shah, who ran the response there, had one of the stronger modeling and analytics teams reporting into him, and he also spent a huge amount of time speaking every day to the public about what we know, what we don’t know, how these non-linear systems work, et cetera, and built a huge amount of trust across the State of Maine in himself and in the public health apparatus and in these models.

So I think there are kind of a generation of leaders that are coming up. I was actually sort of disappointed to see that he wasn’t tapped to lead the CDC. I don’t know anything about the person really who was put in charge of the CDC most recently, but I think we have to start identifying these people that have already proven themselves capable of not just bringing trusted advisors and using algorithms, AI, et cetera, as a part of their decision process, but demonstrating their ability to communicate that to the public and build public trust, especially in the methods and the data that are being used to make decisions.

Jim: Ah, that’s very well said, Sam. I know there are a few influential people out there who listen to this show. So those of you who have any leverage on the public health sector, see if you can encourage the hiring at the decision-maker level to be people that are complexity-aware or at least complexity-friendly, because the problems of today are inherently complex, and if you try to solve complex problems with complicated responses, you’re always going to be behind the curve. That’s always been a theme here of the show.

Let’s turn now to the topic of vaccines. All right? I had a very early guest on the show, a friend of mine, who’s a bit of a maniac, but has a background in vaccines. He actually made his own COVID vaccine in his bedroom lab and gave it to some friends of his, and it apparently worked really early. I mean, he made it in, like he said, 10 days. He said it wasn’t that hard. On the other side, it was actually quite remarkable and totally contrary to historical practice for us to have gotten that mRNA vaccine out as quickly as we did. What do you think about vaccines and being ready to manufacture novel vaccines on short notice? On the other hand, every country, at first, the United States kind of tripped over its dick trying to deploy it, but then we quickly sorted it out. But other countries, even ones that you think of as quite sophisticated, like Germany, had all kinds of problems on the deployment side.

So let’s talk about vaccines along the whole chain from first you identify the pathogen, then you develop and prove enough the vaccine, and then you deploy it in volume so it’s good, or maybe not in volume. To your point earlier, if you can identify early enough, you can just saturate Brooklyn if it turns out that that’s the hotspot. So talk about the whole chain of vaccines and what happened in COVID, the good, the bad, and the ugly, what we’ve learned and how we should be ready for the big one or the next one.

Sam: Yeah. I mean, probably the initial place to start, briefly touching on sort of vaccine hesitancy and anti-vaccine sentiment, it’s useful to remember, actually, I spoke about this at the Santa Fe Institute, all the way back to us using variolation for smallpox, so pre-vaccine, there were coordinated mis- and dis-information campaigns around vaccination. And so one of the things that I think is really important is trying to figure out how we solve the problem of anti-vaccine sentiment is not likely to succeed. In fact, it’s probably going to get a lot harder with generative AI because these generative AI tools would be able to come up with very plausible-sounding, well-referenced concerns that are completely hallucinogenic around vaccines. But I do think it is always worth recognizing. And there’s this great book by Eula Biss called On Immunity. And as a journalist, she’s sort of trying to research vaccination for her children. And the landscape of information is complicated, and it’s scary to stick a needle in your arm for a lot of people.

And I think one of the things that we could do a much better job of on the public health messaging side of things is kind of to try to embrace that aspect of building public trust and also acknowledging the fact that it’s never going to be successful on the anti-vaccine side of things in terms of eliminating that. But there are other ways that we can go about building public trust and demonstrating safety in the vaccines, et cetera.

For example, the CDC just turned off its vaccine safety reporting system, and they turned it off because nobody’s reporting side effects. And why not turn it on and just tell everybody every day that nobody’s reporting side effects because there are no major side effects associated with the vaccines, especially with the boosters, for example. I was hesitant to get my third booster shot because I was down for 24 hours after my first two doses and I was like, maybe I don’t need to do this again to myself, et cetera. I got it anyways, almost no side effects. Everybody I talked to, for the most part, had almost no side effects. Why we’re not singing that from the rooftops boggles my mind. But you asked [inaudible 00:53:32]. Okay.

Jim: I do want to come back and go over the whole [inaudible 00:53:36] chain.

Sam: Yeah, yeah. I will.

Jim: But since you brought up the vaccine hesitancy, I did look at the Johns Hopkins data again this morning, as I mentioned, and I was kind of surprised. US actually did quite good initially on vaccine take-up. We were at 82% of Americans have had at least one dose compared to Switzerland, one of the most well-run countries, stable-minded people, 70%, less than the US, Sweden 77, UK 79, Brazil …

Jim: Less than the US, Sweden 77, UK 79, Brazil 89, kind of on the other side. So, for first doses, we were good. Even the complete primary series, we were quite good, 70%. But down to the bivalent, we’re down to 17%. So again, some of it may have been folks like yourself who, once you’ve had four, the chances of having had one bad reaction, if you think of, say, you have one chance in 8 or 12 of having a reaction, if you run four of them, you’re up near the 50/50 range of having a bad reaction.

I had one relatively bad reaction, it wasn’t that bad. But I went and had my bivalent anyway and I’m about to have my second bivalent. But, something has happened in the info sphere from when we were one of the highest in the world first dose to, I don’t know where other people are in bivalent, but it strikes me. 17%, how many months now in?Over nine months in since the bivalence came out is a pretty disappointing number.

Sam: No, I agree. And I think there’s a lot we can learn from that. And one of the really frustrating things early on is we were kind of supply limited, but not really. And one of the things that’s always going to happen is that people are scared and scrambling for the vaccine. That’s going to go away. You’re going to lose that strong drive on the part of the public to go out and get the vaccine. And so, you need to have a multi-pronged approach, which takes advantage of that initial interest and just get as many shots in the arm as you possibly can during that wave.

But then you kind of have to switch strategies and have one that has very different kind of messaging and marketing, but also makes it just so easy to get vaccinated. You should walk out into your hallway in the apartment building and there should be somebody out there from the local public health agency who’s vaccinating. You should be able to walk into a CVS and get a vaccine right away instead of seeing a sign that says, “We’re out of the bivalent boosters come back tomorrow.” Kind of thing.

And so, that’s the things that we need to learn in the US. The other thing is that mandates for vaccines, it’s a short term bandaid that will have long term repercussions in terms of total vaccination number. This is actually work that came out of the Santa Fe Institute showing that you often end up with lower overall vaccination coverage with mandates because, yes, it’s true that you get a bit of a bump early, but then you get pushback on the part of the public and you end up with lower coverage later on.

And so, many cases, well into even Omicron, there were still places that had vaccine mandates to go into a business. And it’s like, well, but the vaccine isn’t blocking transmission, so it’s doing absolutely nothing societally. It’s doing a huge amount individually, which is why getting vaccinated is so important. But it doesn’t make it less likely that I’m going to infect somebody if I walk into a restaurant and they have a vaccine mandate or I got an airplane and they have a vaccine mandate.

And so, I don’t think we did enough engaging on the societal side with how people are going to make decisions, how there’s going to be pushback, et. And that’s something that we have to plan for for the next one, because it’s exactly the same thing that’s going to play out again. And probably there’ll be even more of a challenge this next time around because if it happens in our lifetimes, we will have all gone through this and the societal memory in the US will already be one that’s kind of primed to push back in a much more coordinated way.

Jim: Yeah, that’s unfortunate, because again, if it’s the big one and there’s vaccine hesitancy, that would be really fucking stupid, right? But it could happen because we have a [inaudible 00:58:16]. The system has moved in a way that may not be returnable to where it was, where we got 81% compliance early on. 81%, if you could get it really fast, is enough to stop most epidemics, right? If we had the surge capacity to manufacture and deploy it, 81% would even stop smallpox probably.

Sam: No, I mean, my biggest concern there, actually, for the big one, is a slightly different one, which is in Massachusetts, you couldn’t get appointments to get the vaccine. We had a huge amount of demand here.

Jim: Yeah. I was logging into our systems at 3:00 in the morning to try to find slots when I first became eligible, and it took me a week to find a slot, right?

Sam: But across the border, in New Hampshire, they had slots available, and they weren’t really supposed to be preventing people from Massachusetts coming over and getting vaccinated, but they were doing it. They were making you attest that you were a New Hampshire citizen, etc. If we’re really looking at a 15%, 20%, 30%, I mean, people are going to be storming across the borders with guns to get these vaccines. And, so I don’t think we’re anywhere near prepared to roll out vaccines in the midst of true public terror for a pathogen that is as deadly as a smallpox or a MERS or a SARS one.

So, in some ways, we’re in a really terrible situation right now because if it’s another big one like SARS-2, there’s going to be a huge amount of hesitancy, public pushback. It’s going to be a big mess to roll out. If it’s a bigger one, we’re just totally unprepared to deploy vaccines in the face of public terror over a 15%, 20%, 30% fatal vaccine. And distributing pro rata by population, which is probably what we’ll do, is great, except you’re probably not going to have demand that’s proportional to that. It’s going to vary by state, it’s going to vary by location, and you just won’t have the kind of orderly compliance that mostly occurred during SARS-CoV-2’s vaccine rollout if it’s a lot worse.

Jim: Yeah. Oh, yeah. It’s very interesting. I don’t know how we prepare for that. But let’s go back to where we were, which is talking about the information chain, from we identify a novel pathogen, we create a good enough vaccine to get it out. And talk to me about how that worked and how that could work in the future, and have we learned some useful lessons from COVID-19?

Sam: Well, obviously, the development of the mRNA vaccines and their deployment is one of the engineering and science marvels of probably all of human history. Obviously we’ve been working on this, I say we, I’m not a part of it. We’ve been working on this for 20 years in terms of the mRNA vaccine technology. So it’s not like it was just birthed out of somebody’s head in the middle of the pandemic. We were ready for it. And that’s actually an important, it probably shouldn’t even be a footnote. An important point to make is one of the reasons, well, one, the reasons we invest in basic science is because it’s just important to do basic science. Another reason we invest in basic science is it’s often hard to predict what you’re going to need until you need it. And all of a sudden, we’ve been investing in this mRNA technology for 20 years. Most people didn’t know about it and it kind of saved the day, so to speak.

So for the next big one, there’s probably some underfunded research lab somewhere in the US that’s sitting on the thing that we’re going to need. And it’s only been done because of National Science Foundation or NIH or other kind of government or philanthropic funding, which is why its basic science is so important. But, come back to your question, which I’ve dodged a few times now, so I’m answer it is, the current pipeline, you have to have the genome sequence. That’s going to happen really fast. Well, fast enough to get it over to the mRNA labs.

One thing that I’m skeptical of and have quite a bit of concern around is the overconfidence in how quickly we’re going to be able to develop an mRNA vaccine and for how many pathogen threats mRNA vaccines will actually be feasible. The mRNA folks sort of seem to say everything can be done quickly, and that’s certainly not what I’ve seen in terms of updating the vaccines, right? They told us, 30, 60 days, we’ll have updated vaccines, and we’ve had one update. And even by the time that thing came out, the variant wasn’t even really around anymore. It was a new variant.

In addition, the manufacturers on the private side are not going to push out a semi-effective vaccine early to try to prevent transmission. And so, the private sector is just never going to have the business model to push something out really quickly right at the beginning to try to prevent the pandemic from spreading. If we think that that’s an important strategy, and I do, that has to be the role of the government, right? One of the things that I think government should do is take care of things that have a big societal upside, and it’s hard to see the business case for why the private sector should be investing in it.

So, got to identify the genome, that’s going to be easy. I think there’s big question marks around whether we would encounter a pathogen that we couldn’t build an effective mRNA vaccine around. We’ll probably be able to do it a little bit faster than we did this time, but it took about a year from the time that the genome sequence was made available to the mRNA manufacturers until shots were going in arms in a meaningful way. Now, even if we could cut that in half to six months, that’s still too slow to stop the pandemic. You think of six months from late December 2019, early January 2020. That’s, into the middle of summer, we’d already gone through the first wave in most places. So I think the take home message for me is that the mRNA technology is amazing. It’s completely changed our ability to respond to infectious disease and pandemic threats.

Even at 2x the speed that we saw during the pandemic, it’s not fast enough to stop a pandemic. And so, we either have to have investment in staging in vaccines ahead of time against plausible threats, or we have to have test trace isolate that can keep the number’s low enough until the vaccines are deployed and we can squash it, right? So I don’t see a strategy where we’re going to be able to manufacture and deploy mRNA vaccines against a novel threat fast enough. We can certainly do it faster and that will save a huge number of lives. But if we’re talking about preventing pandemics, I just don’t see the evidence that we’re going to be able to do it fast enough to actually stop a pandemic.

Jim: Interesting. So, if we think about a layered strategy, vaccines won’t be Phase 2, right? They’ll have to be Phase 3 after trace and isolate, which puts a big burden on trace and isolate. Which again, the United States was pretty incompetent at.

Sam: Yeah, absolutely. And I don’t really know what the solution is in the US because you have to have testing infrastructure in place. Again, we talked a little bit about the role universities could play there. It’s very clear that people either can’t or won’t take action, usually can’t until you get that positive diagnostic test back. And the one thing that was crystal clear is, if you don’t get the test results back in 24 hours, you really might as well not run the test from the perspective of public health control.

And so again, at Northeastern University, part of the reason we built our own testing center is that we knew from the math that you had to get the test results back within 24 hours. And the only way we could guarantee that would happen is if we did it ourselves, because if you outsource it, Quest is great, etc., but if they can’t get it back in 24 hours, maybe we don’t have to pay them as much. But that’s still, there’s no real enforcement. There’s no real way to make sure that you get it in 24 hours.

The thing that we could do, and I think this is maybe one of the bigger failings, and we learned all the wrong lessons, is around digital contact tracing in the US. Something like 80 million people in the United States ended up with the contact tracing app installed on their phone that Google and Apple facilitated. I don’t know if that, I think that app probably stopped zero transmission events in the whole US. I got notified a few times, but every time I got notified, it was a week after the exposure had occurred. And anyone that knows anything about public health in the US, as soon as they saw the deployment strategy, knew that this was going to fail because it put all the burden on the state health agencies to run these systems.

And the state health agencies are not funded to be able to run a technology platform like this. Many times, they had to build their own apps before they could even use them. And so, I think because we deployed the apps in the wrong way, public health officials kind of came to the conclusion that digital contact tracing can’t work. And if we can’t change minds about that in the part of decision makers, I don’t see any other way that it happens in the US except for putting resources in the hands of the public in leveraging technology. I just don’t see any other way.

Jim: Now, did any countries do any, say, Western or advanced economy countries do a good job with contact testing and contact tracing and isolation?

Sam: Yeah. So the best example, so South Korea is the shining example, and this is because of MERS in South Korea. So there’s a social contract between the public and the Korea CDC that if a certain set of triggers are hit, high resolution mobility data are released to the CDC for contact tracing. That was a huge part of why South Korea was so successful. Japan, for example, part of the reason they were so successful is that they understand complex systems, and you probably heard about this cluster busting, right? And so, if something is spreading randomly like a gas mixing in the room, which is how a lot of people that don’t know any better model infectious diseases, it doesn’t really matter if, like if I test positive, if I go forward and try to find people I contacted, or whether I go backwards and try to find out who infected me.

But if it’s a highly heterogeneous social network, the power law or most of, you have far fewer connections than most of your friends, etc., it’s a so-called friendship paradox, your friends have more friends than you do. It’s always better to go backwards because if I get infected, it’s much more likely that I got infected by a super-spreader, then I become a super-spreader myself. And so, what Japan does is, say I test positive, they go back and they find who infected me, and then they go out from that person and they cluster bust. And so, Japan showed us how it could be done.

There have been papers actually published out of Switzerland. Marcel Salathé, who is a professor in Geneva, has published on this from Switzerland, from the UK, etc., that their digital contact tracing systems actually did save quite a lot of lives and did interrupt transmission. But again, the key piece there is that the public can kind of report immediately, and that immediately sends out an alert to everyone who was contacted. It doesn’t go through some intermediary and take weeks later. It’s kind of instantaneous. So, there are examples of how to do this.

It’s just that you can’t have kind of a government interloper in the middle who’s going to wait a week before they send out the alert. And you have to understand how social network dynamics and infectious diseases work. And instead of trying to do forward contact tracing, you have to do reverse contact tracing and cluster busting. And you can see this in a lot of countries, how different countries put this together in different packages and were successful with it.

Jim: Is there anybody in authority in the United States who knows this and is doing anything about it?

Sam: I am sure there are people in authority in the United States that know about it and are trying. I’ve also been around the room with high level folks recently from, pick your favorite three letter federal agency that is involved in pandemic response, who have told me, full stop, they don’t think that contact tracing can work in the US. And I think part of the reason they say that is because, this goes back to my point about how a lot of people in charge of the public health agencies, they don’t know anything about social networks and they don’t know anything about complex systems. And they’re approaching this from sort of a freshman 101 understanding of infectious disease dynamics. And it’s not like being a bit naive means that you’re a little bit wrong. It’s the difference between being able to deploy effective contact tracing and prevent pandemics, and just being able to generate a lot of misery and death without actually doing much.

Jim: Yeah, that’s not good. Not good. Again, there are some decision makers out there that listen to The Jim Rutt Show. Get your shit together, talk to Sam and his friends and let’s make sure that we do, because I can see it in my head how you design such a system with no bureaucrats in the middle. Not that hard. This might be a thing for a philanthropist to do. Talk to Sam and his friends and let’s build it and have it on standby. I bet it wouldn’t cost more than $10 million to build it. It’s not that big a deal. Now deploying it, and have it ready.

Sam: Right. And I actually think there are probably creative ways of paying for it. If I’m putting data onto this system, that data might be valuable for other business functions that I could monetize as a part of these apps that are ongoing. And I think there are ways of doing it there. The privacy thing is it’s a red herring. There are plenty of ways of building it that are privacy preserving. Although one of the ways that I sort of like to talk about this is, in South Korea, the public’s privacy is invaded by the government and they benefit from it. In the United States, our privacy is invaded. We do benefit in ways that we don’t understand from it, but certainly not on the public health side of things, right?

So we’re never going to have a situation where it’ll be publicly palatable for the sharing of high resolution telco data. That will never happen. But that’s not what we’re talking about here. So I think people kind of use that privacy thing to sort of distract from what we could actually build that doesn’t really require anything that’s invasive or not respectful of privacy.

Jim: I’m going to push back on that one a little bit.

Sam: Yeah, go ahead.

Jim: With a hypothesis that that would be fucking stupid if we took that as a working assumption for, in the case of the big one. Anything is worth doing in the case of the big one, so we ought to have standby authority, and maybe it requires an 80% vote of the House and the Senate and the President. Some super consensus. But we ought to have the authority to have whatever we need in the case of, let’s say, a terroristically deployed, 100 locations, late Cold War, weaponized Soviet smallpox, right? We need to do what we need to fucking do. And I don’t know if we have the stomach for that, but it certainly seems to be stupid not to.

Sam: No, no, I agree. And so, I mean, well, I was… I don’t like to agree when somebody pushes back because that makes the conversation less interesting. But one of the things that we really failed at during the pandemic was clearly communicating why it is we’re doing what we’re doing. I remember, I spent a lot of time on Boston Sports radio shows. I tried to basically say, it was all pro bono, I tried to say yes to basically every interview, especially local, just to tell people what was going on. And one of the hosts asked, “I’m trying to figure out how it’s compatible that restaurants are open, but the governor doesn’t want us to have at-home gatherings for Thanksgiving.” And I said, “Those are incompatible. Either they’re both safe or they’re not safe.”

And we would have these very convoluted strategies around when we would open and close and what the business regulations were. And kind of the analogy that I give is, it would be sort of like if the weather report said, “Carry around an umbrella until we tell you to stop at some point in the future and we have no information about when that might be,” people would stop carrying around umbrellas because why would you do it? And so, I think what you’re pointing out is one of the big things that we’re missing, which is let’s have a discussion around what it is that we would need to stop the big one. I don’t see how you do it without high resolution telecommunications data.

Okay. So then if we want to stop the big one, we’ve got to have a mechanism to activate those data, and either one of three things is going to happen. The government is going to use it anyways, and they might use it in a way that we don’t think is appropriate or they might decide to use it in a way that we don’t think is appropriate in terms of what the chain of command is. They’re not going to use it and we’re all going to die, or we’re going to get out in front of this thing and have the hard conversations and figure out, okay, well we would be comfortable if it was a pathogen with this fatality rate, this rate of spread, those things we can measure early enough.

And then what has to happen is that we need a two-thirds vote in the House and the Senate, or we need two-thirds of the states’ legislators that, we cook up whatever you were saying, that becomes the way that we make sure that the public and the voters are engaged. Because instead, if we do nothing now, then what will happen is that yeah, we’re either fucked, or the government will do something anyways but we won’t have had a say in what it is they’re going to do. And right now, we just sort of have our head in the stand waiting for something bad to happen instead of picking our head up out of the sand and trying to figure out what we can do about it.

Jim: Yep, exactly. And you would think that the lesson learned from this is we really ought to be thinking about all scenarios much worse than this one and do that preparation. Because your point is, probably what happens if it’s the big one, well, it depends who’s in power, right? If it’s a non-insane person in power, which unfortunately we can no longer count on, they probably just do it anyway, right? But we don’t really want that precedent for somebody for… I like your idea, and I’m sure of our jointly developed idea here is to identify some threshold of scariness, and a mechanism for political validation that scariness has occurred, and that we are going to violate constitutional provisions for a while.

Remember, Abraham Lincoln famously said, “A constitution is not a suicide pact,” And he violated the Constitution in numerous ways during the Civil War. But we need to have a principled and politically accountable pulling of that trigger so that people can have confidence that this was done in good faith. And Republicans, Democrats, independents all voted for it. Maybe throw the Supreme Court in too, since it’s going to be an extra constitutional provision, right? It’s going to say, “There’s some super consensus that we can get that allows us to violate the Constitution for a brief period of time in the face of a first class emergency. But the constituencies that have voted for this and pulled this lever, safety lever, are so broad that this will not is unlikely to be abused.” Something like that.

Sam: Well, and I think there’s also stages, right? So I mean, having anonymized high resolution mobility data, critically important during the pandemic, this was shown time and time and again all over the world, and those data are far less sensitive. We could have lower thresholds and it wouldn’t be violating people’s privacy. It wouldn’t potentially trigger any constitutional crises. And so, even those things we could be planning for, and we’re just not, as far as I know, really even engaging in any of those conversations. And I think, as you said, I mean, probably the biggest lesson we haven’t learned, which is a lesson you can see if you just go back and look at past pandemics, is that people don’t learn anything from pandemics.

There’s this sort of collective amnesia in part because this was very traumatic, what happened to most of us, even those of us that didn’t directly lose loved ones, social isolation for the periods of time that we went through, people that had their first job experiences remote, the students in colleges and universities who spent years remote or isolated in small social groups. All of that is traumatic, and it doesn’t require death, which a lot of us experienced, or sickness or financial consequences, etc. And we haven’t really dealt with much of that at all. We’ve just sort of tried to move on from it. And it’s important to try to move on from things, but if we don’t reflect, it’s just going to happen again.

Jim: Yeah, exactly. And that’s why I wanted to get you on the show, to talk about these issues. Now, hopefully, a hopeful sign at least, is that some of the countries that did best were those that had SARS MERS scares, right? As you said, Korea had a really bad scare, right? And maybe got themselves prepared. Maybe, maybe we’ll be scared enough by this, but unfortunately, there’s this sort of mimetic propagation of crazy ideas. Bill Gates is going to put a tracking chip in your butt with the vaccine, and some wackadoodle running for this presidency on the Democratic side, some wacko in-

Jim: For the presidency on the democratic side, some wacko anti-vaxxer, these are not good things. And so we may have produced a crazy immune reaction in our meme space. What do you think about that?

Sam: I think in some ways, well, I think we need to worry about some of the folks that are running for president, independent of the pandemic risk associated with them. I think they’ll do a plenty good job. Part of the problem with a good president is… I actually think for the most part, Biden is doing a pretty good job, but he’s boring. And there’s a ton of infrastructure work happening across the country that we’ve been putting off almost for a generation. Across the board, there are things that people care about. Like, there’s no more individuals in private prisons at the federal level anymore. There’s a ton of good stuff happening. It’s just, for the most part, it’s pretty boring. I feel like if you have a president that’s really doing their job, they probably aren’t in the news a lot. It’s not exciting a lot of people, it’s just bureaucratic good governance. And again, it doesn’t mean I agree with everything. It doesn’t mean I necessarily, whether you think you should run again or not. I’m not saying any of that. I’m just saying that good governance tends to be boring and-

Jim: Like Eisenhower, one of the most boring presidents we ever had. But now the historians are going back and looking at his administration and say it was a lot better than we thought, right?

Sam: Exactly. So I think there’s plenty of concern around there, but I don’t want us to… We don’t have to solve the anti-vax problem. We don’t have to solve the conspiracy theory problem to prevent a pandemic. My concern is that individuals in government feel like, “Well, if we can’t solve the problem of conspiracy theories, then we can’t prevent pandemics.” And that it’s just not the case. It’s true that the conspiracy theories are killing thousands of kids all over the planet, because measles vaccine rates are low now and polio and all sorts of other vaccine preventable diseases. So there are really good reasons to go after these anti-vaccine sentiments, because kids, other people are dying all over the world, all over the US from things that they shouldn’t be dying of. But that’s not a pandemic issue, especially because early on, if there’s another pandemic threat, no one’s going to have the luxury of really being that afraid of the vaccine because it’s that or die.

And so I think instead we need to be focusing on some of these more pragmatic solutions that I think are being lost in the conversation. One example that sticks in my mind, and I don’t know if anybody’s done an analysis around this, maybe somebody’s listening knows about it and can tell us this. Sure Trump not being president probably were in a much better position for the pandemic. Although I actually think maybe if Trump had actually listened to some of the right advisors, he probably could have stopped the pandemic, because Trump is, I disagree with just about everything about him, but he’s one of the best storytellers and political operatives that we’ve ever encountered. And I think he really thought that this wasn’t going to be a big problem, because he probably would’ve stopped it because that’s probably the only thing that actually caused him the election.

But sidestepping that, if you look back, H1N1, Ebola, Zika, most of the big public health infectious disease responses that happened in recent memory happened under Democrat administration. And so most of the people that I know that were political appointees were on the outside looking in. And they would’ve been on the outside looking in for any Republican administration, because these were high level folks who aren’t going to get reappointed under a Republican administration. And so I do actually think there was an effect of not necessarily Democrat or Republican, but having a lot of the expertise in the federal response sitting on the outside looking in at this federal response.

And so maybe one of the things that we need to have, and I know groups like the new Academy of Sciences are working on this sort of scientific reserve, is we need some way of, and again, it’s not going to work if there’s a president that’s like Trump, but if there was say a reasonable Republican who had been elected that that person can call up the Democrat appointees that actually responded to 2009 H1N1, and Ebola, and others, and kind of deputize them into important, at least advisory roles in the government during this period of emergency.

And we don’t really have anything in place for that if we realize that, oh wait, all the people that know anything about responding to the situation we’re in administrations of the other political party and we have no way of activating them. And that’s a problem that we could solve. Now again, you can’t solve it if there’s a psychopath in charge, but we could solve it if there was a reasonable person of the other political party in charge. And we haven’t even really worked on that problem.

Jim: Yeah. Well, a very great idea. Good idea. Somebody ought to… Again, philanthropists out there, I noticed some of those that listen to the show too, fund something like this. So let’s wrap up here. I’m going to attempt to take what I think I heard from you on how we probably have to respond, because of realities to the big one. First, and correct me as I go here, because I’m just trying to infer from our conversation. First, we have to detect something is happening. And some of that it might be clinical, it might be from wastewater analysis, particularly of this more generic variety. So first detect and presumably there’s no testing really, initially. And so there’s ad hoc, symptomatic detection and maybe isolation, if it’s looking bad. Then, look, [inaudible 01:27:23] actually written this shit down, so I’m trying to think it through. A very important window is how quickly can we get tests that are at least okay.

And further, I think we have to have some threshold to say when tests are okay enough for the early stage. And the level of testing quality that is acceptable later may be different as I understand it, than early even 50/50 testings is probably okay early when it’s pretty rare. So that, well, maybe that’s not true. False positives might not be good. 50% false negatives might be okay. But anyway, so somebody needs to be able to make the call, because the tests are really critical for test trace and isolate. So therefore minimizing the time to get a good enough test and knowing what a good enough test is critical. Is that part of the theory strategy?

Sam: That’s exactly right so far. So you have to quickly detect, and that is something that we have some resources against, especially now with wastewater. And then the most critical window is how quickly can we get tests out and running?

Jim: Okay, so we got tests running there are good enough, whatever that means from a network epidemiology perspective. And that will have to do to some degree with the actual nature of contagion. Because COVID-19 was aerosol, droplet, contagion. Other things are touch, or there’s all kinds of different ways diseases can be spread. And the next thing we have to have, would be very good to have, is a ready to go testing trace and isolate, both the technology and the infrastructure in place to actually make that happen and particularly be able to deploy it very intensely in hotspots. Is that the next thing?

Sam: Exactly.

Jim: Okay. And then presumably in the meantime, in parallel, as soon as we have the thing sequenced, which these days is easy, as you pointed out, we need to fire up the vaccine engine. But you pointed out the fairly scary point that there’s no guarantee that we’re going to find a vaccine quickly. In some sense, we got lucky with COVID-19. One of the good few good things I can say about Trump is he did push a bunch of chips on the table and said, “Just go for it motherfuckers.” He even gave it a fancy name, what was it, Lightspeed or something, right?

Sam: Yeah, the warp speed I think, or-

Jim: Warp speed, that was it. So one of the few good things he did was just went all in on vaccines. I don’t know why he didn’t take credit for it, the idiot, but that’s him. But we certainly should do that, because if you think about the opportunity cost to throw a couple of billion dollars at it initially is giant return on fat tail distribution, like we’re likely to see in pandemics.

Sam: Well, I remember, but I don’t want to interrupt your flow, but I remember Bill Gates promising he was going to do that. He said he was going to take the five best vaccine targets and put them immediately into manufacturing and whichever one ended up getting approved, we’d be ready. And he never did it. It seemed like a great idea at the time. And certainly also want to make sure Trump gets credit for the vaccines that came out. And I’m glad that he didn’t get reelected, but I’m also glad that we had the vaccines and I don’t know if another administration would’ve done that.

Jim: Yeah, exactly. That’s one thing you got to give him credit for. Now, interesting. I mentioned this guy before Brian Hanley. It was current 002 on my show who made his own homemade vaccine. His proposal, I think he said at the time, when was this? Let me pull this up. It was May 26th when it was published. So I actually did the interview with him probably around May 15th, 2020, so still pretty early. He said at that point there were 19, I believe it was, vaccines that were in the lab. His proposal was release them all, let anybody manufacture and put them in the public domain and just throw them out there, but rigorously track the side effects. And yes, a few people will die and he calculated might be a few hundred and then quickly find the ones that are the least harmful and the most effective and ramp them up. And we had enough knowledge in May of 2020 to do that. What do you think of that theory?

Sam: I think it’s probably a good idea. If we’re looking at something that’s 10 times as fatal or more, as SARS-CoV-2. I think the backlash that you’re going to get on the anti-vaccine and hesitancy side of that kind of strategy it’s probably not worth it. Especially because by May, a lot of places in the US that really got hit hard were starting to exit, especially getting into June. And so there was a pretty good lull up until the fall of number of cases. So I think that that’s actually not a bad idea if it’s more severe, but I think the backlash from the side effects is going to be so severe that it certainly would’ve done more harm than good I think during COVID.

Jim: Yeah, that’s interesting. That’s interesting. This is where good wisdom in our decision making is going to be critical. My doctor, my personal physician, his wife is a infectious disease person, and she was of course right in the middle of all this, and I still recall him telling me in, I think it was March 2020, that they believed already that the case fatality rate would be around 0.7%. And that was pretty close. And she was quite solid on that number. She said, “I’d be very surprised if it’s more than 1%, and it might be less than 0.7.” But 0.7, point estimate. In March of 2020, if that number 0.7% were taken as a given for planning, that would’ve been gigantic for thinking about what to do, because we would’ve ruled out Brian Henley’s let the 19 vaccines role. On the other hand, if the number had been 7%, we might have decided something different. If it had been 20%, we almost certainly would go more extreme. So there needs to be some wisdom center for getting the best available data and making these high level strategic decisions on how to respond.

Sam: No, I completely agree. And that was one of the visions that we had at the Rockefeller Foundation when I went and joined. And I still think that we need an independent non-governmental, non-WHO organization, similar to a Santa Fe Institute. That’s not a political body, it’s not a think tank, although it is involved in a little bit more policy development. So it’s more think tank than SFI, but not all the way in that direction. And it’s not that there’s a problem with the governments, there are problems with the governments. It’s not that there’s a problem with the WHO, there are problems with the WHO, but they all have different missions.

And I think there’s this gap around the thing that you’re actually talking about, which is developing the playbooks for different kinds of infectious disease, outbreak scenarios. What needs to happen, and then developing the policy mechanisms around them that will be both national and international, and require NGO cooperation and other intergovernmental multilaterals to participate, but who maybe aren’t as beholden to member states as the WHO is, aren’t as tied to politics as the governments are. And again, this non-governmental organization will have its own weaknesses, because it’ll be beholden to whose ever funding it and a variety of other things. But it will compliment what’s happening inside of the governments and then what’s happening outside of the governments in the multilateral public health agencies.

Jim: And here’s some other thing, I need to publish this essay. I’ve written an essay called the Department of Wicked Risks, suggesting that US government establish a cabinet level post for thinking about all of our wicked risks and doing planning in advance, plus having a $5 billion instant intervention fund that they can throw at anything anytime they want. And one of the parallels I give is the military has files on almost any possible scenario.

For instance, if Albania were to invade Montenegro, there is some staff officer in the Pentagon who has in his drawer the official response of the military, “All right, we move an aircraft carrier near to make sure they don’t fuck something up.” I don’t know, I don’t know what it is, but I think we have one. We probably don’t have that red file approach, that I call that, for 15% death, 10% death, 5% death scenario. And we should, because somebody has to make these wisdom calls, because that’s a wisdom call. Do you let all the vaccines loose right now and thousands of people might die, “Oh, well, from the vaccines, but we save hundreds of millions of lives,” or is that the wrong thing to do? Somebody must to have a wisdom call and trusting politicians to do that unadvised pretty hard.

Anyway, let’s get back to this, my little scenario. So lets say things work, we get testing pretty quick. But let’s say vaccines are harder than they were for COVID-19, or at least as hard. So we’re got a year to hold the line. What do we need to do? And let’s say, let’s pick, it’s that it’s SARS level, so 15% fatality rate and let’s make it as infectious as the original COVID-19. So pretty infectious, but not at the maximum. How do we hold it together for let’s call it a year until the vaccine gets here?

Sam: I don’t know if we could, I think have to stop it with test-trace-isolate.

Jim: So have to stomp it down.

Sam: And we know how to do this. And the math is actually pretty straightforward. We’ve published on this, there’s groups from London School that had published on this. For a virus like the Wuhan strain of SARS-CoV-2, well, for any pathogen, most of the chance that they cause an epidemic involves two numbers. One number is this infamous R0 or R-naught, not which is the average number of secondary infections in a susceptible population from one infected individual. But actually the R-naught is not the biggest player. The biggest player is actually the variability in the R-naught that shows up. And so the standard calculations for R-naught assume that it’s a plus on process, which means that the mean, and I know what it means, but I’m just saying it for the listeners, it means the mean and the variants are the same. And so you don’t really have super spreading in the traditional sense.

So the second number that matters, and this is the one that is most important early on, is the reliance on super spreading for sustained transmission. And so viruses like Ebola are really heavily reliant on super spreading. You turn off the super spreading and they quickly go extinct on their own. And SARS-CoV-2, the original Wuhan strain, was actually pretty heavily reliant on super spreading. If you remember, there were lots of introductions in the US that didn’t lead to long chains of transmission. And so you plug in, we know what both of those numbers are for SARS-CoV-2 original Wuhan, the R-naught was probably between three and five, and the degree of super spreading it’s parameterized with this negative binomial distribution, the kappa parameter, which is probably somewhere between 0.3 and 0.8. You get both of those numbers, you plug it into a pretty simple equation and what pops out the other side is you need 90, 95% success on your contact tracing in terms of isolation to stop it.

Now if it’s much less than 90%, the chance that whatever pathogen that shows up is going to cause a pandemic is pretty low. So if you only need… So Ebola is probably in the 60, 70% containment range. That’s why it’s pretty straightforward to stop Ebola. That’s why countries with without a lot of resources can stop Ebola, because you don’t need to have 90% containment. You can do it with 60, 70. So if it’s much less than 90, it’s not really likely to be a problem. If it’s much over 95, that’s getting into omicron territory, influenza territory, there’s probably not a lot you’re going to be able to do unless you’re China, or unless you have really sophisticated digital contact tracing like they do in South Korea. And so I’m actually pretty convinced that almost any pathogen that’s actually going to be a threat and that we can actually do something about aside from just die, is going to require between 90 and 95% containment to stop and we can reverse engineer what we need to do going from that number.

Because again, for a pathogen that is 15, 20% fatal, society will collapse before the vaccine gets here. And so we have to stop it, we have to stop it, or we have to anticipate what it’s going to be and have the vaccines pre-staged and ready to go. I think realistically you’d need to have mass vaccination rolled out certainly within the first six months, but probably within the first 90 days to six months. And you can’t do that de novo, it has to be something that’s pre-staged. So either you’ve got to have the vaccine already done, and ready to go, and the distribution network set up and everything else, and I just don’t think that’s ever going to happen. Or you’ve got to have test-trace-isolate that can get you 90, 95% containment and you’ve got to have that ramped up in the first 30 to 60 days.

Jim: All right, well, I love this. We actually have an answer that is supported by the math, and it fits any disease that fits the mathematics, and you can calculate that relatively early on. But we need to have the command and control situations and the infrastructure in place to make it happen. If the big one hit the United States tomorrow, are we ready?

Sam: No.

Jim: What does it take to get ready?

Sam: I think in order to get ready, we have to have wastewater surveillance always on multi pathogen with the novel detection AI that I’ve been discussing deployed across the US deployed at strategic airports and ports of entry. We’re getting there, that’s actually the best thing that we have going for us right now is our investment in wastewater, but we need a lot more, and we need a lot more on the technology side. We have to have the ability to go from genome sequence, to mass clinical testing within 30 to 45 days. We’re not even close to that, but we could do it if we invested in the university labs that are already in place. It could be done. And then make sure that we have the right FDA regulations, et cetera, around the emergency use authorizations. Because one of the things that we probably want is your analogy with the vaccines. We’d want the universities to develop their own primers, get them out there as fast as we can, start the PCR testing, and then share the knowledge and eventually the best one will win out via natural selection processes.

So we have to have that scaled up. And then we have to have digital contact tracing. And it needs to both involve technology applications on people’s devices, but the ability to leverage high resolution mobility data quite quickly to identify areas where we would need to intervene and respond. And that’s going to require the kind of social contract that you and I were talking about earlier where we have some of these difficult conversations around what are the triggers that release certain kinds of data, what are the processes for doing that, et cetera.

And then the final thing, and this is something that we haven’t really talked about, so I’ll just mention at the end, I’ve been working with this new nonprofit called [inaudible 01:44:05], who’s founded by Professor Lauren Ancel Meyers, whose University of Texas, Austin, and also SFI science Board. Phil Siegel and Molly Peroni, who are background in business, private equity, et cetera. And what they’re doing is building a universe of pathogen threats to try to populate that folder, you talked about if possible scenarios that we need to be prepared for. So we’re going to build all this stuff I just talked about, and then we need to be regularly pressure testing it to make sure that it can actually work in the face of the big one.

Jim: Wow. I love it. Policy people who happen to be listened or people who more likely, no policy people? Get them to listen to this episode. This, I think, everything I can think about Sam just nailed it. But it requires a significant amount of investment, but none of these things strike me as undoable.

Sam: I think it’s all very doable. And I think also, and we touched on this a few times, it’s one of the challenges for pandemic preparedness is that you have to have people imagine a black swan event and put a lot of money down against something that we just can’t ever imagine is going to happen. Now we can, so we’ve got that going for us. But the wastewater surveillance, tons of applications for routine infections, one of the best markers for sepsis changes in background levels of E. coli infection in the population because a lot of sepsis is readmit for untreated, or undertreated, or resistant urinary tract infections. And so wastewater surveillance that’s looking for E. coli infections, great marker for sepsis. Sepsis is one of the most expensive things in the United States. There are tons of applications for this stuff that don’t require pandemics.

The same thing with clinical testing. We need way more clinical diagnostic testing for infectious diseases in the United States, and we can leverage the university’s low cost, bring healthcare costs down through these clinical testing mechanisms at the universities, et cetera. So I think there’s a way of packaging all this, that it’s all getting ready for the big one, and when the big one comes along, we’re going to stop it and we are going to do something that will save more money, more lives and livelihoods than anyone can even imagine. But it’s going to pay for itself in multiples in peace time. And so that’s why I think doing this is so important. Yes, it will require some investment and a little bit of vision on the part of the government, but I think there’s a way to put this package together where it pays for itself in multiples in terms of the economic benefit just from routine infection diseases and bringing healthcare costs down.

Jim: Wow. Well, I really want to thank Sam. I figured we’d have an interesting conversation, but this has been a plus plus conversation.

Sam: I really enjoyed it, Tim. I really was excited to have you reach out to talk about this. It’s been something I’ve been thinking about a lot and also really, really enjoyed the conversation and gave me a bunch of other new things to think about.

Jim: Yeah, this has really been great. Thank you very much. That’s Sam Scarpino at Northeastern University, in Boston. Anybody has any papers or references on the things that we question? Send them to and we’ll put them up on the episode pages assuming Sam takes a look at them and says they’re not cranked bullshit, that is. So anyway, thanks again.

Sam: Thanks so much, Jim.