In response to a question about evidence that surfaces are not spreading the virus: 

Good question, I wondered whether I should write more about it then. I think one's prior beliefs/priorities matter a lot here, so let me be explicit about mine first. I think there's a limit to how many precautions people will follow, especially over the length of time we need to stop this pandemic. The more things we ask people to do, or the more complex they are, the less likely they are to be followed. And if people stop following some guidelines and nothing bad happens, they will be more likely to stop following other, more important ones too. So it's important to focus efforts on getting people to follow a few important and simple guidelines for the sake of general compliance. At the individual level, it can be perfectly rational to go beyond these guidelines. With that as preamble:

Essentially nobody challenges the idea that transmission by fomites (particles on surfaces) is possible. The question is whether it happens in the real world, and at a frequency that's high enough for us to mandate/suggest specific actions. The WHO considers fomites to be a plausible mode of transmission, but their report also states: "Despite consistent evidence as to SARS-CoV-2 contamination of surfaces and the survival of the virus on certain surfaces, there are no specific reports which have directly demonstrated fomite transmission". Their communication of scientific evidence has been poor, so I looked into what epidemiologists & virologists were saying, especially on Twitter. After months of contact tracing around the world (albeit much less than ideal), I've encountered discussion of only 3 cases where transmission by fomites (particles on surfaces) may be more plausible than other explanations, and that's being generous (see first Twitter thread below). Even these cases are very far from certain. And infection rates within households seem to be lower than one would expect if surfaces were important for transmission.

Since it's hard to show a negative, there's no paper I can point you to which spells this out clearly, or states precisely what the relative risks of surfaces vs. droplets/aerosols are - the numbers are still unknown! But the specialists have generally downgraded their perceptions of the risk of surface transmission, though they hedge their public statements appropriately. See the articles & tweets linked below.

Three caveats: (a) it's a hard topic to study, so it's possible that fomite transmission has happened where contact tracing has been unsuccessful, (b) fomite transmission may have been incorrectly attributed to aerosols in spaces like offices, and (c) since hand-washing and sanitising was one of the major initial recommendations, we may have stopped transmission via fomites in the real world. If we ease up on that, it may start to happen.

Despite those caveats, I think that the balance of evidence so far suggests that surfaces are not important. I understand the desire to take precautions, but personally don't sterilise things I bring home, and did not do this even when the risks were higher here. I have recommended to concerned family that they could consider just leaving things on a balcony for a while if they wanted to be very safe. Virus numbers on plastic decrease by a couple of orders of magnitude in two days in cool, dry conditions; it's much faster when warmer and more humid, and on most other surfaces.

[I've linked to a few papers below, but they seem less helpful than they appeared. I found the threads on Twitter more helpful because they were to the point and open to immediate challenge from other experts.]

Papers:

https://www.nejm.org/doi/full/10.1056/nejmc2004973 (can survive on surfaces)
https://msphere.asm.org/content/msph/5/4/e00441-20.full.pdf (...but decays faster at higher temp & humidity)
https://academic.oup.com/.../doi/10.1093/cid/ciaa905/5868534 (hospital surfaces have viral RNA but no viable viruses found)
https://www.thelancet.com/action/showPdf?pii=S1473-3099(20)30561-2 (much-publicized commentary, not the most useful, I think)
https://wwwnc.cdc.gov/eid/article/26/9/20-1798_article (suspected fomite transmission, weak evidence and could well be aerosols)
https://wwwnc.cdc.gov/eid/article/26/6/20-0412_article (suspected fomite transmission, weak evidence and could well be aerosols)
https://www.cdc.gov/mmwr/volumes/69/wr/mm6914e1.htm... (suspected fomite transmission, weak evidence)

Articles:

https://www.who.int/.../modes-of-transmission-of-virus... (WHO report mentioned above)
https://www.krisp.org.za/.../StAugustinesHospitalOutbreak... (hospital outbreak in which physical contact or fomites are suggested but without much evidence, see page 20) ". Summary at https://www.sciencemag.org/.../study-tells-remarkable...
https://www.cbc.ca/.../coronavirus-surfaces-groceries... (general article, several experts offer their opinions)

Tweets:
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https://twitter.com/DiseaseEcology/status/1279097818351726592 (good thread summarising the best known case while highlighting its rarity)
https://twitter.com/Bob_Wachter/status/1263673015591530496
https://twitter.com/CathNoakes/status/1282230720778457088
https://twitter.com/firefoxx66/status/1260905943933620226 (see rest of the thread too)
https://twitter.com/TheBinderLab/status/1254166676515454978
https://twitter.com/LucyStats/status/1282112670230106112 (contrary opinion)

UPDATE a week later: A recent Atlantic article on the topic summarises this pretty well: https://www.theatlantic.com/ideas/archive/2020/07/scourge-hygiene-theater/614599/ 

​It does lean a bit on that commentary piece that I thought was not very helpful (among other things, it misrepresents the goals of the papers on rate of viral decay on surfaces). But that's a minor weakness.

I mentioned in my last post that an increase in US virus deaths was expected this week after 2 months of steady decline.

Well, it's here (see bottom right graph).

Earlier, cases were increasing but deaths decreasing. This mismatch had multiple possible explanations, and this week's reversal supports the main one I wrote about - that we had been catching cases earlier than before. There were more hopeful explanations, such as that we had shielded vulnerable populations successfully.

The worse news is that this will probably grow for weeks. First, because we've got about 4 weeks of case increases baked in. Second, because many of the recent cases were from young people. Given the competence with which this has been handled, they have probably passed them on to older people, who will fall sick later and start to die later, but at much higher rates.

What a shitshow.



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In response to a question about whether the daily death curve would eventually match the daily cases curve, implying about 4k deaths per day (after accounting for undertesting in April):

Mercifully the better projections don't foresee anything quite that extreme; it looks more like 4-6k per week rather than per day. I don't fully understand why that is, but I think it's largely because the age distribution of recent cases has skewed younger and younger. That has reversed recently (see this plot for Florida, for e.g. https://twitter.com/.../status/1283134585665200131/photo/1) and that will probably show up as an increase in another 3-4 weeks. Big uncertainties, as you know, especially because this involves forecasting policy and behaviour to some extent.

Those forecasts I mentioned: https://covid19-projections.com/us & https://viz.covid19forecasthub.org/. (The first shows deaths per day, the latter per week).

Coronavirus news #7. As always, please point out my errors. I started making notes a couple of weeks ago before getting side-tracked. In the meantime, we've had 2 million new reported cases - about 20% of the total.

1) About 4000-5000 people are reported to die everyday because of this virus, or about 3% of all deaths. Globally, that has been stable for nearly 2 months. The true number is almost certainly higher, but it's unlikely to be by a whole lot (high uncertainty in India and some other places, though). Please remember that the people who don't die don't all recover completely. Many, many more are being struck with long-term damage to their health. That includes a substantial number that don't have any symptoms and may not even realise it now; many asymptomatic people show signs of lung damage in scans. So though it's normal to have one's standards for safety slip after all this time and with fewer immediate consequences in our daily lives, please be safe. Wear a mask.

2) Though the US mostly leads the news, Brazil and possibly Mexico are likely in worse shape, with India bidding to take this miserable crown. South Africa also seems fairly likely to join that group. Nobody really knows what's happening in Russia, because there's clear signs that some of the data being released are junk. Unlike the other countries, the US has actually been declining in deaths per day since the beginning of May. Brazil, Mexico, South Africa and India are still increasing, and the first two have substantially more daily deaths than the US. There has been a worrying drop-off in reporting (even by scientists) about the state of the virus in the developing world, with Brazil being a partial exception.

3) The US has seen explosive growth in cases in the last three weeks but deaths per day have actually declined since early May. There's multiple reasons for this. A greater proportion of new cases are in younger people (~10-100X less likely to die), we have developed better methods to manage severe illnesses, and perhaps most importantly, we are catching cases earlier. The last point implies that the lag between increases in cases and increases in deaths should be increasing. It used to be about 2 weeks; it may be 3 or 4 now. If this hypothesis is true, we should see increases in deaths across much of the US in another week or so. We can be fairly confident that the growth in cases is not simply because of more testing, because many of the outbreaks are also seeing an increase in the percentage of positive tests - a sign that an increasing number of cases is being missed.

4) Europe shouldn't feel too thrilled. After getting things under control, they've messed up the reopening and experienced about a month of increasing daily cases. Switzerland has finally mandated mask usage in public transportation. I think that ought to be the minimum policy change that we should aim for. There seems to be reasonable evidence that mandatory mask usage and closing some activities that involve crowds or closed spaces (e.g. bars) would be sufficient to kill the pandemic. Mask usage alone does a lot of the heavy lifting. Even tighter restrictions would do it faster but might be overkill if the situation is not yet out of control.

5) Antibodies are the focus of 2 important types of testing: (i) testing to figure out if someone has had the disease and will therefore be immune, and (ii) testing to figure out what proportion of the population has been infected by the disease ('seroprevalence studies'). This is how we get exposed/infected numbers like 5% of the Spanish population (it's similar in the US). But we now know that antibodies actually decay below our ability to detect them relatively fast, roughly on the scale of months. This does not mean that these people have lost immunity; they almost certainly retain the ability to produce more antibodies in the future if re-infected by the virus. Also, some indeterminate (but probably low) number of people apparently tend to not show much of an antibody response. However, most (if not all) people develop another type of immunity that is mediated by specialised T-cells. These provide long-term immunity and are generally ignored because they are much harder to test for. They are not quite as effective as antibodies but are likely important, though we don't know much about their role in COVID immunity yet. Bottom line: (a) we are still fairly confident that people develop immunity after infection, (b) the antibodies we test for decrease over time but we retain immunity, (c) this antibody decrease & T-cell response adds an unknown but probably small bias to our estimates of how much of the population has been exposed.

6) There appears to be some pre-existing immunity in people who were infected by SARS-1 many years ago and by an unknown coronavirus. There are 7 documented coronaviruses circulating in human populations, but there is likely an unknown one circulating in South-East Asia that has protected populations there through this 'cross-immunity'.

7) Most evidence points towards us being very far from any sort of herd immunity. If the governments of the US, India & Brazil give up on containing this, I would say we are heading towards millions of deaths with high probability (given their failure so far, we are headed there already with moderate probability). To speculate even further, tens of millions is not implausible in this scenario.

8) Last month, I wrote that perhaps 80% of new cases are caused by 10% of infected people (superspreaders). This has important implications for how to do contact tracing. The standard method is to find everyone an infected person was in contact with and notify/quarantine them. But since they were almost certainly infected by a superspreader, an improvement on this is to identify the superspreader who passed it to them and then trace everyone they were in contact with. This 'backward contact tracing' can be thought of as a second level that makes the whole procedure much more effective at stopping an outbreak. That said, contact tracing isn't feasible when you have a massive ongoing outbreak.

9) There is now plausible but inconclusive evidence that the virus has adapted during its spread. A mutation that increases the spread in limited lab experiments has also come to dominate in new cases around the world in the last 3-4 months. But it could have spread more just by chance, by being in the first cases that spread to new places. However, the mutation does not appear to do anything to the virus' lethality, so this evolution has not made things any better for us. And it does not change anything about how we should prepare for or treat it.

10) Despite all the press about treatments, no specific medication we have so far is close to being a cure. Hydroxychloroquine does not do much and has wasted time and money. Remdesivir and Dexamethasone have relatively weak effects or limited use-cases; they will save lives but are not cures. When used most effectively, dexamethosone appears to save about 25% of lives lost. This is progress, but we need a lot better. Both also have severe, dangerous side-effects that can kill. We are on the way to having monoclonal antibody treatments, probably within a few months. This would be a big improvement but is probably going to be expensive. The US appears to be doing its best to corner the market on these right now, though that investment should stimulate more development.

11) Children appear to be about 1/3 to 1/2 as likely to get infected. And they are much less likely to fall seriously ill or die once infected; they have ~100X lower probability of dying if infected, relative to people over 80. This has obvious implications for reopening schools and colleges. I think doing so is probably feasible if coupled with distancing, mandatory masking, and mass testing on a regular basis to catch outbreaks early. But the details matter a lot.

12) There's now even more evidence that surfaces are not that important for spreading the virus.

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In response to a question about whether we were headed in the right direction at this time:

Absolutely in the wrong direction in the US right now.

We still don't have enough tests or protective equipment, mask usage is not high enough, people in outbreak areas appear to still be frequenting indoor restaurants (less than normal, but still), new cases are going up rapidly, and the federal government & the CDC continue to be disastrous (more on that soon).

The main good news is that deaths per day are much lower than May, but as I said above, I expect that to increase soon. There's a phenomenal amount of scientific talent, of course, but it's not much good if the people in charge are incompetent, malicious or craven (or some combination of the above).

Other that that, the prospect of monoclonal antibodies, some advances on treatment, and some progress on the vaccine front are all encouraging. But none of them is close to deployment.

Coronavirus news #6. As always, please point out my errors. Not an expert in this specific domain, but I have relevant training and am trying to keep up to date. I encourage those of you with relevant expertise to also spread your understanding as best you can.

1) It's happened without much fanfare, but it seems as though contact with surfaces is no longer thought to be a very important method of spreading the virus. In March, there was a lot of advocacy around using gloves, washing hands, & avoiding face touching. As more evidence has poured in, the cautions and analyses have shifted towards focussing strongly on inhalation of viruses. I have yet to see clear research on the relative risks (please tell me if you know!), but I think this is a fair summary of epidemiologists' present beliefs. I'm not saying that viruses do not spread through contact with surfaces, so continue to take reasonable precautions. But I offer this to allay the fears of friends who go to incredible lengths to sanitise everything they buy or that enters their house. Letting new acquisitions sit in the sun for a week is overkill.

2) Brazil and India have exponentially increasing case numbers despite lockdowns - in India's case, one of the most brutal in the world. The outbreaks are concentrated in some regions, so it is possible that they will get contained. But given exhaustion with the cruelly mismanaged lockdowns (at least in India), I'm doubtful they will be. And they have
20% of the world's population between them.

3) As a consequence, the situation right now is far worse than I think most people realise. Global daily deaths are slowly decreasing (currently ~3000 per day), driven by improvements in the situation in Europe and the US, which were hit worst. The news is moving on to the economy, tourism, protests, and so on as local situations seem to stabilise, and people get bored or desperate. But this apparent progress can be quickly reversed by just one or two new outbreaks that can happen anywhere, and these seed new outbreaks in turn. We do not have a single pandemic, but a patchwork. Regions/countries with outbreaks can be isolated, but the success rate needed to prevent them seeding new outbreaks is very high. Most countries have not displayed the competence needed. We are stuck in this situation till we have a vaccine.

4) As India's & Brazil's numbers rise, global daily deaths will start to increase again. We are now looking at possibly millions to even tens of millions of deaths. This probably seems unlikely to you and I hope it's totally wrong. But in March, the possibility of tens of thousands of deaths was seen by many as unwarranted pessimism, and hundreds of thousands as wild fantasy. And yet here we are. We ought to learn something from this about how unreliable gut impressions about worst-case scenarios and tail risks are. And perhaps eventually turn that insight towards another area where scientists have spent decades venting their spleens about tail risks: climate change.

5) A better argument for why millions of deaths is plausible: a few weeks ago, Spain and France did the biggest & best random testing programs run so far, helping to fill a massive gap in basic data. These found that the infection fatality rate is about 1%, just as epidemiologists have been saying since at least March. Remember that infection fatality rate is the % of people who ever got infected that die, which is the number we are most interested in. Most reports have been about the case fatality rate, which leaves out all the people who got infected but did not know about or report it; this varies a lot based on medical system and reporting practices. Also, about 5% of those countries had been infected (i.e. had antibodies) at the time. If the virus were to continue to spread, you would not get 20 times as many deaths, but you would get very large numbers that are in line with those that basic epidemiological models predicted months ago. Apply that logic and the basic numbers to other parts of the world and you gets millions to tens of millions.

6) A particularly worrisome pattern: there are many more young people infected and hospitalised in India and some other countries than was expected. There's multiple reasons why this may be, such as exposure patterns and data biases. There are more scary possibilities but right now no real evidence for them. But even so, outbreaks among young people are a massive threat to countries with much younger populations, where the hope was that the vulnerable elderly could be isolated while the young slowly return to work.

7) Since I'm thoroughly sick of the endless debate around Sweden and its tactics, allow me to point out stories from other countries that are not discussed much. Take Mongolia and Vietnam, which have had zero deaths between them with a combined population of 100 million. Zero. And they share a border with China! Senegal, though further away, has had about 40 deaths in a population of 31 million. Ghana: about 35 deaths among 16 million people. Ethiopia: 12 deaths out of 115 million. All these countries are relatively poor and lack the capacity of European and American healthcare systems, in terms of manpower, training, and technological sophistication. What they share is that they took action in January, while more developed countries did nothing. I'll add that they are also younger, but I think that is a less important factor. Ghana and Ethiopia are noteworthy, because I understand they implemented better contact tracing than most of Europe or the US. Ghana also tested large numbers of people by using pooled testing, an old method I discussed in the very first of these posts in March. Germany and India have also been using the same strategy, which should have been employed months ago. I was personally terrified about outbreaks in developing countries, and want to highlight that many of them have outperformed the wealthiest countries to an impressive degree, one that ought to shock us. They may yet suffer badly, but they have done well so far.

8) Reopening in many countries is politically inevitable now and justified in many cases. Did the lockdowns work? It's a question that's going to be contested very strongly because of the political and economic implications. But please keep in mind that this is not exactly a yes/no question. There was not a single type of 'lockdown'. Instead, there was a wide range of activity restrictions, ranging from stay-at-home with almost no exceptions (China, India, Italy, France) to limitations on gathering places such as restaurants & movie theatres but not much else (Switzerland) to essentially no legal limitations, just recommendations (Sweden, Ethiopia). There were successes in countries in all these categories. So a case could be made that the strictest stay-at-home orders were not needed, at least in areas without high population densities. But let's put that in context. Strict restrictions were entirely justifiable at the time given the limited information we had and the very real threat of having healthcare systems overwhelmed (as happened in northern Italy). Shutdowns were protection against very real tail risks. Additionally, even the places with no limitations did have big reductions in gatherings and foot traffic because most people are not idiots and generally took more care than usual (more on this in the next point). So the absence of stay-at-home orders did not mean that economies did well; businesses lost a lot of customers because people chose to stay away from each other.

9) It's increasingly clear that disease spread is largely driven by superspreaders. The numbers are far from precise, but something like 10% of infected people cause 80% of new infections, while perhaps 70% do not infect anybody. This is a more extreme 'clustering' than many other diseases. We don't know if there's anything particularly different about that 10% that makes this happen, in terms of physiology or immunology. But this represents an important opportunity: if those superspreading events can be contained, the epidemic may die out by itself. [The following is my speculation] I suspect this is why even weak reductions in population activity were extremely effective in suppressing the disease. And why many places have not seen surges in cases after reopening. When people took the logical step of avoiding the most crowded areas (stadiums, public transportation, bars, restaurants, etc), they effectively prevented a lot of potential superspreading events. I'd like to stress this point: it shows that even weak compliance with distancing recommendations/rules can be immensely beneficial for the whole population. This is worth keeping in mind as the lockdowns are lifted, new outbreaks happen, and plenty of people can't be arsed to obey the resulting lockdown reimposition.

10) As countries reopen, there is going to be intense debate and lobbying about what to allow. Given what we know, crowded places/events with a lot of people expelling a lot of air are probably the riskiest. An incomplete list would be: gyms, sports stadiums, concerts, university dorms & big classes, some places of worship (there seems to be a weirdly high number of reported outbreaks among choirs), nightclubs, some kinds of restaurants & bars. There's some evidence that younger kids don't get infected much and so reopening schools may be less of a concern (only moderate confidence in this claim right now). I expect places of worship will be opened sooner than ideal, so we ought to be talking to religious leaders about how best to manage the consequences of the outbreaks that will ensue.

11) As we reopen, there are going to be new outbreaks. In an even mildly competent world, we'd have built up the capacity to do lots of testing, tracing, and isolation of newly infected cases. I don't think we have done this to the degree needed in a lot of countries. Since we have not done this, a second, poorer option is cycles of shutdowns and reopenings as outbreaks are detected and controlled. Except plenty of societies are barely tolerating the first shutdown, so subsequent shutdowns seem almost guaranteed to be ignored. So what happens instead? I expect we'll see plenty of businesses change how they function for the near future till we have this under control. Some businesses may also start offering exceptions to these restrictions if customers can provide proof of immunity from antibody tests. This will essentially provide extra services to people who have immunity, creating a market for both fake test results and for people to voluntarily get infected. A while ago I mentioned that governments manage this by providing people with official 'immunity passports'. This is understandably opposed by civil liberties advocates, but we might end up with a messy private version of this instead.

12) I mentioned universities earlier and want to expand on this. A combination of factors are going to send a lot of universities - especially in the US - into financial freefall. The risk in crowding lots of people together into classes & dorms, the poorer educational experience of video conferencing, high tuition fees, immigration restrictions cutting off high-paying foreign students. and the inevitable recession-driven slashing of government funding (in the US) are all going to hit the bottom line. Also, universities have apparently been mismanaged to the extent that many do not have the financial reserves to weather these storms (if they can't even manage money, why on earth did we let the corporate world start running them?). The famously large endowments are not (according to university spokespeople) funds that can be used to manage the crisis, because money willed to the university comes with specific conditions attached. Using them to tide over general budget shortfalls apparently violates a bunch of legal agreements, ones which universities are less happy to break than say, union-negotiated job contracts and pension liabilities. The biggest universities will probably manage somehow, in part by taking in students who might otherwise have gone to lower-rung universities. At least some of those lower-rung universities may have to have to radically change or close down. Hopefully some good will come from the necessary experimentation. Teaching in the lockdown has kicked many of us out of our rut and may help improve what we do. With more support and practice, we could perhaps be teaching more students, better. But it seems likely to be a bleak few years to be an academic, especially an early-career one.

13) I've argued previously that you should ignore the headline of the day, because most science papers offer provisional results, the media communicates science badly, and you will end up misinformed. I stand by that, but feel obligated to talk about one study in the Lancet that claimed that hydroxychloroquine does not help with COVID and actually kills people instead. For obvious political reasons, this story spread like wildfire. Well, there are massive problems with that study, and not of the usual scientists-disagree-about-how-to-interpret-everything kind. There's an extremely good chance that it is a hoax and the data completely made up. Here's one valuable critique you can read: http://freerangestats.info/.../implausible-health-data-firm . Note that this does not mean that hydroxychloroquine is actually good.

14) We're likely to see more protests of all kinds soon, and not just in the US. These protests are extremely likely to spread the virus. If you argue that the goals of a specific protest are more important than the possibility of spreading the virus, be prepared to listen when a similar argument is made by those protesting for goals you dislike. Dismissing their arguments out of hand will lead to charges of hypocrisy, and people who disagree with you politically will have less reason to listen to your advocacy on any topic. In any case, we should be preparing for outbreaks in all these cities where protests happen. The sad fact, though, is that contact tracing is going to be a much harder sell when protestors view it as a way for authorities to track down and suppress political dissent. Contact tracing that maintains privacy may be vital here.

15) Slow vaccine progress continues to be made on a variety of fronts. Two of the best initiatives on that front are those by the Gates Foundation and Operation Warp Speed by the US government, both of which are spending billions to build capacity for vaccines that we do not have yet. Most of that money will end up being spent on vaccines that do not work. But if one or two work, it could save millions of lives and trillions of dollars. This is the kind of targeted, wise initiative that we need more of, and not just to deal with this virus.

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In response to 2 questions about my speculation in point #9 that weak measures may be sufficient to stop superspreading:

(i) about modelling rare events

A toy model should be relatively simple to implement. If you want to get fancier, here's some resources you might find interesting/useful:
https://www.nature.com/articles/nature04153 (old & general, and already supports the basic intuition)
https://covid.idmod.org/.../Stochasticity_heterogeneity... (very new, specific to COVID)
https://epidemicsonnetworks.readthedocs.io/.../index.html (Python module for modelling epidemics on networks)

(ii) explaining my intuition behind why weak measures can stop superspreading:

I'm going to invoke some realistic numbers for this based on what we now know about COVID:

Imagine 10 people are infected. 7 of them do not pass it on; actually, let's say they *cannot* pass it on, for argument's sake. Of the remaining 3 people, 2 pass the infection on to 1 other person each. Let's say this is to a family member or someone they are closely associated with. The disease spread by these 9 people may be unaffected by distancing & lockdowns, but it only results in 2 infections.

For the disease to continue to spread, the remaining 1 person has to infect more than 8 people, since the initial 10 has to infect more than 10 or it dies out. In ordinary times, this may happen when they encounter crowds at the office, or church, or a restaurant, or on the bus, or a concert, or so on.

When people are distancing and the most crowded areas are shut down or avoided, this one infective person encounters fewer people and at lower densities. This makes them much less likely to pass it on to more than 8 people. Even if people are not strictly following the rules or the lockdown is quite mild, they may infect only 4 or 5 more. The newly infected cohort is 7 people (2 + 5), which is lower than the previous cohort. Since the same logic applies to them, over time the number of infected dies down and goes to zero.

Basically, preventing a few people from each infecting 10 people is easier than preventing lots of people from each infecting 2 people.

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In response to a question about a Medium article about Covid being a 'blood-vessel disease': 

It does seem to be a plausible mechanism, though the Medium title is hyperbole. There's been a couple of months of reporting on this, and the story does seem to be gaining in prominence (see this from yesterday, for example: www.sciencemag.org/news/2020/06/blood-vessel-attack-could-trigger-coronavirus-fatal-second-phase )

There's an odd angle to this story that I spent some time on. The Medium article cites only one scientific paper, so I took at look at it. Bizarrely, it shares a couple of authors with the hydroxychloroquine paper that appears to be a hoax (the one I wrote about above in point #13). That made me worry about how reliable this paper was, so I dug into that a bit. As best I can tell, the shared co-authors were not the main players in the (alleged but very likely) hoax. I'd guess they were innocent; their other co-authors on the dodgy paper were from a company that seems to have fabricated the data. It does call these doctors' judgement into question, though.

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In response to a question about the role of population density and infrastructure:

I agree that density & infrastructure are likely to be very important, and probably a major reason why New York was hit so horribly. And yeah, that also implies huge differences between states, which is likely to make co-ordinating policy tougher. Low-density states are generally Republican and already relatively sceptical of scientists. If they are fortunate and escape big outbreaks, they are likely to become even less supportive of public health efforts, including vaccination when that becomes possible.
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Europe basically suspended Schengen when it closed all borders, and each country chose its own path and felt the consequences of its own decisions. US states will be pursuing different strategies but won't be able to close borders, which makes the outcomes dependent partly on the policies of their neighbours. I expect this will cause a lot of friction.

In response to a question about the WHO covering for China:

I'm no fan of the Chinese government, and I think the WHO has taken some pretty lousy political decisions in the past few years (it screwed up on Ebola before this). I also agree that the WHO has deferred too much to China on this. But much of this popular story you refer to seems to me to be an effort by governments to shift blame and excuse their own negligence.

China contributes a relatively small portion of its funds. You know who contributes more? The US. And the UK. And Germany. And Japan. And the EU. And the Gates Foundation. Even goddamned Rotary International pays more than China.

Of course, maybe money is not the main factor. After all, the director-general was elected with support from China. So who runs the WHO? It has 194 member states and an executive board of 34 members that is chaired by a leader that rotates geographically. The chair probably doesn't have much power, but FWIW, it was led by Japan till a week ago - hardly a shill for China. Where's the US in all this? Oh, it's not bothered to nominate anyone to its executive board seat, which has been left vacant for years. This is consistent with the US government's choice to ignore or weaken pretty much every international organisation. If the US chooses to ignore these organisations, is it any wonder that other entities increase in influence, if only by virtue of being at the table?

The WHO made statements in January and February that were stupid and wrong, even given only the information available publicly. But you can call it a strategy: they were probably trying to coax China into giving their experts access to Wuhan to study what was going on. To some extent it worked, China did let them in. It was not worth the damage caused by the misinformation. But the WHO has no power to force any government to do anything, so they probably thought mollifying the Chinese leadership was the best option they had. Especially when the only powerful country that could back them in this fight, the US, was in absentia and busy praising the Chinese leadership for their efforts.

Most importantly, however, plenty of countries did get the obvious message back in January and February and took action. Vietnam has had 0 deaths and 300 cases. Mongolia has had 0 deaths and 200 cases. These are relatively weak, poor countries that share a border with China. They simply jumped into action immediately, based largely on information that you could read in any international newspaper at the time. Even Kerala had a plan in place in January.

So whatever influence China may have at the WHO, most of the lives lost have been because of the incompetence of authorities in the US and Europe. This was not inevitable. There was more than enough information available in January and February to take action, and for reasons that I do not understand, most governments and health authorities twiddled their thumbs.

The WHO is a convenient scapegoat for their failures to save the lives of hundreds of thousands (likely over a million before this is over) and the livelihoods of hundreds of millions.

Coronavirus news #4. An update to the last post about the IHME model. Bottom line: there's still good reason to be sceptical of its predictions.

1) I had expressed scepticism about a graph on the IHME website. It confused some epidemiologists too, but one of them finally figured out what was going on. It was driven by a combination of the nature of the model (atypical and not ideal, but not wrong), poor visualisation choices combined with a lack of explanation (uncertainty in the 'fitted' part of the graph was hidden without explanation), and bad luck (the date of max uncertainty was not simply the next day; it had remained stable from the previous week). Too long to explain here, but you can read more here if you're interested: https://twitter.com/CT_Bergstrom/status/1249135767613554690. I partially withdraw this particular criticism; it's definitely bad but not as egregious as it seemed. The other points still stand, and unfortunately some more have cropped up:

2) People with actual expertise in this figured out that the model has a strange quirk: it assumes that once the peak is reached, the epidemic will decline at the same speed at which it rose (once social distancing is in place). There is absolutely no reason to expect this to be true, and the patterns in China and a few other countries do not match this; the decline is generally quite a bit slower. This is not important for the model's main purpose (predicting peak hospital usage) but does matter because people & governments are making plans based on these predictions of numbers of deaths. A more thorough explanation of this is here: https://twitter.com/CT_Bergstrom/status/1250304069119275009

​3) A group of statisticians and epidemiologists tested how well the model predicted deaths on the following day and it did badly. The model was 'fitted' with data till March 29 and made predictions for deaths in all US states on March 30. Every prediction had a '95% prediction interval'; these represent a range of possibilities for the number of expected deaths. If the model worked well, 95% of the predictions should fall within those intervals. In reality, less than 30% did. In other words, the model was very overconfident in its expected range of possibilities - and this is just for predictions on the next day. The model has since been updated and this group will test the new predictions soon. Details in the full report here.

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In response to a question about herd immunity:

Herd immunity is great, the question is how we get there. There are two paths: either we vaccinate most people or most people get infected. Most people getting infected likely means that many millions will die, especially if it happens quickly enough for medical facilities to get swamped. A vaccine will apparently take 1-2 years to develop. Lockdowns for that kind of time frame are basically impossible because people will revolt. If it were possible, it would still lead to a lot of deaths (I have no idea how many) through the damage to incomes and economies & the consequent drop in medical care and degradation of supply chains.

So we're buying ourselves time to prepare right now with shorter lockdowns, working to understand the virus and disease better, develop treatments and testing capabilities. We are probably going to reopen before the public health experts and doctors think is ideal because the public will demand it. I expert partial reopenings in many countries in 2-4 weeks. Switzerland and a few countries actually have a declining total number of infections, so a slight reduction of the lockdown is justifiable. How we manage the reopening will be crucial: Have we put in place the infrastructure to do testing and tracing on a large scale (necessary to avoid large loss of life, despite the privacy concerns)? How small do we start? How do we manage the inevitable jockeying between different entities that want their industry/business/hobby to be allowed? What is the sequence of reopening steps to follow? What planning do we put in place to trigger a second lockdown if the inevitable second wave of cases starts to threaten again?

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In response to a question about reinfection:

Reinfection seems to be way down the list of most experts' concerns right now, and with good reason. Partly there's not enough data, though it has been looked at recently on a small scale. The general consensus seems to be that it would be extremely unusual for this virus to NOT lead to at least some post-infection immunity, because that's what happens with most comparable viruses. So it's a reasonable (but definitely important) assumption till we know more. The reports of re-infections have so far been rare and in some cases don't seem very reliable because of issues with testing.

But if we make the pessimistic assumption that immunity declines with time till it is eventually useless, whether herd immunity takes hold will I think depend on the rates of disease spread and the rate at which immunity declines. And it will be temporary anyway, since this scenario assumes everyone will lose their immunity.

Basically, most realistic paths end with us having herd immunity through vaccination.

If you want to read more about immunity to viruses, this seems like a good place to start (kind of technical, though):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899649/


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In response to a question about the Swedish strategy and the modelling it was based on: 

This led me down a rabbit hole! First, I discovered that Worldometer, my usual source of data on deaths and cases, shows a bizarre weekly pattern in its data for Sweden, with very few deaths on weekends. And it's not a reporting problem, since there's no spike on Mondays. Digging into it further, the original data source does NOT show this weekly pattern, so I don't know what is going on [EDIT: this was because there were reporting lags and the original source would update its numbers when the data came in. But Worldometer would take only the latest day's number and ignore updates to previous days].

But back to the question: I'm not familiar with the Swedish modelling work because the only link I found explaining it was a while paper in Swedish. But I don't think that anyone is really trying to achieve herd immunity in the way that this is understood. Even the weird initial UK plan was not exactly about trying to achieve herd immunity; it was in some sense a side effect. Like with Sweden now, the plan to not lock down was based on the assumption that people will not tolerate the strict and long lockdown that would be needed to completely stop the disease spread. Or that the economic and consequently human costs of such a long lockdown would be unbearable. So given that a long, total lockdown is not possible, how best do we manage the situation? A short, strict lockdown would suppress the disease for now but lead to the same spike once the lockdown is lifted.

The Swedes argue that allowing a slow spread right now through weak measures is the best option available. Assuming they have no shortage of medical supplies (the best argument for a lockdown is preventing medical facilities from being overwhelmed), their plan may be wrong but it's not totally ridiculous. Sweden has a low density of population, so the risks are probably lower than most countries (Stockholm and perhaps some other cities will be more at risk). Switzerland has enforced a relatively weak lockdown (though still much stronger than Sweden) but had a lot of success containing the spread, so this is one point in favour of weak measures. And Sweden retains the ability to enforce a lockdown when things get worse (which they will) and have the population being willing to go along with it.

In the meantime, Michigan just had masses descend on the state capital to block roads (and hospitals!) to protest the short lockdown they have already experienced. What happens when things get worse and stronger measures are needed? I don't envy politicians and administrators having to take these decisions.

Ultimately, short-term lockdown followed by intense testing and tracing still seems the best strategy. But there's so much unexplained variation between countries that it's hard to claim with any confidence that the Swedish approach will fail.