Teaching meets COVID-19 research

Semester is starting to loom large, lessons start in four weeks. I will be teaching several things, including biological physics – a course where I also try and blend in some learning of estimation. Of course, for biological physics I currently have no shortage of real-world examples. So let’s look at one that involves some estimation. Question: If Guildford’s nightclub Casino is full to capacity, what is the probability* that none of the patrons are asymptomatic carriers of COVID-19? Casino’s capacity is 1,500. ONS data on the fraction of the population that are infected is here. A reasonable estimate for the fraction of people infected with COVID-19, that do not know it, is somewhere in the range say one in five to one in three.

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The problem is that people are prepared to pay for the cherry, but they won’t pay for the cake

The title is a quote from the excellent Vaxxers by Sarah Gilbert and Cath Green, on how they led teams to develop (with others and with AstraZeneca) the Oxford-AstraZeneca vaccine, and to bring it into use to vaccinate millions, including me. It is very readable, as well as being an inspiring read. If you are looking for your next book, I strongly recommend this one. The quote is from the final chapter, and I think it is worth quoting some more from that chapter:

Academic vaccine projects that attract funding are almost always to make a vaccine for a specific disease, not to do the underpinning work on more general improvements …. This work could have cut months off our response time, and the amounts we were asking for … look laughably tiny compared with the hundred of billions we have had to spend on fighting this pandemic. … [A] significant chunk of the UK funding … has come from the UK’s Official Development Assistance budget – a budget that has just been cut.

I recognise and sympathise with the frustration that vital underpinning research can be almost impossible to get funded. In many cases over 90% of attempts to get funding being rejected and funders often want you to show how-paradigm-shifting etc is your research. But many processes that we rely on, from making vaccines to rubber gloves, have parts that are poorly understood and done at the moment in a rather empirical way. This is partly because no funding body is interested in funding work to understand how they work, and so make them work better and faster.

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It is better to learn from others mistakes, than to blindly repeat them

Above is a plot of the number of children being admitted to hospitals in the American state of Alabama, due to infection with COVID-19. This is per day and per 100,000 of the population. To put it into context, the population of England is about 56 million, so three children admitted to hospital per 100,000 is about 1,500 children admitted to hospital each day. The data is from the American Centres for Disease Control COVID-19 dashboard. Note the over 300% rise in hospital admissions in the last week. In the USA school starts earlier than in UK, I think term starts in Alabama in early/mid-August. As you can see, the consequences of the schools reopening on transmission of COVID-19 among children, is dramatic. Many schools in Alabama don’t require masks, I guess many of them are not taking action on ventilation. The Delta variant of COVID-19 is very contagious, and so if you crowd unmasked children together in poorly ventilated classrooms, you get what you see above.

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Are infected hamsters really so much more dangerous?

I’m reading a preprint by Hawks and coworkers. They used controlled lab experiments with hamsters to show that when infected the hamsters breath out infectious SARS-CoV-2 — the virus that causes COVID-19. This is in small (less than 8 micrometres in diameter) droplets, that can travel several metres across a room. This result is not a surprise but it is good to show this. Surprisingly, given how contagious COVID-19 is, showing definitively that you have infectious virus is technically very challenging, so it is good to see it being done. It confirms that we can catch COVID-19 from an infected person that may be across a room from us, and so social distancing by a metre or two may reduce the risk, but does not eliminate it.

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The number of secondary-school age children infected with COVID-19 has tripled in a month, so is it time to abandon social distancing and masks?

Above is the estimated fraction of secondary-school age (years 7 to 11) children that are infected with COVID-19, as a function of time from 1st June to 3rd July, 2021. The solid curve is the best estimate, while the dotted curves are the bottom and top of a 95% confidence interval. It is estimated that we are 95% confident that the true fraction of children infected lies between the two dotted curves. The data is for England and is from the UK government’s ONS. At the start of June, about 0.3% or 1 in 300 children in this age range had COVID-19. As of early July it is about 1% or 1 in 100*. And it is still going up. Schools break up in a few weeks which will I guess stop the rise, but perhaps not before it is has hit 2%.

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How virus-containing droplets are made

CSIRO ScienceImage 6552 Dripping tap Perth WA 1975

Transmission of COVID-19 likely starts with production of a small droplet that contains one or more SARS-CoV-2 viruses. This occurs somewhere in the lungs, throat, or mouth of an infected person. We have almost no data on this process as it occurs inside the body of an infected person, but we do know how droplets are generally made. One mechanism is named after Lord Rayleigh and Joseph Plateau, and we have all seen it in action. We see it every time we turn a tap a little bit on, and it drips. The stream of water from the tap breaks up into droplets, and the same thing may be happening inside us every time we breath.

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Absence of evidence for the hands part of “hands, face, space, fresh air”

One of the studies that convinces many (including me) that COVID-19 is mostly transmitted directly across the air, is a “superspreader” event in a restaurant in Guangzhou, China. It looks like a single infected person infected five people at other tables, in addition to four people on the same table as them. The restaurant was very badly ventilated, but there was a system that just circulated air around the table the infected person sat at, and the other two tables where people become infected. This is all perfectly consistent with the infected person breathing out virus that is then carried by air currents across the restaurant, and breathed in by people at another table. However, we can’t rule out alternative mechanisms, for example what is called the fomite route.

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Understanding the transmission of COVID-19 requires interdisciplinary teams

Covid-19: Health staff in plea for better protection is a depressing headline to be reading at any time, let alone a year and half into a pandemic. NHS healthcare workers have less protection to infection than those in many other countries, for example, the USA. Totally understandably many in the NHS are not happy about this. The Royal College of Nursing is just one of the unhappy organisations. The official infection-prevention guidelines were updated on 1st June but are still pretty hopeless, with pages on ensuring masks are stored in a “clean, dry area” (page 19) – which is a nice I guess but hardly an essential point – but almost nothing on the fact that proper FFP3 PPE masks offer you much more protection than a surgical mask.

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Hands, face, space, fresh air?

The government now tells us “hands, face, space, fresh air”* to reduce transmission of COVID-19, but the evidence supporting these four measures is very weak. By contrast the evidence showing that the Oxford AstraZeneca vaccine I had a few weeks ago is safe, is much much stronger, and assessed much more rigorously.

Let’s take them in order:

  1. “Hands”: There is essentially no good evidence that washing hands and surfaces reduces the likelihood of catching COVID-19.
  2. “Face”: by which they mean masks. We understand fairly well how mask work, colleagues at Bristol have a paper recently out in Physics of Fluids, and this is just a small part of a lot of work over the past year, that has assessed how effective masks (of different types) are. So we have a reasonable idea of how effective a given type of mask is at filtering out virus-containing droplets of a given size, but unfortunately, we have little idea of what size of droplet are transmitting COVID-19. Vaccines like those for COVID-19 are typically tested via a randomised controlled trial (RCT), we have almost no RCT data here.
  3. “Space”: by which they mean 1 or 2 m “social distancing”. As you can tell by the various limits of 1 m, 2 m, 6 feet, etc suggested by different countries there is no well justified distance beyond which you are safer. But basic geometry tells you that the concentration of virus will be highest right in front of an infected person, in their breath, so there is sound logic behind not getting too close, especially if you are facing someone. No RCT data here either.
  4. “Fresh air”: There a observations of “superspreader” events in which multiple people are infected, and they are strongly associated with people being together indoors, and in rooms with poor ventilation, i.e., air that is the opposite of fresh. We also have a reasonable understanding of the mechanism, and a simple model (Wells-Riley model).

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Building back better buildings

The UK government of Boris Johnson has pledged to build back better. We can all form our opinions as to how much good will come of this pledge, but an international group of scientists have made a suggestion for how learn from the pandemic and improve all our health in this week’s Science magazine. Morawska et al‘s point is that since, the 19th nineteenth century in the UK’s case, we have taken decisive action to combat the spread of typhus, cholera and other diseases spread by infected water. Now in the 21st century it is past time to pull our fingers out and take comparable action against diseases spread by infected air, such as tuberculosis, and COVID-19.

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