BF2S Forums Pandemic thread

Last edited by uziq (2020-04-30 10:10:47)

Last edited by Larssen (2020-04-30 10:30:46)

uziq wrote:

epidemics are a fact of human life and have been throughout our species history. we need to think about developing measures that will limit and contain them, as and when they do occur, in a very small and globalised world. it's no good banning the consumption of one food. viruses mutate. they spread from animal to animal, and eventually, occasionally, wind up in humans. we not part of a different biosphere. we are not masters of all Nature. it's going to happen and we cannot extract ourselves from it.

there is no proof that it came from eating bats. earliest best guess was pangolins. frankly the more we look into it, the less certain it even seems that the first mutation occurred in the wet market. a virus mutating and hopping to humans isn't exactly like a smoking gun. there isn't a chalked body outline on the floor surrounded by police tape.

Last edited by Dilbert_X (2020-04-30 16:57:22)

Dilbert_X wrote:

uziq wrote:

epidemics are a fact of human life and have been throughout our species history. we need to think about developing measures that will limit and contain them, as and when they do occur, in a very small and globalised world. it's no good banning the consumption of one food. viruses mutate. they spread from animal to animal, and eventually, occasionally, wind up in humans. we not part of a different biosphere. we are not masters of all Nature. it's going to happen and we cannot extract ourselves from it.

there is no proof that it came from eating bats. earliest best guess was pangolins. frankly the more we look into it, the less certain it even seems that the first mutation occurred in the wet market. a virus mutating and hopping to humans isn't exactly like a smoking gun. there isn't a chalked body outline on the floor surrounded by police tape.

There's no reason to be transporting either wild bats or pangolins, both well known disease vectors, to food markets.

OK so lets not worry about how pandemics are caused, we'll just figure out how to deal with them when they happen, cure being so much easier than prevention.
We can deal with a total lockdown and no world trade, say, two years in every ten as we try to figure out a vaccine?

You can build a simple mathematical model of an epidemic in a spreadsheet, using three columns to represent the Susceptible, the Infectious and the Recovered and calculating daily totals to show how an imaginary population is affected. The SIR model has two mathematical formulae controlling the flow from Susceptible to Infectious and from Infectious to Recovered. These formulae tell us how many people to subtract each day from the Susceptible population and add to the Infectious, and how many to subtract from the Infectious and add to the Recovered. The number of people moved out of the Susceptible group is calculated from the average number of contacts each individual has, the likelihood that a contact is with an infectious person, and the likelihood that such contacts will lead to infection. The number moved from Infectious to Recovered is simply the number of infectious individuals multiplied by the average rate of recovery.

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The teams that have been advising the government have now published accounts of their models. The one from the London School of Hygiene and Tropical Medicine (LSHTM) is superficially similar to mine. Susceptible people pass through a latent phase between becoming infected and being infectious, and then either have a mild, or subclinical, version of the disease, or a more serious illness with both a preclinical phase and a clinical phase requiring a stay in hospital. It is assumed that the mild cases are only half as infectious as the more severe cases.

Only one of the parameters in my model – the average number of contacts per person per day – is a fact about human behaviour. This is the parameter that can be manipulated when we attempt to alter the course of a pandemic. In the LSHTM model a separate value for the average number of contacts was calculated for every five-year age band in each of the 186 county-level administrative units in England, Wales, Scotland and Northern Ireland. To do this, demographic data on the proportion of people in each age group in each county was combined with data from an EU-funded study from 2008 (which seems to have been carried out in anticipation of a need for this kind of modelling) that surveyed 7290 people of different ages and asked them about the number of people they typically encountered at home, at work, at school or elsewhere. In my model the transitions between phases were determined by applying an average figure to everyone in each group at a particular time. In the LSHTM model the probability of each individual moving from one phase to the next at a given time was drawn from a range of values taken from early analyses of data from Wuhan. The length of time between onset and death, for example, is modelled using data that a Japanese team collated on 44 patients for whom those dates were reported either on Chinese government websites or in news stories.

The model predicted that, if nothing was done to mitigate the effects of the epidemic in the UK, 85 per cent of the population would be infected, there would be 24 million clinical cases and 370,000 deaths. At its peak, 220,000 ICU beds would be required. In February this year the number of adult ICU beds open in England was 4122. The effects of different policies – school closures, social distancing, shielding of the elderly and self-isolation of symptomatic individuals – and of combinations of them were simulated by adjusting the average number of contacts. The most effective single strategy, shielding the elderly, still resulted in 220,000 deaths and a need for 120,000 ICU beds, as well as 230,000 other hospital beds. There are about 100,000 general and acute NHS hospital beds currently available in England.

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The LSHTM team also modelled the impact of more aggressive strategies, such as the use of repeated lockdowns, triggered when the number of ICU beds occupied by Covid-19 patients reaches a particular number. If the threshold was set at a thousand ICU beds, the number of cases could be kept to four million and the number of deaths to 51,000. The downside is that 73 per cent of the time between now and December 2021 would be spent in lockdown, by which point only 11 million people would have been infected and, unless a vaccine had been found, the epidemic would be far from over.

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The burden of the pandemic has so far fallen mainly on countries in South-East Asia, which coped with it relatively well, and Europe and North America, where the results have been more variable. Its spread will be global. We don’t have the data for many low and middle-income countries that would allow us to run detailed simulations of the kind I have described here. The Imperial team used a simple SIR model, adding survey data, where it exists, to estimate age-specific contact rates, which were then combined with demographic data and the Infection Fatality Rate estimates from China. The results suggest that, if nothing is done, the pandemic will lead to seven billion infections and forty million deaths worldwide. These figures could, in theory, be halved if various mitigation strategies were deployed, but healthcare systems everywhere would still be overwhelmed. The conclusion for the world is the same as it was for the UK. The only option is suppression, and its consequences, economic and social, are unknown.

Last edited by uziq (2020-05-01 04:02:29)

Last edited by uziq (2020-05-01 06:10:57)