I’m seeing people share these kinds of plots on excess deaths to try and claim there isn’t COVID problem currently. But look at data for week 29 Mar 2020 - if this lagging metric had been used to drive action, nothing would've been done until *early April* (i.e. far too late) 1/
As anyone who’s worked on epidemics will tell you, there are imperfect data streams early on, and more conclusive data later. But as above shows, sitting around waiting for all the data is not an option in a fast moving outbreak. 2/2
(Source of above plot: cebm.net/covid-19/covid…)
Data up to 16th October now available, showing overall deaths have risen above range from previous 5 years, reflecting recent increase in deaths involving COVID-19:

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More from @AdamJKucharski

26 Oct
There are two main ways to estimate the reproduction number for SARS-CoV-2, and I'd like to discuss the one that doesn't get so much attention... 1/
Most reported R values use a 'top-down' method, which estimates R from the growth pattern in various surveillance datasets (e.g. ), but there is also a 'bottom-up' method, which my @cmmid_lshtm colleagues have been using to track R... 2/
The basic idea is that R depends on four components: duration of infectiousness; opportunities for transmission (i.e. contacts); transmission probability during each opportunity; and population susceptibility... 3/
Read 8 tweets
25 Oct
A common feature of a growing epidemic is that the % of cases detected by surveillance systems typically declines (just as the % detected typically increases as epidemics are brought under control)... 1/
In week ending 24 Sep, ONS estimated around 8,400 new infections per day in England (ons.gov.uk/peoplepopulati…). And on 24 Sep, the 7-day average for daily reported cases in UK was around 6,800. 2/
By week ending 16 Oct, ONS estimate was around 35,000 new infections per day in England (ons.gov.uk/peoplepopulati…), with 7-day average for UK cases by 16 Oct at around 18,500. 3/
Read 5 tweets
24 Oct
I think the below modelling output provides a useful illustration of how to evaluate forecasts. A short thread... 1/
First, let's be clear about difference between a 'scenario' and 'forecast'. Scenarios explore specific 'what if' questions, e.g. 'What if we don't introduce any control measures?' - Below are some examples from the March Imperial UK modelling report (imperial.ac.uk/mrc-global-inf…). 2/
In contrast, epidemic forecasts provide an answer to the question 'What do we think is most likely to happen?' More on scenarios vs forecasts here: washingtonpost.com/outlook/2020/0… 3/
Read 11 tweets
21 Oct
The COVID-19 pandemic has shown power of open data and analytics in research, but these activities often aren't recognised in traditional academic metrics. New perspective piece with @rozeggo & @sbfnk: journals.plos.org/plosbiology/ar…. I'd also like to highlight some examples... 1/
- Curation of open data sources, such as line list data by @MOUGK @davidmpigott et al (github.com/beoutbreakprep…), case tracking by @TexasDownUnder et al (coronavirus.jhu.edu/map.html), testing from @OurWorldInData (ourworldindata.org/coronavirus-te…)... 2/
Read 9 tweets
19 Oct
A short thread about a dead salmon and implausible claims based on epidemic curves... 1/
A few years ago, some researchers famously put an Atlantic salmon in an fMRI machine and showed it some photographs. When they analysed the raw data, it looked like there was evidence of brain activity... wired.com/2009/09/fmrisa… 2/
Now of course there wasn’t really any activity. It was a dead salmon. But it showed that analysing the data with simplistic methods could flag up an effect that wasn’t really there. Which leads us to COVID-19... 3/
Read 9 tweets
14 Oct
'Herd immunity' has been reached during previous epidemics of influenza, measles and seasonal coronaviruses. But it's subsequently been lost (and then regained). What are some of the reasons for this? 1/
Here we're using technical definition of 'herd immunity', i.e. sufficient immunity within a population to push R below 1 in absence of other control measures. But reaching this point doesn't mean R will stay below 1 forever. Here four things to be aware of... 2/
A: Population turnover. Over time, new births mean an increase in % of population susceptible. This will eventually lead to R>1 and new (but smaller) outbreaks - the more transmissible the infection, the sooner this recurrence will happen. More: 3/
Read 8 tweets

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