We’ve been investigating Ct values as a proxy for viral load of symptomatic (pillar 2) Covid-19 cases in England in the last 18 months. Work-in progress report (w/ @seabbs) at epiforecasts.io/covid19_ct_pil… and a few observations in this thread. 1/9 First, a caveat. This is all based on pillar 2 testing and therefore affected by test-seeking behaviour. We know about reported dates of symptom onset but not how severe symptoms were, and/or what prompted people to seek a test. This can bias the results shown here. 2/9

Many now focus on the amazing prevalence data published weekly by ONS for tracking SARS-CoV-2 in the UK. There's a few additional epidemiological quantities that can be derived from it, which we're putting in a weekly report that is based on the ONS data. w/ @seabbs 1/9 First, incidence of infections. Using previous estimates by @HellewellJoel et al. we relate positivity to new infections, taking into account that it can take a few days from infection to PCR positive, and probability of testing positive varies over the course of infection. 2/9

Lots of speculation on generation intervals of omicron and whether it might different to ones of previous variants. So here are a few things that I think are worth bearing in mind. 🧵 1/16 We can think of the generation interval, i.e. the time between becoming infected and infecting others, as being made up of two components. One is given by how an individual’s infectiousness changes from the time since infection. 2/16

Evidence from the UK testing programme in educational settings suggests that rapid test specificity exceeds 99.9%. A brief thread on how we found this and why 99.9% isn’t necessarily enough. Short note (w/ @StfnFlsch) available at cmmid.github.io/topics/covid19… 1/7 Every time a large-scale survey is conducted with a diagnostic test one can calculate a lower bound of test specificity by assuming all positive test results were false positives. 2/7

Is the new variant of SARS-CoV-2 more transmissible than others and if yes by how much? We @cmmid_lshtm are currently looking at this by comparing reproduction numbers between local areas in England (w/ @seabbs). WORK IN PROGRESS, NOT PEER REVIEWED. 1/10
raw.githubusercontent.com/epiforecasts/c… Looking at this week-by-week, there seems to be a trend where areas that see more S-gene target failure (SGTF, a proxy for detection of the new variant) have higher reproduction numbers. WORK IN PROGRESS, NOT PEER REVIEWED. 2/10

Much attention has recently focused on increases in the reproduction number R across the UK, with some speculation on the impact that reopening schools may have had. But for that it is too early to tell. 1/8 First, the numbers. According to latest SAGE estimates, R in the UK and England was between 1 and 1.2. gov.uk/guidance/the-r… According to the REACT infection survey, the reproduciton number in England was between 1.4 and 2.0. imperial.ac.uk/medicine/resea… 2/8