Thread by @IsaacATFlorence

Although Twitter doesn’t need another thread of individual thoughts on the latest PHE variant technical briefing, as half the team behind the new outbreaks and clusters data, I feel it’s important to highlight a few things about this data which are missed in discourse here 1/

Data from the Case and Incident Management System (CIMS) is hugely biased towards Health Protection Team (HPT) prioritisation. During Covid this means what data is captured there varies through time and by region ... 2/

... (due to different incidence meaning fluctuating work but with largely constant staffing levels). This means that looking at trend data from CIMS is only an accurate picture of what gets managed by HPTs. 3/

Since Alpha variant (B.1.1.7), all the subsequent variants have been intensely managed by HPTs, as their small numbers made them containable. This means CIMS data on Alpha variants is not at all comparable to any other variant work, due to Alpha outbreaks not getting onto CIMS 4/

As Delta variant’s case numbers have risen, there are more outbreaks in all settings and some of those settings are prioritised. For example outbreaks related to schools are intensively managed and so will all end up on CIMS. 5/

Additionally think about the magnitude of vaccine coverage change since the emergence of the Beta variant (for example), and whether community transmission has occurred. These have all varied and so outbreak data between variants at different times are not directly comparable. 6/

Then why create and present this data, you ask? I imagine 90% of you will agree that PHE publishes extraordinary amounts of data and analyses, more than anywhere in the world, in order to be both transparent and engage the public with our work to protect the nation ... 7/

It’s not perfect, it doesn’t give you an exact or easy-to-understand answer, but I am confident it’s by far the best data we’ve got, so we’ve shared it. It’s why I spent >50 hours working on it between Saturday and Tuesday night/Wednesday morning. 8/

(Somewhat tangentially, this is why applied epidemiology is different, it’s about creating a coherent picture from as many distinct, massively patchy datasets as possible. If you just look at one set of numbers, you won’t get the best picture). 9/

Although I personally fear that several commentators are right and schools are a major site of transmission of delta variant, ***I vehemently believe that this data isn’t, and can’t, show that***. What I think is more likely ... /10

... is that vaccines protection older age groups and surge PCR-testing in schools creating vastly higher case-ascertainment in those age groups is more likely the reasoning behind why Delta case rates are relatively higher in schools. /12

TL;DR - PHE provides outbreak-level data to show what health protection teams are managing but it isn’t that helpful to understand transmission. The case-level data is much better and provided in the tech briefing. P.s. read the supporting text of the report, it’s helpful! /13

Thread annex: The full report is brilliant and does contain world-class analysis that gives a great picture of what truly is going on. Read it all, not just the Twitter threads. The genomics work in particular I am continually in awe of. 14/ ENDS.