I can answer this one, or more specifically the PHE can. The tl; dr of this technical briefing is that the new strain tests positive on two assays (N, ORF1ab) and negative on a third (S), and that up to some noise this is currently the only strain to do so. So the number of PCR tests that are both S-negative and COVID-positive is a good indication of the spread of the new strain, without the need for genome sequencing. This document makes this argument precise, and then produces a painful graph on page 8 showing the ‘S dropout’ proportion at the Milton Keynes Lighthouse lab (Buckinghamshire). Mid December they show a proportion of over 60%.
This has led to me to update towards the new variant being as aggressive as previously feared, because unlike genome sequencing PCR test data does not lag several weeks behind. Combined with the fact that genome sequencing is done sporadically at best (if I understand correctly, nextstrain data explains the UK has sequenced 85 samples since September, with neighbouring countries showing similar numbers) I think it may already be more widely spread/beyond containment in a lot of European countries. Edit: Oskar Mathiasen gives a difference source with incompatible numbers, I am no longer confident in this point.
I also share shminux’ fears that this more aggressive strain may be difficult to contain with just the measures we have taken so far.
I can answer this one, or more specifically the PHE can. The tl; dr of this technical briefing is that the new strain tests positive on two assays (N, ORF1ab) and negative on a third (S), and that up to some noise this is currently the only strain to do so. So the number of PCR tests that are both S-negative and COVID-positive is a good indication of the spread of the new strain, without the need for genome sequencing. This document makes this argument precise, and then produces a painful graph on page 8 showing the ‘S dropout’ proportion at the Milton Keynes Lighthouse lab (Buckinghamshire). Mid December they show a proportion of over 60%.
This has led to me to update towards the new variant being as aggressive as previously feared, because unlike genome sequencing PCR test data does not lag several weeks behind.
Combined with the fact that genome sequencing is done sporadically at best (if I understand correctly,nextstrain dataexplains the UK has sequenced 85 samples since September, with neighbouring countries showing similar numbers) I think it may already be more widely spread/beyond containment in a lot of European countries.Edit: Oskar Mathiasen gives a difference source with incompatible numbers, I am no longer confident in this point.I also share shminux’ fears that this more aggressive strain may be difficult to contain with just the measures we have taken so far.
85 seems incongruent with this source https://covidcg.org/?tab=global_sequencing
Good point, I’m likely misinterpreting nextstrain website then.