1 THREAD on latest COG data on B1.617.2 (so called "India" variant) in England
COG sequences positive tests from the community (~50% of them), all travellers to UK & from surge testing. Data is updated almost every day.
What does it tell us about spread?
sars2.cvr.gla.ac.uk/cog-uk/#shiny-…
COG sequences positive tests from the community (~50% of them), all travellers to UK & from surge testing. Data is updated almost every day.
What does it tell us about spread?
sars2.cvr.gla.ac.uk/cog-uk/#shiny-…
2 COG data is not entirely representative because it over-represents surge and traveller cases.
Sanger data removes traveller and surge cases to try to get a picture of community transmission, but Sanger only updates once a week.
What if we compare the two?
Sanger data removes traveller and surge cases to try to get a picture of community transmission, but Sanger only updates once a week.
What if we compare the two?
3 This compares the number of sequenced tests of B.1.617.2 that appear in COG (black) and Sanger (blue).
Over time there is much more overlap between the two showing that community cases are growing and that COG is becoming more representative of community cases (Sanger).
Over time there is much more overlap between the two showing that community cases are growing and that COG is becoming more representative of community cases (Sanger).
4 In fact, if we look at the number of Sanger cases of B.1.617.2 as a percentage of COG cases in England, we can see that week to 8th May (most recent), it's now 90%.
This suggests that COG cases are currently a reasonable proxy for community cases.
This suggests that COG cases are currently a reasonable proxy for community cases.
5 In fact, if you look at the percentage of all cases that are B.1.617.2 between COG and Sanger over time, they track each other pretty well and differences have narrowed over time.
This gives further support to using COG as a more real time proxy for community cases.
This gives further support to using COG as a more real time proxy for community cases.
6 So what is the latest COG data showing? Well, data from samples after 8th May are still very incomplete (I estimate about a third complete from numbers of B.1.1.7 ("Kent") variant) but nonetheless show a continued increase in proportion of tests that are B.1.617.2 - almost 37%.
7 So - to sum up - COG is the data that is most frequently updated. It's not perfect but I think it's good enough to say that spread of B.1.617.2 is continuing at expense of B.1.1.7 ("Kent").
And it certainly is NOT all travellers to the UK.
And it certainly is NOT all travellers to the UK.
8 Most recent week is too incomplete to say whether spread is slowing much.
I *hope* it is - we want to contain this and so we need local measures in outbreak areas to work!
But ultimately we want B.1.617.2 cases to decrease - not increase. And no sign of that yet. /END
I *hope* it is - we want to contain this and so we need local measures in outbreak areas to work!
But ultimately we want B.1.617.2 cases to decrease - not increase. And no sign of that yet. /END
PS: Caveat 1: B.1.617.2 became a variant of concern 7th May - so surge testing only started after that. This might affect COG data for most recent week - we'll need to compare with Sanger again on Monday.
PPS Caveat 2: Sanger doesn't perfectly clean the COG data so there might be some residual travel related data. Both contain some duplicates.
But Sanger and COG are consistent with picture from the gold standard Public Health England VOC reports (somewhat unpredictably published)
But Sanger and COG are consistent with picture from the gold standard Public Health England VOC reports (somewhat unpredictably published)
the title to that chart is wrong - should say "number of Sanger cases of B.1.617.2 as a percentage of COG cases in England"
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