Read on Twitter
Many are interested in using the 69/70 deletion to scan for cases of the new #SARSCoV2 variants.
As it can impact some primers (seen as an 'S drop-out' in PCR), it can be a high-throughput way to check for the 'SE England' variant - but some important things to remember!
1/5
As it can impact some primers (seen as an 'S drop-out' in PCR), it can be a high-throughput way to check for the 'SE England' variant - but some important things to remember!
1/5
First, the 69/70 deletion has arisen multiple times independently: not everything with 69/70 is the SE England variant!
You can see that 69/70del appears many times here: notably it's associated with 501Y.V1 (English variant) AND 453 & 439.
2/5
https://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69&r=country
You can see that 69/70del appears many times here: notably it's associated with 501Y.V1 (English variant) AND 453 & 439.
2/5
https://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69&r=country
In particular, S:N439K is widespread across Europe, and about 3/4 of the sequences in this cluster have the 69/70del.
So there's a fair chance a 69/70del in continental Europe is part of this cluster, not the 'new variant' from England.
3/5
https://nextstrain.org/groups/neherlab/ncov/S.N439K?c=gt-S_69&f_region=Europe&label=clade:S.N439K&r=country
So there's a fair chance a 69/70del in continental Europe is part of this cluster, not the 'new variant' from England.
3/5
https://nextstrain.org/groups/neherlab/ncov/S.N439K?c=gt-S_69&f_region=Europe&label=clade:S.N439K&r=country
In the UK & particularly SE England, using the 69/70del as a proxy for the variant works because it is in many areas the most common variant.
In other places, where frequency is expected to be lower, it's very important to double-check S drop-out results!!
4/5
In other places, where frequency is expected to be lower, it's very important to double-check S drop-out results!!
4/5
Finally, the South African variant (501Y.V2) does *not* have the 69/70 deletion - but we know it has also been import outside of SA.
So, if also interested in looking for 501Y.V2, don't depend on 69/70del - it won't pick this up!
5/5
So, if also interested in looking for 501Y.V2, don't depend on 69/70del - it won't pick this up!
5/5
