search

rsv-lineages / lineage-designation-A

RSV-A lineage definitions and proposals
4 stars 1 forks source link

A.D.5.2 sublineages #12

Open rneher opened 1 week ago

rneher commented 1 week ago

A.D.5.2 is the dominant clade atm and has a few recognizable sublineages with mutations in F

image

AngieHinrichs commented 4 days ago

FWIW, autolin (with a minimum sample size of 10) finds seven sufficiently distinctive A.D.5.2 potential sublineages:

sublineage      sampleCount      mutations
A.D.5.2.X1      60      F:S377N,F:A107T,G:T238A,M2-2:I85V,P:K88R,NS1:L104I,G:T235I,L:A1927T
A.D.5.2.X2      30      G:F101L,G:H258Y,G:I235T,G:V225A,L:*2166Q,G:T235I,L:A1927T
A.D.5.2.X3      31      F:S105N,M2-1:R4K,F:V533I,L:T104A,L:T1927S,G:T235I,L:A1927T
A.D.5.2.X4      19      F:V379A,G:Y273H,L:A1787T,G:T235I,L:A1927T
A.D.5.2.X5      11      L:T1927A,F:I59V,F:N124T,G:S317F,L:*2166Q,G:T235I,L:A1927T
A.D.5.2.X6      16      G:Q140R,G:S283P,L:T1942I,N:I104V,P:E239D
A.D.5.2.X7      11      G:G232R,L:T104A,L:T1927S,G:T235I,L:A1927T

Here's what they look like in Auspice: image Some of them are rather small with a lot of internal divergence and may not be worth it (should I use a larger minimum sample size?), and X4 looks like it died out in 2023.