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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.3.1 + S:F59S + Orf1a:E36D + Orf10:I4V (60 from 17 countries including Brazil and Georgia) #1615

Closed FedeGueli closed 1 month ago

FedeGueli commented 3 months ago

Just spotted a sublineage of KP.3.1 carrying the convergent and beneficial (in Jn.1) mutation S:F59S , it has been sampled two times by GBW airport surveillance from travellers from Spain and Brazil and it has been locally sampled in Spain , all very recent. Interestingly these samples have mutations both toward the 5' end (G373T) and toward the 3' end of the virus with one mutation in Orf10 and two mutations in the 3' end UTR (4/5) (A29567G, G29706T G29781T) Two samples have a further spike mutation S:A260T but likely from the same traveller. It is interesting that three out of six defining mutations are G>T trasversions.

Defining mutations: Kp.3.1 > orf1a:E36D (G373T), A9235G, S:F59S (T21738C), Orf10:I4V (A29567G), G29706T , G29781T (4/5)

New Query: A9235G, T21738C, G15372T by @aviczhl2 in #1756 Old Query: G373T, A9235G

Samples: 5 ( 3 Spain , 1 Spain via GBW 1 Brazil via GBW) IDs:EPI_ISL_19162492, EPI_ISL_19191338, EPI_ISL_19191730, EPI_ISL_19193946, EPI_ISL_19193970

Tree:

Screenshot 2024-06-13 alle 22 00 08

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_249b2_b4bbd0.json?c=userOrOld&label=id:node_6996822

FedeGueli commented 3 months ago

ping @corneliusroemer @ryhisner not sure if interesting for you but you are def the 3' UTR man here!

ryhisner commented 3 months ago

Yeah, this is super interesting! The other notable thing is that although G373T is in the ORF1a coding region, it's still part of an extensive stem-loop structure that resembles the 5' UTR and which I think likely plays a role in the structural functions of the 5' UTR. Looking at the conventional secondary RNA structures, there's no obvious connection between the 3' UTR mutations, but there could still be something non-obvious happening.

And I think there's a decent change G373T is in someway connected to one of the 3' UTR mutations. I'll try to do some investigating to see what the posited connections between the 3' UTR and 5' UTR are. I know I've seen a few secondary structure maps that laid out possible places where they could interact.

ryhisner commented 3 months ago

Here's a view of where those 3' UTR mutations are located. s2m is of course mostly deleted (∆29734-29759) in all Omicron, but according to a couple analyses I've seen, the s2m deletion isn't expected to cause any major changes in the rest of the 3' UTR structure.

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ryhisner commented 3 months ago

And here's G373 in the context of the 5' UTR (from the same study)

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FedeGueli commented 3 months ago

Thank you @ryhisner ! Great!

FedeGueli commented 3 months ago

8 with GBW samples from Spain,Brazil, Iceland

FedeGueli commented 3 months ago

13

FedeGueli commented 3 months ago

it expands further but seems quite slow

FedeGueli commented 2 months ago

Sudden spike for this one now 23. Spain uploaded from 4 different regions this means this was able to spread geographically despite KP.3.1.1

FedeGueli commented 2 months ago

49 3 new countries (Ru, Nor, Isr)

FedeGueli commented 1 month ago

60 Greece Sweden

aviczhl2 commented 1 month ago

Designated KP.3.1.8 via https://github.com/cov-lineages/pango-designation/commit/a22c382df095611bcccc8adc43a17047ea37d6d5

Over-There-Is commented 1 month ago

This lineage is not able to be identified by usher yet. @angiehinrichs

AngieHinrichs commented 1 month ago

This lineage is not able to be identified by usher yet. @AngieHinrichs

Sorry, I took a vacation last week and now there are 75 new lineages to annotate on the tree. (Not to mention the hundreds of emails). I will annotate them ASAP, hopefully today & tomorrow.