sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
43 stars 2 forks source link

EG.5.1.1/JN.1.4.5 recombinant (9 seqs, Australia) #1357

Closed xz-keg closed 6 months ago

xz-keg commented 9 months ago

One more previous singlet registered in #991 gets company.

EG.5.1.1--Pango#2426(JN.1.4+Orf8:S103L) Breakpoint between 14890 and 15755 image

Additional mutations:C14889T,C17766T, C28948T,G29527T N:Q418H

C14889T from an EG.5.1.1 branch(many candidates) C28948T from a sub-branch of Pango#2426 C17766T, G29527T are private

GISAID query: C28948T,C14889T,C18894T No. of seqs: 3(Australia)

First:EPI_ISL_18815003, 2023-1-16 Latest: EPI_ISL_18841427, 2023-1-17

usher image

CaitlinSelway commented 8 months ago

Hi @aviczhl2, to add to this post there are 5 more genomes from Australia (see names below) that are expected to have the same recombinant profile as the profile you have posted (one with some missing data). These have been uploaded to GISAID.

hCoV-19/Australia/SA1252254/2024 (sample with missing data) hCoV-19/Australia/SA1254671/2024 hCoV-19/Australia/SA1254675/2024 hCoV-19/Australia/SA1254672/2024 hCoV-19/Australia/SA1254685/2024

xz-keg commented 8 months ago

Hi @aviczhl2, to add to this post there are 5 more genomes from Australia (see names below) that are expected to have the same recombinant profile as the profile you have posted (one with some missing data). These have been uploaded to GISAID.

hCoV-19/Australia/SA1252254/2024 (sample with missing data) hCoV-19/Australia/SA1254671/2024 hCoV-19/Australia/SA1254675/2024 hCoV-19/Australia/SA1254672/2024 hCoV-19/Australia/SA1254685/2024

Thanks. BTW are you sure about hCoV-19/Australia/SA1252254/2024 ?It doesn't have EG.5.1.1 signature mutations and JN.1.4 signature mutations.

CaitlinSelway commented 8 months ago

I don't mind if it's not counted in the numbers for this purpose. Based on nextclade (see image), it was missing data in the regions for mutations defining this new recombinant, possibly due to low sequencing depths in these regions, but had a very similar arrangement of the genome.

image

xz-keg commented 8 months ago

I don't mind if it's not counted in the numbers for this purpose. Based on nextclade (see image), it was missing data in the regions for mutations defining this new recombinant, possibly due to low sequencing depths in these regions, but had a very similar arrangement of the genome.

I think that one is a sandwich recomb of this recomb and JN.1. It has the signature mutation 29527 for this recomb, but clearly it isn't JN.1.4 in the middle. Indicating it has a breakpoint after 28948(and before 29527)

It also doesn't have 14889 and 13627, which may due to its 1st BP is before 13627(and after 12815)

FedeGueli commented 8 months ago

i ve put it un der closer monitoring i think it will be worth a proposal soon

FedeGueli commented 8 months ago
Screenshot 2024-02-15 alle 10 03 07

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_a37d_dd08a0.json?c=userOrOld&label=id:node_6961022

There is an unrelated (in my view but help wanted) sibling of this one that has popped up in US with 2 samples : USA/CA-HLX-STM-7SSQDSMDZ/2024|EPI_ISL_18834967|2024-01-01 hCoV-19/USA/CA-CDC-QDX91916022/2024|EPI_ISL_18895341|2024-01-26

the previous singlet was reported in #991

FedeGueli commented 8 months ago

Screenshot 2024-02-15 alle 10 03 07 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_a37d_dd08a0.json?c=userOrOld&label=id:node_6961022 There is an unrelated (in my view but help wanted) sibling of this one that has popped up in US with 2 samples : USA/CA-HLX-STM-7SSQDSMDZ/2024|EPI_ISL_18834967|2024-01-01 hCoV-19/USA/CA-CDC-QDX91916022/2024|EPI_ISL_18895341|2024-01-26

the previous singlet was reported in #991

for sure unrelated due lacking orf8:103 so it is another JN.1.4 sublineage and another recombinant event.

xz-keg commented 8 months ago

for sure unrelated due lacking orf8:103 so it is another JN.1.4 sublineage and another recombinant event.

1383

xz-keg commented 8 months ago

Seems that one of the seqs is removed from GISAID. Now the count is 7.

FedeGueli commented 8 months ago

for sure unrelated due lacking orf8:103 so it is another JN.1.4 sublineage and another recombinant event.

1383

thank you

xz-keg commented 8 months ago

No new seqs

xz-keg commented 7 months ago

1 more from Australia

xz-keg commented 6 months ago

No new seqs