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

[xz-keg]

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

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

[CaitlinSelway]

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]

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]

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.

[xz-keg]

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]

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

[FedeGueli]

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]

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]

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

1383

[xz-keg]

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

[FedeGueli]

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

1383

thank you

[xz-keg]

No new seqs

[xz-keg]

1 more from Australia

[xz-keg]

No new seqs