A Quite Ancient EG.5.1* lineage with Orf3a:D27H and S:E1092D involved in a recent recombination (#1154) (250 Sequences)

[krosa1910]

Formerly mentioned by @NkRMnZr in #1048 (Edited)

I was tracking C22916T (under T22917G it makesS:R452W ) mutation within my HV.1* sequence and I accidentally discovered a recombination of EG.5.1* with JN.1* as EPI_ISL_18566568 (see #1154), which is not uncommon considering the sheer amount of the two parent lineages.
Yet the latter part contains some mutation I do not know S:E1092D. E and D are not too common within XBB* so it makes me interested and investigate the lineage. Indeed there seems to bury a small lineage there.
Parent: EG.5.1*
Mutations Added: EG.5.1*-》G25471C (Orf3a:D27H)-》T14835C, A24838C (S:E1092D), T28226C
Gisaid Inquiry: T14835C,A24838C,T28226C
Geographic Distribution:
Earliest Sequence: EPI_ISL_18113849 US, 2023-07-23
Latest Sequence: EPI_ISL_18708628, Canada, 2023-12-20
Geographic Distribution: North America-24 Canada, 1 Peurto Rico, 51USA ; Asia-1 Shanghai, 3 South Korea; South America-7 Ecuador Oceania-11 Australia, 5 New Zealand; Europe-1 Belgium, 4 Denmark, 44 England, 4 France, 7 Germany, 7 Greece, 15 Ireland, 5 Netherlands, 1 Portugal, 33 Scotland, 3 Spain, 4 Sweden, 1 Switzerland
Its comparison with EG.5.1* parent:

Usher：https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1b4f7_7bd2c0.json?f_userOrOld=uploaded%20sample

Some of the recent sequences seem to get S:K444R, and if that is not misled by England clusters then it could give a little more vis viva to this old branch

[xz-keg]

parent of branch 7 of #1048

[FedeGueli]

parent of branch 7 of #1048

dead one luckily.

[FedeGueli]

This kind of lineages without a super fit but with a good persistance are always interesting , maybe is that orf3a:D27H 8 close to the orf3a:S26L in all Delta) pushing some different expression of putative Orf3b Orf3C and so? i sicerely dont jnow anything about that. maybe @ryhisner or @oobb45729 could check that.

[krosa1910]

This kind of lineages without a super fit but with a good persistance are always interesting , maybe is that orf3a:D27H 8 close to the orf3a:S26L in all Delta) pushing some different expression of putative Orf3b Orf3C and so? i sicerely dont jnow anything about that. maybe @ryhisner or @oobb45729 could check that.

Yeah, it look like quite fit to me, and also it is evident in other lineages, yet this one seems like it is the sole survivor now

[oobb45729]

This kind of lineages without a super fit but with a good persistance are always interesting , maybe is that orf3a:D27H 8 close to the orf3a:S26L in all Delta) pushing some different expression of putative Orf3b Orf3C and so? i sicerely dont jnow anything about that. maybe @ryhisner or @oobb45729 could check that.

The mutation of ORF3a:D27H also results in ORF3c:Q5H. The mutation of ORF3a:S26L is also results in ORF3c:Q5*. Some Deltas further gained ORF3a:D27Y/ORF3c:Q5Y.

[FedeGueli]

This kind of lineages without a super fit but with a good persistance are always interesting , maybe is that orf3a:D27H 8 close to the orf3a:S26L in all Delta) pushing some different expression of putative Orf3b Orf3C and so? i sicerely dont jnow anything about that. maybe @ryhisner or @oobb45729 could check that.

The mutation of ORF3a:D27H also results in ORF3c:Q5H. The mutation of ORF3a:S26L is also results in ORF3c:Q5*. Some Deltas further gained ORF3a:D27Y/ORF3c:Q5Y.

Thank you!

[krosa1910]

Mexico and Ecuador？ very weird recent lineages，lets keep watching it a bit

[krosa1910]

Weird, this one does not look too fit but seems to still move on, I would still keep it as of now.

[FedeGueli]

no 2024 sample from this closing it