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Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryan Hisner via out of frame Orf7b:F13- (13 seqs) #585

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FedeGueli opened this issue Aug 10, 2023 · 1 comment
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Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes.

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@FedeGueli
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FedeGueli commented Aug 10, 2023

While checking the last batch from Singapore i noticed that also GJ.1.2 has gained the out of frame deletion at Orf7b:13 described by @ryhisner about FR.1 , XBC.1 and GP.1 (see here) and extended explanation >(here)
Schermata 2023-08-10 alle 14 07 43

Luckily this out of frame deltion occured at the same time with a nuc/AA mutation so we can track it and see it on [USHER]:
Orf1a:T4418I (C13517T)
(https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33ef6_4c81b0.json?c=userOrOld&label=id:node_7202734)
Schermata 2023-08-10 alle 14 00 24
Schermata 2023-08-10 alle 14 00 49

So defining mutations for this sublineage are:
GJ.1.2>> C7819G > Orf1b:S997P (T16456C) > Orf1a:T4418I (C13517T), Orf7b:F13del( 27795_27796del)

Gisaid Query : del27795_27796,G28209C,C13517T

Samples : 12 all from Singapore
EPI_ISL_17849968, EPI_ISL_17957199, EPI_ISL_17957352,
EPI_ISL_18006736-18006737, EPI_ISL_18015376, EPI_ISL_18056922-18056924,
EPI_ISL_18082823-18082824, EPI_ISL_18082828

@FedeGueli FedeGueli changed the title Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by @Ry Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryanr Hisner via out of frame Orf7b:F13- (13 seqs) Aug 10, 2023
@FedeGueli FedeGueli added the Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. label Aug 10, 2023
@FedeGueli FedeGueli changed the title Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryanr Hisner via out of frame Orf7b:F13- (13 seqs) Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryanr Hisner via out of frame Orf7b:F13- (12 seqs) Aug 10, 2023
@FedeGueli FedeGueli changed the title Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryanr Hisner via out of frame Orf7b:F13- (12 seqs) Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryan Hisner via out of frame Orf7b:F13- (12 seqs) Aug 10, 2023
@FedeGueli FedeGueli changed the title Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryan Hisner via out of frame Orf7b:F13- (12 seqs) Recent singaporean GJ.1.2 sublineage gained the brand new Orf7b described by Ryan Hisner via out of frame Orf7b:F13- (13 seqs) Aug 28, 2023
@FedeGueli
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it seems not going no where. Good to have it tracked for a bit in any case .

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 4, 2023
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