XBB.1.28 saltation with ORF1a:G2814S (nsp4_G51S), S:L461I, S:N556S and ORF7a:P34L (45 seqs, 5 countries)

[NkRMnZr]

Defining Mutations: XBB.1.28 > T514C, G6850A, G8705A(ORF1a:G2814S), T18351C, C22943A(S:L461I), C23086T(S:Y508Y), A23229G(S:N556S), C27494T(ORF7a:P34L)
Query: G8705A, T18351C, A23229G
Earliest seq: 2023-05-21 (EPI_ISL_17770005, Shanghai, China, with travel history to: Ethiopia)
Latest seq: 2023-06-28 (EPI_ISL_18034530, Guangdong, China with unknown travel history)
Sampled Countries: China (2, Shanghai, Guangdong), India (1, Hyderabad)

Genomes:

`EPI_ISL_17770005, EPI_ISL_18034530, EPI_ISL_18042397`

Saltation Profile:
mutation on nearest branch:

nuc	unique	G6850A, G8705A, T18351C, C22943A, A23229G, C27494T
nuc	homoplasies	C11455T, G22770A, C23086T
ORF1ab	unique	G2814S
S	unique	L461I, N556S
S	homoplasies	R403K
ORF7a	unique	P34L

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_34b96_22a000.json?label=id:node_3665218

Trivia:

• 2 Chinese sequences are associated with travel history

Shanghai/SCDC-HG0523-1064/2023|EPI_ISL_17770005|2023-05-21

FEATURES             Location/Qualifiers
     source          1..29792
                     /organism="Severe acute respiratory syndrome coronavirus 2"
                     /mol_type="genomic RNA"
                     /isolate="SARS-CoV-2/human/CHN/SH-HG20230523-1064/2023"
                     /isolation_source="Pharyngeal swab"
                     /host="Homo sapiens; Host_age: 55; Host_sex: Male"
                     /country="China:Shanghai"
                     /collection_date="2023-05-21"
                     /note="Passage_details/history: Original;
                     Additional_host_information: Patient infected while
                     traveling in Ethiopia"

• Guangdong/GDCDC_GZHG_1246/2023|EPI_ISL_18034530|2023-06-28 is sampled by Guangzhou Customs without metadata showing exact travel history.
• S:L461I only sampled about 400 times during the whole pandemic, and is not predicted to have any significant impact on immune escape, nor binding affinity, nor fitness; S:N556S is about the same rarity, and is predicted to be slightly deleterious.

[xz-keg]

This doesn't have 486P

[NkRMnZr]

Tracking updates:

08-15, 1 more from Sweden: EPI_ISL_18099936

[FedeGueli]

No seqs incoming, tracking it privately

one more from Sweden EPI_ISL_18099936

[NkRMnZr]

5th from Virginia: EPI_ISL_18160357

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38142_f61460.json?f_userOrOld=uploaded%20sample

[FedeGueli]

closing this for now, nothing happened. in more than one month.

[Over-There-Is]

45 now, including 7 submitted by Ethiopia

[xz-keg]

Yeah a lot of old seqs of this branch are submitted recently.