JN.1.4 Saltation [12 AA subs, 5 in Spike] (Hong Kong, 4 seq, 2 pts?)

[ryhisner]

Description Sub-lineage of: JN.1.4 Earliest sequence: 2024-9-20, Hong Kong, EPI_ISL_19464534 Most recent sequence: 2024-10-10, Hong Kong, EPI_ISL_19498393 Continents circulating: Asia (2) Countries circulating: Hong Kong (2) Number of Sequences: 2 GISAID Nucleotide Query: T21652A, G21701A Alternative query by Fed: C5365T,C7851T, T10636C CovSpectrum Query: Nextcladepangolineage: Substitutions on top of JN.1.4: Spike: N30K, V47I, S151I, R346T, D936H ORF9b: I5T, L64P ORF1a: H388Y, P1786L, V2276A, A2529V, Q2574H, A4285V ORF1b: L137F Nucleotide: C1427T, C4543T, C5192T, C5365T, C5622T, G5629T, T7092C, C7851T, T7855C, G7987T, T10636C, A12508G, C13119T, C13876T, T21652A, G21701A, G22014T, G22599C, A24325G, G24368C, C27630T, T28297C. T28474C

Phylogenetic Order of Mutations (edited after the tree on Nov 10 by Fed) : C13119T (ORF1a:A4285V) → C5622T (ORF1a:P1786L) → C5365T → C7851T, T10636C, C13876T, T21652A, G21701A, G22599C, T28474C ( ORF1a:A2529V, ORF1b:L137F, S:N30K, S:V47I, S:R346T, Orf9b:L64P)
→→ C1427T,C4543T, C5192T, G5629T, T7092C, T7855C, G7987T, A12508G, G22014T, A24325G, G24368C, C27630T, T28297C (ORF1a:H388Y,ORF1a:Q2574H, ORF1a:V2276A, S:S151I, S:D936H, ORF9b:I5T)

C1427T, C4543T, C5192T, C5365T, C5622T, G5629T, T7092C, C7851T, T7855C, G7987T, T10636C, A12508G, C13119T, C13876T, T21652A, G21701A, G22014T, G22599C, A24325G, G24368C, C27630T, T28297C. T28474C

USHER Tree updated as November 10 By Fed

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2376f_1463c0.json?f_userOrOld=uploaded%20sample&label=id:node_7102870

Evidence (Not updated) Metadata indicate these two sequences are from different patients. The first sequence had 14 mixed nucleotides, likely indicating a chronically infected patient. Five of those mixed-nuc mutations were fixed in the second sequence, including two spike mutations. The second sequence had one mixed nucleotide, which isn’t uncommon for sequences from Hong Kong. Both of the ORF9b mutations (I5T and L64P) are commonly found in chronic-infection sequences.

Assuming the metadata is correct (not always the case), this second case could be a close contact of the first, with no further transmission. Or the second sequence could be an indication of some low-level circulation. In either case, this branch almost certainly arose from a chronic infection in the first patient. The closest sequences on the tree were collected over 10 months ago.

Genomes (Not updated)

Genomes

EPI_ISL_19464534, EPI_ISL_19498393

[xz-keg]

worth noting Chinese provinces near Hong Kong(Guangdong, Fujian, Guangxi, Hunan) have submitted 0 seqs for more than a year. Any branch in Hong Kong may (or may not) have large base of underrepresented circulation.

Can it involve some form of recombination with KP.2.25.1?

[FedeGueli]

Third sequence of this but likely another sample from same 78yr patient

[FedeGueli]

Third sequence of this but likely another sample from same 78yr patient

Oh wait @ryhisner i must have re found it later and made a query to track it (without matching it with this issue until now) : C5365T,C7851T, T10636C , that query gives me 4 samples. 3 of them from a single patient likely

[FedeGueli]

@ryhisner i have added the query , updated the tree and edited the phylogenetic order of mutations to respect the actual tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2376f_1463c0.json?f_userOrOld=uploaded%20sample&label=id:node_7102870

I have added a "not updated" label on the sections i didnt touch if you want to review them

[FedeGueli]

Looking at the tree it could be also that an Immunocompromised patient infected his/her caregiver but i dunno if it could be true