XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (191/105/51 seq, May 8)

[ryhisner]

Full credit to @FedeGueli for tracking this mutation (and hundreds of others!) in the XBB.1.5 spike diversity issue, #1510. Fede had documented this long before I noticed the trend.

Description for Lineage 1 — XBB.1.5 + S:K304Q Sub-lineage of: XBB.1.5 Earliest sequence: 2023-1-18, USA, Texas — EPI_ISL_17120697 Most recent sequence: 2023-3-11, USA, Pennsylvania — EPI_ISL_17279077 Countries circulating: USA Number of Sequences: 58 GISAID AA Query: Spike_K304Q, NSP13_S36P, -Spike_F486S, -N_I131R, -N_Q260L, -NSP1_L149R GISAID Nucleotide Query: T16342C, A22472C, -T711G, -T10204C, -A29052T, -T28665G CovSpectrum Query: Nextcladepangolineage:XBB.1.5* & A22472C & !T711G & !T10204C & !A29052T & !T28665G Substitutions on top of XBB.1.5: Spike: K304Q Nucleotide: A22472C

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_K304Q_Lineage_1_subtreeAuspice1_genome_38b97_dd0fe0.json

Evidence S:K305Q is a mutation that, before XBB.1.5, had only occurred about 20 times throughout the entire pandemic. Now there appear to be at least three substantial sublineages of XBB.1.5 that have acquired it independently, and all seem to be growing fairly quickly, though sample sizes are too small at this point to draw any conclusions about their growth potential. This seems to me a strong indication that something about XBB.1.5 permits S:K304Q where all previous lineages did not. Whether or not this mutation is advantageous or not remains to be seen.

Genomes

Genomes

EPI_ISL_16916659, EPI_ISL_16919295, EPI_ISL_16919734, EPI_ISL_16919737, EPI_ISL_16957540, EPI_ISL_16962358, EPI_ISL_16992526, EPI_ISL_16992992, EPI_ISL_17009307, EPI_ISL_17023378, EPI_ISL_17027198, EPI_ISL_17035090, EPI_ISL_17035242, EPI_ISL_17037387, EPI_ISL_17037430, EPI_ISL_17084701, EPI_ISL_17084948, EPI_ISL_17085120, EPI_ISL_17085161, EPI_ISL_17099098, EPI_ISL_17120697, EPI_ISL_17139282, EPI_ISL_17139821, EPI_ISL_17140243, EPI_ISL_17147035, EPI_ISL_17147482, EPI_ISL_17170014, EPI_ISL_17170022, EPI_ISL_17170040, EPI_ISL_17170342, EPI_ISL_17170360, EPI_ISL_17170361, EPI_ISL_17170389, EPI_ISL_17180109, EPI_ISL_17181363, EPI_ISL_17181379, EPI_ISL_17181861, EPI_ISL_17191626, EPI_ISL_17193231, EPI_ISL_17193497, EPI_ISL_17193717, EPI_ISL_17197256, EPI_ISL_17224080, EPI_ISL_17237229, EPI_ISL_17238375, EPI_ISL_17238663, EPI_ISL_17248802, EPI_ISL_17249727, EPI_ISL_17250474, EPI_ISL_17251207, EPI_ISL_17251260, EPI_ISL_17259478, EPI_ISL_17279077, EPI_ISL_17280091, EPI_ISL_17280202, EPI_ISL_17286996, EPI_ISL_17287145, EPI_ISL_17287166,

Description for Lineage 2 — XBB.1.5.3 (S:A411S) + S:K304Q, N:I131R Sub-lineage of: XBB.1.5.3 (S:A411S) Earliest sequence: 2023-1-18, USA, Nevada — EPI_ISL_16859435 Most recent sequence: 2023-3-13, USA, California — EPI_ISL_17279134 Countries circulating: USA Number of Sequences: 38 GISAID AA Query: Spike_K304Q, NSP13_S36P, N_I131R GISAID Nucleotide Query: T16342C, A22472C, T28665G CovSpectrum Query: Nextcladepangolineage: Substitutions on top of XBB.1.5.3: Spike: K304Q N: I131R Nucleotide: A22472C, G22793T, T28665G

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5.3_K304Q_Lineage_2_subtreeAuspice2_genome_38b97_dd0fe0.json

Evidence See comments on Lineage 1 above.

Genomes

Genomes

EPI_ISL_16859435, EPI_ISL_16991536, EPI_ISL_16991537, EPI_ISL_17001566, EPI_ISL_17073180, EPI_ISL_17084827, EPI_ISL_17084952, EPI_ISL_17102474, EPI_ISL_17146251, EPI_ISL_17146707, EPI_ISL_17169365, EPI_ISL_17179782, EPI_ISL_17179979, EPI_ISL_17180086, EPI_ISL_17180099, EPI_ISL_17182039, EPI_ISL_17183338, EPI_ISL_17183340, EPI_ISL_17183343, EPI_ISL_17183345, EPI_ISL_17194646, EPI_ISL_17197035, EPI_ISL_17204095, EPI_ISL_17205263, EPI_ISL_17205266, EPI_ISL_17224677, EPI_ISL_17224851, EPI_ISL_17224852, EPI_ISL_17250682, EPI_ISL_17261170, EPI_ISL_17264663, EPI_ISL_17271707, EPI_ISL_17278484, EPI_ISL_17278531, EPI_ISL_17278596, EPI_ISL_17279134, EPI_ISL_17279748, EPI_ISL_17286477

Description for Lineage 3 — XBB.1.5 + S:G261V, S:K304Q, N:Q260L Sub-lineage of: XBB.1.5 Earliest sequence: 2023-1-25, USA, Iowa — EPI_ISL_16853962 Most recent sequence: 2023-3-10, USA, Florida — EPI_ISL_17287229 Countries circulating: USA (13), Mexico (11), Denmark (7), South Korea (1) Number of Sequences: 32 GISAID AA Query: Spike_K304Q, NSP13_S36P, N_Q260L GISAID Nucleotide Query: T16342C, A22472C, A29052T CovSpectrum Query: Nextcladepangolineage:XBB.1.5 & A22472C & A29052T Substitutions on top of XB.1.5: Spike: G261V, K304Q N: Q260L Nucleotide: G22344T, A22472C, A29052T

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_K304Q_Lineage_3_subtreeAuspice3_genome_38b97_dd0fe0.json

Evidence (See comments for lineage 1 above.) This lineage is likely most prevalent in Mexico or Central America and likely is the most globally widespread of the three XBB.1.5 + S:K304Q lineages described here.

Genomes

Genomes

EPI_ISL_16853962, EPI_ISL_16991186, EPI_ISL_16991332, EPI_ISL_17007616, EPI_ISL_17026377, EPI_ISL_17048537, EPI_ISL_17048801, EPI_ISL_17066276, EPI_ISL_17167717, EPI_ISL_17170127, EPI_ISL_17170170, EPI_ISL_17170222, EPI_ISL_17170233, EPI_ISL_17170262, EPI_ISL_17170273, EPI_ISL_17172014, EPI_ISL_17196744, EPI_ISL_17196752, EPI_ISL_17210284, EPI_ISL_17210289, EPI_ISL_17210319, EPI_ISL_17223535, EPI_ISL_17268872, EPI_ISL_17270146, EPI_ISL_17270151, EPI_ISL_17270155, EPI_ISL_17270158, EPI_ISL_17272393, EPI_ISL_17272466, EPI_ISL_17273319, EPI_ISL_17286216, EPI_ISL_17287229

[oobb45729]

K304Q? That's intriguing. I was wondering about what S50L would do yesterday. S50L is a known chronic infection marker but it is relatively rare (for a C to U mutation) otherwise. S50 is very close to K304.

[FedeGueli]

Thx Ryan! it was the american par of S:I410V in Europe, they popped up quite at the same time and grew fast since. Happy you finally proposed them!

[ryhisner]

It looks like 304 is also very close to 275-278 and somewhat close to 957 and 960, at least based on this tool made by @OliasDave, which is the only way I know of figuring out the proximity of different spike sites. https://ukcovid.xyz/proximity.php?targetposition=304

[xz-keg]

363/143/61 now.

[FedeGueli]

363/143/61 now.

Lineage 1 doubled in two months, not super fast but probably worth a designation. @aviczhl2 did any of them acquired some further mutations?

[xz-keg]

T16342C, A22472C, -T711G, -T10204C, -A29052T, -T28665G

53 of them have the convergent Orf1a:T4175I (XBB.1.9/XBB.1.42/XBB.1.23/XCC/BF.30/BA.2.1/BF.35/BN.1.4.1)

[FedeGueli]

Branch 1 designated XBB.1.5.104 via https://github.com/cov-lineages/pango-designation/commit/9e084183db3a025a240f59341931fefe883c09a5

MIlestone missing

[FedeGueli]

Branch 2 designated JK.1 via https://github.com/cov-lineages/pango-designation/commit/f9cd6630833036fef458c16132bb13a3bade400f

(Lineages note corrected from JH.1 to JK.1 , annotation for readers)

Milestone missing.

[HynnSpylor]

Yeah the partially alias of BQ.1.2.2 and XBB.1.5.3 are conflict. @corneliusroemer

[corneliusroemer]

Oh damn, I'll fix it, sorry for the confusion

[DailyCovidCases]

Please close this issue

[DailyCovidCases]

Please close this issue