KP.2.3 (pre C28714T branch) with ORF1a:Q884E / nsp3_Q66E (301 seqs, 8+4 countries); Further with S:Q677H (multiple sub-branches) and S:F1103L

NkRMnZr commented 1 month ago

Transferred from sars-cov-2-variants/lineage-proposals#1959

Defining Mutations: KP.2.3 (pre-C28714T) > C2915G (ORF1a:Q884E) Query: C2915G, G25593T Earliest seq: 24-04-23 (EPI_ISL_19126207, New York) Latest seq: 24-08-23 (EPI_ISL_19364611, Iowa) Sampled Countries: USA (107: TX/27, FL/17, NY/12, NE/5, CA/6, IA/4, NJ/4, OH/6, IL/3, PR/3, CO/2, DE/2, GA/2, MI/2, NC/2, AZ, CT, LA, MA, PA, VA + GBW ex. Dominican Republic/1, India/1, South Africa/1, Sweden/1); Canada (32: ON/24, QC/5, AB, BC, SK), New Zealand (3), France (1), Moldova (1), Netherlands (1), Spain (1)

Further Spike Additions:

Main Branch > C1714T > G23593T (S:Q677H); Query: C1714T, C2915G, G23593T
Main Branch > T25705C (ORF3a:F105L) > C7823T (ORF1a:H2520Y) > T24869C(S:F1103L, which makes it F1103L, V1104L); Query: C7823T, T24869C

Genomes:

for `lineages.csv` commit: ``` Canada/AB-ABPHL-120569/2024 Canada/BC-BCCDC-722620/2024 Canada/ON-KHS-03660-v1/2024 Canada/ON-KHS-03806-v1/2024 Canada/ON-PHL-202410429/2024 Canada/ON-PHL-202411355/2024 Canada/ON-PHL-202411376/2024 Canada/ON-PHL-202411426/2024 Canada/ON-PHL-202411427-v2/2024 Canada/ON-PHL-202411574/2024 Canada/ON-PHL-202411612/2024 Canada/ON-PHL-202411615/2024 Canada/ON-PHL-202411617/2024 Canada/ON-PHL-202411816/2024 Canada/ON-PHL-202411817/2024 Canada/ON-PHL-202411818/2024 Canada/ON-PHL-202412008/2024 Canada/ON-PHL-202412260/2024 Canada/ON-PHL-202412268/2024 Canada/ON-PHL-202412281/2024 Canada/ON-PHL-202412282/2024 Canada/ON-PHL-202412288/2024 Canada/ON-PHL-202412290/2024 Canada/ON-PHL-202412314/2024 Canada/ON-PHL-202412316/2024 Canada/ON-PHL-202412317/2024 Canada/QC-L00763066001/2024 Canada/QC-L00772952001/2024 Canada/QC-L00773761001/2024 Canada/QC-L00773800001/2024 Canada/QC-L00776797001/2024 Canada/SK-RRPL-722813/2024 France/PAC-RELAB-IPP07553/2024 Moldova/Nr-121C/2024 Netherlands/ZH-RIVM-139868/2024 NewZealand/24YA6142/2024 NewZealand/24YA6184/2024 NewZealand/24YA6185/2024 PuertoRico/PR-CVL-025086/2024 PuertoRico/PR-CVL-025546/2024 PuertoRico/S-7148/2024 Spain/CT-HUVH-E39707/2024 USA/AZ-CDC-LC1110093/2024 USA/CA-CDC-LC1110094/2024 USA/CA-CDPH-500140772/2024 USA/CA-CDPH-6000019614/2024 USA/CA-CDPH-6000020198/2024 USA/CA-CDPH-6000020456/2024 USA/CA-CDPH-6000020459/2024 USA/CA-GBW-GKISBBBD55936/2024 USA/CO-CDPHE-42084757/2024 USA/CO-CDPHE-42084781/2024 USA/CT-UM-G44S58W9/2024 USA/DE-CDC-LC1110950/2024 USA/DE-CDC-LC1114022/2024 USA/FL-CDC-LC1105641/2024 USA/FL-CDC-LC1107238/2024 USA/FL-CDC-LC1107297/2024 USA/FL-CDC-LC1107746/2024 USA/FL-CDC-LC1110501/2024 USA/FL-CDC-LC1110542/2024 USA/FL-CDC-LC1110603/2024 USA/FL-CDC-LC1111083/2024 USA/FL-CDC-LC1111092/2024 USA/FL-CDC-LC1114469/2024 USA/FL-CDC-LC1115710/2024 USA/FL-CDC-LC1115790/2024 USA/FL-CDC-LC1117538/2024 USA/FL-GBW-GKISBBBB71982/2024 USA/FL-PLMI-6HW-25353/2024 USA/FL-UM-G44S51Z5/2024 USA/FL-UM-G44S56D5/2024 USA/FL-UM-G44S56E1/2024 USA/GA-CDC-LC1113339/2024 USA/GA-EHC-8044X/2024 USA/IA-SHL-2463826/2024 USA/IA-SHL-2469247/2024 USA/IA-SHL-2469248/2024 USA/IA-SHL-2484871/2024 USA/IL-NRIPHL_RIPHL_14666/2024 USA/IL-RIPHL_14666_G/2024 USA/IL-RIPHL_33103_G/2024 USA/LA-EVTL22608/2024 USA/MA-CDC-LC1107473/2024 USA/MI-MDHHS-SC45283/2024 USA/MI-UM-L379256547/2024 USA/NC-CDC-LC1112955/2024 USA/NC-USAFSAM-S22822/2024 USA/NE-NM_L378215230/2024 USA/NE-NM_L379114546/2024 USA/NE-NM_L379169916/2024 USA/NE-NPHL24-412/2024 USA/NE-NPHL-421/2024 USA/NJ-CDC-LC1104013/2024 USA/NJ-CDC-LC1110926/2024 USA/NJ-CDC-LC1112640/2024 USA/NJ-CDC-LC1113165/2024 USA/NJ-GBW-GKISBBBD37619/2024 USA/NY-CDC-LC1105026/2024 USA/NY-CDC-LC1111809/2024 USA/NY-CDC-LC1112081/2024 USA/NY-CDC-QDX96017830/2024 USA/NY-GBW-GKISBBBD28888/2024 USA/NY-NYULH-20521/2024 USA/NY-PRL-240820_81H02/2024 USA/NY-PRL-240828_81D06/2024 USA/NY-SUNYQB-XL2319/2024 USA/NY-SUNYQB-XW77236/2024 USA/NY-URMC-O6S1P118-1/2024 USA/NY-URMC-O7S1P415-1/2024 USA/NY-URMC-O7S1Q042-1/2024 USA/OH-PLMI-5H5-25107/2024 USA/OH-PLMI-5H5-25183/2024 USA/OH-PLMI-7CH-25498/2024 USA/OH-PLMI-7CH-25519/2024 USA/OH-PLMI-7CL-26202/2024 USA/OH-PLMI-7CR-26098/2024 USA/PA-CDC-LC1105818/2024 USA/TX-CDC-LC1113312/2024 USA/TX-HMH-M-143665/2024 USA/TX-HMH-M-143785/2024 USA/TX-HMH-M-143976/2024 USA/TX-HMH-M-143984/2024 USA/TX-HMH-M-144318/2024 USA/TX-HMH-M-144857/2024 USA/TX-HMH-MCoV-143376/2024 USA/TX-HMH-MCoV-143399/2024 USA/TX-HMH-MCoV-143436/2024 USA/TX-HMH-MCoV-143447/2024 USA/TX-HMH-MCoV-143537/2024 USA/TX-HMH-MCoV-143556/2024 USA/TX-HMH-MCoV-143593/2024 USA/TX-HMH-MCoV-144464/2024 USA/TX-HMH-MCoV-144564/2024 USA/TX-HMH-MCoV-144615/2024 USA/TX-HMH-MCoV-145093/2024 USA/TX-KVI400860/2024 USA/TX-KVI400861/2024 USA/TX-KVI400876/2024 USA/TX-KVI400928/2024 USA/TX-KVI400957/2024 USA/TX-PHH-CS-03991/2024 USA/TX-UHS-UTHSA11339-P0/2024 USA/TX-UHS-UTHSA11559-P0/2024 USA/TX-UHS-UTHSA11689-P0/2024 USA/VA-VTVAS3-GSC45451/2024 ``` epi_isl accessions: `EPI_ISL_19306575, EPI_ISL_19303158, EPI_ISL_19331547, EPI_ISL_19345730, EPI_ISL_19293885, EPI_ISL_19343672, EPI_ISL_19343693, EPI_ISL_19343733, EPI_ISL_19357922, EPI_ISL_19343864, EPI_ISL_19343900, EPI_ISL_19343903, EPI_ISL_19343905, EPI_ISL_19358010, EPI_ISL_19358011, EPI_ISL_19358012, EPI_ISL_19358197, EPI_ISL_19386376, EPI_ISL_19386384, EPI_ISL_19386397, EPI_ISL_19386398, EPI_ISL_19386404, EPI_ISL_19386406, EPI_ISL_19386428, EPI_ISL_19386430, EPI_ISL_19386431, EPI_ISL_19310499, EPI_ISL_19364403, EPI_ISL_19364409, EPI_ISL_19364442, EPI_ISL_19364475, EPI_ISL_19318558, EPI_ISL_19267102, EPI_ISL_19357673, EPI_ISL_19293206, EPI_ISL_19363246, EPI_ISL_19363112, EPI_ISL_19363113, EPI_ISL_19268761, EPI_ISL_19358927, EPI_ISL_19284679, EPI_ISL_19158790, EPI_ISL_19298058, EPI_ISL_19298096, EPI_ISL_19347620, EPI_ISL_19232894, EPI_ISL_19319450, EPI_ISL_19383898, EPI_ISL_19383900, EPI_ISL_19254680, EPI_ISL_19333298, EPI_ISL_19333309, EPI_ISL_19367503, EPI_ISL_19316852, EPI_ISL_19350067, EPI_ISL_19197432, EPI_ISL_19288969, EPI_ISL_19288991, EPI_ISL_19288967, EPI_ISL_19317191, EPI_ISL_19317341, EPI_ISL_19317074, EPI_ISL_19316965, EPI_ISL_19316986, EPI_ISL_19349942, EPI_ISL_19379546, EPI_ISL_19379547, EPI_ISL_19379661, EPI_ISL_19210381, EPI_ISL_19307193, EPI_ISL_19328934, EPI_ISL_19367376, EPI_ISL_19367507, EPI_ISL_19350327, EPI_ISL_19344192, EPI_ISL_19270996, EPI_ISL_19306324, EPI_ISL_19306366, EPI_ISL_19364611, EPI_ISL_19307413, EPI_ISL_19314335, EPI_ISL_19273141, EPI_ISL_19343374, EPI_ISL_19289004, EPI_ISL_19261832, EPI_ISL_19302579, EPI_ISL_19347613, EPI_ISL_19368766, EPI_ISL_19260083, EPI_ISL_19287247, EPI_ISL_19301073, EPI_ISL_19306318, EPI_ISL_19318919, EPI_ISL_19153918, EPI_ISL_19316792, EPI_ISL_19346943, EPI_ISL_19346979, EPI_ISL_19300557, EPI_ISL_19197251, EPI_ISL_19347054, EPI_ISL_19347562, EPI_ISL_19126207, EPI_ISL_19339318, EPI_ISL_19359975, EPI_ISL_19362691, EPI_ISL_19381178, EPI_ISL_19311423, EPI_ISL_19341344, EPI_ISL_19285057, EPI_ISL_19325543, EPI_ISL_19356822, EPI_ISL_19273217, EPI_ISL_19273292, EPI_ISL_19324422, EPI_ISL_19324434, EPI_ISL_19378816, EPI_ISL_19367921, EPI_ISL_19197364, EPI_ISL_19349561, EPI_ISL_19348953, EPI_ISL_19349073, EPI_ISL_19348880, EPI_ISL_19349140, EPI_ISL_19349307, EPI_ISL_19366278, EPI_ISL_19335440, EPI_ISL_19335465, EPI_ISL_19335236, EPI_ISL_19335225, EPI_ISL_19335327, EPI_ISL_19335260, EPI_ISL_19335271, EPI_ISL_19365880, EPI_ISL_19365612, EPI_ISL_19365561, EPI_ISL_19366042, EPI_ISL_19278940, EPI_ISL_19278967, EPI_ISL_19329248, EPI_ISL_19352341, EPI_ISL_19352355, EPI_ISL_19354144, EPI_ISL_19295159, EPI_ISL_19337576, EPI_ISL_19347850, EPI_ISL_19294103`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e31f_d86970.json?label=id:node_7054901

Trivia:

ORF1a:Q884E (C2915G) only sampled about 170 times during the whole pandemic, probably due to low frequency of C>G mutation, 85% of the seqs are on this specific branch which doesn't seem to be slow: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1a%3AQ884E

ryhisner commented 1 month ago

Transferring my comment from the original post below.

Nucleocapsid engages in a crucial interaction with this region of NSP3, residues 1-111 (ORF1a:819-929), called Ubl1. Without this interaction, coronaviruses basically cannot replicate.

The structure below depicts the Ubl1-N interaction, and I've colored Ubl1:Q66 (ORF1a:Q884) in magenta. I've shown the atoms in the residues closest to Q884. The light blue is Ubl1 and the soft pink is the region of nucleocapsid that interacts with Ubl1 (N:191-263). It looks like ORF1a:Q884 faces away from N, so I'm not sure whether it would affect this interaction or not.

Over-There-Is commented 1 month ago

Q677H 57

FedeGueli commented 1 month ago

Q677H 57

@NkRMnZr please add S:Q677H branch to the proposal

NkRMnZr commented 1 week ago

multiple S:Q677H sub-branches (at least 3), the major one goes: main proposal > C1714T > G23593T (S:Q677H), query: C1714T, C2915G, G23593T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ebf3_f631a0.json?label=id:node_7335143

cov-lineages / pango-designation

KP.2.3 (pre C28714T branch) with ORF1a:Q884E / nsp3_Q66E (301 seqs, 8+4 countries); Further with S:Q677H (multiple sub-branches) and S:F1103L #2767