KP.2.3 (pre C28714T branch) with ORF1a:Q884E / nsp3_Q66E (130 seqs, 7+4 countries) #1959
Comments
|
This is very fast likely boosted by Texas and Canadian clusters. |
|
130 seqs, and compatible with KP.3.1.1*(much faster than KP.2.3*). I think this shall be proposed.
|
xz-keg
changed the title
xz-keg
added
To be proposed
|
agree |
|
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. |
|
transferred to cov-lineages/pango-designation#2767 |
Defining Mutations:
KP.2.3 (pre-C28714T)>C2915G (ORF1a:Q884E)Query:
C2915G, G25593TEarliest seq: 24-04-23 (
EPI_ISL_19126207, New York)Latest seq: 24-08-23 (
EPI_ISL_19364611, Iowa)Sampled Countries: USA (90: TX/22, FL/12, NY/11, NE/5, CA/4, IA/4, NJ/4, OH/4, IL/3, PR/3, CO/2, DE/2, GA/2, MI/2, AZ, LA, MA, NC, PA, VA + GBW ex. Dominican Republic/1, India/1, South Africa/1, Sweden/1); Canada (23: ON/15, QC/5, AB, BC, SK), New Zealand (3), France (1), Moldova (1), Netherlands (1), Spain (1)
Genomes:
for
lineages.csvcommit:epi_isl accessions:
EPI_ISL_19126207, EPI_ISL_19153918, EPI_ISL_19158790, EPI_ISL_19197251, EPI_ISL_19197364, EPI_ISL_19197432, EPI_ISL_19210381, EPI_ISL_19232894, EPI_ISL_19254680, EPI_ISL_19260083, EPI_ISL_19261832, EPI_ISL_19267102, EPI_ISL_19268761, EPI_ISL_19270996, EPI_ISL_19273141, EPI_ISL_19273217, EPI_ISL_19273292, EPI_ISL_19278940, EPI_ISL_19278967, EPI_ISL_19284679, EPI_ISL_19285057, EPI_ISL_19287247, EPI_ISL_19288967, EPI_ISL_19288969, EPI_ISL_19288991, EPI_ISL_19289004, EPI_ISL_19293206, EPI_ISL_19293885, EPI_ISL_19294103, EPI_ISL_19295159, EPI_ISL_19298058, EPI_ISL_19298096, EPI_ISL_19300557, EPI_ISL_19301073, EPI_ISL_19302579, EPI_ISL_19303158, EPI_ISL_19306318, EPI_ISL_19306324, EPI_ISL_19306366, EPI_ISL_19306575, EPI_ISL_19307193, EPI_ISL_19307413, EPI_ISL_19310499, EPI_ISL_19311423, EPI_ISL_19314335, EPI_ISL_19316792, EPI_ISL_19316852, EPI_ISL_19316965, EPI_ISL_19316986, EPI_ISL_19317074, EPI_ISL_19317191, EPI_ISL_19317341, EPI_ISL_19318558, EPI_ISL_19318919, EPI_ISL_19319450, EPI_ISL_19324422, EPI_ISL_19324434, EPI_ISL_19325543, EPI_ISL_19328934, EPI_ISL_19329248, EPI_ISL_19331547, EPI_ISL_19333298, EPI_ISL_19333309, EPI_ISL_19335225, EPI_ISL_19335236, EPI_ISL_19335260, EPI_ISL_19335271, EPI_ISL_19335327, EPI_ISL_19335440, EPI_ISL_19335465, EPI_ISL_19337576, EPI_ISL_19339318, EPI_ISL_19341344, EPI_ISL_19343374, EPI_ISL_19343672, EPI_ISL_19343693, EPI_ISL_19343733, EPI_ISL_19343864, EPI_ISL_19343900, EPI_ISL_19343903, EPI_ISL_19343905, EPI_ISL_19344192, EPI_ISL_19345730, EPI_ISL_19346943, EPI_ISL_19346979, EPI_ISL_19347054, EPI_ISL_19347562, EPI_ISL_19347613, EPI_ISL_19347620, EPI_ISL_19347850, EPI_ISL_19348880, EPI_ISL_19348953, EPI_ISL_19349073, EPI_ISL_19349140, EPI_ISL_19349307, EPI_ISL_19349561, EPI_ISL_19349942, EPI_ISL_19350067, EPI_ISL_19350327, EPI_ISL_19352341, EPI_ISL_19352355, EPI_ISL_19354144, EPI_ISL_19356822, EPI_ISL_19357673, EPI_ISL_19357922, EPI_ISL_19358010-19358012, EPI_ISL_19358197, EPI_ISL_19358927, EPI_ISL_19359975, EPI_ISL_19362691, EPI_ISL_19363112-19363113, EPI_ISL_19363246, EPI_ISL_19364403, EPI_ISL_19364409, EPI_ISL_19364442, EPI_ISL_19364475, EPI_ISL_19364611UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3d18b_5a170.json?label=id:node_7077590
Trivia:
ORF1a:Q884E (C2915G)only sampled about 150 times during the whole pandemic, probably due to low frequency ofC>Gmutation, 80% of the seqs are on this specific branch which doesn't seem to be slow.The text was updated successfully, but these errors were encountered: