EG.5.1.1 with ORF1a:L3919F (nsp7_L60F), ORF1a:A656V (nsp2_A476V) and S:L455F (215 seqs, 25 countries)

[NkRMnZr]

Taken from Branch 31 of Multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C12020T(ORF1a:L3919F), T24496C > C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)
Query: C6541T, C12020T, G22927T, -C8982A, -C28087T
Earliest seq: 2023-08-21 (EPI_ISL_18216560, Galway, Ireland)
Latest seq: 2023-10-01 (EPI_ISL_18372127, Ontario, Canada)
Sampled Countries: UK (19: EN/16; WS/2; SC/1), Ireland (10), USA (2: FL; OH), Canada (1: ON), China (1: HB), Sweden (1)

Genomes:

EPI_ISL_18216560, EPI_ISL_18244531, EPI_ISL_18254216, EPI_ISL_18263700, EPI_ISL_18263710, EPI_ISL_18263712, EPI_ISL_18273572, EPI_ISL_18273769, EPI_ISL_18275799, EPI_ISL_18281553, EPI_ISL_18281559, EPI_ISL_18281563, EPI_ISL_18281565-18281566, EPI_ISL_18281571, EPI_ISL_18286405, EPI_ISL_18288159, EPI_ISL_18290901, EPI_ISL_18301950, EPI_ISL_18302430, EPI_ISL_18302969-18302970, EPI_ISL_18302981, EPI_ISL_18315490, EPI_ISL_18332019, EPI_ISL_18332514, EPI_ISL_18332960, EPI_ISL_18355820, EPI_ISL_18355868, EPI_ISL_18363053, EPI_ISL_18366468, EPI_ISL_18367062, EPI_ISL_18372127, EPI_ISL_18373373

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_877_69f060.json?f_userOrOld=uploaded%20sample&label=id:node_3449912

Trivia:

• There's a discussion of this branch whether simply being HK.3-dropout or independently acquires S:L455F, also @FedeGueli suggests that both ORF1a:L3919F and ORF1a:A656V are predicted to be beneficial according to Bloom/Neher calculator.

[NkRMnZr]

Tracking updates

23-10-14, 6 seqs from USA EPI_ISL_18379416, EPI_ISL_18379870, EPI_ISL_18379894, EPI_ISL_18379898, EPI_ISL_18389579, EPI_ISL_18389606
10-20, 10 seqs from France, Ireland, UK, and USA
10-28, 8 seqs from Canada, Iceland, Norway, UK and USA EPI_ISL_18420691, EPI_ISL_18426052, EPI_ISL_18432840, EPI_ISL_18433721, EPI_ISL_18435948, EPI_ISL_18436773, EPI_ISL_18439655, EPI_ISL_18442486
11-05, 8 seqs from Canada, Israel, Thailand, Sweden and UK EPI_ISL_18444518, EPI_ISL_18444726, EPI_ISL_18449883, EPI_ISL_18451715, EPI_ISL_18451717, EPI_ISL_18452904, EPI_ISL_18464846

11-18, 16 seqs from Belgium, Canada, Colombia, Croatia, France, Germany, Ireland, Spain, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29d27_a239c0.json?f_userOrOld=uploaded%20sample&label=id:node_3503615

EPI_ISL_18466623, EPI_ISL_18466858, EPI_ISL_18473136, EPI_ISL_18474903, EPI_ISL_18476748, EPI_ISL_18489703, EPI_ISL_18491792, EPI_ISL_18491795, EPI_ISL_18492414, EPI_ISL_18496211, EPI_ISL_18497075, EPI_ISL_18497313, EPI_ISL_18497787, EPI_ISL_18512059, EPI_ISL_18516967, EPI_ISL_18517010

11-25, 14 seqs from Austria, Canada, Ireland, Japan, Sweden, UK and USA

EPI_ISL_18520859, EPI_ISL_18522548, EPI_ISL_18523215, EPI_ISL_18523326, EPI_ISL_18524193, EPI_ISL_18524272, EPI_ISL_18524927, EPI_ISL_18524939, EPI_ISL_18525306, EPI_ISL_18525310, EPI_ISL_18530585, EPI_ISL_18532268, EPI_ISL_18532475, EPI_ISL_18536364

12-02, 18 seqs from Austria, Canada, France, Ireland, Singapore, UK and USA

EPI_ISL_18544601, EPI_ISL_18545469, EPI_ISL_18545492, EPI_ISL_18545506, EPI_ISL_18548046, EPI_ISL_18548842, EPI_ISL_18549413, EPI_ISL_18552735, EPI_ISL_18554463, EPI_ISL_18558694, EPI_ISL_18559304-18559305, EPI_ISL_18559309-18559310, EPI_ISL_18559312, EPI_ISL_18560198, EPI_ISL_18568371, EPI_ISL_18575342

12-06, 25 seqs from Canada, Ireland, UK and USA

EPI_ISL_18578224, EPI_ISL_18579014, EPI_ISL_18581324, EPI_ISL_18581381, EPI_ISL_18581474, EPI_ISL_18581505, EPI_ISL_18581653, EPI_ISL_18581684, EPI_ISL_18581821-18581822, EPI_ISL_18581827, EPI_ISL_18581929, EPI_ISL_18581942, EPI_ISL_18582067, EPI_ISL_18582346, EPI_ISL_18582479, EPI_ISL_18582853, EPI_ISL_18582889-18582891, EPI_ISL_18582966, EPI_ISL_18582971, EPI_ISL_18582973, EPI_ISL_18582985, EPI_ISL_18583197

12-14, 26 seqs from Austria, Canada, France, Germany, Italy, Japan, Poland, Thailand and USA

EPI_ISL_18595159, EPI_ISL_18596724, EPI_ISL_18596886, EPI_ISL_18598747, EPI_ISL_18600366, EPI_ISL_18602176, EPI_ISL_18602323, EPI_ISL_18603442, EPI_ISL_18605937, EPI_ISL_18609380, EPI_ISL_18609757, EPI_ISL_18610167, EPI_ISL_18610583, EPI_ISL_18610594, EPI_ISL_18614378, EPI_ISL_18619722, EPI_ISL_18620141, EPI_ISL_18620646, EPI_ISL_18620961, EPI_ISL_18621614, EPI_ISL_18622251, EPI_ISL_18623194, EPI_ISL_18624378, EPI_ISL_18624681, EPI_ISL_18624685, EPI_ISL_18633034

24-01-13, 49 seqs from Austria, Canada, China, Denmark, Israel, Italy, Japan, Malaysia, Netherlands, Singapore, Slovakia, Sweden, UK and USA

EPI_ISL_18638158, EPI_ISL_18641212-18641218, EPI_ISL_18641220, EPI_ISL_18643643, EPI_ISL_18643653, EPI_ISL_18651114, EPI_ISL_18652253, EPI_ISL_18652321, EPI_ISL_18654257, EPI_ISL_18660691, EPI_ISL_18660695, EPI_ISL_18666663, EPI_ISL_18669817, EPI_ISL_18672401, EPI_ISL_18673199, EPI_ISL_18674407, EPI_ISL_18675201, EPI_ISL_18684769, EPI_ISL_18689894, EPI_ISL_18691551, EPI_ISL_18692246, EPI_ISL_18692265, EPI_ISL_18699579, EPI_ISL_18701270, EPI_ISL_18702445, EPI_ISL_18704061, EPI_ISL_18704145-18704146, EPI_ISL_18704211, EPI_ISL_18705695, EPI_ISL_18707361, EPI_ISL_18707822, EPI_ISL_18707829, EPI_ISL_18707897, EPI_ISL_18711109, EPI_ISL_18716343, EPI_ISL_18716351, EPI_ISL_18719608, EPI_ISL_18721339, EPI_ISL_18723884, EPI_ISL_18741062, EPI_ISL_18757213, EPI_ISL_18758633

[FedeGueli]

I see 49 with C6541T, C12020T, G22927T, -C28087T why?

[NkRMnZr]

10-20, 10 seqs from France, Ireland, UK, and USA

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_10ca4_2f2650.json?f_userOrOld=uploaded%20sample&label=id:node_3473368

EPI_ISL_18389843, EPI_ISL_18389916, EPI_ISL_18392497, EPI_ISL_18396736, EPI_ISL_18398160, EPI_ISL_18398181, EPI_ISL_18401133, EPI_ISL_18404443, EPI_ISL_18407000

[NkRMnZr]

I see 49 with C6541T, C12020T, G22927T, -C28087T why?

a typo

[FedeGueli]

Thx

[DailyCovidCases]

Please close this issue

[Over-There-Is]

247

[FedeGueli]

247

old ones