Sublineage of BA.5.2 (ORF1b:T1050N) with S:K444Q & ORF7a:A55V (92 seq)

[ryhisner]

Description

Sub-lineage of: BA.5.2 (ORF1b:T1050N)
Earliest sequence: 2022-9-17, USA, Minnesota — EPI_ISL_15227102
Most recent sequence: 2022-11-22, New Zealand — EPI_ISL_15956989
Countries circulating: New Zealand (68), Australia (17), USA (2), South Korea (1), Thailand (1)
Number of Sequences: 89
GISAID Query: Spike_K444Q, NS7a_A55V
CovSpectrum Query: Nextcladepangolineage:BA.5.2* & ORF7a:A55V & S:K444Q
Substitutions on top of BA.5.2 (ORF1b:T1050N):
Spike: K444Q
ORF7a: A55V
Nucleotide: A8197G, T19896C, C21595T, A22892C, C25710T, C27557T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BA.5.2%20(T1050N)%20%2B%20K444Q%20%2B%20ORF7aA55V%20-%20subtreeAuspice1_genome_a48d_770360.json

Evidence
Of the 89 sequences in this lineage, 68 were uploaded today, all from New Zealand. S:444 is probably the most prominent antibody escape mutation in the current global context. I’ve previously described (in issues #1110 and #1272) how S:K444Q stands out on the Bloom Lab RBD Heat Map as having the most favorable combination of ACE2 affinity and RBD expression of any of the 19 possible AA substitutions on a BA.2 background.

S:K444Q also appears to be the second-best mutation for evading neutralizing antibodies from breakthrough-infection convalescent sera.

This hasn’t, however, translated into real-world success in terms of the prevalence of this mutation. S:R444Q has occurred in a number of BA.5 lineages, but all have either died out or have shrunk to insignificant levels. This lineage appears to be an exception, though its growth seems primarily confined to New Zealand and Australia.

Genomes

Genomes

EPI_ISL_15227102, EPI_ISL_15399291, EPI_ISL_15416413, EPI_ISL_15732157, EPI_ISL_15736397, EPI_ISL_15784105, EPI_ISL_15797328, EPI_ISL_15797567, EPI_ISL_15797771, EPI_ISL_15797799, EPI_ISL_15797897, EPI_ISL_15797930, EPI_ISL_15820571, EPI_ISL_15832186, EPI_ISL_15832312, EPI_ISL_15832602, EPI_ISL_15832620, EPI_ISL_15848882, EPI_ISL_15870943, EPI_ISL_15917287, EPI_ISL_15941947, EPI_ISL_15955562, EPI_ISL_15955659, EPI_ISL_15955875, EPI_ISL_15955900, EPI_ISL_15956016, EPI_ISL_15956060, EPI_ISL_15956289, EPI_ISL_15956335, EPI_ISL_15956349, EPI_ISL_15956371, EPI_ISL_15956403, EPI_ISL_15956438, EPI_ISL_15956444, EPI_ISL_15956445, EPI_ISL_15956483, EPI_ISL_15956484, EPI_ISL_15956552, EPI_ISL_15956567, EPI_ISL_15956646, EPI_ISL_15956665, EPI_ISL_15956699, EPI_ISL_15956731, EPI_ISL_15956759, EPI_ISL_15956792, EPI_ISL_15956872, EPI_ISL_15956915, EPI_ISL_15956968, EPI_ISL_15956971, EPI_ISL_15956978, EPI_ISL_15956986, EPI_ISL_15956989, EPI_ISL_15957065, EPI_ISL_15957069, EPI_ISL_15957088, EPI_ISL_15957090, EPI_ISL_15957097, EPI_ISL_15957208, EPI_ISL_15957449, EPI_ISL_15957456, EPI_ISL_15957490, EPI_ISL_15957512, EPI_ISL_15957710, EPI_ISL_15957783, EPI_ISL_15957806, EPI_ISL_15957903, EPI_ISL_15958112, EPI_ISL_15958122, EPI_ISL_15958131, EPI_ISL_15958151, EPI_ISL_15958176, EPI_ISL_15958217, EPI_ISL_15958246, EPI_ISL_15958254, EPI_ISL_15958264, EPI_ISL_15958290, EPI_ISL_15958298, EPI_ISL_15958329, EPI_ISL_15958334, EPI_ISL_15958335, EPI_ISL_15958370, EPI_ISL_15958382, EPI_ISL_15958450, EPI_ISL_15958541, EPI_ISL_15958625, EPI_ISL_15958689, EPI_ISL_15958786, EPI_ISL_15958824

[InfrPopGen]

Thanks for submitting. We've added lineage BA.5.2.45 with 19 newly designated sequences, and 0 updated designations. Defining mutations C21595T (S:K444Q), A22892C (following C25710T).

[icestorm972]

FYI
As I've seen some S:K444Q rising in my Germany RKI DESH data analysis tonight

I took a closer look:

There are now 4 (representative) samples in total

• 1x BA.5.2.45 (BA.2 + S:K444Q + ORF7a:A55V)
  • 2022-11-17: IMS-10122-CVDP-BA1B523F-9940-494B-BE3B-57CFED6E2EF5
• 3x undesignated Sublineage of BA.5.1.5 with S:K444Q, S:V1264L (15 seq) #1272 (BA.5.1.5 + S:K444Q + S:V1264L):
  • 2022-11-07: IMS-10013-CVDP-C7EB07C4-5508-4D4B-A4B8-49B5E7D16F3C
  • 2022-11-15: IMS-10116-CVDP-58564FA6-9DBB-42F0-8E12-4AFA00FA812C
  • 2022-11-21: IMS-10116-CVDP-77FDC025-BDFA-4632-8DE5-6B10B5E752CA

CC @corneliusroemer