Description
Description
Sub-lineage of: BQ.1.1
Earliest sequence: 2022-9-15, Malaysia, EPI_ISL_15942617
Most recent sequence: 2022-11-15, Indonesia — EPI_ISL_15966070
Countries circulating: Indonesia (8), Malaysia (1)
Number of Sequences: 9
GISAID Query: Spike_K182E, Spike_Q218H, Spike_P1162L
CovSpectrum Query: Nextcladepangolineage:BQ.1* & S:K182E & S:Q218H
Substitutions on top of BQ.1.1.:
Spike: K182E, Q218H, P251L, P1162L (and A829S for 4/9 sequences)
Nucleotide: T19293C, A22106G, G22216T, C22314T, T23716C, C25047T, A28834G
USHER Tree
The bottom branch here appears to lack S:P251L but that is almost certainly an artifact. All four sequences lack coverage in that area. Also, the long branch is 100% artifactual, the seven “reversions” obviously being due to lack of sequencing coverage in the RBM. Only the ORF1a:P1947S (C4754T) mutation on that branch is real.
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BQ.1.1%20%2B%20K182E%2C%20Q218H%2C%20P251L%2C%20P1162L%20-%20subtreeAuspice1_genome_26c49_8934f0.json
Evidence
The first sequence in this lineage is the only one from Malaysia and was collected on September 15, though it was only uploaded November 29. The other eight sequences, all from Indonesia, were collected nearly two months later—one on Nov 2 and the rest between Nov 11-15. There are many countries in this region with little to no sequencing, so it seems likely this lineage has been circulating in significant numbers somewhere in SE Asia.
There is really not much diversity in this lineage considering the two-month time difference between the Malaysian sequence and the others. As stated above, the long branch on the tree is definitely an artifact.
Notably, four of the more recent sequences (collection dates Nov 2, 11, 11, 15) also have S:A829S. It's possible that A829S is also present in the other four Indonesian sequences but is not indicated due to the relatively poor quality of those sequences.
Genomes