DV.7.1.4+Orf1a:L3829F(126 seqs, 9 countries)

[xz-keg]

DV.7.1.4+C12473T+C11750T,A14979G(Orf1a:L3829F)

GISAID query: C12473T, A14979G, C11750T (broadened) No. of seqs: 40(Israel, Belgium, Canada, Netherlands)

First: EPI_ISL_18224604, 2023-8-25 Latest: EPI_ISL_18251467, 2023-9-6

usher

[FedeGueli]

Very likely the usual canadian cluster

[krosa1910]

Everything starts with Canada-OH-PHL23, and that is a high indication of cluster.

[alex-m-a]

Thanks all. The majority (25+) of these cases are associated with a known cluster within a healthcare facility.

Note that "ON-PHL-23" is simply the lab ID nomenclature used by the provincial reference laboratory that sequences cases from a variety of patient settings including, but not limited to, suspected outbreaks in healthcare facilities.

[xz-keg]

Thanks all. The majority (25+) of these cases are associated with a known cluster within a healthcare facility.

Note that "ON-PHL-23" is simply the lab ID nomenclature used by the provincial reference laboratory that sequences cases from a variety of patient settings including, but not limited to, suspected outbreaks in healthcare facilities.

Thanks!

Any reports on this? What's the infection rate(number of people infected/total residents)? Maybe we can compare such clusters with the BA.2.86 cluster(attack rate 33/38) to have some insight of relative infectiveness of DV.7.1.

[alex-m-a]

Sorry no additional information is available at this time.

[FedeGueli]

Sorry no additional information is available at this time.

Thank you very much!

[ryhisner]

There are now sequences from Belgium, the Netherlands, and Israel in this lineage. ORF1a:L3829F and ORF1a:K3353R are both known to be advantageous in diverse lineages. Furthermore, ORF1a:L3829F has already independently evolved six times in DV.7.1 according to Usher. This one could fly, and ought to be moved to the main page, IMO.

One interesting branch in Israel has ORF3a:S74F, N:T334I, and the 3-nuc, ORF1b TRS motif with ORF1b:G2610N / NSP16_G213N.

[FedeGueli]

There are now sequences from Belgium, the Netherlands, and Israel in this lineage. ORF1a:L3829F and ORF1a:K3353R are both known to be advantageous in diverse lineages. Furthermore, ORF1a:L3829F has already independently evolved six times in DV.7.1 according to Usher. This one could fly, and ought to be moved to the main page, IMO.

One interesting branch in Israel has ORF3a:S74F, N:T334I, and the 3-nuc, ORF1b TRS motif with ORF1b:G2610N / NSP16_G213N.

Thx Ryan I am checking it , the query returns 28 from Canada maybe worth expanding the proposal to the whole branch: (updating)

[FedeGueli]

Agree with Ryan here @aviczhl2 you can broaden the proposal starting with C11750T (Orf1a:L3829F):

Query: C12473T, A14979G, C11750T Samples 40 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_37cf7_7c3be0.json?label=id:node_7736289

[krosa1910]

Maybe not very important, but there seems to be a S:T240I cluster in Canada, Ontario?

It has 38seqs although very likely a small cluster, classic Canada ones.

[xz-keg]

Maybe not very important, but there seems to be a S:T240I cluster in Canada, Ontario?

It has 38seqs although very likely a small cluster, classic Canada ones.

That was the original proposal.

[FedeGueli]

78 now

[xz-keg]

82, France and USA

[Over-There-Is]

subbranch of DV.7.1.4

[xz-keg]

117, South Korea, Switzerland

[xz-keg]

126,China

[FedeGueli]

Please propose it :https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=DV.7.1*&nucMutations1=C12473T%2CA14979G%2CC11750T&analysisMode=CompareToBaseline&