New DJ.1.1 sublineage with ORF8:W45S, S:Y144-, Nuc:T15516C mutations circulating in Peru, USA.

[Wen1953]

A) Description
New possible DJ.1.1 sub-lineage with ORF8:W45S, S:Y144-, Nuc:T15516C mutations proposed by the Group of SARS-CoV-2 Genomic Surveillance of the Instituto Nacional de Salud (INS) from Peru.

B) Earliest sequence: 2022-09-16
EPI_ISL_15934005

C) Most recent sequence: 2022-11-15
EPI_ISL_15944205

D) Countries circulating:
Peru (109)
USA(2)

E) Genomes
genomes.csv

F) Evidence
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_9b2b_e25990.json?c=userOrOld

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF8%3AW45S%2CS%3AY144-&nextcladePangoLineage=BA.5.1.25*&

Proposed lineage name
DJ.1.1.X

[FedeGueli]

Notably this sublineage has further acquired S:K147N

[FedeGueli]

Notably this sublineage has further acquired S:K147N

Dear @Wen1953 ( and cc @InfrPopGen @corneliusroemer @AngieHinrichs) i think there is something wrong in this proposal or better saying there is not just one lineage but they are two lineages !! Both of them rooting in Orf8:W45S :

The first one is invisible due the fact Usher doesnt show deletions and starts right after C18747T and counts 80 sequences (see here
Gisaid query for the FIRST one collecting all the bottom branches after C18747T : NS8_W45S,Spike_Y144del,N_T265S finds 84 sequences

Expand for EPI_ISLs

EPI_ISL_15804877-15804878, EPI_ISL_15804880-15804881, EPI_ISL_15804883, EPI_ISL_15804894-15804895, EPI_ISL_15804898, EPI_ISL_15804903, EPI_ISL_15805499, EPI_ISL_15805503-15805504, EPI_ISL_15805506, EPI_ISL_15805516, EPI_ISL_15805529, EPI_ISL_15805531, EPI_ISL_15805534, EPI_ISL_15805541, EPI_ISL_15805552, EPI_ISL_15805556, EPI_ISL_15805977, EPI_ISL_15806029, EPI_ISL_15849955, EPI_ISL_15861393, EPI_ISL_15901822, EPI_ISL_15913645, EPI_ISL_15933041, EPI_ISL_15934129, EPI_ISL_15934131-15934133, EPI_ISL_15934137-15934138, EPI_ISL_15934146, EPI_ISL_15934155, EPI_ISL_15934167, EPI_ISL_15934180, EPI_ISL_15934197, EPI_ISL_15934199, EPI_ISL_15934209, EPI_ISL_15934228-15934229, EPI_ISL_15934345, EPI_ISL_15934352, EPI_ISL_15934357, EPI_ISL_15934359, EPI_ISL_15934371-15934374, EPI_ISL_15934378, EPI_ISL_15934381, EPI_ISL_15934394, EPI_ISL_15934419, EPI_ISL_15934649, EPI_ISL_15936781, EPI_ISL_15943111, EPI_ISL_15943157, EPI_ISL_15943164, EPI_ISL_15943169-15943170, EPI_ISL_15943173, EPI_ISL_15943175-15943178, EPI_ISL_15943181, EPI_ISL_15943194, EPI_ISL_15943197-15943198, EPI_ISL_15943213, EPI_ISL_15943229, EPI_ISL_15943238, EPI_ISL_15944216, EPI_ISL_15944220, EPI_ISL_15944248, EPI_ISL_15944252, EPI_ISL_15944267, EPI_ISL_15948699, EPI_ISL_15960597, EPI_ISL_15987456, EPI_ISL_16007080, EPI_ISL_16011232, EPI_ISL_16013193

The second one is the one i mentioned above and starts after T15516C then acquiring S:K147N and counts 99 seqs (see here
Gisaid query for the SECOND one at the top of the tree with S:147N : NS8_W45S,Spike_K147N,N_T265S finds 104 sequences

Expand for EPI_ISLs

EPI_ISL_15804879, EPI_ISL_15804882, EPI_ISL_15804884, EPI_ISL_15804886, EPI_ISL_15804891, EPI_ISL_15804897, EPI_ISL_15804901, EPI_ISL_15804905, EPI_ISL_15805497, EPI_ISL_15805500-15805502, EPI_ISL_15805513, EPI_ISL_15805518, EPI_ISL_15805520-15805521, EPI_ISL_15805523, EPI_ISL_15805525, EPI_ISL_15805528, EPI_ISL_15805530, EPI_ISL_15805535, EPI_ISL_15805537-15805539, EPI_ISL_15805545-15805548, EPI_ISL_15805551, EPI_ISL_15805553, EPI_ISL_15805555, EPI_ISL_15806026, EPI_ISL_15806028, EPI_ISL_15806043, EPI_ISL_15815793, EPI_ISL_15842130, EPI_ISL_15934005, EPI_ISL_15934010, EPI_ISL_15934127, EPI_ISL_15934130, EPI_ISL_15934134-15934136, EPI_ISL_15934140-15934141, EPI_ISL_15934143-15934145, EPI_ISL_15934147-15934150, EPI_ISL_15934152-15934154, EPI_ISL_15934163, EPI_ISL_15934182, EPI_ISL_15934192, EPI_ISL_15934204, EPI_ISL_15934265, EPI_ISL_15934281, EPI_ISL_15934363-15934365, EPI_ISL_15934368-15934369, EPI_ISL_15934380, EPI_ISL_15934388-15934389, EPI_ISL_15934391-15934392, EPI_ISL_15934399-15934400, EPI_ISL_15934411, EPI_ISL_15934413-15934415, EPI_ISL_15934624, EPI_ISL_15934631-15934632, EPI_ISL_15934641-15934642, EPI_ISL_15934716, EPI_ISL_15934720, EPI_ISL_15935023, EPI_ISL_15943109, EPI_ISL_15943153, EPI_ISL_15943159-15943160, EPI_ISL_15943166, EPI_ISL_15943203, EPI_ISL_15943207, EPI_ISL_15943236, EPI_ISL_15943239, EPI_ISL_15944205, EPI_ISL_15944213, EPI_ISL_15944227, EPI_ISL_15944239, EPI_ISL_15944268, EPI_ISL_16002601, EPI_ISL_16006702, EPI_ISL_16006709, EPI_ISL_16007479, EPI_ISL_16009250,

[FedeGueli]

Both these two sublineages are growing : S:144del reached 99 sequences,
instead S:147N reached 133 sequences

[Wen1953]

Hi @FedeGueli. It seems to be that many samples have C18747T, ORF8:W45S, S:Y144- and appears to be a new sublineage inside DJ.1.1. Likewise another sublineage is emerging from that defined by T15516C mutation as I described lines above. @InfrPopGen @corneliusroemer @chrisruis could it be?
Also, I thought that due to the high increasing of DJ.1 in many countries could be very useful to have a new version of pangolin. The last version is from October and it seems to be outdated.

[AngieHinrichs]

Also, I thought that due to the high increasing of DJ.1 in many countries could be very useful to have a new version of pangolin. The last version is from October and it seems to be outdated.

The latest pangolin-data release is v1.16 which is from November 7th, so one month old today. Two days ago @aineniamh tagged pango-designation release v1.17 and we are working on updating the pangoLEARN model and minimized UShER tree for the next pangolin-data release, so stay tuned for pangolin-data v1.17 hopefully soon.

[Wen1953]

Thanks @AngieHinrichs @aineniamh. We appreciate all your efforts and contributions made to continue with genomic surveillance. We hope to hear from you soon.

[FedeGueli]

Hi @FedeGueli. It seems to be that many samples have C18747T, ORF8:W45S, S:Y144- and appears to be a new sublineage inside DJ.1.1. Likewise another sublineage is emerging from that defined by T15516C mutation as I described lines above. @InfrPopGen @corneliusroemer @chrisruis could it be? Also, I thought that due to the high increasing of DJ.1 in many countries could be very useful to have a new version of pangolin. The last version is from October and it seems to be outdated.

@Wen1953 i actually think they are two and not one only:
the lineage starting with T15516C has not the S:144deletion as you can see from here: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AY144-&nucMutations=T15516C&nextcladePangoLineage=BA.5.1.25*&aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

while many sequences with C18747T have S:144del

Covspectrum finds around 300 sequences with C18747T and 49% of them has S:147N and 36% has 144del
.

Back to gisaid i found now 110 sequences for NS8_W45S,Spike_Y144del,N_T265S
and 146 for NS8_W45S,Spike_K147N,N_T265S

Both the lineages are growing quite fast and are worth to be designated.

@InfrPopGen @corneliusroemer

[InfrPopGen]

In terms of designatable clades, there appears to be a parental clade, beginning with nt:C18747T, but that would have to designated one node rootward at ORF8:W45S, and within this (off one of the nt:C18747T multifurcations) a sub-clade with S:K147N, but (unlike its sister branches) this one is lacking the S:Y144- deletion (as noted by @FedeGueli). At the moment the apparent growth advantages (with BA.5.1.25*) are about the same for both the larger clade, and its S:K147N sub-clade, over 3 months in Peru, being 28% Current adv. 14-42% and 24% Current adv. 10-38%, respectively. Before designating a heirarchy of DJ.1.1 sublineages, it is probably worth waiting to see if one of these possible pango lineages markedly out competes the other(s).

[FedeGueli]

Thanks @InfrPopGen for the analysis in the meanwhile they both keep on growing : the one with S:144Del reached 144 samples and the other with S:147N reached 173.

[ryhisner]

Hi, @Wen1953 and @LuisBarcenaF, I noticed a small, five-sequence branch of the S:K147N part of this lineage that appears to have a S:N444K reversion, a mixed nucleotide at S:N460, and, most intriguingly, S:R452V in four of the five sequences, which involves two nucleotide mutations. The fifth sequence, which is not yet on GISAID, appears to have S:R452G (a one-nucleotide mutation) and was collected about 10 days after the others.

There is a fair bit of missing coverage in these sequences, but almost all in non-spike regions of the genome. If you can give any insight into these peculiar sequences, I'd very much appreciate it. Thanks.
EPI_ISL_16039431-16039434

https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/DJ.1.1%20%2B%20L452V%2C%20etc%20-%20subtreeAuspice1_genome_11432_f03260.json

[InfrPopGen]

Thanks for submitting. We've added lineage DJ.1.1.1 with 329 newly designated sequences, and 0 updated. Defining mutation A22003T (S:K147N) (following T15516C). For now only the S:K147N sub-clade is designated because the other sub-clade makes up most of the remainder of DJ.1.1 and is a polytomy. If the situation changes in the future please re-propose the S:Y144- sub-clade (or the fast growing sub-clade of it!).

[Wen1953]

Thanks @InfrPopGen