Issue to Register Singlet Recombinants that shall be not be removed by usher (starting from 2024-9-24 ) Part III

[aviczhl2]

https://github.com/sars-cov-2-variants/lineage-proposals/issues/991 Part I https://github.com/sars-cov-2-variants/lineage-proposals/issues/1675 Part II https://github.com/sars-cov-2-variants/lineage-proposals/issues/2086 Part III

Successor issue of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1675

Anything with >5 reversion(refer to the last checkpoint ,usually a designation) or >20 private mutations(distance to the last node) may be removed by usher. However some of them are real recombinants.

There are quite a few recombinants meeting this criteria. Whenever you happen to see any of them, please register them here to help those recombinant singlets not becoming invisible, hence when a 2nd seq appears we may easily realize the cluster.

As github only displays ~50 comments at the same time for each issue, better refresh this issue for every 50 comments so that searching for specific recomb is easier.

[FedeGueli]

LZ.2/XDV.1 with LZ.2 acquiring Orf9b/N from XDV as another LB.1/XDV recombinant proposed today by @aviczhl2

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_d4de_521ff0.json?label=id:node_7138446 Query: C10440T, T28297C,T2032C Samples: 3 all from Singapore

Proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/2093

[aviczhl2]

LZ.2/XDV.1 with LZ.2 acquiring Orf9b/N from XDV as another LB.1/XDV recombinant proposed today by @aviczhl2 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_d4de_521ff0.json?label=id:node_7138446 Query: C10440T, T28297C,T2032C Samples: 3 all from Singapore

Make a separate proposal?

[FedeGueli]

EPI_ISL_19437426 JN.1.67.1/XDV.1 recombinant with XDV.1 taking everything from JN.1.67.1 (branch with G1126A) between 0 >> 14775

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_288ff_524ab0.json

[FedeGueli]

EPI_ISL_19430059 KP.1.1.5 got N/Orf9b from XDV.1 tree

[FedeGueli]

EPI_ISL_19445458 pooled GBW MB.1.1.1/KP.3.1.1 exchanging 31del for 22N 31F . Very likely not real

[FedeGueli]

EPI_ISL_19450478 XDV.1.5 got Orf10:S23F could be a recombinant with EG.5.1??

[aviczhl2]

EPI_ISL_19450478 XDV.1.5 got Orf10:S23F could be a recombinant with EG.5.1??

If there is no reversions likely convergent evolution. EG.5.1 has died off for a long time and Orf10:23 is a convergent site.