Complex recombinants(and maybe recomb of recombs) in Italy (4 seqs)

[aviczhl2]

There seems to be a complex branch in Italy that shares some same very unique mutations but different in other parts of the virus. There shall be something that recomb/contams with major JN.1 variants (JN.1.4/ JN.1.11.1/JN.1.16+S:Q493E)

GISAID query: G16283C, A19080T, T19081C,C28958A No. of seqs: 4(Italy)

JN.1+A6425G, G16283C, A19080T, T19081C, T22208C(rev), G23604C(rev), A23854C ,T3431G(rev), T9344C(rev), C10078T, T14408C(rev), A15756T(rev), C16308T, C17634T, G18163A(rev), T18738A, T26060C(rev), A26709G(rev)

ORF1ab | N2054D, C5340S, E6272D, W6273R,L1056V(rev), F3027L(rev), L4715P(rev), V5967I(rev), F6158L S | F216L(rev), R681P(rev), K764N ORF3a | I223T(rev) M | T63A(rev)

EPI_ISL_18831265, 18831266, with JN.1.4-defining, 2024-1 EPI_ISL_19261041, with JN.1.11.1-defining (S:F456L+S:V1104L), 2024-6 EPI_ISL_19261040, with S:F456L+S:Q493E, 2024-6

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26393_73ed10.json?f_userOrOld=uploaded%20sample&label=id:node_6250736

[FedeGueli]

I would not exclude some sort of artifact being all by the same lab but worth looking into it. thx.

[ryhisner]

All from the Lombardy lab, so I would guess these are artifacts. Lots of bad sequences from that lab.

[aviczhl2]

No new seqs