P.2 (Zeta)/XBB.1.5* Recombinant, Singlet, Brazil

[ryhisner]

Description

Recombinant of: P.2 and XBB.1.5*
Breakpoint: 20055-21617
Most recent sequence: 2024-2-4, Brazil, Santa Catarina, Ararangua — EPI_ISL_18971336
Continents circulating: South America (1)
Countries circulating: Brazil (1)
Number of Sequences: 1
GISAID Nucleotide Query: G970T, A4091T
CovSpectrum Query: [10-of: C100T, T3295C, T3766C, C4012T, C4586T, C5622T, T6218C, C6402T, C7688A, C8956T, C9924T, T10573C, T10667G, C11669T, C11824T, C12053T, A12964G, T14408G, T15738C, C16342T, C17104T, T17220C, C19586T, G20937A]
Private Substitutions on top of P.2:
ORF1a: E102K, E235D, R545V (2-nuc), I1276F, V1393M, P1786L, P2046L, V2252G, A3220V, C3423Y, R3802C
ORF1b: H1213Y, T2040I
Nucleotide: T3295C, C4012T, C4586T, C5622T, T6218C, C6402T, C7688A, C8956T, T10573C, C11669T, T15738C, C16342T, C17104T, T17220C, C19586T, G20937A

Private Substitutions on top of XBB.1.5:
Spike: N481I
N: G96V
E: D72N
ORF3a: K16E, T89I, M125L
ORF9b: V93L
Nucleotide: C22530T, A23004T, C23673T, A25438G, A25765T, C25658T, G26458A, G28202A, G28560T, C28657T, C29203T

Nucleotide Deletions: ∆A28254 (creates N/ORF9b TRS extended homology with TRS-L)
Nucleotide Insertions: ins27899T (frameshift leads to stop codon at 27953-27955)

USHER Tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5764_1f4f0.json?c=gt-nuc_10667&gmax=11667&gmin=9667&label=id:node_3795707

Evidence
I noticed this sequence because it has several mutations typically found in chronic infections. There is a lot of dropout, but there were are no Omicron mutations in ORF1ab and plenty of unfamiliar ones, which made me think this had to be a recombinant with a pre-Omicron variant. It turns out to share eight nucleotide mutations with P.2 (Zeta), including some very rare ones: C100T (5' UTR), T3766C (synonymous), T6218C (synonymous), C9924T (ORF1a:A3220V), T10667G (ORF1a:L3468V), C11824T (synonymous), C12053T (ORF1a:L3930F), A12964G (synonymous), and T14408G (ORF1b:L314R).

As P.2 was prevalent in Brazil, this makes sense. P.2 circulated in Brazil mainly from November 2020 to February 2021, which means this person has been infected with P.2 for three years.

There is unfortunately a lot of dropout in ORF1ab, so there are likely other mutations that weren't registered. The exact areas of dropout are listed below:

Nucleotide Dropout—1341-1400, 1581, 1946-2252, 7200-7545, 7548, 7558, 7769-7797, 9950-10245, 14704, 16395, 16486, 16492, 16494, 16617-16647, 20409-20441, 24221, 24444-24445, 24448-24450, 24453, 24455, 24457, 24459, 24462
Amino Acid Dropout—ORF1a:359-379, ORF1a:439, ORF1a:561-663, ORF1a:2312-2428, ORF1a:2431, ORF1a:2502-2511, ORF1a:3229-3327, ORF1b:413, ORF1b:1007, ORF1b:1009, ORF1b:1051-1060, ORF1b:2314-2325, S:887, S:961, S:963-967

Genomes

Genomes

EPI_ISL_18971336

[FedeGueli]

"Zed is back" (cit.)! unbelievable!

[Over-There-Is]

P.2> A12964G> T3766C> T6218C> C7834T (6 seq)
GK.1 (non GK.1.1)

G569A, G970T, C1898G, G1899T, T3295C, C4012T, A4091T, G4442A, C4586T, C5622T, C6402T, T7020G, C7688A, C8956T, T9139C, C9924T, G10533A, T10573C, T11542C, C11669T, T13282C, T14408G, A14493G, A16410G, C17104T, T17220C, T19278C, C19586T, G20937A, C22530T, A23004T, A25438G, A25765T, G26458A, ins27899T, C27903T, G28202A, del28254, G28560T, C29203T

[FedeGueli]

P.2> A12964G> T3766C> T6218C> C7834T (6 seq) GK.1 (non GK.1.1)

G569A, G970T, C1898G, G1899T, T3295C, C4012T, A4091T, G4442A, C4586T, C5622T, C6402T, T7020G, C7688A, C8956T, T9139C, C9924T, G10533A, T10573C, T11542C, C11669T, T13282C, T14408G, A14493G, A16410G, C17104T, T17220C, T19278C, C19586T, G20937A, C22530T, A23004T, A25438G, A25765T, G26458A, ins27899T, C27903T, G28202A, del28254, G28560T, C29203T

Donors?

[Over-There-Is]

P.2> A12964G> T3766C> T6218C> C7834T (6 seq) GK.1 (non GK.1.1)
G569A, G970T, C1898G, G1899T, T3295C, C4012T, A4091T, G4442A, C4586T, C5622T, C6402T, T7020G, C7688A, C8956T, T9139C, C9924T, G10533A, T10573C, T11542C, C11669T, T13282C, T14408G, A14493G, A16410G, C17104T, T17220C, T19278C, C19586T, G20937A, C22530T, A23004T, A25438G, A25765T, G26458A, ins27899T, C27903T, G28202A, del28254, G28560T, C29203T

Donors?

Yeah, the donors are the branch I listed. And the rest are the private mutations.

[FedeGueli]

P.2> A12964G> T3766C> T6218C> C7834T (6 seq) GK.1 (non GK.1.1)
G569A, G970T, C1898G, G1899T, T3295C, C4012T, A4091T, G4442A, C4586T, C5622T, C6402T, T7020G, C7688A, C8956T, T9139C, C9924T, G10533A, T10573C, T11542C, C11669T, T13282C, T14408G, A14493G, A16410G, C17104T, T17220C, T19278C, C19586T, G20937A, C22530T, A23004T, A25438G, A25765T, G26458A, ins27899T, C27903T, G28202A, del28254, G28560T, C29203T

Donors?

Yeah, the donors are the branch I listed. And the rest are the private mutations.

Thanks good job