Potential BA.2.3.20/BA.5.2 recombinant (25 sequences as of 2022-12-01)

[c19850727]

I am proposing this potential recombinant with only 7 sequences based on its scattered geographical distribution and concerning mutation profiles.

Description

Recombinant between: BA.2.3.20 and BA.5.2*
Earliest sequence: 2022/09/19 (Australia-WA)
Most recent sequence: 2022/10/31 (Japan, local case)
Countries circulating: Australia, Austria, Italy, Japan, Singapore, US-TX and US-MN.
Potential breakpoint: somewhere between Spike S1 and ORF3a (23015-25809)

Mutation profile:

Private mutations: ORF1a:C936Y, ORF1a:A2584V
GISAID query: NSP3_C118Y, NSP4_A146V, M_D3N

About the potential BA.5.2 donor: according to Cov-spectrum, the potential BA.5.2 donor might be a undesignated Philippine sub-branch with C25896T, which had a peak prevalence of ~50% in the Philippines in early August.

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_35689_fe2e00.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G3072A,T25810C,C25896T,G26529A,T26858C,C27012T,C27259A,C27382G,T27383A,C27384T,C27513T,A28330G,A28550C

Genomes:

EPI_ISL_15026956, EPI_ISL_15306600, EPI_ISL_15306899, EPI_ISL_15312824, EPI_ISL_15421221, EPI_ISL_15482232, EPI_ISL_15578495

[FedeGueli]

Thx @c19850727 great catch as usual. This could be the riight "" train"" for BA.2.3.20:
It recombined with the fastest of the main BA.5 branches inheriting the Orf9b:16G mutation that seems being a key for the BA.5.2* family to reach global dominance earlier past august.
I would like to notice that this recombination took rid of Orf6:61L mutation that was deeply analyzed by last Krogan lab paper : https://www.biorxiv.org/content/10.1101/2022.10.19.512927v1
In this paper the Krogan team showed as Orf6 mutated makes the virus lose some of its capability of evade/antagonize innate immune system, attenuating it.

[cvejris]

This is gonna be big... Thanks @FedeGueli for the summary - the recombination pattern here is exactly the same as in XBD, which adds weight to your reasoning!

[thomasppeacock]

Recommending this based on the geographical spread and the unique parent lineages (as the 3' end of the BA.5 genome is where it is hypothesised to contain some fitness advantages over BA.2 or BA.4)

[c19850727]

one more uploaded from the Philippines. Collected back in September though.

[ryhisner]

Another from this lineage uploaded today from Malaysia. Collection date October 18. EPI_ISL_15660403

[c19850727]

12 sequnces as of 2022-11-10, newly found in Switzerland.

[c19850727]

13 sequences as of 2022-11-12, newly found in Australia-NSW.

[c19850727]

14 sequences as of 2022-11-15, newly found in Singapore ex-Philippines.

[ryhisner]

Make that 15 sequences: another travel-sequence from the Philippines, this one sequenced in Japan. Collection date November 1. EPI_ISL_15784498

This recombinant has to be present in the Philippines in substantial numbers.

[c19850727]

16 sequences as of 2022-11-17. Newly found in Germany.

[ryhisner]

Another uploaded last night from USA, California, along with one from France the day before.
EPI_ISL_15880948, EPI_ISL_15839998

Up to 19 sequences now I believe and spread throughout the world. Seems worthy of designation to me.

[ryhisner]

Additional sequence of this lineage from Germany yesterday. EPI_ISL_15904795

[c19850727]

23 sequences as of 2022-11-29.

[ryhisner]

Two more sequences of this uploaded in the past 24 hours, one from Switzerland and one from Japan. The one from Japan has S:K478E, which creates a new sgmRNA. EPI_ISL_15966208, EPI_ISL_15967636

[corneliusroemer]

Done, designated as XBJ, thanks for the issue and continued insights.

[FedeGueli]

This is going on growing. To be clear this has S:E484R as BA.2.3.20 (someone got fooled by the screenshot from Usher)

Covsperctrum query : A28330G + ORF1a:C936Y, ORF1a:A2584V
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1a%3AC936Y%2CORF1a%3AA2584V&nucMutations=28330G&aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

[JosetteSchoenma]

XBJ