XDH: BN.1/XBB.1 + S:486P+ Orf8:G8* + orf9b:I5T recombinant [1 Belarus/Shanghai, 1 England, 3 Lithuania as of 2023-06-02]

[corneliusroemer]

Came across this doublet of sequences from Shanghai and England, looking like they are the same recombinant:

hCoV-19/Shanghai/SCDC-HG-0518-887/2023|EPI_ISL_17725101|2023-05-17
hCoV-19/England/PHEC-YYEAHG9/2023|EPI_ISL_17721826|2023-05-14

Not sure anyone has spotted these already.

https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1930d_91a900.json

Gisaid query: T4744C,T7477C (the coolest ive ever seen, edited by Fed)

[FedeGueli]

Today i have found another of the same kind , but unrelated BN.1.2.3/XBB.1+Orf8:G8* https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_35594_84d460.json?c=gt-ORF1ab_47&label=id:node_7234439

With the notable mutation S:Q965E

[corneliusroemer]

But yours is a singlet @FedeGueli, singlets are much more boring than something discovered on opposite sides of the world ;)

[corneliusroemer]

Here's another one, now Lithuania 👀 hCoV-19/Lithuania/MB230509-0128/2023|EPI_ISL_17742697|2023-05-02

It's actually 3 from Lithuania, late April/early May.

hCoV-19/Lithuania/MB230509-0128/2023 hCoV-19/Lithuania/MB230503-0131/2023 hCoV-19/Lithuania/MB230503-0143/2023

https://next.nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4bd46_a22950.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Same tree so i ll update the title

[FedeGueli]

@corneliusroemer having Orf9b:I5T and being sequenced from very far places in the globe i suggest you to propose. Set yourself the nr of sequences to be reached.

[Over-There-Is]

Belarus?!

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/HG20230518-887/2023"
                 /isolation_source="Pharyngeal swab"
                 /host="Homo sapiens; Host_age: 49"
                 /country="China:Shanghai"
                 /collection_date="2023-05-17"
                 /note="Passage_details/history: Original;
                 Additional_host_information: Patient infected while
                 traveling in Belarus"

[FedeGueli]

Belarus?!

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/HG20230518-887/2023"
                 /isolation_source="Pharyngeal swab"
                 /host="Homo sapiens; Host_age: 49"
                 /country="China:Shanghai"
                 /collection_date="2023-05-17"
                 /note="Passage_details/history: Original;
                 Additional_host_information: Patient infected while
                 traveling in Belarus"

thx it makes sense

[xz-keg]

There seems to be a side branch of this. Another BN.1/XBB recombinant locally in China. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice29_genome_1e814_8cc5b0.json

[FedeGueli]

No new sequence. closing it.

[Over-There-Is]

24 now (exactly 21)

[FedeGueli]

reopening this for a while. @corneliusroemer this kept circulating in Lithuania

[corneliusroemer]

Just saw the new one from South Korea, worth designating I think given the time it's around and the range of countries and being around 25 sequences which isn't totally insignificant

[FedeGueli]

Designated XDH

[Over-There-Is]

3 sequences uploaded on 08-17 are duplicated to sequences uploaded on 06-02. And not only Belarus, Latvia and Estonia did not uploaded any sequences collected in 2023. It's believable that this lineage is also circulating there.