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Nextstrain build for mpox virus
https://nextstrain.org/mpox
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Mpox Clade I delineation? #265

Open woguta opened 1 month ago

woguta commented 1 month ago

Has Mpox clade I been designated as Clade Ia and Clade Ib? And is this being reflected in the nextstrain? If so, what mutations are considered? Please, assist. Thank.

Walter

rneher commented 1 month ago

Hi Walter,

the definitions of the clade I subclades are here: https://github.com/nextstrain/mpox/blob/master/nextclade/resources/clade-i/clades.tsv

The Nextclade dataset for clade I has these definitions implemented:

https://clades.nextstrain.org/?dataset-name=nextstrain/mpox/clade-i

let us know if you have additional questions.

woguta commented 1 month ago

Thank you. Looking forward to have all the references clade also updated. Merci.

woguta commented 1 month ago

Also, asking for reference material(s) or article(s) as to cite when writing for publication. This about the implementation as concerns clade I. Thank you.

BryanTegomoh commented 1 month ago

@woguta, you might find this helpful: Nature Medicine Article. The paper discusses the distinction between Clades Ia and Ib, similar to the rationale for separating Clades IIa and IIb. Currently, Clade Ib is only represented by genomes from the Kamituga outbreak in the DRC, there's a need for more representative isolates for clearer classification.

I noticed that @corneliusroemer has updated the clades.tsv file to reflect new nucleotide positions for Clades Ia and Ib, which aligns with the recent findings. You can view the changes here: Updated clades.tsv.

Might be worth considering how these changes impact your ongoing work. Best of luck!!

woguta commented 3 weeks ago

Dear Richard and Bryan,

Thank you all for this. I really appreciate it.

Best regards, Walter Oguta Walter

On Thu, 15 Aug 2024 at 21:37, Bryan Tegomoh @.***> wrote:

@woguta https://github.com/woguta, you might find this helpful: Nature Medicine Article https://www.nature.com/articles/s41591-024-03130-3. The paper discusses the distinction between Clades Ia and Ib, similar to the rationale for separating Clades IIa and IIb. Currently, Clade Ib is only represented by genomes from the Kamituga outbreak in the DRC, there's a need for more representative isolates for clearer classification.

I noticed that @corneliusroemer https://github.com/corneliusroemer has updated the clades.tsv file to reflect new nucleotide positions for Clades Ia and Ib, which aligns with the recent findings. You can view the changes here: Updated clades.tsv https://github.com/nextstrain/mpox/blob/9d3b8ea9f5b4916c3459a6796fda4fc823b54951/nextclade/resources/all-clades/clades.tsv#L5-L12 .

Might be worth considering how these changes impact your ongoing work. Best of luck!!

— Reply to this email directly, view it on GitHub https://github.com/nextstrain/mpox/issues/265#issuecomment-2292302298, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6PUWMQNJK7OETNXAO57JFTZRUNSDAVCNFSM6AAAAABMGJVOR6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGMYDEMRZHA . You are receiving this because you were mentioned.Message ID: @.***>