Mpox Clade I delineation?

[woguta]

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]

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]

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

[woguta]

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]

@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]

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 <#265 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6PUWMQNJK7OETNXAO57JFTZRUNSDAVCNFSM6AAAAABMGJVOR6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGMYDEMRZHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>