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hodcroftlab / covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
https://covariants.org/
GNU Affero General Public License v3.0
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XBB1.5 23A #376

Closed patvalcom closed 1 year ago

patvalcom commented 1 year ago

Hi, On the web interface Nextclade, when I submit a fasta which has the lineage XBB1.5, the clade is still assigned to 22F and not to 23A. Is it normal ? Maybe you plan a change of the database including the 23A for the web interface ?

thanks for your help Patricia

MikeMavrok commented 1 year ago

i can help with that

emmahodcroft commented 1 year ago

Hi @patvalcom , I think you may have posted this issue in the wrong place - This is the CoVariants github, which is separate from Nextclade. You can post an issue on Nextclade here: https://github.com/nextstrain/nextclade

However, 23A (XBB.1.5*) is already part of the Nextclade web interface, so sequences should be assigned to that if they are truly XBB.1.5. It's possible your sequence isn't being assigned because it carries just some XBB.1.5 mutations, rather than all of them? It may be worth looking at your sequence quality and what mutations your sequence has, exactly.

patvalcom commented 1 year ago

HI,

thanks for your answer, I did not think that my sequence might not be informative enough even if I had 99.5% of coverage.

I will have a look at the mutations.

Sorry for the inconvenience, but at least I know now that the XBB1.5 is alreaday part of the web interface ;-)

Thanks

PAtricia

De : Emma Hodcroft @.***> Envoyé : lundi 20 mars 2023 14:46 À : hodcroftlab/covariants Cc : Combes Patricia; Mention Objet : Re: [hodcroftlab/covariants] XBB1.5 23A (Issue #376)

Hi @patvalcomhttps://github.com/patvalcom , I think you may have posted this issue in the wrong place - This is the CoVariants github, which is separate from Nextclade. You can post an issue on Nextclade here: https://github.com/nextstrain/nextclade

However, 23A (XBB.1.5*) is already part of the Nextclade web interface, so sequences should be assigned to that if they are truly XBB.1.5. It's possible your sequence isn't being assigned because it carries just some XBB.1.5 mutations, rather than all of them? It may be worth looking at your sequence quality and what mutations your sequence has, exactly.

- Reply to this email directly, view it on GitHubhttps://github.com/hodcroftlab/covariants/issues/376#issuecomment-1476265037, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5IX4Z4Z5BVJT4K6JFF6N7TW5BNSXANCNFSM6AAAAAAV6NEJ5U. You are receiving this because you were mentioned.Message ID: @.***>