cov-lineages / lineages-website Goto Github PK

Hi there,

I am missing basically several lineages in this file:
e.g.
EE.4
EF.2

last update was on the 28/01, but the latest data rather end of Feb.

Greets

I might be missing something here, so please excuse me if this issue is irrelevant.

I noticed the B.1.1.529 variant "node" is missing from the lineages.yml meaning contrary to other variants, there is no name field associated with B.1.1.529. It does show up as a parent of the BA.1 variant though.

It was not the case up until commit 1570749 before / after
Is this intentional ?

Cheers

Hi!
I've noted that on occasion some of the children of a lineage won't be included, particularly if there is a jump in the nomenclature. For example, BF.1 is a descendant of BA.5, but doesn't appear in the list of BA.5's children. The parent of BF.1 is listed as B.1.1.529.5.2.1, so I could imagine it's possible that this is due to there being multiple names for BA.5.2.1? Or perhaps I can reconstruct this relationship between BF.1 and BA.5 some other way using the lineages.yml file?

Thanks so much for the incredible resource and help!
Josh

Hi!

I've noticed that data/lineages.yml hasn't been updated in almost a month. Is this file going to continue to be updated (presumably by running grinch)?

Thanks again for this great resource!
Josh

As I understand it pango.network is also managed by this team. In any case I did not find another repository or contact details. Remove the issue if this isn't correct.

Link at https://www.pango.network/the-pango-nomenclature-system/list-of-designated-lineages/ is broken. It is currently https://cov-lineages.org/lineages.html while the correct URL is https://cov-lineages.org/lineage_list.html.

It appears the lineage_data.full.json has not been updated for about a month. Based upon the text on the Pango website, this JSON file should have the "full set of lineages"; however, it appears to have fallen behind compared to other sources. For example, the DT lineage is not listed.

Will this be updated, and if not, what would be the preferred source for timely lineage lists? Perhaps this location instead?

Hello! I realized that the table of Summary of Currently Defined Constellations cannot be properly shown in the webpage (https://cov-lineages.org/constellations.html). Perhaps there's any error?

It is inconsistently placed after the BA.* lineages and not below B.1.621.1.

Just gives blank page (Safari).

It seems like a number of lineages were removed in b0bfdd9

I was wondering if there is any information about why they were removed/how to redesignate specimens assigned to those lineages.

I've attached a list of the removed files. Appreciate the help!

missing_lineages.txt

I like to occasionally browse this lineage list: https://cov-lineages.org/lineage_list.html

It's great, that it mentions which designation issue the lineage was created from. It would be amazing, if this wasn't just text but linked directly to the Github issue.

This should be easy to implement, just add the link in the metadata in the designation repo. This can easily be machine generated.

See example (done with dev tools, the link of course has to be different

The rules and committee webpage has been down for over a week.
I tried emailing [email protected], but my message bounced, suggesting to me that the domain name was not renewed.
I could not find any public announcement or github issue.

I appreciate that this is the github repo for cov-lineages.org, not for www.pango.network.
Nevertheless, because this repo is web-related (and one site links to the other) it seemed like the best place to post this question.
I'm sorry if this is impertinent, but I imagine that others will have the same question, and thought this was better than emailing individual people associated with the Pango Network.

Fortunately past versions of the site have been preserved at archive.org.

I am a big fan of the work you all do, so I hope the site can be restored (or the content moved elsewhere for possible future updates).

Hi there,

I just ran an analysis and came across a case of BQ.1.13.1. This lineage is not to find in the annotation-json file.
--> looks like this is solved.

I am still missing XBB.1.9 (?)

Greets

I managed to install pangolin natively using this script - the standard one doesn't work

conda create -n pangolin
conda activate pangolin
conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
conda config --env --set channel_priority strict
conda config --env --set subdir osx-64
mamba install pangolin #or conda if mamba is not installed

Link for the Pando software (http://pando.tools/) goes to an advertisement webpage with my browser.

--mahmut

Hi there,

is this issue connected to one of the others, listed here?
I do not see any lineages listed.

Greets

Fixed by #5

SARS-CoV-2 Variant B.1.1.529 was indicated as a Variant of Concern by the WHO last Friday. Could it be added to the cov-linages website? (https://cov-lineages.org/index.html#global_reports)

WHO: Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern