New Lineages Update: 20 new lineages active through 2023-02-09

[jmcbroome]

Lineage Name	Parent Lineage	Size	Earliest Appearance	Latest Appearance	Regions	Nucleotide Changes	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Open Sequence FASTA	EPI ISLs	Amino Acid Changes
auto.CH.1.1.1.1	CH.1.1.1	1564	2022-12-11	2023-02-03	England, Wales, and Denmark	C1545T,T24991A,A19886G,T15591C,C25721T,T4402A	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF3a:A110V,ORF1ab:K6541R,ORF1ab:A427V
auto.BQ.1.1.18.1	BQ.1.1.18	2261	2022-12-11	2023-02-01	Japan	T1562A,C25714T,G28079T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:C433S,ORF3a:L108F
auto.XBB.1.12	XBB.1	3198	2022-12-11	2023-02-01	USA, Guatemala, and Mexico	G27915T,C1884T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:A540V,ORF8:G8*
auto.BA.5.2.48.1	BA.5.2.48	2062	2022-12-11	2023-02-03	China, Japan, and SouthKorea	C11824T,C28994A	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	N:Q241K
auto.BQ.1.1.5.1	BQ.1.1.5	2105	2022-12-11	2023-02-02	USA	A6790G,G11828A,G20518A	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:D6752N,ORF1ab:V3855I
auto.BQ.1.1.33	BQ.1.1	2283	2022-12-11	2023-01-30	USA, England, and Canada	C19547T,C25821T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:S6428L
auto.BA.5.2.6.1	BA.5.2.6	1253	2022-12-11	2023-02-02	Japan	C26645T,C20115T,C19602T,C1929T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:A555V,E:I9T
auto.BQ.1.29	BQ.1	1460	2022-12-11	2023-02-05	USA, Germany, and Japan	C26833T,T12667C,A28389T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	N:Q39L,M:A104V
auto.BF.7.16	BF.7	690	2022-12-11	2023-02-02	Japan	T7111C,C16470T,A26219G,C1915T,A27747C,C28153T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF8:T87I,ORF7a:R118S
auto.BQ.1.1.20.1	BQ.1.1.20	1365	2022-12-11	2023-02-03	Denmark	C24771T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	S:A1070V
auto.BA.5.1.13	BA.5.1	1419	2022-12-11	2023-02-02	Denmark	C11530T,C2142T,C15720T,C25046T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:P626L,S:P1162S
auto.BQ.1.2.2	BQ.1.2	2377	2022-12-11	2023-01-28	Canada and USA	G26314C	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	E:V24L
auto.BF.7.15.1	BF.7.15	546	2022-12-11	2023-02-02	Japan	G28077A,G12170A,A1558G	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF8:V62M,ORF1ab:I431M,ORF1ab:A3969T
auto.XBB.1.5.4	XBB.1.5	820	2022-12-11	2023-02-02	England, USA, and Canada	T17124C,G14209T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:V4649F
auto.BN.1.3.6	BN.1.3	1922	2022-12-11	2023-01-28	Japan, USA, and SouthKorea	G27043A,G11146T,C7390A,C593T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	M:R174Q,ORF1ab:H110Y,ORF1ab:M3627I
auto.BF.5.4	BF.5	5205	2022-12-11	2023-01-28	Japan	C16954T,A8882G,C21114T,A28402G	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:I2873V
auto.CH.1.1.10	CH.1.1	1072	2022-12-11	2023-02-03	England, Ireland, and Germany	G3791A,C21811T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:A1176T
auto.BN.1.5.2	BN.1.5	871	2022-12-11	2023-01-31	England, Wales, and USA	A10258G,G20774A	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:G6837D
auto.BN.1.4.2	BN.1.4	708	2022-12-11	2023-01-30	Denmark	T3347C,G16912T,G18634A,C8782T	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:F1028L,ORF1ab:V5550L,ORF1ab:V6124M
auto.BQ.1.1.13.1	BQ.1.1.13	691	2022-12-11	2023-02-01	England and Scotland	G13822A	View On Cov-Spectrum	View On Taxonium (Public Samples Only)	Download Example Sequence FASTA (LAPIS)	Get EPI ISLs	ORF1ab:V4520I

[aineniamh]

All looking great so far, love the informative table with the PR too!
For the actual PR to pango-designation main, the auto lineage names shouldn't be prefixed with auto in the lineage_notes.txt file lineage field, the description should include that it's auto-generated, but including a different pattern will likely break websites, pipelines and aliasor scripts without an update. We could always add an additional field to the file that describes whether it's an autolineage or a manually curated lineage.
At this point we could also consider whether we want to start hosting the non-aliased name and more metadata about the lineage in the lineage_notes.txt too.
Plans are to release a pango-designation v2.0 with the introduction of autolin, so an opportunity to make some other changes too!
Really great work though, so excited for this to be put into use!

[corneliusroemer]

but including a different pattern [in lineage notes] will likely break websites, pipelines and aliasor scripts without an update

I don't think we currently make any real guarantees about the format of lineage_notes.txt - this is like a changelog for human consumption, but still of course good to be consistent.

At this point we could also consider whether we want to start hosting the non-aliased name and more metadata about the lineage in the lineage_notes.txt too.

I'm not quite sure what you mean, can you give an example? I think if we want to add structured data we should start fresh with something with a strict schema, notes are free text.

Here is some structured data I derive from various sources: https://raw.githubusercontent.com/corneliusroemer/pango-sequences/main/data/pango-consensus-sequences_summary.json

These are all auto-generatable without any manual curation - I guess that pattern is more useful for us. The less humans involved the less chance of inconsistency. But then some things aren't really auto-deductible. Would be curious what you are thinking of adding specifically.

Plans are to release a pango-designation v2.0 with the introduction of autolin, so an opportunity to make some other changes too!

If we use semver we'd only bump major version if we break backwards compatibility - what are we planning on breaking? I can't think of something off the top of my head.

[jmcbroome]

Thanks Aine! Reiterating my qualifications from the slack discussion, this particular example does not include the modeling step (as I was wanting to iterate more quickly while I check whether links are being generated and displayed correctly) and the EPI_ISL download link is misformatted in this particular PR (it will be fixed in the real one).

With regards to names, I've been including the "auto." prefix in order to be explicit in all cases about what I'm generating versus what's already in the system. I can simply remove the prefix easily enough, but there will be likely inconsistencies/potential name collisions. We will also have to keep in mind that we may need to change the names of new proposed lineages- for example, if we propose two sibling lineages XXX.1 and XXX.2, then reject 1 and accept 2, we need to rename XXX.2 to XXX.1 for consistency. That will probably be relatively rare, though, and could be handled on a case-by-case basis.

Also, in this particular case, it's claiming that all of the lineages were first sampled on 2023-12-11 - that's because I removed samples prior to that from consideration for this run. I may need to move the date further back, or otherwise look into having it more correctly report the earliest date.