Add Orthomarburgvirus marburgense species taxon (taxonId: 3052505)

[anna-parker]

This is a copy of a dataset I created here: GenSpectrum/nextclade-datasets#4

You can view the dataset by running

https://clades.nextstrain.org/?dataset-server=https://raw.githubusercontent.com/genspectrum/nextclade-datasets/add_marburg/data

The example sequences: data/marburg/unreleased/sequences.fasta are a subsample of 20 marburg sequences with over 10% coverage.

I also added clades and lineages:

Example sequences fall with their corresponding sequence in the tree:

Tree built here:
https://github.com/anna-parker/marburg-virus-tree/tree/main

[rneher]

Thanks, Anna. This looks good! The example sequences are probably too many though.

It might also be interesting to make the default ref_node the clade founder. This should work by setting
default = '__clade_founder__' in the dataset config in the tree.json.

Instead of __root__ here

[ivan-aksamentov]

Again, not a huge expert on this particular virus, but my usual concern is that the path is too generic:

data/community/genspectrum/marburg

It's like having a flu named just flu. Not very future-proof or clear.

Paths are immutable, global, unique identifiers of datasets and they cannot be nested in the existing dataset paths. So once /marburg is taken, the /marburg/A and /marburg/hello/world are no longer available.

If any immediate identification or sub-classification groups come to mind, it's better to include them into the path. Or, as a lazy solution, a path segment with ref sequence accession.

The usual candidate keywords could be in the readme:

Orthomarburgvirus marburgense species taxon (taxonId: 3052505), members of this species are called marburgviruses. However, the species has two distinct lineages: ravn virus (RAVV) and marburg virus (MARV). Alignments use the official INSDC marburg virus reference sequence NC_001608.3.

as well as and in the genbank readme:

https://www.ncbi.nlm.nih.gov/nuccore/NC_001608.3

LOCUS       NC_001608              19111 bp    cRNA    linear   VRL 13-AUG-2018
DEFINITION  Marburg marburgvirus isolate Marburg
            virus/H.sapiens-tc/KEN/1980/Mt. Elgon-Musoke, complete genome.
ACCESSION   NC_001608
VERSION     NC_001608.3
DBLINK      BioProject: [PRJNA485481](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA485481)
KEYWORDS    RefSeq.
SOURCE      Orthomarburgvirus marburgense
  ORGANISM  [Orthomarburgvirus marburgense](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3052505)
            Viruses; Riboviria; Orthornavirae; Negarnaviricota;
            Haploviricotina; Monjiviricetes; Mononegavirales; Filoviridae;
            Orthomarburgvirus.
REFERENCE   1  (bases 1 to 19111)
  AUTHORS   Enterlein,S., Volchkov,V., Weik,M., Kolesnikova,L., Volchkova,V.,
            Klenk,H.D. and Muhlberger,E.
  TITLE     Rescue of recombinant Marburg virus from cDNA is dependent on
            nucleocapsid protein VP30
  JOURNAL   J. Virol. 80 (2), 1038-1043 (2006)
   PUBMED   [16379005](https://www.ncbi.nlm.nih.gov/pubmed/16379005)
REFERENCE   2  (bases 11291 to 19109)
  AUTHORS   Muhlberger,E., Sanchez,A., Randolf,A., Will,C., Kiley,M.P.,
            Klenk,H.D. and Feldmann,H.
  TITLE     The nucleotide sequence of the L gene of Marburg virus, a
            filovirus: homologies with paramyxoviruses and rhabdoviruses
  JOURNAL   Virology 187 (2), 534-547 (1992)
   PUBMED   [1546452](https://www.ncbi.nlm.nih.gov/pubmed/1546452)
REFERENCE   3  (bases 1 to 19111)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (22-OCT-2007) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   4  (bases 1 to 19111)
  AUTHORS   Muhlberger,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2005) Department of Virology, Philipps University
            Marburg, Robert-Koch-Str. 17, Marburg 35037, Germany
COMMENT     REVIEWED [REFSEQ](https://www.ncbi.nlm.nih.gov/RefSeq/): This record has been curated by NCBI staff. The
            reference sequence was derived from [DQ217792](https://www.ncbi.nlm.nih.gov/nuccore/DQ217792).

If there's only one marburg and will ever be, then ignore this :)

[anna-parker]

@ivan-aksamentov thanks! I renamed to community/genspectrum/marburg/HK1980/all-lineages (H = human, K= Kenya, 1980 = collection date)

[ivan-aksamentov]

I allowed myself to push the rebuild (instead of the bot :)

This way we can preview how indexing and autosuggestions work. Also, it is better to test things in this PR, not some other things at a remote location (genspectrum repo), to make sure we test what we have here, not there:

https://master.clades.nextstrain.org/?dataset-server=gh:anna-parker/nextclade_data@add-marburg@/data_output

At this point LGTM, but I'll let science team to do the final decision and merge if all good.

[rneher]

LGTM. happy to see that the clade founder thing works!