Sub-country geolocation was removed from 50 RSV sequences despite biosample still having the information #533
Description
At Pathoplexus we use the NCBI datasets CLI to ingest publicly available sequences. Whenever there's a change to the data we get from ncbi datasets, we update the records on our end - even if there's not a new version of the sequence on NCBI.
This is how we noticed that a few days ago, 50 RSV sequences stopped containing location information. Example accession: OZ211384.1, biosample is SAMEA117552821
It seems that the geolocation parsing changed for this record? The biosample still has the information.
Here's the full list of changes, courtesy of @anna-parker. Some taxon IDs changed as well - maybe that's related:
# Left of arrow is new, right of arrow is old (slightly confusingly so beware)
50 rows changed
insdcAccessionFull: OZ224588.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224589.1
geoLocAdmin1: "" => "SG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224590.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224591.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224593.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224594.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224595.1
geoLocAdmin1: "" => "TI"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224596.1
geoLocAdmin1: "" => "BE"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224597.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224599.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224600.1
geoLocAdmin1: "" => "SG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224601.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224602.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224603.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224604.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224605.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224606.1
geoLocAdmin1: "" => "SG"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224608.1
geoLocAdmin1: "" => "ZH"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224609.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224610.1
geoLocAdmin1: "" => "VD"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ224611.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2025-02-19"
insdcAccessionFull: OZ211289.1
geoLocAdmin1: "" => "VD"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211292.1
geoLocAdmin1: "" => "SZ"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211297.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211298.1
geoLocAdmin1: "" => "BE"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211302.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211306.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211308.1
geoLocAdmin1: "" => "ZH"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211310.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211311.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211340.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211341.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211345.1
geoLocAdmin1: "" => "VD"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211349.1
geoLocAdmin1: "" => "SZ"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211351.1
geoLocAdmin1: "" => "GE"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211356.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211357.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211358.1
geoLocAdmin1: "" => "SO"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211363.1
geoLocAdmin1: "" => "VD"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211364.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211365.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211366.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211370.1
geoLocAdmin1: "" => "BS"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211371.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211374.1
geoLocAdmin1: "" => "SO"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211375.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211377.1
geoLocAdmin1: "" => "AG"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211384.1
geoLocAdmin1: "" => "BL"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211397.1
geoLocAdmin1: "" => "GR"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"
insdcAccessionFull: OZ211398.1
geoLocAdmin1: "" => "ZH"
ncbiUpdateDate: "2025-09-26" => "2024-12-22"
ncbiVirusName: "Human respiratory syncytial virus A" => "Respiratory syncytial virus"
ncbiVirusTaxId: "208893" => "12814"