Bundibugyo database contains unwanted patent sequences

[thibaut-hourlier]

Describe the possible issue

As set of 10 sequences imported from GenBank were submitted to INSDC to support patents applications. These sequences are subsequences from known Bundibugyo sequences. They bring duplication and mutations found may not be representative of real world data.

Evidence of the problem

https://patentscope.wipo.int/search/en/WO2016069853

• PP_006X65H.1 => https://www.ncbi.nlm.nih.gov/nuccore/LQ278388.1
• PP_006X66F.1 => https://www.ncbi.nlm.nih.gov/nuccore/LQ278392.1
• PP_006X67D.1 => https://www.ncbi.nlm.nih.gov/nuccore/LQ278396.1

https://patentscope.wipo.int/search/en/WO2016069853

• PP_006X5S9.1 => https://www.ncbi.nlm.nih.gov/nuccore/HC918458.1
• PP_006X5T7.1 => https://www.ncbi.nlm.nih.gov/nuccore/HC918461.1
• PP_006X5U5.1 => https://www.ncbi.nlm.nih.gov/nuccore/HV753272.1
• PP_006X5V3.1 => https://www.ncbi.nlm.nih.gov/nuccore/HV753275.1
• PP_006X5W1.1 => https://www.ncbi.nlm.nih.gov/nuccore/HZ164395.1
• PP_006X5XZ.1 => https://www.ncbi.nlm.nih.gov/nuccore/HZ164398.1

https://patents.google.com/patent/WO2016189490A1/en

• PP_006X6B5.1 => https://www.ncbi.nlm.nih.gov/nuccore/MS811591.1

Suggested change

It would be great if the patent section of GenBank is filtered out from imports in Pathoplexus. These sequence are likely to be sequence fragments of real world pathogens and would not represent the isolates from the pathogen.

I would suggest the deletion of all these sequences from Pathoplexus.

Full list of affected sequences

• PP_006X5S9.1
• PP_006X5T7.1
• PP_006X5U5.1
• PP_006X5V3.1
• PP_006X5W1.1
• PP_006X5XZ.1
• PP_006X65H.1
• PP_006X66F.1
• PP_006X67D.1
• PP_006X6B5.1

[arthurshem86]

I have checked the sequences in question both on PPX and Genbank. I agree that these should be revoked. Below are the sequences and their GenBank records.

PP_006X65H.1 - GenBank title Sequence 220 from Patent WO2016069853
PP_006X66F.1 - GenBank title Sequence 224 from Patent WO2016069853
PP_006X67D.1 - GenBank title Sequence 228 from Patent WO2016069853

PP_006X5S9.1 - GenBank title Sequence 8 from Patent WO2010057650
PP_006X5T7.1 - GenBank title Sequence 11 from Patent WO2010057650
PP_006X5U5.1 - GenBank title JP 2012509073-A/3: Vector comprising multiple homologous nucleotide sequences
PP_006X5V3.1 - GenBank title JP 2012509073-A/6: Vector comprising multiple homologous nucleotide sequences
PP_006X5W1.1 - GenBank title JP 2015128443-A/3: Vector comprising multiple homologous nucleotide sequences
PP_006X5XZ.1 - GenBank title JP 2015128443-A/6: Vector comprising multiple homologous nucleotide sequences

PP_006X6B5.1 - GenBank title Sequence 13 from Patent WO2016189490