Mpox & Hantavirus — exclude artificial/patent sequences from PAT division of GenBank

[emmahodcroft]

Description

Flagged by David N (reported via email).

Several artificial sequences from the PAT (patent) division of GenBank are currently being ingested into Pathoplexus. These sequences are not meaningful for phylogenetic analysis and should either be filtered out during curation or excluded from ingestion entirely.
The sequences are identifiable by their GenBank molecule type or patent-derived title. Examples are provided below for both Mpox and Hantavirus.

Mpox

Molecule type: Modified Microbial Nucleic Acid

• PP_000T136.1

Hantavirus

Molecule type: Modified Microbial Nucleic Acid

• PP_006VT18.1
• PP_006VVCJ.1
• PP_006VVDG.1
• PP_006VVEE.1
• PP_006VVFC.1
• PP_006VVGA.1

Title: COMPOSITIONS FOR USE IN IDENTIFICATION OF VIRAL HEMORRHAGIC FEVER VIRUSES

• PP_006VQGF.1

Title: METHODS AND REAGENTS FOR DIAGNOSING HANTAVIRUS INFECTION

• PP_006VVVH.1
• PP_006VVWF.1
• PP_006VVUK.1
• PP_006VQN2.1
• PP_006VQYG.1
• PP_006VQZE.1
• PP_006VR0C.1
• PP_006VR1A.1
• PP_006VR28.1

Title: NOVEL CLASS 2 TYPE II AND TYPE V CRISPR-CAS RNA-GUIDED ENDONUCLEASES

• PP_006W1PM.1

Proposed action

It needs to be checked (and confirmed by a second curator) that the sequences listed above really do appear to be patents/constructs.

Then:
Revoke/exclude the above sequences.

Consider implementing a systematic filter to prevent ingestion of PAT-division GenBank sequences going forward, as these are generally artificial constructs with no value for phylogenetic analysis.

[emmahodcroft]

Checking these sequences by searching the PPX accession then clicking through to the Genbank page. I can verify these are all indeed patent sequences and thus should be revoked. Second review needed!

Mpox

Molecule type: Modified Microbial Nucleic Acid
(also mentions 'Patent')

• PP_000T136.1 - ✅

Hantavirus

Molecule type: Modified Microbial Nucleic Acid
(these also mention 'Patent')

• PP_006VT18.1 - ✅
• PP_006VVCJ.1 - ✅
• PP_006VVDG.1 - ✅
• PP_006VVEE.1 - ✅
• PP_006VVFC.1 - ✅
• PP_006VVGA.1 - ✅

Title: COMPOSITIONS FOR USE IN IDENTIFICATION OF VIRAL HEMORRHAGIC FEVER VIRUSES
(also mentioned 'Patent')

• PP_006VQGF.1 - ✅

Title: METHODS AND REAGENTS FOR DIAGNOSING HANTAVIRUS INFECTION
(also mentions Patent - Novartis!)

• PP_006VVVH.1 - ✅
• PP_006VVWF.1 - ✅
• PP_006VVUK.1 - ✅
• PP_006VQN2.1 - ✅
• PP_006VQYG.1 - ✅
• PP_006VQZE.1 - ✅
• PP_006VR0C.1 - ✅
• PP_006VR1A.1 - ✅
• PP_006VR28.1 - ✅

Title: NOVEL CLASS 2 TYPE II AND TYPE V CRISPR-CAS RNA-GUIDED ENDONUCLEASES
(also mentions Patent)

• PP_006W1PM.1 - ✅

[arthurshem86]

Thanks alot Emma. I have reviewed all these sequences in Pathoplexus as well as their GenBank records and I agree that they are indeed patent sequences and should be revoked.

[emmahodcroft]

Thanks Arthur. Ok, let's coordinate on a time to do this, after the other pending revisions are cleared. Once that's done let's find a time and we can work on it together.

[arthurshem86]

Sure! Let me follow up on slack for the best time