ANDV dataset - same virus is repeated Chile-9717869

[ammaraziz]

Describe the possible issue

The new ANDV build includes what is essentially duplicates of the same virus sequenced multiple times. Their origin appears to be uploads from craig venture institute. Only the M segment was uploaded.

Evidence of the problem

1. The phylotree on nextstrain has the same ID "9717869_XX"
2. Same uploader
3. All have this note (see genbank):

/note="derived from construct in VSV containing GnGc the M segment of Andes virus strain Chile-9717869; Passage history: passage 18 (128xIC50s of neutralizing mAb) in

Suggested change

Remove the duplicates

Full list of affected sequences

There could be more but these are the ones I found on nextstrain M tree:

strain	unique_id
PP_006VQN2.1	nan/nan/nan-1
PP_006W0E7.1	Chile-9717869/nan/nan-2
PP_006VQYG.1	nan/nan/nan-2
PP_006VVUK.1	nan/nan/nan-7
PP_006VNZG.1	Chile-9717869/nan/nan-1
PP_006VY05.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_18/2002/nan/nan-1
PP_006VYAK.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_38/2002/nan/nan
PP_006VY7R.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_37/2002/nan/nan
PP_006VY6T.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_17/2002/nan/nan-1
PP_006VXPT.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_16/2002/nan/nan-1
PP_006VZ04.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_03/2002/nan/nan-2
PP_006VYEB.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_01/2002/nan/nan-2
PP_006VXTK.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_01/2002/nan/nan-1
PP_006VY8P.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_03/2002/nan/nan-1
PP_006VXZ7.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_02/2002/nan/nan-1
PP_006VYG7.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_13/2002/nan/nan-2
PP_006VYDD.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_15/2002/nan/nan-2
PP_006VYCF.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_14/2002/nan/nan-2
PP_006VYK0.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_06/2002/nan/nan-2
PP_006VYTJ.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_04/2002/nan/nan-2
PP_006VYXA.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_05/2002/nan/nan-2
PP_006VYY8.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_08/2002/nan/nan-2
PP_006VYPS.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_07/2002/nan/nan-2
PP_006VYJ2.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_09/2002/nan/nan-2
PP_006VXSM.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_09/2002/nan/nan-1
PP_006VXVF.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_08/2002/nan/nan-1
PP_006VY21.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_07/2002/nan/nan-1
PP_006VYNU.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_20/2002/nan/nan
PP_006VZ12.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_21/2002/nan/nan
PP_006VYZ6.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_19/2002/nan/nan
PP_006VYUG.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_18/2002/nan/nan-2
PP_006VYWC.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_16/2002/nan/nan-2
PP_006VYF9.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_17/2002/nan/nan-2
PP_006VYH4.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_02/2002/nan/nan-2
PP_006VYLY.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_24/2002/nan/nan
PP_006VYSL.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_23/2002/nan/nan
PP_006VYMW.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_22/2002/nan/nan
PP_006VYVE.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_10/2002/nan/nan-2
PP_006VYRN.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_11/2002/nan/nan
PP_006VYQQ.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_12/2002/nan/nan-2
PP_006VXWD.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_05/2002/nan/nan-1
PP_006VXXB.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_04/2002/nan/nan-1
PP_006VXUH.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_06/2002/nan/nan-1
PP_006VXRP.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_12/2002/nan/nan-1
PP_006VY5V.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_45/2002/nan/nan
PP_006VY9M.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_44/2002/nan/nan
PP_006VXNV.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_10/2002/nan/nan-1
PP_006VY3Z.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_39/2002/nan/nan
PP_006VXY9.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_15/2002/nan/nan-1
PP_006VXQR.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_13/2002/nan/nan-1
PP_006VXMX.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_14/2002/nan/nan-1
PP_006VY4X.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_41/2002/nan/nan
PP_006VYBH.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_42/2002/nan/nan
PP_006VY13.1	ANDV/Oligoryzomys-longicaudatus/CHL/9717869_40/2002/nan/nan

I think Chile-9717869/1997/Chile pathoplexus id PP_006W0D9.1 is the original as it contains other segments (see this tree, thanks Emma! https://nextstrain.org/groups/hodcroftlab/andv/L:groups/hodcroftlab/andv/M)

[emmahodcroft]

I've checked a few of these and agree they seem to be a set of passages.
I assume all those with the same name would be the same series of passage - The few at the top with slightly different names may be worth double-checking.

[m-a-martin]

Thanks for bringing this to our attention.

PP_006VQN2.1, PP_006W0E7.1, PP_006VQYG.1, PP_006VVUK.1, and PP_006VNZG.1 do not actually share that note.

PP_006VNZG.1 and PP_006W0E7.1 appear to be duplicated GenBank records and both have records for the L, M, and S segments.

Based on release dates and sequence methods in GenBank, PP_006W0D9.1 appears to be re-sequencing of the same strain.

Suggested Change

I suggest revoking PP_006VY05.1 PP_006VYAK.1 PP_006VY7R.1 PP_006VY6T.1 PP_006VXPT.1 PP_006VZ04.1 PP_006VYEB.1 PP_006VXTK.1 PP_006VY8P.1 PP_006VXZ7.1 PP_006VYG7.1 PP_006VYDD.1 PP_006VYCF.1 PP_006VYK0.1 PP_006VYTJ.1 PP_006VYXA.1 PP_006VYY8.1 PP_006VYPS.1 PP_006VYJ2.1 PP_006VXSM.1 PP_006VXVF.1 PP_006VY21.1 PP_006VYNU.1 PP_006VZ12.1 PP_006VYZ6.1 PP_006VYUG.1 PP_006VYWC.1 PP_006VYF9.1 PP_006VYH4.1 PP_006VYLY.1 PP_006VYSL.1 PP_006VYMW.1 PP_006VYVE.1 PP_006VYRN.1 PP_006VYQQ.1 PP_006VXWD.1 PP_006VXXB.1 PP_006VXUH.1 PP_006VXRP.1 PP_006VY5V.1 PP_006VY9M.1 PP_006VXNV.1 PP_006VY3Z.1 PP_006VXY9.1 PP_006VXQR.1 PP_006VXMX.1 PP_006VY4X.1 PP_006VYBH.1 PP_006VY13.1 as passages of the original strain.

In the absence of any protocol for handling resequenced isolates, I suggest revoking PP_006W0D9.1 and PP_006VNZG.1 and retaining PP_006W0E7.1 as it is linked to the RefSeq record in GenBank.

[emmahodcroft]

Thanks so much for this Martin! I second the revocation of the suggested passage set. I would be happy to either cue this up, or you, and I'll approve.

It's weird that PP_006VNZG.1 and PP_006W0E7.1 seem to be duplicated - I wonder if it's also a resequencing?
Genbank records: AF291704 (2002 submission) and NC_003468 (2018 submission)
Agree that PP_006W0D9.1 references the same sample isolate name ("Chile-9717869"). (Gebank record MT956621)

I am less sure how to handle these possible re-sequences - I'll take to curator chat.

[anna-parker]

It was decided in the curator chat to hold of revoking passages and resequencing results