metadata that can be added to sequence PP_006W0PN.1 and PP_006W0UC.1

[arthurshem86]

Describe the possible issue

There is additional metadata from table S1 from this publication that can be added for the sequences PP_006W0PN.1 and PP_006W0UC.1

Additional information for sequence PP_006W0PN.1

1. Region - Neuquen
2. Town/City - San Martin de los Andes
3. Year - 1999

Assembly Method       :: Cutadapt v. v. 1.7; Prinseq-lite v. v.
                                     0.20.4; Picard v. v. February 2019;
                                     Bowtie2 v. v. 2.1.6
            Coverage              :: 97
            Sequencing Technology :: Illumina

✅ Additional information for sequence PP_006W0UC.1

1. Region - Buenos Aires
2. Town/City - La Plata
3. Year - 2002
4. Sample type - whole blood

Assembly Method       :: Cutadapt v. 1.7; Prinseq-lite v. 0.20.4;
                                     Picard v. February 2019; Bowtie2 v. 2.1.6
            Coverage              :: 100
            Sequencing Technology :: Illumina

[emmahodcroft]

From looking at table S1 in the publiation linked above:

PP_006W0PN.1 links genbank IDs OP555724.1.M/OP555723.1.S - this one seems very complicated, and am unsure how to handle.

In table 1 in the paper, OP555723 (S) and OP555724 (M) are in the same column, implying they are both from 'Rodent tissue; ARG p0'

However in Table S1 this seems otherwise - OP555724 is listed as the M segment from the 'original' host Oligoryzomys longicaudatus named strain 'ARG' in the paper.

OP555723 is listed as the S segment from a golden hamster(s?) infected with the ARG p9 (9th passage of ARG, above). Is this the same virus? Should these be linked? Is the host the hamster or the long-tailed colilargo?

For both the location is San Martin de los Andes, Neuquen, Argetina, 1999

To further confuse things, in Table S1 OP555724 (M) is linked with OP555728 (S) - as if they both came from the same originally infected O. longicaudatus --- but in the genbank record for this it says 'Mesocricetus auratus' (Golden hamster) - so did they mix up in the S1 table???

But looking up OP555729 - the M next to OP555723 (golden hamster) - also says Golden hamster - so doesn't seem to be a straight-up mixup in the Table.....

This is a mess!

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PP_006W0UC.1 links genbank IDs OP555736.1.L/OP555731.1.M/OP555730.1.S - This is strain BA02-C1S - La Plata, Buenos Aires, Argentina. year 2002. From human.

[anna-parker]

As PP_006W0UC.1 appears to be a straight forward curation I will approve and release it (the revision has already been prepared and reviewed by Emma and Arthur, satisfying the two eyes principal) - it is a bit odd that OP555736.1.L is not mentioned in the publication but perhaps it was added later

[anna-parker]

I would propose not revising PP_006W0PN.1 as the paper contradicts itself