Adding metadata to hantavirus sequences

[arthurshem86]

Describe the possible issue

A portion of hantavirus sequences has missing Country, host, strain, region, and date.

These can be added using data compiled by Andrew that can be found here. I have checked the corresponding GenBank records and their consistent.

I will post these in batches by Author. Where segments have different PPX accessions I have indicated with ** in the PPX column and provided the PPX/GenBank ids in that format under the segment column. Otherwise the PPX accession contains the PPX accession while the segment columns contain GenBank ids.

	PPX accession	Segment S	Segment M	Segment L	Virus	Strain	Host	Country	Region	Date	Ref
	PP_0072UW2	previously: PP_006VQ45.1/AF482713.1	previously: PP_006VLVS.1/ AF028025.1	NA	Bermejo	Oc22531	Oligoryzomys chacoensis	Argentina	Oran	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
✅	PP_006VLSY.1	AF482714.1	AF028022.1	NA	Lechiguanas	Of22819	Oligoryzomys_flavescens	Argentina	Entre_Rios	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
	PP_006VLUU.1	AF482715.1	AF028024.1	NA	Oran	Ol22996	Oligoryzomys_longicaudatus	Argentina	Salta	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
	PP_0072UX0	previously: PP_006VQ53.1 / AF482716.1	previously: PP_006VLXN.1 / AF028027.1	NA	Maciel	Bo13796	Necromys_benefactus	Argentina	Pergamino	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
	PP_0072UYY	previously: PP_006VQ61.1 / AF482717.1	previously: PP_006VLYL.1 / AF028028.1	NA	Pergamino	Aa14403	Akodon_azurae	Argentina	Pergamino	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
	PP_006VLWQ.1		AF028026.1			Ol23133	Oligoryzomys_longicaudatus	Argentina			https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002
	PP_006VLTW.1	AF482711	AF028023.1			Hu39694	Homo_sapiens	Argentina	Pergamino	1997	https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002

[emmahodcroft]

For PP_006VLSY.1 - can confirm date of 1997, and host Oligoryzomys flavescens
Confusingly, from the paper cited (https://journals.asm.org/doi/10.1128/jvi.76.8.3765-3773.2002) in Table 1 it says Lechiguanas virus (which is this sample) is from "Lechiguanas Islands, Argentina" - but this is within Entre Rios.

So this seq revision is checked.

(I have released this from pending revisions)

[emmahodcroft]

Checking additional sequences:

I am concerned we're not being consistent about Admin Levels - Pergamino seems to be a city, in the province of Buenos Aires. Therefore Buenos Aires should be the Admin Level 1 and Pergamino Admin Level 2.

PP_006VLTW.1 -- Confirm date, host, location - but from sample info in Table 1 - looks like we could add 'Blood' to 'Anatomical material' - let me know if you agree Arthur. And should have Pergamino as a Admin2 not 1?

PP_006VLUU.1 -- Confirm date, host, location - but again from Table 1 - looks like we could add 'Lung' to 'Anatomical material'
And should have Oran as Admin Level 2, and Salta (province) as Admin Level 1.

PP_006VQ45.1 and PP_006VLVS.1 - Confirm date, host, location - but from Table 1 - can add 'Lung'
And should have Oran as Admin Level 2, and Salta (province) as Admin Level 1.

PP_006VQ53.1 and PP_006VLXN.1 - Confirm date, host -- but location in Table 1 is Maciel - which seems to be in Santa Fe province. (Currently in the table above this is given as Pergamino in both - it's a mistake I guess)
Can also have 'lung' added.
In standing revisions:
VQ53 - has host Necromys benefactus
6VLXN - has host Necromys obscurus (?)
These should match! From paper, should be benefactus.

PP_006VQ61.1 - seems to have host-name scientific missing in the revision - should be Akodon azurae (and 'lung'). Confirm location and date, but should have Pergamino as Admin2 and Buenos Aires as Admin1.
PP_006VLYL.1 - has the host info. Confirm date and location with same comment as above - and 'lung'.

PP_006VLWQ.1 - I don't find Ol23133 in the paper cited - in Table 1 or otherwise. Is this from another paper?
I do see in Genbank that the host is "Oligoryzomys longicaudatus" - however in the standing revision the common name is "mice and others" which is not a correct common name for a specific scientific name.

PP_006VLTW.1 - can confirm host, date, location - however, as above, Pergamino should be Admin2 and Buenos Aires should be Admin1. Should have 'blood' added.

[arthurshem86]

The five sequences highlighted in Table1 from this article https://doi.org/10.1128/jvi.76.8.3765-3773.2002 were from https://doi.org/10.1086/514221. For the human samples cases happened between (1987 - 1996) and thats probably when the samples were collected and frozen. And for the rodent samples lung and kideny tissues were obtained from sacrificed animals that were trapped in (1992 - 1996) thats probably when the samples were collected frozen. These are the meaning of the suffix used: Hu = Human, Of = Oligoryzomys flavescens, Ol = Oligoryzomys longicaudatus, Oc =  Oligoryzomys chacoensis, Bo = Bolomys Obscurus, Akodon azarae. Mapping these back to the sequences in PPX;

PP_006VLTW.1 (Hu 39694) - the exposure site unknown but Pergamino given as the location. Therefore, it can be added as Admin2 and Buenos Airess added as the province (Admin1). The host Homo sapiens

PP_006VLUU (Ol22996) - Oran Admin2 and Salta province Admin1. Host is Oligoryzomys longicaudatus

PP_006VQ45 (Oc22531) and PP_006VLVS (Oc22531)  - Oran Admin2 and Salta province Admin1. Host is Oligoryzomys chacoensis

PP_006VQ53 (13796) - In the article this is given as Necromys benefactus but there is no host or sample collected with linkage from this host from Maciel in the cited paper

PP_006VLXN (Bo13796) - Maciel Admin2 and Sante Fe province (Admin1). The host is Bolomys obscurus not Necromys Benefactus as indicated in the paper

PP_006VLYL (Aa14403) - Pergamino Admin1 and Buenos Aires Admin1. The host is Akodon azarae

[anna-parker]

I have updated the pending revisions with what was discussed above, let me know if I can approve or if one of you would like to do so:

• PP_006VLTW (Hu 39694) - to have Pergamino (admin2) and Buenos Aires (admin1)
• PP_006VLUU - to have Oran (admin2) and Salta (admin1)
• PP_0072UW2 - to have Oran (admin2), Salta (admin1), Argentina (country), 1997 (sampleCollectionDate), Lung (anatomical part)
• PP_0072UX0 - to have Pergamino (Admin2), Buenos Aires (Admin1), Argentina (country), 1997 (sampleCollectionDate), Lung (anatomical part), Necromys benefactus as the paper writes Necromys benefactus (formerly Bolomys obscurus),
• PP_0072UYY - to have Maciel Admin2 and Sante Fe province (Admin1), Argentina (country), 1997 (sampleCollectionDate), Lung (anatomical part)