Skip to content

Commit f4068f2

Browse files
rneherrneher
authored
Merge pull request #448 from nextstrain/andes-update
andv: update with ppx data, add outbreak annotation
2 parents d120960 + 9725273 commit f4068f2

37 files changed

Lines changed: 2434 additions & 17 deletions

‎data/nextstrain/orthohantavirus/andv/l/CHANGELOG.md‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,9 @@
1+
## Unreleased
2+
3+
- Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
4+
- Include 2026 outbreak sequences
5+
- add 2026 outbreak annotation
6+
17
## 2026-05-08T21:17:05Z
28

39
- initial release

‎data/nextstrain/orthohantavirus/andv/l/README.md‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,11 +4,14 @@
44
| :-- | :-- |
55
| name | Andes virus segment L Tree |
66
| authors | [Nextstrain](https://nextstrain.org) |
7-
| reference | NC_003468 |
7+
| reference | [NC_003468](www.ncbi.nlm.nih.gov/nuccore/NC_003468) |
88
| workflow | https://github.com/nextstrain/andv/tree/main/nextclade |
99
| path | `nextstrain/orthohantavirus/andv/l` |
1010

1111

12+
This dataset aligns sequences to the RefSeq entry [NC_003468](www.ncbi.nlm.nih.gov/nuccore/NC_003468) and places the sequences onto a tree build using sequences from INSDC and Pathoplexus.
13+
Sequences from the 2026 outbreak were rapidly shared by several laboratories around the world to facilitate outbreak investigations. These data have been released under RESTRICTED USE terms on Pathoplexus.
14+
We refer to the [summary of the initial investigations by this collaboration on virological.org](https://virological.org/t/preliminary-analysis-of-orthohantavirus-andesense-virus-sequences-from-a-cruise-ship-related-cluster-may-2026/1029) for further details.
1215

1316
## What are Nextclade datasets
1417

‎data/nextstrain/orthohantavirus/andv/l/tree.json‎

Lines changed: 1 addition & 1 deletion
Large diffs are not rendered by default.

‎data/nextstrain/orthohantavirus/andv/m/CHANGELOG.md‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,9 @@
1+
## Unreleased
2+
3+
- Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
4+
- Include 2026 outbreak sequences
5+
- add 2026 outbreak annotation
6+
17
## 2026-05-08T21:17:05Z
28

39
- initial release

‎data/nextstrain/orthohantavirus/andv/m/README.md‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,11 +4,13 @@
44
| :-- | :-- |
55
| name | Andes virus segment M Tree |
66
| authors | [Nextstrain](https://nextstrain.org) |
7-
| reference | NC_003467 |
7+
| reference | [NC_003467](www.ncbi.nlm.nih.gov/nuccore/NC_003467) |
88
| workflow | https://github.com/nextstrain/andv/tree/main/nextclade |
99
| path | `nextstrain/orthohantavirus/andv/m` |
1010

11-
11+
This dataset aligns sequences to the RefSeq entry [NC_003467.1](www.ncbi.nlm.nih.gov/nuccore/NC_003467.1) and places the sequences onto a tree build using sequences from INSDC and Pathoplexus.
12+
Sequences from the 2026 outbreak were rapidly shared by several laboratories around the world to facilitate outbreak investigations. These data have been released under RESTRICTED USE terms on Pathoplexus.
13+
We refer to the [summary of the initial investigations by this collaboration on virological.org](https://virological.org/t/preliminary-analysis-of-orthohantavirus-andesense-virus-sequences-from-a-cruise-ship-related-cluster-may-2026/1029) for further details.
1214

1315
## What are Nextclade datasets
1416

‎data/nextstrain/orthohantavirus/andv/m/genome_annotation.gff3‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,5 +4,6 @@
44
##sequence-region NC_003467.2 1 3671
55
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456
66
NC_003467.2 RefSeq region 1 3671 . + . ID=NC_003467.2:1..3671;Dbxref=taxon:1980456;Name=M;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=M;strain=Chile-9717869
7-
NC_003467.2 RefSeq CDS 52 2004 . + 0 Name=G1;
8-
NC_003467.2 RefSeq CDS 2005 3468 . + 0 Name=G2;
7+
NC_003467.2 RefSeq CDS 52 3468 . + 0 Name=GPC;
8+
NC_003467.2 RefSeq CDS 52 2004 . + 0 Name=Gn;
9+
NC_003467.2 RefSeq CDS 2005 3468 . + 0 Name=Gc;

‎data/nextstrain/orthohantavirus/andv/m/pathogen.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@
1010
"changelog": "CHANGELOG.md"
1111
},
1212
"schemaVersion": "3.0.0",
13-
"defaultCds": "G1",
13+
"defaultCds": "GPC",
1414
"attributes": {
1515
"name": "Andesvirus (segment M)",
1616
"reference name": "Chile-9717869",

‎data/nextstrain/orthohantavirus/andv/m/tree.json‎

Lines changed: 1 addition & 1 deletion
Large diffs are not rendered by default.

‎data/nextstrain/orthohantavirus/andv/s/CHANGELOG.md‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,9 @@
1+
## Unreleased
2+
3+
- Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
4+
- Include 2026 outbreak sequences
5+
- add 2026 outbreak annotation
6+
17
## 2026-05-08T21:17:05Z
28

39
- initial release

‎data/nextstrain/orthohantavirus/andv/s/README.md‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,10 +4,13 @@
44
| :-- | :-- |
55
| name | Andes virus segment S Tree |
66
| authors | [Nextstrain](https://nextstrain.org) |
7-
| reference | NC_0034686 |
7+
| reference | [NC_003466](www.ncbi.nlm.nih.gov/nuccore/NC_003466) |
88
| workflow | https://github.com/nextstrain/andv/tree/main/nextclade |
99
| path | `nextstrain/orthohantavirus/andv/s` |
1010

11+
This dataset aligns sequences to the RefSeq entry [NC_003466](www.ncbi.nlm.nih.gov/nuccore/NC_003466) and places the sequences onto a tree build using sequences from INSDC and Pathoplexus.
12+
Sequences from the 2026 outbreak were rapidly shared by several laboratories around the world to facilitate outbreak investigations. These data have been released under RESTRICTED USE terms on Pathoplexus.
13+
We refer to the [summary of the initial investigations by this collaboration on virological.org](https://virological.org/t/preliminary-analysis-of-orthohantavirus-andesense-virus-sequences-from-a-cruise-ship-related-cluster-may-2026/1029) for further details.
1114

1215

1316
## What are Nextclade datasets

0 commit comments

Comments
 (0)