Merge pull request #196 from nextstrain/moncla-lab-h5

moncla-lab: add initial IAV h5 datasets

data/community/collection.json

@@ -17,6 +17,12 @@
   "dataset_order": [
     "community/isuvdl/mazeller/prrsv2/orf5/yimim2023",
     "community/neherlab/hiv-1",
-    "community/neherlab/hiv-1/hxb2"
+    "community/neherlab/hiv-1/hxb2",
+    "community/moncla-lab/iav-h5/all-clades",
+    "community/moncla-lab/iav-h5/2.3.4.4",
+    "community/moncla-lab/iav-h5/2.3.2.1",
+    "community/moncla-lab/iav-h5/ha/2.3.4.4",
+    "community/moncla-lab/iav-h5/ha/all-clades",
+    "community/moncla-lab/iav-h5/ha/2.3.2.1"
   ]
 }

data/community/moncla-lab/iav-h5/ha/2.3.2.1/CHANGELOG.md

@@ -0,0 +1,5 @@
+## Unreleased
+
+Initial release for Nextclade v3!
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/moncla-lab/iav-h5/ha/2.3.2.1/README.md

@@ -0,0 +1,47 @@
+# H5Nx clade `2.3.2.1` dataset with A/duck/Vietnam/NCVD-1584/2012 reference
+
+| attribute            | value                                    |
+| -------------------- | ---------------------------------------- |
+| authors              |[Jordan Ort](https://lmoncla.github.io/monclalab/team/JordanOrt/), [Louise Moncla](https://lmoncla.github.io/monclalab/team/LouiseMoncla/)|
+| dataset name         | H5Nx clade `2.3.2.1` (provisional)         |
+| reference strain     | A/duck/Vietnam/NCVD-1584/2012(H5N1)      |
+| reference accession  | EPI424984                                |
+
+
+## Authors and contacts
+
+Maintained by: [Jordan Ort](https://lmoncla.github.io/monclalab/team/JordanOrt/)
+
+With the help from: [Louise Moncla](https://lmoncla.github.io/monclalab/team/LouiseMoncla/), Todd Davis, Tommy Lam, Samuel Shephard, Richard Neher
+
+## Scope of this dataset
+This dataset uses a current H5 candidate vaccine virus (CVV) from clade `2.3.2.1` (A/duck/Vietnam/NCVD-1584/2012) as a reference and is suitable for the analysis of H5 sequences belonging to clade `2.3.2.1` and its sub-clades `2.3.2.1a` through `2.3.2.1g`. Sequences belonging to other clades cannot be annotated by this dataset and will be left `unassigned`.
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the provisional nomenclature defined by the WHO/FAO/WOAH H5 Nomenclature Working Group
+ * Sequence quality control (QC)
+ * Phylogenetic placement
+ * Annotations for glycosylation sties, HA cleavage site sequence, and presence/absence of a polybasic cleavage site
+
+## Clades of H5Nx avian influenza viruses
+
+The WHO/FAO/WOAH H5 Nomenclature Working Group define "clades" using HA gene seguences, and define clades as genetically distinct, monophyletic groups of viruses. Viruses falling into a given clade share a common ancestor with significant bootstrap support and have low levels of within-clade diversity. [Past nomenclature updates](https://onlinelibrary.wiley.com/doi/10.1111/irv.12324) have required viruses in the same clade to be monophyletic with bootstrap suppor of at least 60%, with within-clade pairwise distances of less than 1.5%. These requirements are sometimes relaxed, and clades are periodically updated to account for expanding viral diversity.
+
+Clade `2.3.2.1` viruses and their descendants have circulated since 2007 and are endemic in Southeast Asia. These viruses have diversified into eight additional sub-clades, named `2.3.2.1a` through `2.3.2.1g` due to high circulating diversity within the clade.
+This Nextclade dataset incorporates these provisional `2.3.2.1` sub-clades.
+
+## Alternative, and complementary approaches for H5 clade assignment
+Two additional tools exist for assigning clades to H5 viruses that accommodate the recent `2.3.2.1` clade splits.
+
+1. [LABEL](https://wonder.cdc.gov/amd/flu/label/): this command-line tool is built and maintained by Sam Shepard, and performs clade assignment for all current `2.3.4.4` and `2.3.2.1` clade splits.
+2. [BVBRC Subspecies Classification Tool](https://www.bv-brc.org/app/SubspeciesClassification): this is a drag and drop tool that classifies a variety of viruses, including influenza A H1N1, H3N2, and H5N1.
+
+The clade assignments in this Nextclade dataset were validated against LABEL assignments and shown to be generally well-matched across subclades. The figure below shows a direct comparison of assignments for 1671 HA sequences from GISAID, performed using LABEL and this NextClade dataset for clade `2.3.2.1` and its subclades.
+
+![Figure 1: Comparison between LABEL and Nextclade for 2.3.2.1 assignments](https://raw.githubusercontent.com/moncla-lab/h5nx-Clades/main/jordan-h5-clades/testing-nextclade-datasets/2321/files/20240430_2321.png)
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html