hcv: initial import

data/nextstrain/collection.json

@@ -103,6 +103,7 @@
     "nextstrain/flu/h2n2/mp",
     "nextstrain/flu/h2n2/ns",
     "nextstrain/ndv/class-2/NC_075404",
-    "nextstrain/ndv/class-1/AB524405"
+    "nextstrain/ndv/class-1/AB524405",
+    "nextstrain/hcv/AF009606"
   ]
 }

data/nextstrain/hcv/AF009606/CHANGELOG.md

@@ -0,0 +1,4 @@
+## Unreleased
+- Initial dataset creation
+- GFF3 annotation with CDS
+- Reference FASTA AF009606.1

data/nextstrain/hcv/AF009606/README.md

@@ -0,0 +1,65 @@
+# Hepatitis C virus dataset (all genotypes) with reference H77
+
+| Key               | Value                                                                                                                                                                                                                |
+| ----------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name              | Hepatitis C virus (all genotypes)                                                                                                                                                                                    |
+| authors           | [Richard Neher](https://neherlab.org), [Duyen Bao Le](https://www.uniklinik-duesseldorf.de/institut-fuer-virologie/forschung/ag-timm/team), [Stefannie Hoffmann](https://www.uniklinik-duesseldorf.de/institut-fuer-virologie/forschung/ag-timm/team), [Andreas Wagner](https://www.uniklinik-duesseldorf.de/institut-fuer-virologie/forschung/ag-timm/team)                                                                    |
+| reference         | `NC_038882.1` (isolate H77, genotype 1a)                                                                                                                                                                             |
+| workflow          | TODO                                                                                                                                                                                                                 |
+| path              | TODO                                                                                                                                                                                                                 |
+| clade definitions | HCV genotypes and subtypes following the ICTV consensus classification ([Smith et al., 2014](https://doi.org/10.1002/hep.26744); genotype 8: [Borgia et al., 2018](https://doi.org/10.1093/infdis/jiy401))          |
+
+## Scope of this dataset
+
+This dataset assigns genotypes and subtypes to hepatitis C virus (HCV)
+sequences of all known genotypes (1–8), and reports mutations relative to the
+H77 reference (`NC_038882.1`, genotype 1a).
+
+HCV is highly diverse: genotypes differ by more than 30% and subtypes by
+15–30% at the nucleotide level. Since all sequences are aligned against a
+single genotype 1a reference, sequences of other genotypes will show many
+mutations relative to the reference. Highly variable and gap-rich regions of
+the alignment (e.g. in NS5A and the 3' end) are excluded from phylogenetic
+placement.
+
+The dataset is designed for near full-length genomes or sequences spanning
+the complete coding region. TODO: describe performance on partial sequences
+(e.g. NS5B, core/E1 or E2 fragments).
+
+## Reference sequence and reference tree
+
+The reference sequence is the RefSeq `NC_038882.1` of isolate H77 (genotype
+1a). Amino acid mutations are reported for the mature proteins core, E1, E2,
+p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B.
+
+The reference tree contains near full-length genomes from GenBank, sampled
+evenly across genotypes and subtypes. Genotypes and subtypes of the tips are
+based on the NCBI taxonomy; clades in the tree are defined by the most recent
+common ancestor of all tips of a genotype or subtype.
+
+## Features
+
+This dataset supports:
+
+- Assignment of genotypes (`clade`)
+- Assignment of subtypes (`subtype`)
+- Phylogenetic placement
+- Sequence quality control (QC)
+
+## Genotypes and subtypes
+
+HCV is classified into 8 genotypes and more than 90 subtypes. Genotypes are
+labeled by numbers (1–8) and subtypes by a genotype number followed by a
+letter (e.g. 1a, 3b). The genotype is reported in the `clade` column and the
+subtype in the `subtype` column of the Nextclade output.
+
+Subtypes that are rare in public databases may be represented by few
+sequences in the reference tree, or not at all. Sequences of such subtypes
+are assigned the genotype, but may not get a subtype assignment.
+Recombinant viruses (e.g. 2k/1b) are not labeled as such and are assigned
+the genotype and subtype of their closest relative in the tree.
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation:
+<https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html>