Add BA.2.86 dataset

data/nextstrain/collection.json

@@ -24,6 +24,7 @@
     "nextstrain/sars-cov-2/MN908947",
     "nextstrain/sars-cov-2/BA.2",
     "nextstrain/sars-cov-2/XBB",
+    "nextstrain/sars-cov-2/BA.2.86",
     "nextstrain/flu/h1n1pdm/ha/CY121680",
     "nextstrain/flu/h1n1pdm/ha/MW626062",
     "nextstrain/flu/h1n1pdm/na/MW626056",

data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md

@@ -0,0 +1,7 @@
+## Unreleased
+
+Initial release for Nextclade v3!
+
+This dataset is converted from the corresponding older dataset for Nextclade v2. You can find old versions of datasets here: https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/sars-cov-2/BA.2.86/README.md

@@ -0,0 +1,50 @@
+# Nextclade dataset for "SARS-CoV-2 relative to BA.2" based on reference "BA.2" (sars-cov-2-21L/BA.2)
+
+
+## Dataset attributes
+
+| attribute            | value                | value friendly                           |
+| -------------------- | -------------------- | ---------------------------------------- |
+| name                 | sars-cov-2-21L       | SARS-CoV-2 relative to BA.2              |
+| reference            | BA.2                 | BA.2                                     |
+
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+
+
+### What are the SARS-CoV-2 clades?
+
+Nextclade was originally developed during COVID-19 pandemic, primarily focused on SARS-CoV-2. This section describes clades with application to SARS-CoV-2, but Nextclade can analyse other pathogens too.
+
+<figure>
+  <a href="https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg">
+    <picture>
+      <img
+        src="https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg"
+        alt="Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain"
+      />
+    </picture>
+  </a>
+  <figcaption>
+    <small>
+      Fig.1. Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain (<a href="https://github.com/nextstrain/ncov-clades-schema/">source</a>)
+    </small>
+  </figcaption>
+</figure>
+
+Since its emergence in late 2019, SARS-CoV-2 has diversified into several different co-circulating variants. To facilitate discussion of these variants, we have grouped them into __clades__ which are defined by specific signature mutations.
+
+We currently define more than 30 clades (see [this blog post](https://nextstrain.org/blog/2021-01-06-updated-SARS-CoV-2-clade-naming) for details):
+
+- 19A and 19B emerged in Wuhan and have dominated the early outbreak
+- 20A emerged from 19A out of dominated the European outbreak in March and has since spread globally
+- 20B and 20C are large genetically distinct subclades 20A emerged in early 2020
+- 20D to 20J have emerged over the summer of 2020 and include three "Variants of Concern" (VoC).
+- 21A to 21F include the VoC __delta__ and several Variants of Interest (VoI).
+- 21K onwards are different clades within the diverse VoC __omicron__.
+
+Within Nextstrain, we define each clade by its combination of signature mutations. You can find the exact clade definition in [github.com/nextstrain/ncov/defaults/clades.tsv](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). When available, we will include [WHO labels for VoCs and VoIs](https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/).
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).

data/nextstrain/sars-cov-2/BA.2.86/genome_annotation.gff3

@@ -0,0 +1,18 @@
+##gff-version 3
+##sequence-region MN908947 1 29903
+# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
+# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
+# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
+# seqname	source	feature	start	end	score	strand	frame	attribute
+MN908947	GenBank	gene	266	13468	.	+	.	gene_name=ORF1a
+MN908947	GenBank	gene	13468	21555	.	+	.	gene_name=ORF1b
+MN908947	GenBank	gene	25393	26220	.	+	.	gene_name=ORF3a
+MN908947	GenBank	gene	21563	25384	.	+	.	gene_name=S
+MN908947	GenBank	gene	26245	26472	.	+	.	gene_name=E
+MN908947	GenBank	gene	26523	27191	.	+	.	gene_name=M
+MN908947	GenBank	gene	27202	27387	.	+	.	gene_name=ORF6
+MN908947	GenBank	gene	27394	27759	.	+	.	gene_name=ORF7a
+MN908947	GenBank	gene	27756	27887	.	+	.	gene_name=ORF7b
+MN908947	GenBank	gene	27894	28259	.	+	.	gene_name=ORF8
+MN908947	GenBank	gene	28274	29533	.	+	.	gene_name=N
+MN908947	GenBank	gene	28284	28577	.	+	.	gene_name=ORF9b