data: initial commit of community neherlab/HIV-1 dataset

data/community/collection.json

@@ -15,6 +15,7 @@
     ]
   },
   "dataset_order": [
-    "community/isuvdl/mazeller/prrsv2/orf5/yimim2023"
+    "community/isuvdl/mazeller/prrsv2/orf5/yimim2023",
+    "community/neherlab/hiv-1"
   ]
 }

data/community/neherlab/hiv-1/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release of an HIV-1 dataset for subtype classification. 

data/community/neherlab/hiv-1/README.md

@@ -0,0 +1,35 @@
+# EXPERIMENTAL: HIV-1 group M subtype and CRF classification
+
+| Key                    | Value                                                                                                               |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------|
+| authors                | [Richard Neher (U Basel)](https://neherlab.org), [Thomas Leitner (LANL)](https://public.lanl.gov/tkl/)              |
+| data source            | LANL database and Genbank                                                                                           |
+| workflow               | [github.com/neherlab/HIV-nextclade](https://github.com/neherlab/HIV-nextclade)                                      |
+| nextclade dataset path | neherlab/HIV-1                                                                                                      |
+| reference              | [NC_001802](https://www.ncbi.nlm.nih.gov/nuccore/NC_001802)                                                         |
+
+This Nextclade data set aligns sequences to the HXB2 reference and finds the closest match in a reference tree build from the [2021 Super filtered Alignment](https://www.hiv.lanl.gov/content/sequence/NEWALIGN/help.html#filter) provided by LANL.
+Due to extensive recombination in HIV-1 group M, the tree is not a proper phylogenetic tree, but a collection of trees inferred for each subtype or recombinant form. These individuals trees are then grafted together. Rare CRFs, URFs, or subtypes represented less then 3 times in the reference alignment are labeled as subtype `other`.
+
+Note that the classification is **EXPERIMENTAL** and might be unreliable for sequences that lack a close representative in the tree. 
+The closeness to sequences in the reference set is quantified by the `private mutations` 
+As a general guide, the more private mutations a sequence has, the less reliable the subtype assignment will be. 
+
+Note that alignments of sequences that are far from the subtype B HXB2 reference will have 
+
+## Reference sequence HXB2 (NC_001802)
+
+This data set uses the NCBI reference sequence [NC_001802](https://www.ncbi.nlm.nih.gov/nuccore/NC_001802) based on the HXB2 genome [K03455](https://www.ncbi.nlm.nih.gov/nuccore/K03455.1). The primary reason for choosing it is to ensure amino acid substitutions in conserved proteins such as `Pol` are numbered consistently.
+Note that this sequence as a few problems, including a premature stop-codon in `nef`.
+
+## Treatment of indel-rich regions
+
+There are multiple regions in the HIV-1 genome where deletions and insertions are common. Such regions are often not consistently aligned when aligning sequences individually to a reference. For the purposes of finding closely matching sequences in the reference tree, these regions are ignored. Specifically, tree placement ignores
+
+ - The LTR before the beginning of `gag` (until position 336 in `NC_001802`)
+ - Positions 5780 until 5870 at the end of `vpu` and the beginning of `gp120`
+ - Positions 6160 until 6240 in `gp120`. 
+ - Position 6940 unitl 7020 in `gp120`.
+ - The 5' LTR from end of `nef` (positions 9863 until the end of the genome)
+
+

data/community/neherlab/hiv-1/genome_annotation.gff3

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+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_001802.1 1 9181
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11676
+NC_001802.1	RefSeq	region	1	9181	.	+	.	ID=NC_001802.1:1..9181;Dbxref=taxon:11676;gb-acronym=HIV-1;gbkey=Src;genome=genomic;mol_type=genomic RNA;note=strain for reference annotation
+NC_001802.1	RefSeq	CDS	1799	2095	.	+	.	Name=pro;gbkey=Prot;protein_id=NP_705926.1;product=aspartic peptidase;ID=id-NP_057849.4:489..587;experiment=DESCRIPTION:[PMID:2537531],DESCRIPTION:[PMID:2548279],DESCRIPTION:[PMID:3290901];Note=The proteinase domain of Gag-Pol (in the form of homodimer) mediates all the cleavages in the polyprotein. Cleaves itself from the polyprotein late in particle assembly.
+NC_001802.1	RefSeq	CDS	2096	3775	.	+	.	Name=RT-p66;gbkey=Prot;product=p66 subunit;protein_id=NP_705927.1;ID=id-NP_057849.4:588..1147;experiment=DESCRIPTION:[PMID:1374166],EXISTENCE:[PMID:4316300];Note=transcribes single stranded viral RNA genome into double stranded proviral DNA%3B HIV-1 reverse transcriptase is composed of the p66 subunit (this protein) and the p51 subunit that lacks the RNAse H domain of the larger subunit
+NC_001802.1	RefSeq	CDS	2096	3415	.	+	.	Name=RT-p51;gbkey=Prot;protein_id=NP_789739.1;ID=id-NP_057849.4:588..1027;product=reverse transcriptase p51 subunit;Note=HIV-1 reverse transcriptase is composed of the p66 subunit and the p51 subunit (this protein) that lacks the RNAse H domain of the larger subunit
+NC_001802.1	RefSeq	CDS	3776	4639	.	+	.	Name=INT;gbkey=Prot;product=integrase;protein_id=NP_705928.1;ID=id-NP_057849.4:1148..1435;experiment=DESCRIPTION:[PMID:7983732],DESCRIPTION:[PMID:8035478];Note=mediates integration of the viral DNA into the infected cell chromosome
+NC_001802.1	RefSeq	CDS	336	731	.	+	.	Name=p17;gbkey=Prot;product=matrix;protein_id=NP_579876.2;ID=id-NP_057850.1:1..132;experiment=DESCRIPTION:[PMID:12032547],DESCRIPTION:[PMID:1710290],DESCRIPTION:[PMID:8610175];Note=viral structural protein%3B forms the outer structural shell of HIV-1 virions%3B involved in the nuclear import of the HIV-1 preintegration complex
+NC_001802.1	RefSeq	CDS	732	1424	.	+	.	Name=p24;gbkey=Prot;product=capsid;protein_id=NP_579880.1;ID=id-NP_057850.1:133..363;Note=viral structural protein%3B forms the core of HIV-1 virions;experiment=DESCRIPTION:[PMID:15208690],DESCRIPTION:[PMID:16041386],DESCRIPTION:[PMID:21248851]
+NC_001802.1	RefSeq	CDS	1425	1466	.	+	.	Name=p2;product=p2;gbkey=Prot;protein_id=NP_579882.1;ID=id-NP_057850.1:364..377;Note=Processing of Gag-Pol by the protease domain dimer starts with cleavage between the p2 and nucleocapsid proteins.
+NC_001802.1	RefSeq	CDS	1467	1631	.	+	.	Name=p7;gbkey=Prot;protein_id=NP_579881.1;product=nucleocapsid;ID=id-NP_057850.1:378..432;experiment=DESCRIPTION:[PMID:1639074],DESCRIPTION:[PMID:7666546];Note=viral structural protein%3B coats the genomic RNA inside the virion core%3B binds and delivers full-length viral RNAs into assembling HIV-1 virions
+NC_001802.1	RefSeq	CDS	1632	1679	.	+	.	Name=p1;product=p1;gbkey=Prot;protein_id=NP_787042.1;ID=id-NP_057850.1:433..448;Note=important for virus infectivity%2C protein processing%2C and genomic RNA dimer stability
+NC_001802.1	RefSeq	CDS	1680	1835	.	+	.	Name=p6;product=p6;gbkey=Prot;protein_id=NP_579883.1;ID=id-NP_057850.1:449..500;experiment=DESCRIPTION:[PMID:10085158],DESCRIPTION:[PMID:15527852];Note=important for incorporation of Vpr into assembling HIV-1 virions%3B helps mediate efficient virus particle release from infected cells
+NC_001802.1	RefSeq	CDS	4587	5165	.	+	0	Name=vif;gbkey=CDS;gene=vif;product=Vif;locus_tag=HIV1gp3;protein_id=NP_057851.1;ID=cds-NP_057851.1;Dbxref=GenBank:NP_057851.1,GeneID:155459
+NC_001802.1	RefSeq	CDS	5105	5319	.	+	0	Name=vpr;gbkey=CDS;gene=vpr;product=Vpr;locus_tag=HIV1gp4;protein_id=NP_057852.2;ID=cds-NP_057852.2;exception=artificial frameshift;Dbxref=GenBank:NP_057852.2,GeneID:155807;Note=An artificial frameshift eliminating the orf-disrupting nucleotide at position 5320 is introduced to obtain the typical HIV-1 Vpr protein sequence. For this particular HIV-1 strain%2C HXB2%2C only a short (78 amino acid long) variant of the Vpr sequence can be obtained by translation of nucleotides 5105 through 5341 without the frameshift
+NC_001802.1	RefSeq	CDS	5321	5396	.	+	1	Name=vpr;gbkey=CDS;gene=vpr;product=Vpr;locus_tag=HIV1gp4;protein_id=NP_057852.2;ID=cds-NP_057852.2;exception=artificial frameshift;Dbxref=GenBank:NP_057852.2,GeneID:155807;Note=An artificial frameshift eliminating the orf-disrupting nucleotide at position 5320 is introduced to obtain the typical HIV-1 Vpr protein sequence. For this particular HIV-1 strain%2C HXB2%2C only a short (78 amino acid long) variant of the Vpr sequence can be obtained by translation of nucleotides 5105 through 5341 without the frameshift
+NC_001802.1	RefSeq	CDS	5377	5591	.	+	0	Name=tat;gbkey=CDS;gene=tat;product=Tat;locus_tag=HIV1gp5;protein_id=NP_057853.1;ID=cds-NP_057853.1;Dbxref=GenBank:NP_057853.1,GeneID:155871;Note=the length of Tat varies depending on virus strain or clade
+NC_001802.1	RefSeq	CDS	7925	7970	.	+	1	Name=tat;gbkey=CDS;gene=tat;product=Tat;locus_tag=HIV1gp5;protein_id=NP_057853.1;ID=cds-NP_057853.1;Dbxref=GenBank:NP_057853.1,GeneID:155871;Note=the length of Tat varies depending on virus strain or clade
+NC_001802.1	RefSeq	CDS	5516	5591	.	+	0	Name=rev;gbkey=CDS;gene=rev;product=Rev;locus_tag=HIV1gp6;protein_id=NP_057854.1;ID=cds-NP_057854.1;Dbxref=GenBank:NP_057854.1,GeneID:155908
+NC_001802.1	RefSeq	CDS	7925	8199	.	+	2	Name=rev;gbkey=CDS;gene=rev;product=Rev;locus_tag=HIV1gp6;protein_id=NP_057854.1;ID=cds-NP_057854.1;Dbxref=GenBank:NP_057854.1,GeneID:155908
+NC_001802.1	RefSeq	CDS	5608	5856	.	+	0	Name=vpu;gbkey=CDS;gene=vpu;product=Vpu;locus_tag=HIV1gp7;protein_id=NP_057855.1;ID=cds-NP_057855.1;Dbxref=GenBank:NP_057855.1,GeneID:155945;Note=Vpu and gp160 are translated from different reading frames of the same bicistronic mRNA
+NC_001802.1	RefSeq	CDS	5855	7303	.	+	.	Name=gp120;gbkey=Prot;protein_id=NP_579894.2;ID=id-NP_057856.1:29..511;experiment=DESCRIPTION:[PMID:24179160];product=Envelope surface glycoprotein gp120;Note=mediates binding of HIV-1 to CD4 and cellular co-receptors%3B cooperates with gp41 to mediate fusion of viral membrane with cellular membrane during virus entry into cells
+NC_001802.1	RefSeq	CDS	7304	8338	.	+	.	Name=gp41;gbkey=Prot;protein_id=NP_579895.1;ID=id-NP_057856.1:512..856;product=Envelope transmembrane domain;Note=cooperates with gp120 to mediate fusion of viral membrane with cellular membrane during virus entry into cells
+NC_001802.1	RefSeq	CDS	8343	8963	.	+	0	Name=nef;gbkey=CDS;gene=nef;product=Nef;locus_tag=HIV1gp9;protein_id=NP_057857.2;ID=cds-NP_057857.2;transl_except=(pos:8712..8714%2Caa:Trp);Dbxref=GenBank:NP_057857.2,GeneID:156110;Note=This particular nucleotide sequence has a premature stop codon in place of a well-conserved tryptophan codon at position 8712-8714 that truncates the HIV1 Nef protein sequence to a 123 amino acids-long N-terminal portion (not shown).

data/community/neherlab/hiv-1/pathogen.json

@@ -0,0 +1,70 @@
+{
+    "alignmentParams": {
+        "penaltyGapOpen": 8,
+        "penaltyGapOpenInFrame": 12,
+        "penaltyGapOpenOutOfFrame": 14,
+        "gapAlignmentSide": "left",
+        "excessBandwidth": 50,
+        "terminalBandwidth": 50,
+        "kmerLength": 10,
+        "kmerDistance": 50,
+        "minMatchLength": 40,
+        "allowedMismatches": 8,
+        "windowSize": 30
+    },
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    },
+    "placementMaskRanges":[
+      {"begin":0, "end":336},
+      {"begin":5780, "end":5870},
+      {"begin":6160, "end":6240},
+      {"begin":6940, "end":7020},
+      {"begin":8963, "end":9181}
+    ],
+    "deprecated": false,
+    "enabled": true,
+    "experimental": false,
+    "files": {
+        "pathogenJson": "pathogen.json",
+        "changelog": "CHANGELOG.md",
+        "examples": "sequences.fasta",
+        "genomeAnnotation": "genome_annotation.gff3",
+        "readme": "README.md",
+        "reference": "reference.fasta",
+        "treeJson": "tree.json"
+    },
+    "official": true,
+    "qc": {
+      "frameShifts": {
+        "enabled": true,
+        "scoreWeight": 20
+      },
+      "missingData": {
+        "enabled": true,
+        "missingDataThreshold": 2000,
+        "scoreBias": 500
+      },
+      "mixedSites": {
+        "enabled": true,
+        "mixedSitesThreshold": 40
+      },
+      "privateMutations": {
+        "cutoff": 700,
+        "enabled": true,
+        "typical": 600,
+        "weightLabeledSubstitutions": 1,
+        "weightReversionSubstitutions": 2,
+        "weightUnlabeledSubstitutions": 1
+      },
+      "stopCodons": {
+        "enabled": true,
+        "ignoredStopCodons": [
+          {"cdsName": "p6", "codon":49}
+        ],
+        "scoreWeight": 40
+      }
+    },
+    "schemaVersion": "3.0.0"
+  }