Allow addition of unreleased INRB data

phylogenetic/build-configs/inrb/auspice_config.json

@@ -0,0 +1,83 @@
+{
+  "title": "Genomic epidemiology of mpox clade I viruses: INRB build",
+  "maintainers": [
+    {"name": "INRB", "url": "https://inrb.net/"},
+    {"name": "Nextstrain team", "url": "http://nextstrain.org"}
+  ],
+  "data_provenance": [
+    {
+      "name": "INRB, DRC"
+    },
+    {
+      "name": "GenBank",
+      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
+    }
+  ],
+  "build_url": "https://github.com/nextstrain/mpox",
+  "colorings": [
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "division",
+      "title": "Province",
+      "type": "categorical"
+    },
+    {
+      "key": "location",
+      "title": "Health Zone",
+      "type": "categorical"
+    },
+    {
+      "key": "source_private",
+      "title": "INRB (private data)",
+      "type": "boolean"
+    },
+    {
+      "key": "host",
+      "title": "Host",
+      "type": "categorical"
+    },
+    {
+      "key": "GA_CT_fraction",
+      "title": "G→A or C→T fraction",
+      "type": "continuous"
+    },
+    {
+      "key": "dinuc_context_fraction",
+      "title": "NGA/TCN context of G→A/C→T mutations",
+      "type": "continuous"
+    },
+    {
+      "key": "recency",
+      "title": "Submission Recency",
+      "type": "categorical"
+    },
+    {
+      "key": "date_submitted",
+      "title": "Release Date",
+      "type": "categorical"
+    },
+    {
+      "key": "date",
+      "title": "Collection date",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "country"
+  ],
+  "display_defaults": {
+    "color_by": "country",
+    "map_triplicate": false,
+    "distance_measure": "num_date",
+    "transmission_lines": false
+  }
+}

phylogenetic/build-configs/inrb/config.yaml

@@ -0,0 +1,11 @@
+# Custom config file for INRB Clade-I builds.
+# This should be used as an additional config on top of the clade-i config, i.e.
+# --configfile defaults/clade-i/config.yaml build-configs/inrb/config.yaml
+
+
+# Custom INRB footer contents & auspice config
+description: "build-configs/inrb/description.md"
+auspice_config: "build-configs/inrb/auspice_config.json"
+
+# INRB builds inject private data
+private_data: true

phylogenetic/build-configs/inrb/description.md

@@ -0,0 +1,37 @@
+
+### Laboratories involved in genomic surveillance of mpox in the DRC
+Institut National de Recherche Biomédicale (INRB) through :
+* Pathogen Genomics Laboratory, Epidemiology and Global Health Department, INRB, Kinshasa
+* Rodolphe Merieux INRB Goma Laboratory, Goma
+* Mpox National Reference Laboratory, Virology Department, INRB, Kinshasa
+
+### Genomic surveillance of mpox in the DRC
+This work is made possible by the open sharing of genetic data among research groups and constitutes a part of the genomic surveillance of mpox in the DRC, led by the Ministry of Public Health, Hygiene and Prevention through INRB, DSE, PNLFHMPX and INSP. The provincial health divisions and health zones affected by the mpox outbreak are also involved in genomic surveillance efforts.
+
+Data will be shared via virological.org and [Nextstrain](https://nextstrain.org/) , and will be continuously updated as new mpox sequences are generated . If you intend to use these sequences before their publication, please contact Profs.  Placide Mbala and Steve Ahuka for request and coordination.
+
+### Partner institutions
+* These sequences were generated by the Pathogen Genomics Laboratory at INRB in the DRC in partnership with :
+* Africa-CDC/ASLM
+* AFROSCREEN consortium
+* Institute of Tropical Medicine, Antwerp, Belgium
+* ARCTIC Network
+* Biosurv international, UK
+* TransVIHMI :Université de Montpellier, Institut de Recherche pour le Développement (IRD), Institut National de la Santé et de la Recherche Médicale (INSERM) ;  Montpellier ;  France,
+* UCLA
+* USDA
+* WHO
+
+### Acknowledgements
+This work was funded by :
+* Africa Pathogen Genomics Initiative through CARES grants ;
+* Agence Francaise de Dévelopement through the AFROSCREEN project (grant agreement CZZ3209, coordinated by ANRS-MIE Maladies infectieuses émergentes in partnership with Institut de Recherche pour le Développement (IRD) and Pasteur Institute) and PANAFPOX project funded by ANRS-MIE.
+* Belgian Directorate-general Development Cooperation and Humanitarian Aid and the Research Foundation - Flanders (FWO, grant number G096222 N );
+* Department of Defense, Defense Threat Reduction Agency, Monkeypox Threat Reduction Network;
+* USDA Non-Assistance Cooperative Agreement #20230048;
+* International Mpox Research Consortium (IMReC) through funding from the Canadian Institutes of Health Research and International Development Research Centre (grant no. MRR-184813);
+* US NIAID/NIH grant number U01AI151799 through the Center for Research in Emerging Infectious Disease-East and Central Africa (CREID-ECA)
+
+
+#### List of abbreviations:
+**DRC**: Democratic Republic of the Congo; **DSE**: Direction de la Surveillance Epidémiologique ; **INRB**: Institut National de Recherche Biomédicale ; **INSP**: Institut National de Santé Publique ; **PNLFHMPX**: Programme National de Lutte contre les Fièvres Hénorragiques et le Mpox ; **UCLA**: University of California Los -Angeles ; **WHO**: World Health Organization ; **USDA**: United States Department of Agriculture

phylogenetic/defaults/clade-i/auspice_config.json

@@ -21,6 +21,16 @@
       "title": "Country",
       "type": "categorical"
     },
+    {
+      "key": "division",
+      "title": "Province",
+      "type": "categorical"
+    },
+    {
+      "key": "location",
+      "title": "Health Zone",
+      "type": "categorical"
+    },
     {
       "key": "host",
       "title": "Host",
@@ -53,13 +63,16 @@
     }
   ],
   "geo_resolutions": [
-    "country"
+    "region",
+    "country",
+    "division",
+    "location"
   ],
   "display_defaults": {
     "color_by": "country",
     "map_triplicate": true,
     "distance_measure": "num_date",
-    "transmission_lines": false
+    "transmission_lines": true
   },
   "filters": [
     "country",

phylogenetic/defaults/clade-i/config.yaml

@@ -3,7 +3,7 @@ genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 include: "defaults/clade-i/include.txt"
 clades: "defaults/clades.tsv"
-lat_longs: "defaults/lat_longs.tsv"
+lat_longs: "defaults/clade-i/lat_longs.tsv"
 auspice_config: "defaults/clade-i/auspice_config.json"
 description: "defaults/description.md"
 tree_mask: "defaults/tree_mask.tsv"
@@ -45,8 +45,10 @@ clock_rate: 1.465e-06
 clock_std_dev: 6.7e-07
 divergence_units: "mutations"
 
+color_ordering: "results/clade-i/color_ordering.tsv"
+
 traits:
-  columns: "country"
+  columns: region country
   sampling_bias_correction: 3
 
 ## recency

phylogenetic/defaults/clade-i/include.txt

@@ -0,0 +1,7 @@
+# Ensure we include 2 Ia and Ib samples so we can use them to check clade assignment
+# Clade Ia
+PP601197
+KJ642618
+# Clade Ib
+PP601222
+PP601209