Add enterovirus family

data-intuitive · Mar 11, 2024 · a9d9c51 · a9d9c51
2 parents 3d2e482 + c143ff1
commit a9d9c51
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Showing 32 changed files with 250 additions and 6 deletions.
diff --git a/_js/_ojs_family.qmd b/_js/_ojs_family.qmd
@@ -6,9 +6,6 @@
 familyAnnotations = annotations
   .filter(virus => virus.family == virusFamily)
 
-// console.log("family: ")
-// console.log(familyAnnotations)
-
 function virusInfo(_family, _virus) {
   const info = 
     familyAnnotations.filter(row => row.abbreviation == _virus && row.family == _family)
@@ -37,8 +34,6 @@ annotatedViruses =
     .filter(virus => virus.virus_of_interest == "Yes")
     .map(virus => addGrouped(virus))
 
-// console.log(annotatedViruses)
-
 // Create a sublist of viruses with toolbox
 // Take into account groups by selecting unique entries
 toolboxAnnotatedViruses =
@@ -51,6 +46,7 @@ toolboxAnnotatedViruses =
 // Derive a virus object from the ID
 // The ID can be either a virus_id (from the ictv tree) or a group_abbreviation
 virusIdToVirus = (virus_id) => {
+
   // lookup the virus_id in the full list of viruses
   const fullList =
     annotatedViruses

diff --git a/_js/family.qmd b/_js/family.qmd
@@ -168,8 +168,10 @@ renderedTree = tree
   // Transform the tree (translate and prune)
   // based on the input Excel file for this virus family
   .traverse_and_compute(node => {
+
     const virus_id = node.data.name
     const isLeaf = tree.isLeafNode(node)
+
     if (isLeaf) {
       const virus = virusIdToVirus(virus_id)
       const isVirusOfInterest = (typeof virus !== "undefined") ? (virus.virus_of_interest == "Yes") : false
@@ -205,7 +207,6 @@ renderedTree = tree
     'container': "#tree-container"
   })
   .style_nodes( (element, data) => {
-
     // the virus_id is how the virus is encoded in phylotree newick file
     const virus_id = data.data.name  
     
@@ -280,6 +281,8 @@ clearNodes = () => {
     .select("text").attr("class", "phylotree-node-text-hl")
 }
 
+// console.log(renderedTree)
+
 showTree = renderedTree
   .svg
   .node()

diff --git a/enteroviruses/EV-A71.qmd b/enteroviruses/EV-A71.qmd
@@ -0,0 +1,19 @@
+---
+params:
+  family: enteroviruses
+  virus: Enterovirus-A71 (EV-A71)
+---
+
+```{r}
+#| echo: false
+ojs_define(virusFamily = params$family)
+ojs_define(virus = params$virus)
+```
+
+{{< include /_js/virus-breadcrumb.qmd >}}
+
+{{< include _EV-A71.qmd >}}
+
+{{< include /_js/_ojs_data.qmd >}}
+{{< include /_js/_ojs_family.qmd >}}
+
diff --git a/enteroviruses/EV-D68.qmd b/enteroviruses/EV-D68.qmd
@@ -0,0 +1,19 @@
+---
+params:
+  family: enteroviruses
+  virus: Enterovirus-D68 (EV-D68)
+---
+
+```{r}
+#| echo: false
+ojs_define(virusFamily = params$family)
+ojs_define(virus = params$virus)
+```
+
+{{< include /_js/virus-breadcrumb.qmd >}}
+
+{{< include _EV-D68.qmd >}}
+
+{{< include /_js/_ojs_data.qmd >}}
+{{< include /_js/_ojs_family.qmd >}}
+
diff --git a/enteroviruses/_EV-A71-relevance-fig.qmd b/enteroviruses/_EV-A71-relevance-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-A71_medical_relevance.jpg)
diff --git a/enteroviruses/_EV-A71-relevance.qmd b/enteroviruses/_EV-A71-relevance.qmd
@@ -0,0 +1,7 @@
+This virus appears to have evolved only recently with the first known strain isolated in 1965. 
+
+It was associated with an outbreak of neurological disease in the United States in 1969. 
+
+It then spread to Europe with outbreaks there in Bulgaria (1975) and Hungary (1978). 
+
+It has since spread to various countries in Asia (China, Japan, Taiwan, Cambodia and Vietnam) where it has been responsible for several very large epidemics.
diff --git a/enteroviruses/_EV-A71-symptoms-fig.qmd b/enteroviruses/_EV-A71-symptoms-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-A71_symptoms.png)
diff --git a/enteroviruses/_EV-A71-symptoms.qmd b/enteroviruses/_EV-A71-symptoms.qmd
diff --git a/enteroviruses/_EV-A71-toolbox.qmd b/enteroviruses/_EV-A71-toolbox.qmd
diff --git a/enteroviruses/_EV-A71-transmission-fig.qmd b/enteroviruses/_EV-A71-transmission-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-A71_transmission.png)
diff --git a/enteroviruses/_EV-A71-transmission.qmd b/enteroviruses/_EV-A71-transmission.qmd
diff --git a/enteroviruses/_EV-A71.qmd b/enteroviruses/_EV-A71.qmd
@@ -0,0 +1,60 @@
+::: {.panel-tabset}
+
+## Symptoms
+
+::: {.virus-figure}
+
+{{< include _EV-A71-symptoms-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-A71-symptoms.qmd >}} 
+
+:::
+
+## Transmission
+
+::: {.virus-figure}
+
+{{< include _EV-A71-transmission-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-A71-transmission.qmd >}} 
+
+:::
+
+## Medical relevance
+
+::: {.virus-figure}
+
+{{< include _EV-A71-relevance-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-A71-relevance.qmd >}} 
+
+:::
+
+## Toolbox
+
+::: {.virus-toolbox}
+
+{{< include _EV-A71-toolbox.qmd >}} 
+
+:::
+
+```{ojs}
+//| output: none
+//| echo: false
+
+renderVirusToolbox("enteroviruses", "EV-A71")
+
+```
+:::
diff --git a/enteroviruses/_EV-D68-relevance-fig.qmd b/enteroviruses/_EV-D68-relevance-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-D68_medical_relevance.jpg){width=50%}
diff --git a/enteroviruses/_EV-D68-relevance.qmd b/enteroviruses/_EV-D68-relevance.qmd
@@ -0,0 +1,8 @@
+First described in 1962 in children hospitalized for pneumonia and bronchiolitis. 
+
+Since its discovery, during the long period of surveillance up to 2005, EV-D68 was reported only as a cause of sporadic outbreaks. 
+
+In August 2014, the United States and Canada experienced the first few cases of what resulted in the largest known EV-D68 outbreak in history. Unexpectedly, this outbreak of severe respiratory infections coincided with an upsurge in acute flaccid paralysis and cranial nerve dysfunction in children, which has caused concerns in the global community. Similar outbreaks were also seen in different European countries and Asian countries like Japan.
+
+Subsequent EV-D68 epidemics were also seen in 2016 and 2018. 
+
diff --git a/enteroviruses/_EV-D68-symptoms-fig.qmd b/enteroviruses/_EV-D68-symptoms-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-D68_symptoms.png)
diff --git a/enteroviruses/_EV-D68-symptoms.qmd b/enteroviruses/_EV-D68-symptoms.qmd
@@ -0,0 +1 @@
+
diff --git a/enteroviruses/_EV-D68-toolbox.qmd b/enteroviruses/_EV-D68-toolbox.qmd
diff --git a/enteroviruses/_EV-D68-transmission-fig.qmd b/enteroviruses/_EV-D68-transmission-fig.qmd
@@ -0,0 +1 @@
+![](img/EV-D68_transmission.png)
diff --git a/enteroviruses/_EV-D68-transmission.qmd b/enteroviruses/_EV-D68-transmission.qmd
diff --git a/enteroviruses/_EV-D68.qmd b/enteroviruses/_EV-D68.qmd
@@ -0,0 +1,60 @@
+::: {.panel-tabset}
+
+## Symptoms
+
+::: {.virus-figure}
+
+{{< include _EV-D68-symptoms-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-D68-symptoms.qmd >}} 
+
+:::
+
+## Transmission
+
+::: {.virus-figure}
+
+{{< include _EV-D68-transmission-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-D68-transmission.qmd >}} 
+
+:::
+
+## Medical relevance
+
+::: {.virus-figure}
+
+{{< include _EV-D68-relevance-fig.qmd >}} 
+
+:::
+
+::: {.virus-text}
+
+{{< include _EV-D68-relevance.qmd >}} 
+
+:::
+
+## Toolbox
+
+::: {.virus-toolbox}
+
+{{< include _EV-D68-toolbox.qmd >}} 
+
+:::
+
+```{ojs}
+//| output: none
+//| echo: false
+
+renderVirusToolbox("enteroviruses", "EV-D68")
+
+```
+:::
diff --git a/enteroviruses/_details.qmd b/enteroviruses/_details.qmd
@@ -0,0 +1,19 @@
+:::: {.panel-tabset #vb-tabset}
+
+## EV-A71
+
+{{< include  _EV-A71.qmd >}}
+
+:::{ style="text-align:center;font-weight:500" }
+[open virus page](/enteroviruses/EV-A71.qmd) / [reload family page](/enteroviruses/)
+:::
+
+## EV-D68
+
+{{< include  _EV-D68.qmd >}}
+
+:::{ style="text-align:center;font-weight:500" }
+[open virus page](/enteroviruses/EV-D68.qmd) / [reload family page](/enteroviruses/)
+:::
+
+::::
diff --git a/enteroviruses/family.xlsx b/enteroviruses/family.xlsx
diff --git a/enteroviruses/img/EV-A71_medical_relevance.jpg b/enteroviruses/img/EV-A71_medical_relevance.jpg
diff --git a/enteroviruses/img/EV-A71_symptoms.png b/enteroviruses/img/EV-A71_symptoms.png
diff --git a/enteroviruses/img/EV-A71_transmission.png b/enteroviruses/img/EV-A71_transmission.png
diff --git a/enteroviruses/img/EV-D68_medical_relevance.jpg b/enteroviruses/img/EV-D68_medical_relevance.jpg
diff --git a/enteroviruses/img/EV-D68_symptoms.png b/enteroviruses/img/EV-D68_symptoms.png
diff --git a/enteroviruses/img/EV-D68_transmission.png b/enteroviruses/img/EV-D68_transmission.png
diff --git a/enteroviruses/index.qmd b/enteroviruses/index.qmd
@@ -0,0 +1,29 @@
+---
+format:
+  html:
+    page-layout: full
+    anchor-sections: true
+    section-divs: true
+    title-block-banner: false
+    title-block-style: plain
+    include-before-body:
+      text: <link rel=stylesheet href='https://unpkg.com/phylotree@1.1.0/dist/phylotree.css'/>
+params:
+  family: enteroviruses
+---
+
+```{r}
+#| echo: false
+ojs_define(virusFamily = params$family)
+```
+
+{{< include /_js/_ojs_data.qmd >}}
+{{< include /_js/_ojs_family.qmd >}}
+
+{{< include /_js/family-breadcrumb.qmd >}}
+
+{{< include /_js/family.qmd >}}
+
+&nbsp;
+
+{{< include _details.qmd >}}
diff --git a/enteroviruses/tree.newick b/enteroviruses/tree.newick
@@ -0,0 +1 @@
+((X02316:0.3252945029543982,GU219984:0.3445215742905273):0.0748826534338975,HRV:0.3347914067628908,((MZ171094:0.1656715162986374,((POL2LAN:0.12555882719160888,V01149:0.12282472919519088):0.004134255140666732,POL3L37:0.12456481459418028):0.04394048404142631):0.11158585149567968,(AY426531:0.32167849764464007,(((MF662690:0.13973831148986954,CAU05876:0.13459539879407595):0.02762466379235956,(AY421764:0.10413457376821139,AY421767:0.10898019034488632):0.05211088544526837):0.17672535662002303,(AF162711:0.14972458691036628,((OQ842446:0.11315331703428427,MN749143:0.12284423324794175):0.0307983483874279,((X80059:0.13135287255662464,X84981:0.12982253882304728):0.021904413924784538,(AY302558:0.1295458988413709,AY302539:0.14024755888376073):0.005691395657548726):0.005711205862142632):0.0020246125047686525):0.11806418394046059):0.028362832606513788):0.015797588352494785):0.12603378673526933);
diff --git a/index.qmd b/index.qmd
@@ -138,4 +138,19 @@ Bunyaviruses
 :::
 :::
 
+::: {.card .g-col-12 .g-col-sm-6 .g-col-md-4}
+::: {.card-img-top}
+[![](/img/virus.jpg)](enteroviruses/index.qmd)
+
+:::
+::: {.card-body}
+::: {.card-title }
+### Enteroviruses
+:::
+::: {.card-text}
+Enteroviruses
+:::
+:::
+:::
+
 :::
diff --git a/src/families.yaml b/src/families.yaml
@@ -6,3 +6,4 @@
 - orthomyxoviruses
 - bunyaviruses
 - filoviruses
+- enteroviruses