80% of infected people are no reported and asymptomatic.
20% of syntomic people showed mild symptoms, referee as West Nile fever (WNF).
1 in 150 people developed the encephalitis or meningitis.
.jpg)
.jpg)
Causes the fatal neurological disease in humans.
Leading of cause of mosquito-borne disease in USA.
In 2018-2020 has cause massive outbreaks in Europe.
In US, in 2021 was reported 2,445 cases of WNV humans, and there were 165 (6.8%) confirmed deaths.
There are no approved vaccines in humans, only in horses. There is no antivirals available at the moment for the prevention or treatment of West Nile infection.
import { encodeTool } from '/_js/functions.js'
FA = FileAttachment
// Load the toolbox
families = await FA("/families.json").json()
_toolbox = await FileAttachment("/toolbox/toolbox.json").json()
toolbox = _toolbox.map( tool => encodeTool(tool) )
// console.log(toolbox)
addEncodedTools = (virus) => {
return ({ ... virus, tools: toolbox.flatMap( tool => virus[tool.encoded] ? tool.id : []) })
}
// Load all Newick tree file and create a dictionary `family -> tree`
nwks = await Promise.all(
families.map(async (family) => {
let tree = await FA("/"+ family + "/tree.newick").text()
return ({ family: family, nwk: tree })
}))
nwksAsMap = Object.fromEntries(nwks.map( el => [el.family, el.nwk] ))
// console.log(nwks)
// Load annotations for viruses for each family
_annotations = await Promise.all(
families.map( async (family) => {
let xls = await FA("/"+ family + "/family.xlsx").xlsx()
let _annotations = xls.sheet(0, { headers: true, range: ":L" })
let _trimmed = _annotations.map( virus => {
let trimmed = {}
Object.keys(virus).forEach( key => {
trimmed[key] = virus[key].trim()
})
return trimmed
})
return _trimmed.map( virus => ({... virus, family: family }) )
}))
// console.log(_annotations)
// Add tools information, just the list of tools ids
annotations = _annotations
.flat()
.map( virus => addEncodedTools(virus) )familyAnnotations = annotations
.filter(virus => virus.family == virusFamily)
function virusInfo(_family, _virus) {
const info =
familyAnnotations.filter(row => row.abbreviation == _virus && row.family == _family)
return info[0]
}
// Handle grouped viruses by extending the model with isGroup: false/true
addGrouped = (virus) => {
const isGroup = (typeof virus.group_abbreviation !== "undefined") && (virus.group_abbreviation !== "")
const virus_pointer = (isGroup) ? virus.group_abbreviation : virus.abbreviation
return (
{ ... virus,
isGroup: isGroup,
virusPointer: virus_pointer,
resVirusId: (isGroup) ? virus.group_abbreviation : virus.abbreviation,
resAbbreviation: (isGroup) ? virus.group_abbreviation : virus.abbreviation,
resVirusName: (isGroup) ? virus.group_virus_name : virus.virus_name
}
)
}
// Create a list of all viruses of interest in the Excel file
// Add group information early on
annotatedViruses =
familyAnnotations
.filter(virus => virus.virus_of_interest == "Yes")
.map(virus => addGrouped(virus))
// Create a sublist of viruses with toolbox
// Take into account groups by selecting unique entries
toolboxAnnotatedViruses =
annotatedViruses
.filter(virus => virus.availability_in_toolbox == "Yes")
.filter((value, index, self) => {
return self.findIndex(v => v.resAbbreviation === value.resAbbreviation) === index;
})
// 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
.filter(v => v.virus_id.replace(/^'+|'+$/g, '') == virus_id || v.abbreviation == virus_id)
//.filter(v => v.virus_id == virus_id || v.abbreviation == virus_id)
// lookup the abbreviation for the group
const groupList =
toolboxAnnotatedViruses
.filter(v => v.group_abbreviation == virus_id)
if (fullList.length > 0) {
return fullList[0]
}
if (groupList.length > 0) {
return groupList[0]
}
}
// Return all matches for a virus ID
virusIdToViruses = (virus_id) => {
// lookup the virus_id in the full list of viruses
const single_virus =
annotatedViruses
.filter(v => v.virus_id.replace(/^'+|'+$/g, '') == virus_id || v.abbreviation == virus_id)
[0]
if (single_virus.isGroup) {
return annotatedViruses
.filter(v => v.group_abbreviation == single_virus.group_abbreviation)
} else {
return [ single_virus ]
}
}
function renderVirusToolbox(family, virus_id) {
// First extract the virus object from the ID or abbreviation
// This takes into account the groups
const virus = virusIdToVirus(virus_id)
if (typeof virus.tools !== "undefined" && virus.tools.length > 0) {
return html`
${toolbox.filter(tool => virus.tools.includes(tool.id) ).map(tool =>
html`
<h2 id="${tool.id}-section">${tool.name}</h2>
<div class="container grid">
<div class="g-col-12 g-col-md-3 toolbox one-tool" style="text-align:center;">
<div id="toolbox-contents" class="tool-container">
<a href="/toolbox/index.html#${tool.id}-section">
<div class="tool-wrapper">
<div id="${tool.id}" class="tool">
<div class="tool-tooltip-text">${tool.name}</div>
${tool.icon.map( i =>
html`<img class="tool-icon" height="${(tool.icon.length > 1) ? 150/tool.icon.length : 100}%" src="${i}"/>`
)}
</div>
</div>
</a>
</div>
</div>
<div class="g-col-12 g-col-md-9">
<p>${tool.description}</p>
</div>
<div class="g-col-1" style="text-align:center;">
</div>
</div>
<div class="col-xs-12" style="height:20px;"></div>
`
)}
`
}
else {
return html`
<p> </p>
`
}
}