VirusBank

html`
  <h3>${virus}</h3>
  <p>&nbsp;</p>
`

Most of the cases are asymptomatic or with mild symptoms (Headache, fever, and myalgia).

Newborns and children up to the age of 15 years are more vulnerable to JE with the increased threat of neurological complications over adult.

High mortality rate, who survives, 20-30% suffer permanent neurologic sequels.

JEV distribution on Asia. Data reported from 2023 at Centers for disease control and prevention. CDC, cdc.gov/japaneseencephalitis/maps/index.html

According with WHO, in 2019 were reporter almost 68,000 cases of JE with 20-30 % mortality rate.

2 millions people living in endemic countries with JEV, Sporadic outbreaks in the Western Pacific and northern Australia are also observed. Recently outbreak was observed in southern Australia 2022.

The major causes of viral encephalitis in Asia.

There are approved vaccine use as pre-travel precaution in endemic countries, where multiple doses of vaccine are recommended. Although large-scale vaccination of susceptible population must be implemented.

There is any antivirals available at the moment for the prevention or treatment of JE infection.

renderVirusToolbox("flaviviruses", "JEV")

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>&nbsp;</p>
    `
   }
}