How to find the name of a virus species

Have you ever wanted to find the official ICTV species name for a virus when all you have is a disease name, common name, or isolate id? This "Find the Species" tool will provide the current taxon name (species or higher taxonomic rank) for a virus when you enter a full or partial name into the search box below. It uses current and past databases from the ICTV (MSL and VMR lists) and NCBI to make the connection with a taxon name. Results are dependent on identifying a match in one of these databases and determining the most recent ICTV virus taxon based on that match. Carefully review your results as they may miss the correct species or may provide an incorrect answer.

Search Process

  1. Search selector: Choose a search strategy from the dropdown selection list:
    1. Exact match: The words of your query in the order entered must match exactly to a word or phrase in our virus database.
    2. All words: Every word in your query (in any order) must be present in a database record to obtain a match.
    3. Any words: Any one of the words in your query (in any order) must be present in a database record to obtain a match.
    4. Contains: Words or parts of words are acceptable in your query text. The search will add a wild card character to both ends of your text to look for partial matches.
  2. Search query: Enter a search query into the search box (replacing the "Enter one or more required words"). Except for the 'Contains' search option below, a search will look for matches between individual words in your query and words in our virus name database. Your query can consist of one or more words separated by blank space (spaces or tabs). A "word" can consist of any combination of letters or numbers.
  3. Results
    1. Hit counts (First line of results.)
      1. Number of hits to ICTV taxa: The number provided represents the number of links that the search was able to identify between your search query and a current ICTV taxon (usually species). Occasionally, a link to a past (no longer used) taxon name will be provided when that taxon has been abolished from the taxonomy and no current taxonomy exists that replaced the abolished taxonomy. The number of hits represents the number of distinct taxa that were identified. Each ICTV taxon hit is displayed in the first column of results, "Current ICTV Taxonomy".
      2. Number of matching names: This represents the number of unique database hits to your query that match an ICTV taxon. There may be multiple hits to database records that link to a single ICTV taxon. Each match is displayed in the second column, "Matching Name".
      3.  Names without a valid taxon match: This is the number of hits to database records that could not be reliably linked to a current (or abolished) ICTV taxon name. This is usually the case for hits to records in the NCBI database that do not have a clear path in their taxonomic lineage to an identifiable ICTV taxon (past or present). These results are displayed in a second table at the bottom of the page. Clicking on the linked number will take you to the table.
    2. Table columns
      1. Current ICTV Taxonomy: The name of the official ICTV taxon into which the virus represented in your search results is most likely classified. Names are linked to an informational page on the taxon including the complete history of the taxon (naming and higher rank classification).
      2. Matching Name: The virus or taxon or other name identified by a match to your query that is present in one of the search database records (see "Search Databases" below"). Names are linked to the database record containing the match.
      3. Name type: The type of database record identified by the match of your query to a name. These are database specific (see below).
      4. Source: The database containing the record that matched your query.
      5. Intermediate name: The taxonomic identification provided by the source database for the name matched by your query. This may be different from the current ICTV taxon since it may refer to an old, deprecated taxon name. The application will use this associated name to lookup the corresponding current taxon name. Links are to the database record that provided the name.

Search Databases

  1. ICTV MSL: The Master Species List. The MSL provides the official current (or past) ICTV virus taxonomy.
    1. Name types: taxon name
  2. ICTV VMR: The Virus Metadata Resource. The VMR provides a list of exemplar viruses (virus isolates) for each virus species. Sequence accession numbers, genome information, and host source are also provided for each exemplar isolate.
    1. Name types: isolate name, isolate abbreviation
  3. NCBI: The NCBI database of virus sequences containing virus isolate names, associated name synonyms, and taxonomic links.
    1. Name types: acronym, authority, common name, equivalent name, GenBank acronym, GenBank common name, includes, in part, scientific name, synonym.

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