Skip to main content

User account menu

  • Log in
ICTV
  • Home
  • About
    • About the ICTV
      • About Virus Taxonomic Classification
      • Charge to the ICTV
      • Statutes
      • Code
      • Organization
      • ICTV History
    • Membership
      • Membership
      • Executive Committee
      • Exec Comm History
      • Life Members
      • National Members
      • Support Personnel
    • Study Groups
    • Recent Updates
  • Taxonomy
    • Taxonomy browser
    • Visual Taxonomy Browser
    • Find the Species
    • Release History
    • Master Species Lists
    • Virus Metadata Resource
    • Taxon Name Etymology
    • Proposals
      • Approved Proposals
      • Pending Proposals
    • Proposal Template Files
  • Report
    • Current Report Chapters
      • Chapter List: Image
      • Chapter List: Text
    • About the ICTV Report
    • Virion Diagrams
    • Virus Properties
    • Help and Information
    • Report Templates
    • Past (9th) Report Chapters
  • Information
    • General Information
    • Information Reports
      • Binomial Nomenclature
      • EC Meeting Reports
      • Plenary Session Reports
    • Meeting Reports
    • News
    • Newsletters
    • Study Group Info
      • Study Group Info
      • Flaviviridae: HCV
      • Hepeviridae Study Group
      • Picornaviridae Study Group
    • Virology Division News
    • History of Virology
  • Forums
    • All Forums
    • General Discussions
    • Taxonomic Discussions
    • Forum Archive
  • Help
    • Email ICTV Help
    • FAQs
    • How-To videos
      • Using the Taxonomy Browser
      • What is the ICTV Master Species List?
      • Using the Master Species List
      • Using the Virus Metadata Resource
      • Using the Find the Species tool
      • Using the ICTV Report
    • Webinar
      • Webinar on Virus Taxonomy
      • Webinar on Finding Information
  • ‏‏‎ ‎

Breadcrumb

  1. Home
  2. A Place for discussions on virus classification and taxonomy

A Place for discussions on virus classification and taxonomy

Primary tabs

  • View
  • Revisions

This forum is a place to discuss topics related to virus classification and taxonomy. To post, you must first be registered as a member of the ICTV web site and be logged into your account.

To help distinguish between different forum threads, please create a separate topic for each unique thread. This can be done by clicking on the 'Add new Forum topic' link on the homepage of each main discussion forum (General and Taxonomic Discussions).

Thank-you

Elliot

_______________________________________________________________________

Elliot J. Lefkowitz, Ph.D. | Professor
Department of Microbiology | https://scholars.uab.edu/display/elliotl
Data Secretary | International Committee on Taxonomy of Viruses | https://ictv.global/
UAB | The University of Alabama at Birmingham
Birmingham, AL
elliotl@uab.edu

tiny fragments of genomes as ICTV species representatives (VMR)

As I understand, ICTV species exemplars can be  used as references for new genomes classification.

Could you , please, explain  how exactly such fragments can be used?

I understand when the genome is partial and contains 70-90% ,but when it is just a tiny fragment?

I would say, it is global problem:-
I think,  ICTV should provide not just  species exemplars, but publish official classification protocols which allow

external users run them on daily basis (If you check globally all existing taxoprops, you will easily find many different
approaches which are not always consistent wtih each other)

for example :VIRIDIC,a very good tool for local analysis,  but it doesn't work on a global scale.
+
very short genome fragments are always  outliers.

 

Profile picture for user igor_t_ru
Wed, 07/06/2022 - 12:45
igor_t_ru

Re: tiny fragments of genomes as ICTV species representatives (V

Hi,

For a new virus species to be created, the ICTV requires that the virus isolate that represents the species (and usually serves as the exemplar virus in the Virus Metadata Resource - VMR) be essentially completely sequenced or at a minimum, be coding complete. Therefore, viruses represented by only genomic fragments are not used as exemplar viruses for species.

Accessing the classification protocols used by each ICTV Study Group (SG) is indeed a problem. Protocols are generally available from taxonomy proposals and also may be available in the family-based ICTV Report chapters. But this is not consistently done, and since the protocols used are SG (family) specific, it takes a good bit of work to reconstruct the methods used by individual SGs. One of the aims of the NIH grant we have that funded this web site, is to provide a single source for accessing all classification protocols. This is on our to-do list for the next year.

Elliot

Profile picture for user Elliot Lefkowitz
Wed, 07/06/2022 - 15:52
Elliot Lefkowitz

New here. Interested in Lentiviruses and all virus taxonomy.

Hi, 

I am fairly familiar with virus taxonomy, but do not know how/where to make proposals for changes.  Nor how to work with GenBank/NCBI to help update/repair their taxonomy tables.  For a couple of examples, I am very familiar with the Lentiviruses and other retroviruses.  Under "Lentivirus" there is one species listed: "Puma Lentivirus", but all the feline lentiviruses should probably be under "Feline Immunodeficiency Virus".  The GenBank/NCBI taxonomy under Lentivirus is quite a mess, as are most other viruses at lower levels of taxonomy. 

In the mid-2000s I worked with Claude Fauquet a bit on the Pairwise Sequence Comparison tool (PASC) tool at NCBI ( https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi?textpage=overview ):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173583/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221606/

https://pubmed.ncbi.nlm.nih.gov/25259891/

I think such a tool and approach is useful, but other considerations, such as host range of the virus, and sampling bias for sequencing, need to be considered along with the pairwise distance plots.  The distances between RNA virus species are quite different than those for DNA viruses.

sincerely,

Brian Foley, PhD

HIV Databases at LANL (https://hiv.lanl.gov )

btf@lanl.gov

Profile picture for user BrianFoley
Wed, 07/06/2022 - 18:03
BrianFoley

Re: New here. Interested in Lentiviruses and all virus taxonomy.

Hi Brian,

New proposals to the ICTV either to propose new taxa or to update existing taxa can be submitted at any time during the year. Generally, the deadline for consideration at the next Executive Committee (EC) is May or June prior to the meeting (usually held in July). Therefore, proposal review for this year is now closed, and the deadline for consideration at the 2023 EC meeting will be May-June, 2023. You may also want to confer with the Chair of the relevant ICTV Study Group (SG). For retroviruses, the list of SG members can be found at https://ictv.global/sc/dna/sg_retroviridae. Instructions and templates for proposal submission can be found at https://ictv.global/taxonomy/templates. 

As for the tools and criteria used to distinguish between taxa that help define and implement the demarcation criteria used to classify a virus into an existing taxon or suggest creation of a new taxon, these tend to be family (SG) specific. PASC is still used by a number of SGs, and other tools are also in use. See my comment above related to accessing classification protocols for a bit more information.

Best,

Elliot

Profile picture for user Elliot Lefkowitz
Thu, 07/07/2022 - 13:29
Elliot Lefkowitz

Please create new forum topics for unique discussion threads

To help distinguish between different forum threads, please think about creating a separate topic for each unique thread. This can be done by clicking on the 'Add new Forum topic' link on the homepage of each main discussion forum (General and Taxonomic Discussions).

Profile picture for user Elliot Lefkowitz
Thu, 07/07/2022 - 13:33
Elliot Lefkowitz
  • 90 views

International Committee on Taxonomy of Viruses

 

Unless otherwise noted, this work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License

Support is provided by the National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, Award U24AI162625

 

Copyright © 2025 (ICTV)  |  Privacy  |  Disclaimer  |