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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

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.

 

Wed, 07/06/2022 - 12:45
igor_t_ru

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

Wed, 07/06/2022 - 15:52
Elliot Lefkowitz

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

Wed, 07/06/2022 - 18:03
BrianFoley

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

Thu, 07/07/2022 - 13:29
Elliot Lefkowitz