SEA-PHAGES | Classificiation with ICTV guidelines

Link to this post \| posted 30 May, 2024 14:03
bgibb	Hi Everyone, One of my MRAs describing phages Argan and Uzumaki just came back from review. One of the reviewers wants us to use ICTV guidelines to classify our phages. The International Committee on Taxonomy of Viruses (ICTV) revamped the process of viral classification, stripping away the use of phage morphology. As far as I can tell, the ICTV website does not provide a useful tool to help classify viruses. The Genbank entries for both phages offer some classification information. In this case, both of these phages have the following full lineage (Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; unclassified Caudoviricetes). This only takes me up through the Class level, and I feel stuck. Has anyone else had to do this? If so, do you have any tips for how I go further, or failing that, how I should respond to the reviewer's request? I have a feeling that this will become more common. Thanks, Bryan

Link to this post | posted 30 May, 2024 14:03

Hi Everyone,

One of my MRAs describing phages Argan and Uzumaki just came back from review. One of the reviewers wants us to use ICTV guidelines to classify our phages.

The International Committee on Taxonomy of Viruses (ICTV) revamped the process of viral classification, stripping away the use of phage morphology.

As far as I can tell, the ICTV website does not provide a useful tool to help classify viruses. The Genbank entries for both phages offer some classification information. In this case, both of these phages have the following full lineage (Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; unclassified Caudoviricetes). This only takes me up through the Class level, and I feel stuck. Has anyone else had to do this? If so, do you have any tips for how I go further, or failing that, how I should respond to the reviewer's request? I have a feeling that this will become more common.

Thanks,

Bryan

Link to this post \| posted 02 Jun, 2024 13:21
delesall	To the best of my understanding, the classification that Genbank uses to replace what we submit is the ICTV classification - so that should satisfy your reviewer (even if it's not meaningful taxonomy in my opinion). Edited 04 Jun, 2024 00:25

Link to this post \| posted 04 Jun, 2024 01:12
viknesh	This is the first time I'm seeing this request. I would leave it at the Class level, and include the morphology.

Link to this post \| posted 04 Jun, 2024 01:51
debbie	Hi all, GenBank has been re-writing the lineage submission lines for quite a while now. There are 2 issues with what they are doing. First, their records are incomplete. The number of phages that we keep entering is difficult to keep up with, so sometimes they don't offer much. Secondly, we don't really ascribe to this lineage and have found that offering a classification of siphovirus, myovirus, or podovirus may be more helpful. Regardless of what write, they overwrite it. Step carefully as you wade into this to get your MRA published. best, debbie

Link to this post | posted 04 Jun, 2024 01:51

debbie

Hi all,
GenBank has been re-writing the lineage submission lines for quite a while now.
There are 2 issues with what they are doing. First, their records are incomplete. The number of phages that we keep entering is difficult to keep up with, so sometimes they don't offer much. Secondly, we don't really ascribe to this lineage and have found that offering a classification of siphovirus, myovirus, or podovirus may be more helpful. Regardless of what write, they overwrite it. Step carefully as you wade into this to get your MRA published.
best,
debbie

Link to this post \| posted 04 Jun, 2024 14:32
bgibb	Thanks for the replies here. Since my initial post, I emailed the editor handling my MRA to ask about this. Apparently, reviewers for MRA are given a template that includes a question about taxonomy and classification, which is why its coming up in the reviews. I submitted two MRAs this Spring, the first also had reviewer comments asking for classification, but the editor in that case left a note to ignore it. The editor of the second MRA did not leave such a note. However, in the email correspondence, he clarified why it was there and offered similar suggestions that Vic and Debbie made in the posts above for responding to the review request for phage classification info. A few years ago I attended a talk by one of the people on ICTV explaining the updated classification system for viruses (and phage). She showed a phylogenetic tree of phage that also included morphology. The two did not align and made a strong case for moving away from using morphology for classification purposes. I don't know enough about the specifics of ICTV classification system to say if its good or not, but its definitely not easy for us to use.

Link to this post | posted 04 Jun, 2024 14:32

bgibb

Thanks for the replies here. Since my initial post, I emailed the editor handling my MRA to ask about this. Apparently, reviewers for MRA are given a template that includes a question about taxonomy and classification, which is why its coming up in the reviews.

I submitted two MRAs this Spring, the first also had reviewer comments asking for classification, but the editor in that case left a note to ignore it. The editor of the second MRA did not leave such a note. However, in the email correspondence, he clarified why it was there and offered similar suggestions that Vic and Debbie made in the posts above for responding to the review request for phage classification info.

A few years ago I attended a talk by one of the people on ICTV explaining the updated classification system for viruses (and phage). She showed a phylogenetic tree of phage that also included morphology. The two did not align and made a strong case for moving away from using morphology for classification purposes. I don't know enough about the specifics of ICTV classification system to say if its good or not, but its definitely not easy for us to use.

Link to this post \| posted 04 Jun, 2024 17:02
DanRussell	I think Graham would probably point out that phages don't really have "lineages" in the traditional sense, which is one of the reasons we don't systematically name them——or use ICTV classifications. Phage genetic material isn't only shared vertically (between different generations), but horizontally as well. Thus, trying to shoehorn phages into classification systems designed for other types of organisms doesn't work well. From a review article Graham wrote in 2008 (this paper): "One of the most striking features of bacteriophage genomes is their apparent mosaic structure; in essence, each genome can be considered as a unique combination of modules that are exchangeable among the population. The size of the modules, their rates of exchange, and the phage genomes carrying them all vary greatly, with phages of different virion morphology, size, and host-range all participants in an orgy of recombination [36]." Hence the advice above. Just explain some version of the above to the reviewer, and let GenBank/ICTV apply whatever designations they see fit!

Link to this post | posted 04 Jun, 2024 17:02

DanRussell

I think Graham would probably point out that phages don't really have "lineages" in the traditional sense, which is one of the reasons we don't systematically name them——or use ICTV classifications. Phage genetic material isn't only shared vertically (between different generations), but horizontally as well. Thus, trying to shoehorn phages into classification systems designed for other types of organisms doesn't work well.

From a review article Graham wrote in 2008 (this paper):

"One of the most striking features of bacteriophage genomes is their apparent mosaic structure; in essence, each genome can be considered as a unique combination of modules that are exchangeable among the population. The size of the modules, their rates of exchange, and the phage genomes carrying them all vary greatly, with phages of different virion morphology, size, and host-range all participants in an orgy of recombination [36]."

Hence the advice above. Just explain some version of the above to the reviewer, and let GenBank/ICTV apply whatever designations they see fit!

Link to this post \| posted 04 Jun, 2024 17:04
DanRussell	And another one from Roger Hendrix, from this paper: Comparative examination of [phage] genomes indicates that the hallmark of phage evolution is horizontal exchange of sequences. This is accomplished, first, by rampant non-homologous recombination between different genomes and, second, by reassortment of the variant sequences so created through homologous recombination.

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Classificiation with ICTV guidelines