Talk:Marseilleviridae

wikitables

@Bervin61: I'm a newbie, but I think I have figured out that you added the wikitables to this article. I think that they disrupt the text greatly (I intend to expand on it) and are not up to date. Do you object to moving them down to a position just before references? Thanks, Viroguy (talk) 23:29, 4 July 2017 (UTC)

@Viroguy: Please update them if they are out of date! All viral families and genera have similar tables, so for the sake of consistency, please leave them (move them if it makes the article better, but the intent was to provide a quick reference). A few years ago I wrote a script to scrape from a few different sources and compose wiki articles automatically. That effort added hundreds of previously missing articles, and expanded hundreds more. I am far from an expert and do not intend to maintain these pages regularly, so will take no offense to someone actually taking an interest in a page and heavily editing my content. Bervin61 (talk) 03:00, 5 July 2017 (UTC)

taxonomy

@Rich Farmbrough, Virion123, Magioladitis, Ruslik0, and Bervin61: Hello folks. My expertise is not with giant viruses, so I've had a fresh look at some aspects of this article. I don't agree with the ICTV taxonomy. The ICTV recognizes 2 genera, one unassigned. As near as I can determine, that was based on an analysis of ONE gene (an RNA polymerase) as shown at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801854/figure/F4/ (which is a figure that is difficult for me to understand in detail, sigh.) The ICTV places Lausannevirus and Tunisvirus in the unassigned genus, just as the figure shows, and I haven't found any other indication of why Lausannevirus and Tunisvirus are lumped together. However, there are 2 publications that show three "lineages", with Lausannevirus and Tunisvirus in separate lineages, and one (albeit with overlapping authors) that shows 4 lineages (groups A, B, C and D), as in this figure https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810266/figure/viruses-08-00076-f001/ That figure (which is visually excellent, IMHO) is based on the total genomes. So, do any of you object to rejecting the ICTV taxonomy and replacing it with the 4 lineages? Thanks, Viroguy (talk) 01:31, 10 July 2017 (UTC)

I would suggest that we present the alternatives. The ICTV are not afraid to radically restructure virus taxonomy, and do so quite often. Nonetheless we should present their current view, and ideally we should show how ideas about taxonomies have changed over time. All the best: Rich Farmbrough, 18:15, 10 July 2017 (UTC).

Yes, I agree. I didn't make it clear above, (sigh) but I was intending to present the whole genome "groups" and note on it the ICTV classifications of the 4 viruses they list. I'm not going to make the image right away to let others voice their opinions. Thanks, Viroguy (talk) 18:45, 10 July 2017 (UTC)

Classifying viruses based on polymerizes is quite common as these proteins are subject to less change than, for instance, surface proteins. So, I do not see a problem here. Ruslik_Zero 19:45, 10 July 2017 (UTC)

I for one do not have a problem with alternative classifications in this taxon. The RNA polymerase is commonly used as a taxonomic marker but this is mostly in the RNA viruses where it seems to be *relatively* conserved. The DNA viruses and this group in particular are so much bigger (orders of magnitude) that basing a classification on a single gene seems a bit daft. These viruses seem to have accumulated bits of DNA from their hosts over time which will complicate any taxonomic system. My own feeling is that the taxonomy here is likely to undergo radical change in the not too distant future as more of these viruses are found.

This group of viruses are not the only group with problems. The fairly well known herpesviruses are in serious need of an overhaul as well. Thy are not alone.

Remember that the ICTV (FYI I'm not a member) are just a bunch of guys (and girls) working on these viruses. They may have more information about them than we do but not much. They have the same tools that we do. This is a messy messy area and not easy for anyone. I myself try to keep up to date with the latest revisions but I will admit that I find this difficult. I am sure I am not alone.

My own feeling is that as far as possible we should stick to the official line from the ICTV - but bear in mind that this will require updates on a regular basis - but if there are reasonable alternative schemes I for one have no objection to these being included. I would be interested to hear what others have to say on this topic. Virion123 (talk) 13:07, 11 July 2017 (UTC)

BTW thank you Viroguy for asking for my opinion on this interesting but messy subject.

Having read the paper linked to above I am even more inclined to agree with Viroguy. Mauve is a very useful programme for this sort of comparison. The basic issue here is what is and is not a viral species? What criteria can be used to classify them. This like Easter is a moveable feast. Back in the day - Linnaeus's day to be more exact - classification was based on different criteria than are used today. RNA dependent RNA polymerase is a good marker for RNA viruses along with morphology and genome organisation. These viruses have relatively few genes and many are surface exposed and subject to immune selection which makes them prone to rapid turnover. Think influenza if you need an example. DNA dependent DNA polyermase (the equivalent of RNA dependent RNA polymerase) and DNA dependent RNA polymerase are much more complex sets of proteins than the RNA dependent RNA polymerase. This combined with the complexity of these genomes makes me think that basing a classification on a single gene is likely to prove problematic. Again for this reason I agree with Viroguy that listing alternative taxonomies seems very reasonable. Virion123 (talk) 13:21, 11 July 2017 (UTC)

BTW thank you Viroguy for listing at least some of the editors with an interest in this area. Hopefully a few more might identify themselves in the near future. I am not sure how many editors are still interested in contributing to this area. With regular updates from the ICTV expected the more hands the better (within reason) Virion123 (talk) 13:33, 11 July 2017 (UTC)

Not that my experience is to be taken as any kind of standard, but as I was adding/editing hundreds of virus articles, I did come across some disputed taxonomies (disputed meaning not currently accepted by the ICTV). I always tried to preserve all information, which meant adding the ICTV taxonomy and including a sub-section with the other thoughts. It looks like that's what Viroguy has done at this point. While everyone is here, I do still have the scripts I used to generate the virus species, genus, and family lists. Are those in need of an update? Bervin61 (talk) 14:20, 12 July 2017 (UTC)

Thanks Bervin61, but scripts are waaaaayyyyy beyond my editing ability at this time. Viroguy (talk) 22:16, 12 July 2017 (UTC)

Dear editor Bervin61. Your scripts are MUCH appreciated. Trying to keep the taxonomy of this area is a major headache and any assistance is appreciated. The downside of scripts is they tend to break things that might be better left alone. If you have not run these scripts since the last revision of the taxonomy - bearing in mind that additional changes have been made since the last release - then it might be worth doing. But be prepared for a lot of rollback. You seem like a sensible sort of chap(ess) so I dont think running these scripts will cause too much lasting damage. Virion123 (talk) 08:18, 13 July 2017 (UTC)

Wow, I'm even happier that I didn't try to use a script! BTW, Aussies would say "mate" as a gender neutral version of chap(ess)! 8-) Viroguy (talk) 20:21, 14 July 2017 (UTC)

order megavirales

Hello again. @Prahlad balaji: added order megavirales to the taxobox. I have resisted doing that myself because as of 2016 the ICTV has not recognized that order. Does anybody else object to that addition? Viroguy (talk) 03:09, 25 July 2017 (UTC)

I would agree with Viroguy. Orders are rarely created by the ICTV. Creation of an order usually require a lot of debate before an order is created.The idea behind this 'order' is that all very large viruses must have a common origin. There is evidence in the literature that this is unlikely to be the case and that this group are the result of convergent evolution. That having been said there are lots of genes etc that have not been analysed properly yet so the jury is definitely out on that point.

It is agreed that morphology is probably a better guide to viral taxonomy than protein or nucleotide identity. However enveloped viruses are common and many share little similarity other than an envelope. Given that the only common characteristic of these viruses is presence of an envelope and large genome size I for one would be very cautious suggesting that these viruses should be considered as a order.

Finally there is some evidence based on a limited number of genes that these viruses actually have different origins.

For these reasons I would support Viroguy's suggestion to remove the proposed taxonomic designation of order for the viruses - at least until the situation is a lot clearer. Virion123 (talk) 11:04, 25 July 2017 (UTC)