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globalbioticinteractions / virus-host-db

Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016).
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suspicious interactions - Virus Host DB records claims that a fish genus (Cynodon) hosts a plant virus (Plant associated genomovirus 3) #7

Open jhpoelen opened 3 weeks ago

jhpoelen commented 3 weeks ago 
          @jhpoelen Certainly!

The claims that are suspicious are as follows: Plant associated genomovirus 3 is a plant virus, with two records in Genbank (nt): NC_076284.1 (identical to MH939438) and MH939439. Based on ICTV taxonomy browser, it was first described in a 2020 submission, with the reference genome being MH939438 (see below screenshot).

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Based on the GenBank record, the virus was isolated from a leaf in a species found in South Africa within the Cynodon genus, which is a grass. Unfortunately, Cynodon shares the same genus name as a dogtooth characin from South America, likely leading to the assumption that the virus is also found in the vertebrate Cynodon too.

Indeed, the Virus-Host DB lists both Cynodon as hosts, one being the grass species, and the other being the fish (see below). Both lists RefSeq as their source. (https://www.genome.jp/virushostdb/2584397)

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I found out about this suspicious interaction as I downloaded the list of viruses with host information from Virus-Host DB (https://www.genome.jp/virushostdb/) and was filtered for only "Vertebrata" under hosts to look at vertebrate hosts with viruses. Chancing upon this record, with a plant-associated virus, I then went to check GloBI, and found that the fish Cynodon was listed as a host for this pathogen. However, it is a suspicious interaction for the fish being a host for plant associated genomovirus 3 as: (1) the virus was recently described from a plant in Africa, (2) the virus was isolated from a plant with the same genus name as the fish, and (3) the fish is found in South America. There is also no evidence to suggest that the fish was found with the virus isolated from it to date.

Hope this helps!

Originally posted by @RandolphQuek in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1007#issuecomment-2297893123

jhpoelen commented 3 weeks ago

@RandolphQuek thanks again for reporting this suspicious record.

Please note that you can click on "discuss" in the GloBI search results to automatically open a new issue that includes a link to the search context

https://www.globalbioticinteractions.org/?interactionType=ecologicallyRelatedTo&sourceTaxon=Cynodon&targetTaxon=Plant%20associated%20genomovirus%203

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jhpoelen commented 3 weeks ago

@RandolphQuek do you mind contacting the curators of the Virus Host DB and let them know about your findings?

RandolphQuek commented 3 weeks ago

Noted, will drop them an email regarding Cynodon and Morus.

Thanks!