Alternative title I thought of after I wrote this: Naming viruses is fractalism
How are new viruses discovered? It used to be an extremely laborious process that generally involved taking the cells of the host you were interested in, plating them in petri dishes (or microtiter plates) and inoculating them with tissue samples from the organism whom you suspected of harboring the virus. These papers nicely illustrate some more modern techniques.
To discover the first (ever) virus of Varroa destructor, Ongus et al (1) collected one gram of mites from a bee colony, washed them, crushed them, purified any virus particles with 2 rounds of centrifugation, reverse transcribed any insect picornavirus-related RNA and then detected by PCR a viral genome that is highly related to Deformed Wing Virus. They named this new thing for the organism it was found in: Varroa Destructor Virus. It’s on my list of 5 all-time favorite list of virus names.
Varroa destructor mite on a bee. I’ll let you draw your own conclusions about how easy it would be to collect 1 gram of these.
Later, in 2016, Levin et al (2) had the even more modern approach of crushing up honey bees and mites (separately), and then directly sequenced the RNA using Illumina technology to amplify ~every sequence in the pool. In those pools the sequencer finds all kinds of things :
Adapted from Levin et al 2016
Those are the percentages of reads from the Illumina sequencer that could be mapped to that virus. Roughly speaking, you can say that 38% of the viral RNA molecules in the bee library clearly were from Deformed Wing Virus. How does the Illumina sequencer *know* that these are viral RNAs? Well, it doesn’t -it just sequences everything. Researchers (humans) have to then sift through the data… I will bet you 100$ that most of the RNA sequences that these machines detected were things like ribosomal RNAs and actin mRNAs – in my experience that constituted a good amount of the RNA in human cells and I doubt bee cells are that different. What the researchers do is digitally filter out all sequences that don’t “look like a viral genome”. So those percentages I put in the table above are the “percentage of RNAs that look like a viral genome”.
Notice that there is more of “the mite’s virus” (VDV1) in the bee than there is in the mite, and vica versa – there is more of “the bee’s virus” (DWV) in the mite than there is in the bee. Remember though, DWVs are pools of related viruses. Recent papers refer to VDV1 as “a DWV”… it seems like a post about how viruses (or any other species of parasite) is named – do you name it for the the organism you found it in (which would make this new virus a Varroa Destructor Virus)? Or do you name it according to its DNA sequence similarity (which would make it another Deformed Wing Virus)? This question pops up frequently because every person who has ever discovered an organism or virus that looks different from all the other described organisms and viruses WANTS it to be a new species, and they usually name it as such. Then, later, as more people find and describe that organism, there is frequently a gentle correction and renaming according to sequence similarity. And that is better – DNA shows true relationships between organisms… we all agree that if a child’s DNA is 50% related to his, he is obligated to help raise that child regardless of their last names. Or at least we should.
Anyhow VDV-1 then is clearly an Iflavirus, like the DWVs. the major conclusion from the Levine paper is that they find two MORE viruses in the mite RNA pool that are ONLY found in the mite RNA pool, NOT the bee RNA pool. They back this up with separate RT-PCR experiments: Varroa Destructor Viruses 2 and 3 can not be found in the bees.
This rabbit hole keeps going, but I’m going to end by asking a question that I can’t answer. In the last two “Add to the list” posts, there are a total of 6 viruses: DWV-A, -B, -C and VDV-1, -2, -3 – but VDV-1 is now considered to be a subgroup within DWV-B (3) – so does that mean we are talking about five viruses here, or six? I’m sure as I read more papers I will find that this has sort of been settled, but my bigger point is that viruses are kind of fractalish. And yes, anyone reading this who has expertise in this area can see that this question is a paper dragon, but the lines of thought produced by turning it around in your mind are extremely juicy.
References
(1) Ongus et al 2004 J. Virol. Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor
(2) Levin et al 2016 Nature Sci Reports. Two novels viruses associated with the Apis mellifera pathogenic mite Varroa destructor
(3) Martin & Bretell 2019 Annual Review of Virology. Deformed Wing Virus in Honeybees and Other Insects