In the Spring of 1977, while I was living out the last months of my pre-Star Wars childhood, the Rothamsted Experimental Station received a package of honeybees from Egypt.  Alive but apparently “diseased”, no description of the disease was given.  After putting the goo from the ground-up bees through a series of spins on a centrifuge (the last being through a sucrose gradient), researchers at Rothamsted fired up their electron microscope and observed round viral particles about 30 nanometers across.  Antibodies specific for known bee viruses didn’t react with these particles, so they named it Egypt Bee Virus. (1)

And that is the last mention of it for 43 years, sort of – I can find references to it in the introductions of a few papers, but I can’t find that anyone worked on it between now and then.  Until this year, when an international group of scientists from Sweden, Germany, Australia, Ethiopia, Belgium, United States, Jordan, India and several different institutions from the United Kingdom, including Rothamsted published a paper to report that the virus is no more – or at least that they can’t find it (2).

Working from freeze dried samples stored at room temperature for ~40+ years at Rothamsted, they reverse transcribed the viral RNA in the samples into cDNA for sequencing.  Apparently the originally purified viruses from 1977 had been used to infect honeybee pupae and that was the material that was freeze dried, although there is no publication describing the results of those infections (its only reported in the materials and methods of this paper).  They find that the Egypt Bee Virus is highly related to the Deformed Wing Viruses. Overall its more closely related to DWV-C than A or B, but it has 2 segments where it’s clearly more related to DWV-A and DWV-B (separately) (2)

Egypt Bee Virus is clearly its own virus

They rename Egypt Bee Virus as Deformed Wing Virus-D (although there is no evidence that it ever caused deformed wings).

Then they screen 300 separate RNA sequence libraries from all over the world for  DWV-D – and they find nothing!  Although none of the libraries are from Egypt, 10 of them are from Ethiopia, which is at least near Egypt- but then again there is no published information about exactly where those bees were from, only that they were shipped from Egypt in 1977.   Finally, the 1979 paper first describing EBV thanks a “Professor S E Rashad of Cairo University” and I found a 1978 article by  Rashad, SE and El-Sarrag, MSA in “Bee World” entitled “Beekeeping in Sudan” (3), which at least borders Egypt and Ethiopia.

I kind of hope this virus is gone… there are many that can replace it, and it’s unlikely it was doing anything useful for anyone, but its absolutely fascinating how viruses can come and go.  Something many people have been thinking about lately as Alpha, then Beta, then Delta and now Omicron arise and then disappear.

As a sort of side-quest I keep coming back to this Professor S E Rashad, whose full name is Salah El-Din Rashad.  I don’t want to glorify war, but that’s a pretty bad-ass name (look it up).  It interests me that in 1977, this guy sends the samples from which the UK scientists discover Egypt Bee Virus, but he isn’t listed as an author.  In my experience in science, that kind of thing wasn’t uncommon – submitting samples to someone else frequently doesn’t mean you are made an author on the papers describing whatever they discover using those samples.  But I am sure its also part of another thing that isn’t uncommon: cutting scientists from less advantaged countries out of authorship.  I did a bit more research on Professor Rashad – he was clearly interacting with UK scientists because he was at a 1976 conference on Apiculture in Tropical Climates in London.  Ultimately the decision on authorship is typically left up to the scientists who are writing and submitting the paper, and its nice to see that researchers in Ethiopia are included as authors on the 2022 paper of Egypt Bee Virus.

References

(1) Bailey et al 1979 Journal of General Virology. Egypt Bee Virus and Australian Isolates of Kashmir Bee Virus

(2)  de Miranda et al 2022 Virology Journal. Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970’s Egypt

(3)  Rashad & El-Sarrag. 1978 Bee World.  Beekeeping in Sudan

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