Michael Eisen is controlled by fungiVerified account

In addition to propagating the E. muscae infection from fly to fly @homiec17 established an in vitro culture of the the fungus alone, which we used to sequence its transcriptome and genome (the genome is a mess - close to a billion bases and basically all transposable elements).

The fungus is in a very poorly studied fungal phylum - basically 1.4 billion years of branch length away from its closest well-characterized relative - and so I was very eager to see what was in its transcriptome (which we got long before the genome) https://en.wikipedia.org/wiki/Zygomycota .

Being the impatient PI that I am, as soon as we got transcriptome reads back from the sequencing facility I began BLASTing them against GenBank to see what was there. Most reads hit nothing. Some hit distantly related fungi.

We had reams of data coming through at the time, and I made a note about this as a weird observation, but, stupidly, didn't follow up on it at the time (I thought the virus was likely an E. muscae TE and took it as a sign that E. muscae infection of Drosophila is common)

However, when we finally got a decent genome assembly, I came back to this observation, and looked in the genome for signs of the virus -- and got nothing. So now I was very confused and my curiosity was piqued.

I looked more closely at our data and at the virus. First, I realized that the in vitro culture was SCREAMING with this virus - on the order of 15% of the reads in the sample were from the virus (there's a lesson here in paying attention to reads that don't align to the genome).

This suggested that the sample from which @somethingsparks identified Twyford virus was infected with E. muscae. Fortunately all of their reads were available at NCBI (thanks!) and we confirmed by aligning reads to our E. muscae genome that indeed it was.

I should stop a minute and say something about the virus - which we have renamed Entomophthovirus (EV) to reflect its host (sorry Twyford). EV is an iflavirus, a family of positive strand RNA viruses related to the more famous picornaviruses https://en.wikipedia.org/wiki/Iflaviridae …

Most known iflaviruses, which are relatively poorly studied, infect insects, and some induce behavioral changes in their hosts.... (more on this later).

We think all this is pretty definitive proof that that we are dealing with a positive strand RNA virus of insect origins that has switched its host to infect a fungal pathogen of of flies. Pretty cool!

I was fascinated by the fact that we didn't just find this virus in the E. muscae strains we found in California - that it was seemed to be infecting Drosophila infected E. muscae in England. And wondered if it was found in all E. muscae.

And once again, there was clear evidence that the mixed fly sample (which contained Drosophila immigrans and several other non-Drosophila species) from which this virus was identified also contained E. muscae.

Knowing that there's a lot more info in GenBank than in the standard BLAST databases, I looked more deeply and found one other, unannotated, example of the virus in transcriptome database. And ... drumroll please ... it was from a cabbage fly infected with E. muscae!

That data was from https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13863 …. They actually sequence mRNA from several independent isolates of E. muscae from two fly species - infected cabbage flies and houseflies - and all had Entomophthovirus as well.

Based on available RNA sequencing data, every time we see Entomophthovirus it is associated with E. muscae, and every time there is E. muscae in a wild fly there also is Entomophthovirus. So this appears from all indications to be a very close association.

Interestingly, one of the in vitro cultures established in https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13863 … doesn't seem to have any Entomophthovirus, suggesting that the fungus doesn't need to virus to survive.

But we always see the virus associated with the fungus in flies. So, either this is a very effective virus, which is interesting in and of itself, or, more tantalizingly, maybe the fungus needs the virus to propagate in flies....

Intriguingly several iflaviruses are known to alter the behavior of their insect hosts: Kakugo virus for example has been shown to be associated with aggressive colony behavior in bees https://www.sciencedirect.com/science/article/pii/S0065352705650014 …

All of which leaves us with the somewhat wild possibility that maybe Entomophthovirus is playing a role - or maybe the main role - in the behavioral manipulation that is characteristic of Entomophthora infection.

This, and a ton of related questions, are now being pursued by the amazing @MaxCoyle4, who all of the experimental work on Entomophthovirus and is now chief Entomophthora wrangler in the Eisen Lab.