I don't think you've overused the word virus. You're not being clear about the taxonomy. It's hard to advise you since I don't know your audience.
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deadrat If you're dealing with people who aren't technical, you might want to start from the bottom: explain the species first.Please let me know if the following revision I have made is fine:
RommelMarburg virus and Ebola virus are the two identified members of the Filoviridae family.I would say, "The Ebola viruses form one of the two commonly-known groups of the Filoviridae family; the other is the Marburg virus group."