Scientific Nomenclature says that:
Italics are used for bacterial and viral taxa at the level of family and below. All bacterial and many viral genes are italicized. Serovars of Salmonella enterica are not italicized
When a sentence with a viral name is in an italicized environment (in a quote, in a reference list), should it be written in italics or roman? In latex, the \emph command provides such a relative "emphasis", with respect to the surrounding sentence.
The general advice is to revert to roman within a block of italics. Here are a couple of sources:
When a title or sentence is italicized, a word that normally would be italicized in running text—such as a foreign word, the scientific name of a plant or animal, or a ship—should appear in roman type. This is called reverse italics. - from the Editorial Style Guide, Purchase College, State University of New York
8.184 Terms within titles. A term in a quoted title that is itself normally italicized, such as a foreign word, a genus name, or the name of a ship, is set in roman type (“reverse italics”). - karencopyedits, quoting The Chicago Manual of Style
