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Regarding the difference between proviruses and prophages, Wikipedia states that "these terms should not be used interchangeably. Unlike prophages, proviruses do not excise themselves from the host genome when the host cell is stressed." However, Khan Academy implies at 3:41 that the two terms are interchangeable. Who is correct?

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Over some 15 years in academia and research, I've taken graduate-level virology classes, worked in multiple phage research labs, and attended dozens of seminars on both bacterial and eukaryotic viruses. I can't recall ever seeing or hearing the term "provirus" used until reading this post.

Sometimes different disciplines in biology will use the same or similar terms somewhat differently. There are, in fact, several examples of commonly used terms in biology that have no universally agreed upon definition. However, according to at least one source that I just found on a plant viruses, a "Provirus is a permanent part of host genome," meaning it is not excised before reproduction. This other source uses provirus to describe integrated HIV, which also doesn't need to be excised in order to reproduce. So there may be some consistency of usage here.

Ultimately, meaning in language comes from the intersection of use and understanding in context. Any time you're talking about viruses that infect bacteria and/or archaea, the terms "virus" and "viral" can almost always be replaced with "phage", but don't always have to be, so could be somewhat interchangeable in that context. Whereas, to my knowledge, "phage" is never used in describing eukaryotic viruses.

So, if you said "provirus" in a phage biology lecture, your audience would likely understand it to have the same meaning as prophage, but if you said "prophage" to describe an integrated human retrovirus or retroelement, you'll almost certainly confuse a part of your audience, so not really interchangeable at all in that context.

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  • $\begingroup$ Since phage are bacterial viruses, every prophage is a provirus, but not all proviruses are prophages. The term "provirus" IS a thing in molecular biology, but as you note is probably much more common in work on retroviruses or eukaryotic genome evolution. $\endgroup$
    – Armand
    Commented Oct 6, 2021 at 19:00
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    $\begingroup$ @Armand I agree about prophages being proviruses. One difference being that lysogenic prophages are excised from the host genome before a lytic replication cycle can begin, where retroviruses can generate genomic viral RNA (and infectious virions) while the provirus remains integrated on the host genome. So IF being a PERMENANT part of the host genome was a necessary property of all proviruses, then prophages would not technically be proviruses. But that would seem like a pretty arbitrary distinction to make (imho). $\endgroup$
    – MikeyC
    Commented Oct 6, 2021 at 21:03

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