Both spellings have been used in English for a long time [0]; "Virgil" is just the far more common of the two. Wikipedia claims that the original spelling "Vergilius" was changed to "Virgilius" some centuries after his death [1], and the latter became the form that spread to other languages.
> classical texts are enmeshed in a dense web of relationships that can surprise and invigorate us, even after thousands of years
"[E]nmeshed in a web of relationships", i.e., intertextual[1].
Further reading: Hermann Broch's novel, The Death of Virgil, and Simone Weil's lesser known compilation of writings, Intimations of Christianity Among the Ancient Greeks.
The web of relationships extends to music as well. After reading that Broch novel, one might enjoy the cycle of works by Jean Barraqué that took their inspiration from The Death of Virgil.
There was (and still is) a whole subfield of scholars trying to find hidden messages in Shakespeare's works. Most of them are cranks. At some point though, Claude Shannon, the father of Information Theory, looked at these claims and suggested an empirical test: does the claimed hidden message contain text well beyond the point of uniqueness (I think it was originally called the unicity point)?
For example, suppose you stumble across the symbols NEZNIVEHZDHRPNABGEBVNRDHVCEVZHFNOBEVF. Someone tells you that it in fact contains a secret message in ROT13, namely the opening line of Vergil's Aeneid. Should you believe them or are they overfitting?
In this case, it turns out that no system of roughly the same complexity as ROT13 (and that includes any of the 26! examples of 1:1 mappings of the letters) produces anything close to this good a match, so the explanation "this is ROT13" accounts for much more than you would expect by chance. For the same reason, in the linked article the acrostic NIKANDROS in a poem by someone of that name (at least when rendered in Greek) looks too good to be a coincidence.
On the other hand, suppose you encounter the word SXLL and someone tells you that it's the encoding of the word BLUE with a Vigenere square (basically A=0, B=1 etc. modulo 26) and the key RMRH. The math works out, but there are as many degrees of freedom in the key as there are in the supposed codeword (this is a one-time pad, for cryptographers) so you could equally well say that SXLL is an encoding of STOP with the key AEXW. This claim does not pass the point of uniqueness (which for the true one-time pad diverges to infinity of course, that's the point!).
By this technique, most claims of secret messages in Shakespeare fall because there's other, equally complex systems that turn up equally plausible different messages.
In a work the size of Vergil's (or Shakespeare's), you are bound to find some supposed acrostics by chance alone, especially if you allow yourself some degrees of freedom (like skipping the occasional line). My question for the claimed Isaiah one is whether this one is really past the point of uniqueness, something so unlikely under the null hypothesis of coincidence that we can be sure it's an actual "easter egg" hidden here. Of course, the fact that ISAIAH SAYS is on-topic for the plot here is Bayesian evidence in favour of it being real.
I came across this in the book The Codebreakers: The Comprehensive History of Secret Communication from Ancient Times to the Internet by the historian David Kahn. I'm afraid I haven't got my copy to hand at the moment, but there seems to be a very reasonably priced Kindle version.
(I'm now half panicked that I might have misattributed to Shannon something that was actually Friedman; both of which feature in the book. The uniqueness point concept seems so obviously information-theoretic to me that I might have made the connection by mistake, it's a while since I read that chapter.)
