Departed can be interpreted as 'Dead/Deceased' or it can mean he has 'left/gone away' ie. "My brother departed, left for another land" or "I departed on the next train"
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Also in regards to "belonged to my brother", it just means he doesn't own it. Ie. it was stolen, or lost when he became corrupted. There is no point in any of the games that you can 100pct say "Virgil is Dead", because everytime the story attempts to explain it they use words and situations that can be interpreted in many ways, such as "departed" ^_^.
If Dante said to Nero "It belonged to my Brother, who is dead" then sure, thats proof enough for me. But it could also be "It belonged to my brother, whom gave it to me for save keeping...".
Sadly, we are still at a loose end when we look at Virgil