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I just think it's impossible that V didn't notice anything about Nero. I mean, Dante did the first time he saw Nero. And Vergil must remember Fortuna...(especially if it was the only time). I think he just doesn't really want to talk about that with Dante during their fight.
Of course he could have thought Nero was Dante's son, or maybe he was not sure about anything, but at least he must have asked himself some questions.
During mission 17, V confides in Nero, like he did with Trish, and I don't think he can do that with everyone. I supposed he must have felt their special connexion... (Besides, V is still able to feel Sparda's power).
+ I wanted to talk about the fact Vergil ''abandoned'' his child while it's precisely that feeling which is the cause of what Vergil has become.