From the girl's previous actions when she tried to force him to sleep, he could already guess the girl's identity but he didn't want to believe it as he felt it to be very unlikely.
He guess that she could be a phenomenal, very likely an undocumented one but he chose not to believe it because he thought that people like her should be hidden. At least that was his thoughts.
Also, from her following reaction after she failed to out Silas to sleep. Silas understood that this wasn't the first time that something like that has happened.
