"奴" is ambiguous and doesn't define gender (
http://www.mrhowtosay.com/kanji/kanji?k=奴).
Alex has been declared a male in Archives II. However, the Archives books are often contradicted in posterior games, so we can't make a conclusion based on that.
In any case, even if Alex was a man by 2009, they may have changed sex. It wouldn't be the first case of trangenerism in the series - Alfred Ashford impersonated his sister Alexia by the time of the Rockfort Island assault, and Morpheus D. Duvall was in the process of sex change by the time of the Spencer Rain incident.
This is only a guess though, so there's no need for big discussions about this.... in the end, nobody will know for sure until it is revealed.
My other guesses would be Polly Burton, who is directly related to Moira and Barry, or Rebecca Chambers, since the developers said they wanted to please the fans, and she's one of the most requested characters -- I can imagine her being fascinated at Umbrella's research and become evil (she's a doctor after all, so she could have been making the experiences which originated the Afflicted).