In Memory of a Lost City, during the boss fight with G-Mutant in Chief Iron's "torture room" (the same place where you find him about to stuff the Mayor's now deceased daughter that he himself killed), if the G-Mutant grabs a hold of you, you'll be thrown into a well full of blood and chum. At first Leon wonders what the hell the stuff is. And then the player realizes that this is the blood that the Chief drained from the mayor's daughter and possibly other victims before he "stuffed" them.
In one of the audio files for Game of Oblivion featuring Alfred and Alexia Ashford, they seem to be congratulating a girl named Tanya on her 13th birthday and thanking her for everything they've learned from her. According to Alexia, she possesses the same intellect level, is of the same age, and the same genetic makeup of Alexia. There's no response from this Tanya as Alexia or Alfred speak to her. Then Alexia talks about being frozen and how she learned so much from Tanya about it. They cryo-genetically froze Tanya and are mocking her in death as Alexia says "Happy Birthday Eternal Thirteen", in which she states Tanya is frozen forever in.
From the same audio file as above, it's puzzling since by the time Alexia was 15, she had injected herself with the Veronica virus and frozen herself. According to her, she and Alfred have congratulated Tanya for the last 15 years on her birthday. If Alexia is frozen as well by this time, how can she be saying all this? Fridge Brilliance kicks in when the player finally realizes that Alexia is indeed frozen and that it's not Alexia talking, but Alfred playing the role of Alexia. He personally saw to it that this girl was frozen simply because she possessed all the qualities Alexia had and reminded him of her, only furthering his pain.
Its also possible to tell it's Alfrexia and not the real Alexia judging by how "her" voice is the more deeper, mature type Alfred uses when posing as her rather than the real Alexia's lighter, child-like voice.
Actually, it makes all the more sense when you realize Tanya never existed. Alfred knew Alexia had to be frozen for 15 years and had to come up with an excuse as to who was still in Antarctica and why Alexia came back. How does he do this? He creates a girl that basically IS Alexia in everything but name, allowing him to keep the illusion Alexia's with him and not locked away in stasis. Tanya never even existed, just another figment of Alfred's shattered mind.
How can you tell that Manuela is infected with the T-Veronica virus? She has something in common with Alexia. She sings.
Steve managed to overcome his mental brainwashing when he saw Claire in danger and wanted to protect her. This foreshadows the fact that Manuela can control the T-Veronica Virus through mental willpower.