User blog comment:Sara J Newgate/new orphan/@comment-25942629-20160925115932

We don't know if they were orphans at the beginning of the series or not. Frankly, we don't know anything about the Kimizuki or Saotome households. They could have been in an orphanage, with their parents, or in a foster home.

The seraph gene may have been done prior to the conception of these children, for all we know. That's normally how gene modification is done, but this is a fictional series, which makes it harder to say.

Yu and Mika originally lived with their parents as well. Mika's parents appeared to have died in a major car accident when he was five or so. It must have been after that that Mika was taken in by the Hyakuya, but we know that his mother was part of a cult, possibly the Hyakuya. His mother appeared to know he was an angel, but she appeared to be quite delusional.

We don't know what happened to Yu's parents before the Apocalypse. We do know that Yu's mom tried to kill him by setting their house on fire and then attempted to set herself on fire as well, but she failed in both regards. We don't know what happened to his dad. During the fire incident, Saito of the Hyakuya Sect picked him up. Since his parents kept calling him "demon spawn," they may have known something about the Seraph of the End experiment as well.