Eden: it's an endless world! manga

Eden - It's an Endless World! summary:

In the panic surrounding a worldwide pandemic which kills 15 percent of the population and cripples many more, a secret organization, the Propater, topples the UN and seizes control of much of the world. A boy and a girl, raised in an abandoned virology research center, immune to the virus, are attacked by the Propater and escape. Based strongly on Gnostic mythology, all major characters are named after gnostic deities, and have analogous roles.