The animals were immune.
My theory (though I am sure it is not solely mine) as to why Sandeman began playing the gene splicing game. Animals were immune to the agent, which is a reason why the snakes could be carriers and not be infected. Plus, animals must be immune, for the earth itself would cease, the familiars would die, if animals were not immune. This is why Sandeman began experimenting with canine DNA, in the hopes of creating a force to survive the agent and battle the familiars, or because the transgenics were meant to save the human race through some other mean.
MRCA. Most Recent Common Ancestor.
The breeding line began with the rape of a girl, and one can assume the people involved with this were the humans that survived the agent. Most Recent Common Ancestor is the idea that people are all, to an extent, related. So the purpose of the breeding line is to secure and maintain (keep in the family) that immunity through various generations and extensions of the line. To create an empire of sorts of immune people, indoctrinated to believe in and continue their practices. That's the purpose of the selective breeding, of everything the cult does. Plus the side projects of creating humans of superior intelligence and strength.
World population, seven billion. An immunity of less than thirty percent.
Not everyone, I suspect, will die from the agent. The familiars shall inherit the earth, not because there will be no one left, but because they will be the most powerful, rule, over those who are left. What kind of life would they lead if they were the only people on earth? They kill the first two because it mimics what originally happened. 2/3 of the human race was killed, 1/3 survived.
The philosophy, the legend, the rituals.
This again refers to the people involved in the original rape and murder.
Evolution. Creation, stasis, obliteration. Theory of Mass Extinction.
The agent came to earth on an asteroid, much like the one which killed the dinosaurs. Dooms day would probably be much like that. The breeding cult is an evolution of sorts, and the creation, stasis, and obliteration is the course of the human race.
From the sole it was so (From the asteroid came the agent, from the womb came the birth)
The seed from which came enlightenment (from the asteroid came the agent, from the boy came immunity, strength. The breeding cults insane version of enlightenment)
Death of the one, death of the two (Refers to the death of the first two children, like the death of the humans on the first dooms day. 2/3 was killed.)
To weed the Garden (The agent rids the earth, the Garden, of the week, of weeds, so the strong, the good plants, may prosper)
An ascetic trial to reach Laurel (Refers to the initiation ritual, the test. Laurel means success, glory)
Survival
The point. Sandeman wanted, first, for his son to survive, and then the human race.
And that's all. Hope it wasn't painfully repetitive – I do not know how many others have come to these conclusions.