The genophage affects the release of hormones in female krogan during pregnancy, creating imbalances that result in a miscarriage rate of 99.9%. A characteristic of the miscarriages is that they develop without a nervous system, assuring no pain or sapience at any point in the pregnancy. The virus is otherwise harmless to adult krogan and krogan children that do carry to term. It is, however, carried by all krogan.
The genophage was invented by the salarians as a solution to the Krogan Rebellions, which were driven by the extremely high rate of krogan population growth. To cope with the extremely hostile environment of Tuchanka, krogan had evolved to produce as many as 1,000 children per year from every female. When removed from their homeworld to fight as proxies in the Rachni War, the krogan population exploded, and they began to invade worlds claimed by the Citadel Council races. Even the intervention of the heavily militarized Turian Hierarchy could not keep the krogan in check.
The salarians developed the genophage specifically to reduce the krogan reproductive rate to what it was on pre-industrial Tuchanka, a hostile environment in which only one krogan child in a thousand survived to maturity. Their intent was to threaten the krogan with deployment of the virus if the krogan did not cease their aggression. The turians considered a threat insufficient, and they deployed the genophage everywhere krogan had established themselves, infecting the entire population. The genophage made the krogan unable to replace the heavy losses they endured in their attritional style of warfare, ending the Krogan Rebellions.
In the 22nd century, the salarian Special Tasks Group determined that the krogan birth rate was slowly increasing. The krogan were adapting to the genophage, with different glands starting to produce the hormones needed to carry a krogan pregnancy to term. The STG assigned a team of scientists lead by Dr. Mordin Solus to modify the genophage, reducing krogan viability back to the intended 1-in-1000 live birth rate.