Following the Doctrine in Council of Trent, does God give a soul to human at conception deprived of sanctifying grace? The Catholic Church teaches, as St. Thomas Aquinas explained, that God intended our first parents to give their descendants the blessings of original justice. When they lost the gifts, however, they could not give them to their posterity. Thus, the 5th session of the Council of Trent (1546) teaches that original sin is transmitted by propagation and not imitation.

However, the contention arises in, if original sin is transmitted by propagation not by imitation. Somehow understanding it biologically implied that the transmission would be thru sexual procreation.. but the Council implied only a metaphysical transmission since the soul is immaterial being...
I will quote the interpretation of Rev. Nicanor Pier Giorgio Austriaco, O.P.
 (Thomistic Evolution site):


  Now, some may read this statement by the Council of Trent – that original sin is transmitted by propagation and not by imitation – as a claim that original sin is transmitted biologically. However, the consequences of original sin are privations in the soul of the human being. Because of the original sin, his soul lacks grace and the preternatural gifts. Thus, when the Council of Trent teaches that the consequences of the original sin are transmitted by propagation and not by imitation, we should understand this as a metaphysical and not a biological claim. As an immaterial spirit, our soul and its properties are not determined by our genes. Instead, when God creates our souls when we are conceived, He creates them without the graces and gifts that we should have inherited from our original parents.


In view of the Catholic Church Teaching defined in Council of Trent: Does God give a human soul deprived of sanctifying grace at conception?
St. Thomas Aquinas writes in Summa Theologica I-II q. 81 a. 1 ad 2:


  Although the soul is not transmitted, because the power in the semen is not able to cause the rational soul [cf. I q. 118 a. 2], nevertheless the motion of the semen is a disposition to the transmission of the rational soul [which God creates ex nihilo]: so that the semen by its own power transmits the human nature from parent to child, and with that nature, the stain which infects it


So, it's the human nature (body+soul composite) that is infected, and semen is only an instrumental cause of bringing about a particular human nature. The corrupted body infects the soul, the rational soul being "the subject of sin" (ibid. arg. 2).

This will shed some light on your question:


Pedro Lumbreras O.P., "Saint Thomas and the Immaculate Conception," Homiletic and Pastoral Review 24, no. 3 (1923): 253-63.