The origin of this phrase in Psalm 2:7 :I will tell of the decree: The Lord said to me, “You are my Son; today I have begotten you.
“this he has fulfilled to us their children by raising Jesus, as also it is written in the second Psalm, “‘You are my Son, today I have begotten you.’ (Acts13:33)
For to which of the angels did God ever say, “You are my Son, today I have begotten you”? Or again, “I will be to him a father, and he shall be to me a son”? (Hebrews 1:5)
So also Christ did not exalt himself to be made a high priest, but was appointed by him who said to him, “You are my Son, today I have begotten you”; (Hebrews 5:5)
And also God confirmed the special role of Jesus as his son at his baptism:
“and behold, a voice from heaven said, “This is my beloved Son, with whom I am well pleased.” (Matt 3:17)
And shortly before he was conceived:
He will be great and will be called the Son of the Most High. And the Lord God will give to him the throne of his father David, … And the angel answered her, “The Holy Spirit will come upon you, and the power of the Most High will overshadow you; therefore the child to be born will be called holy—the Son of God. (Luke 1:32 .. 35)
So the special relationship of Jesus as “only-begotten Son” of God (John 3:16) is confirmed at different points in his life.