The first tonic chord:

Is substituted by a vi degree chord in first inversion:

The II, V, I chords are part of the cycle of fifths chords progression (D - G - C in C major). By using a vi degree before the ii degree we add an additional step to this progression: A - D - G - C.

The first chord of the progression will be replaced not only by vi degree chords, but also by chords that lead to the chord that follows.

The ii degree chord in measure 2:

Is now a secondary dominant of the V degree in third inversion:

The V degree in measure 3:

Is now a simple V degree triad in first inversion:

The tonic chord in measure 4:

Is now a major seventh chord in third inversion:

Bach prepares the seventh using the third (B) from the previous chord. This is the first major seventh chord in the Prelude.