USB only has 4 available pins, and all are already in use.? There is no extra pin for a hardware PPS signal to connect to.
As Alan stated, you could use an FTDI or CP210x USB to TTL adapter board to connect to the 6-pin header and some appropriate application to utilize the PPS signal.
Make sure you get a USB to TTL adapter board that has access to the additional pins.? If the USB to TTL adaptor only has 3 (Gnd, Tx, Rx) or 4 pins (adds Vcc), it will not work.
Match Option Jumpers to the logic correct level of your adapter.
I do not know which applications use the PPS signal.
-------
Rob KB8RCO