National interest exemption

I am applying for a J-1 visa from Germany. I believe that I qualify for an
NIE. However, I would like to travel to the US from India so that my wife
can accompany me. If I travel to the US from India, do I have to get a new
visa or can I just apply for a separate NIE from India?

Just apply separate NIE if you already have a valid J1 visa stamp.