Shai Weiss, chief commercial officer for Virgin Atlantic, said the deal was not linked to the UK's impending exit from the EU.
"I can say really definitively this has nothing to do with Brexit," he said, adding the rationale was entirely commercial. Mr Weiss said the airline did not fly intra-Europe and so the joint venture was not a way to secure such flying rights post-Brexit.
He said the success of its existing joint venture with Delta, which had helped provide so-called feed traffic - passengers who take a short haul flight to a hub airport before travelling on a long haul flight - could now be replicated with passengers from Europe.
If the UK endures a hard Brexit, rules which says airlines have to be majority domestic owned could be enforced. This deal means Virgin Atlantic is only 20 per cent British owned but Mr Weiss said it would overcome such problems if they transpired. If the Brexit deal is more amicable, the airline's majority European ownership will mean it complies with similar rules on the Continent.
Sir Richard sent a letter to the airline's staff outlining the details of the deal, in which he said he would remain the largest individual investor.
The billionaire entrepreneur said the airline industry had consolidated since he launched Atlantic in 1984, going on to say "it's now our turn to put ourselves at the heart of an important alliance".
"With these three partners in place and with me - and one day, the wider Branson family - still very much involved, we have the foundations to make sure this is so," Sir Richard added.
The deal, set to last for at least 15 years once it gains regulatory approval, will, subject to regulatory approval, see the carriers combine their transatlantic routes.
The joint venture will offer more than 300 daily non-stop transatlantic flights from 12 hubs including from Amsterdam, Atlanta, Heathrow, New York's JFK and Los Angeles.
Sir Richard said "one of the best moves" his company made was tying up with Delta Air Lines five years ago, partly to compete with the British Airways and American Airlines alliance.