Fonte told Mais Futebol: "If the interest is there, it is a reason to be flattered to be associated with a club like Manchester United.
"But I have a contract with Southampton, and I'm just focused on my work, to make a great season. I will not deny that Manchester United is one of the biggest clubs in the world and that it makes me happy to be associated with it. But to be Manchester United's player is a big difference."
Southampton coach Claude Puel is expecting Fonte to be professional when he returns to action. The Frenchman considers the player to be an important part of his plans.
Puel said: "I do not think there is a possibility for Jose to leave us. I am sure that he can play all these games. He is very proficient.
"[Fonte has] rejoined training. I do not know if he will start the game [on Saturday] but we will see.
"The window is difficult for the club and the players. Many clubs can be interested in players. That is normal."