All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
First of all, it should be noted that the supplication in question was authentically narrated from the Prophet, sallallaahu ‘alayhi wa sallam. It was narrated on the authority of Anas that the Prophet, sallallaahu ‘alayhi wa sallam, used to say: "Allaahumma inni a‘oothu bika min al-baras, wal-junoon, wal-juthaam, wa sayyi’il-asqaam (O Allaah! I seek refuge in You from vitiligo, madness, leprosy and evil diseases).'' [Ahmad, Abu Daawood and An-Nasaa’i] This proves that it is permissible for a Muslim to say this supplication to seek protection or cure from every disease, whether it is swine flu or any other disease. That is because the words "evil diseases" include all of these diseases. For further information please refer to Fatwa 85932.
Allaah Knows best.