Martin Olsson and Jason Roberts both sat out the 2-0 defeat against Manchester United after going down with the virus.
Allardyce said: "It may come and go for a while but the doctor tells me the strain is at its weakest now rather than getting stronger as the winter comes in. So hopefully we will not catch it again and be okay later on in the season."
Allardyce revealed last Monday that three players had contracted swine flu, one of them Chris Samba.
The defender lost about four or five kilos, according to his manager, but was able to play at Old Trafford.