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Your concern about emerging resistance to new antiviral medications is well founded but in this case misguided. The fact is that influenza is a recurring problem for humankind precisely because it is constantly evolving and changing. Many of us are "immune" to hundreds of strains of the virus and yet "antigenic drift" and "antigenic shift" keep our immune systems guessing. And influenza is NOT a trivial disease. As zinj alluded to in his post, anyone who is at all immunologically weakened...The young, the old, diabetics, the sick are at great risk from influenza. "Flu" directly accounts for thousands of deaths each year. This is why doctors are so insistant on these groups of people getting vaccinated. But vaccination is not universal and in some flu seasons may not be effective. In these cases tamiflu and or relenza may be life saving.
Furthermore the problem of "cross resistance" or HIV becoming resistant to say protease inhibitors because of use of Tamiflu is just biologically inconceivable. Tamiflu is a neuraminidase inhibitor which means it specifically inhibits an enzyme that is necessary for the replication of the influenza virus but (to my knowledge) does not exist in viruses such as Hepatitis or HIV.
The problem of allergic reaction is universal with all medication (including "herbal treatments") and many other products. Certainly some people will develop serious allergy to Tamiflu and Relenza and the like...but this is no different than Penicillin or Aspirin.
With all new medication, especially antimicrobials (antivirals and antibiotics) there are potential far the most likely being that through misuse they will cease to be effective. Methicillin Resistant Staph Aureus (MRSA) for example poses a serious risk...but certainly no more so then generic Staph Aureus posed before the era of antibiotics. The fact is that we have become so accustomed to the success of antibiotics that a return to an era (which we live in TODAY) when they are no longer universally effective is terrifying. Watching a patient die with a resistant infection is horrible. But this is no reason not to try to cure disease especially viral disease. The work that Gilead and others are doing offers promise of a day when deadly and disabling viral diseases are treatable. It is a certainty that at some later point in time strains of these viruses become resistant to our treatments. But that is no reason not to treat them to begin with.

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