I find that this can become carrier discretion. My carriers recommend 59. CPT Assistant, dated 5-2009, also recommends this...
Whether to report one or two units of code 87804, Infectious agent antigen detection by immunoassay with direct optical observation; influenza, varies according to the type of rapid testing method used distinguishing influenza A from influenza B. The rapid detection of influenza virus types A and B may be part of two entirely separate procedures or may be included within the same test device. If the assays provide two separate results (ie, a result for influenza virus A and a result for influenza virus B), it would be appropriate to report two units of code 87804. When two units of code 87804 are submitted, modifier 59, may be used to indicate that the two results represent separate services (codes 87804 and 87804-59).