The internal antigens (M1 and NP proteins) are the type-specific proteins (type-specific antigens) used to determine if a particular virus is A, B or C. The M1 proteins of all members of each type show cross reactivity. The NP proteins of all members of each type also show cross reactivity.

The external antigens (HA and NA) show more variation and are the subtype and strain-specific antigens. These are used to determine the particular strain of influenza A responsible for an outbreak

Flu strains are named after their types of hemagglutinin and neuraminidase surface proteins, so they will be called, for example, H3N2 for type-3 hemagglutinin and type-2 neuraminidase.

If two different strains of influenza infect the same cell simultaneously, their protein capsids and lipid envelopes are removed, exposing their RNA, which is then transcribed to mRNA.

The host cell then forms new viruses that combine antigens; for example, H3N2 and H5N1 can form H5N2 this way.

Because the human immune system has difficulty recognizing the new influenza strain, it may be highly dangerous.