Viruses are obligatory intracellular pathogens requiring host machinery for survival and reproduction. Differing from living organisms, which can grow where nutrients are available, viruses absolutely require hijacking of host machineries to complete their life cycle. Enveloped viruses evolved to have dedicated strategies to passively sense environmental cues to ensure that initiation of infection occurs at the correct moment and place. One general strategy used by enveloped viruses is to precisely control activation of their envelope glycoprotein just prior entry into host cells. Influenza A virus (AIV) is the causative agent of influenza illness and causes both economical and public health problems globally and annually. As a successful pathogen infecting a wide range of animals, IAV excels in sensing the environment to ensure efficient infection by employing two sequential activating steps during viral entry: proteolytic cleavage for priming of the hemagglutinin (HA) and low-pH-triggered conformational changes allowing release of the fusion peptide. Proteolytic cleavage of influenza HA controls viral pathogenesis by influencing viral growth rate and viral tropism. The primary sequence and tertiary structure of the HA determine the overall properties of HA activation and hence, viral pathogenesis. Mutations on the primary sequence of the HA cleavage site affect viral activation in two dimensions, 1) HA activation efficiency and 2) alteration in protease repertoire for HA activation. The former modulates viral growth kinetics and the later is important for viral tropism. Mutations that modifies HA tertiary structure also play an important role in viral activation, in particular virus growth. In this thesis, I describe three interrelated studies of mutations on primary and tertiary structure of HA and their consequence on HA cleavage and viral pathogenesis. These mutations also allow influenza virus to interact with prokaryotic pathogens and open up another dimension in virus-bacteria-host interactions and synergy.