Completed Projects

The early host response to influenza virus is a key determinant of disease severity and subsequent immunity to infection. As such, vaccination strategies against influenza virus should start with an understanding of the host response. In this Project, we will use high-throughput molecular profiling and novel computational methods to build host response networks, identify predictors of vaccine immunogenicity and efficacy, and discover molecular and cellular targets and candidate drugs for use as adjuvants or host-directed antiviral therapy. We will define molecular mechanisms of innate immunity and molecular correlates of robust immune responses and protection following seasonal influenza vaccination. Using computational approaches, we will determine whether existing small molecules or therapeutics can be repurposed for use as adjuvants or broad-spectrum therapies.

This Project will provide new knowledge regarding the host response to influenza virus infection and vaccination that can be used to develop more effective vaccines. In addition, this Project uses novel computational methods that make use of genomic profiles to rapidly screen small molecules and FDA-approved drugs for repurposing as antiviral therapies or vaccine adjuvants. Because many of these compounds have already been evaluated in human subjects, this strategy may significantly reduce the time needed to translate findings into clinical studies.

Our objectives in this project were to understand the cleavage-activation of influenza hemagglutinin (HA) by proteases in the human respiratory tract and how cleavage-activation is modulated during the emergence of new viruses with variant HAs, and in the context of bacterial co-infections.

1.Characterization of circulating influenza viruses with modified HA cleavage sites. We studied the HA protein of several circulating human influenza viruses that have variant cleavage sites, such as the A/Texas/JMS381/2009 H1N1 strain, which has a Ser-Pro substitution at the P2 residue of the cleavage site (IQSR-GLFG to IQPR-GLFG). Our goal to determine how such viruses may be differentially cleaved by the range of proteases available in the human respiratory tract. We also studied emerging influenza in the human population, notably H7N9 viruses at biosafety level 3, A/mallard duck/W452/2014 (H5N8) and A/Xiangxie-Donghu/346/2013 (H10N8). For our studies we use a range of biochemical and cell biological assays, including single-particle membrane fusion analyses with Susan Daniel (Cornell Chemical Engineering).

2. Determine the interplay between influenza and co-infecting bacteria for HA cleavage-activation. To identify key bacterial proteases that could impact influenza pathogenesis, we carried out proteomic analyses using Staphylococcus aureus, which identified several candidate pathogenicity factors including SspB (staphopain B). SspB was shown to cleave and activate HA, but with distinct preference for viruses having a Tyr residue at the P2 cleavage position (instead of the typical Ser residue). These data suggested that the virus may have evolved to take advantage of the presence of the bacterial protease, and mouse models of bacterial co-infection are currently being used to address the question of whether influenza undergo “microevolution” during a bacterial co-infection. Our focus is on the HA cleavage site and the bacterial proteases that may be impacting disease progression.