Whelan also studies the viral life cycle of VSV to identify potential antiviral targets. He identified a specific subunit of the ribosome, RPL40, as being essential to initiate translation of VSV mRNAs. This selective mechanism allows the virus to block translation of host mRNAs without preventing the production of its own proteins. Interfering with this mechanism could lead to antiviral therapies. With Stephen C. Harrison, he used cryo-EM to determine the structure of the L protein of VSV, revealing several potential drug targets.