Date Published: March 18, 2019
Publisher: Public Library of Science
Author(s): Markus Lesch, Madlen Luckner, Michael Meyer, Friderike Weege, Isabella Gravenstein, Martin Raftery, Christian Sieben, Laura Martin-Sancho, Aki Imai-Matsushima, Robert-William Welke, Rebecca Frise, Wendy Barclay, Günther Schönrich, Andreas Herrmann, Thomas F. Meyer, Alexander Karlas, Ana Fernandez-Sesma.
Influenza viruses (IVs) tend to rapidly develop resistance to virus-directed vaccines and common antivirals targeting pathogen determinants, but novel host-directed approaches might preclude resistance development. To identify the most promising cellular targets for a host-directed approach against influenza, we performed a comparative small interfering RNA (siRNA) loss-of-function screen of IV replication in A549 cells. Analysis of four different IV strains including a highly pathogenic avian H5N1 strain, an influenza B virus (IBV) and two human influenza A viruses (IAVs) revealed 133 genes required by all four IV strains. According to gene enrichment analyses, these strain-independent host genes were particularly enriched for nucleocytoplasmic trafficking. In addition, 360 strain-specific genes were identified with distinct patterns of usage for IAVs versus IBV and human versus avian IVs. The strain-independent host genes served to define 43 experimental and otherwise clinically approved drugs, targeting reportedly fourteen of the encoded host factors. Amongst the approved drugs, the urea-based kinase inhibitors (UBKIs) regorafenib and sorafenib exhibited a superior therapeutic window of high IV antiviral activity and low cytotoxicity. Both UBKIs appeared to block a cell signaling pathway involved in IV replication after internalization, yet prior to vRNP uncoating. Interestingly, both compounds were active also against unrelated viruses including cowpox virus (CPXV), hantavirus (HTV), herpes simplex virus 1 (HSV1) and vesicular stomatitis virus (VSV) and showed antiviral efficacy in human primary respiratory cells. An in vitro resistance development analysis for regorafenib failed to detect IV resistance development against this drug. Taken together, the otherwise clinically approved UBKIs regorafenib and sorafenib possess high and broad-spectrum antiviral activity along with substantial robustness against resistance development and thus constitute attractive host-directed drug candidates against a range of viral infections including influenza.
IVs are the cause of seasonal epidemics with up to 500,000 fatalities per year  as well as occasional pandemics with increased infection and mortality rates . Epidemics are usually caused by human IAV strains of the subtypes H1N1 and H3N2, as well as IBVs. The source for influenza pandemics has in the past often been provided by avian IAVs that managed to adapt to humans as a host. Current preventive and therapeutic measures target viral proteins and include vaccination as well as direct-acting antivirals (DAAs). Unfortunately, a single mutation of the targeted site can lower the efficacy of a virus-directed drug by two to three orders of magnitude. Consequently, isolates resistant against all approved DAAs have been identified [3–5]. Thus, there is an urgent need for new anti-IV drugs which are less prone to the development of resistance.
We present here a large-scale comparative loss-of-function screen for IV replication. We also included an avian IAV strain and an IBV strain. An avian strain has only been tested in one other published screen , whereas no IBV strain was in the focus of previous loss-of-function screens. Due to the comparative nature of the present screen, we were able to detect strain-specific differences in host factor requirement. The number identified, several hundred strain-specific genes and gene groups, was unexpectedly large. The impact of these genes and gene groups on viral replication differed in many instances either between the three human IVs versus the avian IV strain and between the three IAVs versus the IBV strains. These differences likely reflect evolutionary divergence (IAV vs. IBV) or adaptation to divergent hosts (human IV vs. avian IV).