Discovery of Genes that Modulate Flavivirus Replication in an Interferon-Dependent Manner.

Establishment of the interferon (IFN)-mediated antiviral state provides a crucial initial line of defense against viral infection. Numerous genes that contribute to this antiviral state remain to be identified. Using a loss-of-function strategy, we screened an original library of 1156 siRNAs targeting 386 individual curated human genes in stimulated microglial cells infected with Zika virus (ZIKV), an emerging RNA virus that belongs to the flavivirus genus. The screen recovered twenty-one potential host proteins that modulate ZIKV replication in an IFN-dependent manner, including the previously known IFITM3 and LY6E. Further characterization contributed to delineate the spectrum of action of these genes towards other pathogenic RNA viruses, including Hepatitis C virus and SARS-CoV-2. Our data revealed that APOL3 acts as a proviral factor for ZIKV and several other related and unrelated RNA viruses. In addition, we showed that MTA2, a chromatin remodeling factor, possesses potent flavivirus-specific antiviral functions induced by IFN. Our work identified previously unrecognized genes that modulate the replication of RNA viruses in an IFN-dependent manner, opening new perspectives to target weakness points in the life cycle of these viruses.

Retinoic Acid Inducible Gene I and Protein Kinase R, but Not Stress Granules, Mediate the Proinflammatory Response to Yellow Fever Virus.

Yellow fever virus (YFV) is an RNA virus primarily targeting the liver. Severe YF cases are responsible for hemorrhagic fever, plausibly precipitated by excessive proinflammatory cytokine response. Pathogen recognition receptors (PRRs), such as the cytoplasmic retinoic acid inducible gene I (RIG-I)-like receptors (RLRs), and the viral RNA sensor protein kinase R (PKR), are known to initiate a proinflammatory response upon recognition of viral genomes. Here, we sought to reveal the main determinants responsible for the acute cytokine expression occurring in human hepatocytes following YFV infection. Using a RIG-I-defective human hepatoma cell line, we found that RIG-I largely contributes to cytokine secretion upon YFV infection. In infected RIG-I-proficient hepatoma cells, RIG-I was localized in stress granules. These granules are large aggregates of stalled translation preinitiation complexes known to concentrate RLRs and PKR and are so far recognized as hubs orchestrating RNA virus sensing. Stable knockdown of PKR in hepatoma cells revealed that PKR contributes to both stress granule formation and cytokine induction upon YFV infection. However, stress granule disruption did not affect the cytokine response to YFV infection, as assessed by small interfering RNA (siRNA)-knockdown-mediated inhibition of stress granule assembly. Finally, no viral RNA was detected in stress granules using a fluorescence in situ hybridization approach coupled with immunofluorescence. Our findings suggest that both RIG-I and PKR mediate proinflammatory cytokine induction in YFV-infected hepatocytes, in a stress granule-independent manner. Therefore, by showing the uncoupling of the cytokine response from the stress granule formation, our model challenges the current view in which stress granules are required for the mounting of the acute antiviral response.IMPORTANCE Yellow fever is a mosquito-borne acute hemorrhagic disease caused by yellow fever virus (YFV). The mechanisms responsible for its pathogenesis remain largely unknown, although increased inflammation has been linked to worsened outcome. YFV targets the liver, where it primarily infects hepatocytes. We found that two RNA-sensing proteins, RIG-I and PKR, participate in the induction of proinflammatory mediators in human hepatocytes infected with YFV. We show that YFV infection promotes the formation of cytoplasmic structures, termed stress granules, in a PKR- but not RIG-I-dependent manner. While stress granules were previously postulated to be essential platforms for immune activation, we found that they are not required for the production of proinflammatory mediators upon YFV infection. Collectively, our work uncovered molecular events triggered by the replication of YFV, which could prove instrumental in clarifying the pathogenesis of the disease, with possible repercussions for disease management.

A Framework for Aquatic Invasive Species Surveillance Site Selection and Prioritization in the US waters of the Laurentian Great Lakes.

Risk-based prioritization for early detection monitoring is of utmost importance to prevent and mitigate invasive species impacts. The Great Lakes Water Quality Agreement, a binational commitment between the United States and Canada to restore and protect the waters of the Laurentian Great Lakes, identifies aquatic invasive species (AIS) as one of ten priority issues (annexes) that must be addressed to ensure the chemical, physical, and biological integrity of the Great Lakes. The Agreement calls out the need for a comprehensive strategy for detecting and tracking new and potentially invasive species. Yet, with a surface water area of 95, 000 square miles (246, 049 square km) and shoreline length of 10, 210 miles (16, 431 km), the Great Lakes represent a daunting challenge for prioritizing where AIS surveillance activities should occur. Our goal was to develop a spatially-explicit and quantitative approach for identifying the highest risk sites for AIS introduction into the US waters of the Great Lakes based on the cumulative risk of new introductions (including range expansions) from a range of pathways and associated taxa. We estimate "invasion risk" scores for nearly 6,000 sites (9 km x 9 km) across the Great Lakes basin using proxy measures for propagule pressure weighted by the proportion of taxa associated with each proxy variable. Proxy variables include human population, number of ship visits, marina size, number of ponds, and number of natural or artificial aquatic connections. In total, we identify more than 1,800 sites with invasion risk scores >0. A small subset of these 1,800+ sites accounts for a majority of predicted propagule pressure and are therefore logical targets for future surveillance and AIS prevention efforts. Many of the highest risk sites are located in western Lake Erie, southern Lake Michigan, and the St. Clair-Detroit River System.