Vineet D. Menachery, Ph.D. - US grants

DESCRIPTION (provided by applicant): Coronaviruses (CoV) are important emerging human viruses, with multiple cross-species transmission events identified over the past 200 years. Human infections with severe acute respiratory syndrome coronavirus (SARS-CoV), the first newly emerged virus of the 21st century, results in acute and organizing phase diffuse alveolar damage, atypical pneumonia, and acute respiratory distress syndrome (ARDS), leading to mortality rates of 10-50 percent, dependent on age. A major component in the success of the SARS-CoV is its ability to manipulate and subvert the host immune response. Studies by our laboratory and others have revealed numerous genes that antagonize the type I interferon (IFN) response including NSP1, ORF3b, and ORF6. In addition, several groups have generated SARS-CoV deletion mutants and demonstrated various levels of attenuation, possibly due to increased type I IFN sensitivity. A central hypothesis in this application is that highly conserved viral gene functions that target type I IFN responses can serve to provide a universal platform for the rational design of vaccine and drug therapeutics affording rapid responses in outbreak settings. Recently, research has focused on viral components involved in type I RNA capping utilized by SARS, other CoV, and many RNA and DNA viruses. In an ordered process, several CoV proteins contribute to the capping process including NSP13 (RTPase), NSP14 (N7-guanine methylation), and NSP10 (scaffold). However, interest has focused on NSP16, a S-adenosylmethionine (SAM) dependent nucleoside 2'-O-methyltransferase (2'-O-MTase) and its critical role in subverting the type I IFN response. Recent works have implicated 2'O- methylation in distinguishing between self and non-self RNA by MDA-5, a RIG-I like recognition molecule, and the IFIT family of interferon stimulated genes (ISGs). These results suggest that 2'-O-MTases like NSP16 play a critical role in immune antagonism during viral infection. Based on these recent findings, we sought to evaluate the impact of 2'O-methylation on SARS-CoV replication and pathogenesis by generating mutants lacking NSP16 2'O-MTase activity. We hypothesize that deltaNSP16 mutant viruses will be exquisitely sensitive to and attenuated in the presence of type I IFN both in vitro and in vivo. We anticipate the absence of type I IFN signaling or specific ISGs including MDA5 and IFIT family members will restore replication and possibly virulence. Due to broad conservation of this activity across RNA and DNA virus families, targeting the 2'O methylation pathways with either vaccine or drug strategies may provide unique, broadly applicable treatment options that can protect against current and emerging viruses.

? DESCRIPTION (provided by applicant): Viral respiratory tract infections are among the leading causes of hospitalization, economic loss, and mortality in the US and worldwide. With the continued threat from emerging pathogens as well as complications from more common respiratory viruses, understanding these infections and their accompanying host responses remain a major priority for global public health. In particular, efforts must also be made to understand these infections within the context of an aging population. While modern germ theory has greatly reduced its burden, infectious disease remains the fourth leading cause of death in aging adults. Coupled with the robust increase in aged populations over the next two decades, these factors highlight the importance of understanding the interplay between infection and the senescent host. While significant progress has been made in understanding the age-related deficiency in adaptive immunity, much less is understood about tissue specific and innate immune cell function in the aging host. Therefore, these studies take a systems based approach to characterize and examine the early tissue-specific and innate immune responses to respiratory virus infection within the context of aging. Utilizing severe acute respiratory syndrome coronavirus (SARS-CoV), the proposal seeks to compare young, middle-aged, and aged mice in order to identify, confirm, and validate major change in pathway and immune activation that contribute to enhanced susceptibility and can be exploited for therapeutic treatment. In addition, the project extends examination into primary human airway and immune cells in order to confirm and validate in vivo finding. Finally, efforts will be made to explore th contribution of broad epigenetic changes to differential responses in young and aged models. Together, these approaches will yield important findings critical to understanding and treating current and future respiratory virus infections in aged populations.

Abstract The coronavirus (CoV) spike protein is a key viral determinant responsible for receptor binding and fusion/entry. The spike protein has also been predicted to be the major factor driving cross-species transmission, allowing the emergence of epidemic strains like SARS- and MERS-CoV. In the first decade after SARS-CoV emergence, changes to the epidemic spike that allowed binding to a new host receptor were thought to underlie this zoonotic emergence. However, our work has shown that bat species already harbor SARS-like CoVs with spike proteins capable of infecting human cells. These results argue that for a subset of bat CoVs, receptor binding and infection of human cells is not the major barrier for emergence. We found that despite equivalent replication in vitro, chimeric viruses containing bat CoV spikes have reduced virulence in vivo. Mice infected with a chimeric SARS-CoV expressing the bat derived SHC014-CoV spike had reduced weight loss and lethality compared to SARS-CoV controls. Importantly, this attenuation occurs despite equivalent replication to SARS-CoV in the lung. The results indicate that virulence is dictated by more than just the ability to infect host cells in vitro. Notably, we also found that the SHC014 spike chimera has reduced infection of the large airways of the lung. These preliminary data shaped our central hypothesis that SARS- CoV virulence is predicated on both host interactions with and viral motifs in the CoV spike protein. Understanding the host and viral mechanisms that drive reduced airway infection may predict in vivo pathogenesis and have critical implications for zoonotic emergence. In this proposal, we explore the host factors and CoV spike changes that attenuate the zoonotic SHC014 spike in vivo. In part one, we examine tropism changes finding that the zoonotic SHC014 spike has impaired upper airway infection. We predict that this incompatibility relates to differences in host protease activity. We subsequently define the specific host proteases that mediate this attenuation using both in vitro and in vivo approaches. In part two, we use mouse-adaptation and structural analysis to predict spike changes responsible for attenuation of the SHC014 spike. We subsequently generate mutant viruses and restore the SHC014 spike or attenuate the SARS spike in vivo. Finally, we evaluate the mechanism of attenuation focusing on spike interactions with host proteases. Together, the proposal identifies host proteases and spike interactions that alter airway infection and dictate virulence following coronavirus infection. These findings provide critical insights for understanding virulence as well as have important implications for emergence and transmission of coronaviruses.

Abstract Both aging and host genetics play a critical role in susceptibility to viral infection. In our proposal, we use the Collaborative Cross (CC), a novel mouse genetic resource, to explore how host genetics impacts age dependent susceptibility to infection. Infection with Severe Acute Respiratory Syndrome coronavirus (SARS- CoV), the first outbreak virus of the 21st century, caused a range of respiratory infection with more serve disease observed in patients over the age of 50. Importantly, aging susceptibility is conserved in mouse models of SARS-CoV infection and increased disease is not due to higher viral load in older animals. The results indicate host responses drive differential disease in the aged. However, age-dependent susceptibility is not completely conserved across the genetically diverse CC populations. Screening eleven CC lines with SARS-CoV infection at 18 months old, we identified seven lines with more disease as they aged, three lines equivalent to their younger controls, and one line more resistant as it aged. Together, our preliminary results indicate that certain genetic elements contribute to age-dependent susceptibly to SARS-CoV infection. Building from this screen, we will generate an F2 cross using a CC line with age-dependent susceptibility and a CC line without; we will then challenge both young and aged F2 mice to further characterize genetic loci that contribute to SARS-CoV disease and to identify QTL specifically associated with aging and age-dependent disease. We anticipate that these novel genetic loci will provide a foundation for understanding the role of genetic diversity in SARS-CoV disease and aging processes. We expect the results to also to inform future treatment approaches for elderly patients.