Research

EMERGING VIRUSES

We are interested in emerging and re-emerging viruses which include a number of different viral families. Many of these viruses are zoonotic, transmitted from animals to humans. One major group of RNA viruses that have historically emerged include arthropod-borne viruses which are transmitted to humans from vector insects. There are three major families of arthropod-borne viruses that are important human pathogens and interestingly these are all small RNA viruses: the flaviiviruses, alphaviruses, and bunyaviruses. We study viruses from each family including flaviviruses such as West Nile virus, dengue virus, and the newly emerged Zika virus. We are studying the alphaviruses including Sindbis and Chikungunya virus as well as the bunyaviruses Rift Valley Fever virus and La Crosse virus. We are interested in exploring the similarities and differences between these viruses and are performing comparative studies to determine mechanisms by which these viruses infect humans and cause disease. We perform genetic and small molecule screens in insect and human cells and explore the mechanisms involved. Tick-borne diseases are also on the rise, and we have begun to expand our studies to include arboviruses that are transmitted by these arthropods.

In addition to arthropod-borne viruses, respiratory viruses are also a large group of emerging viruses. The influenza virus infects the globe yearly and has led to large-scale pandemics in the past. More recently, we have observed increasing incidents of coronavirus spillover which in the last year has led to a pandemic of enormous proportions. These viruses infect the respiratory tract but lead to different outcomes. We are comparing influenza and other respiratory viruses to SARS-CoV-2 as well as studying different coronaviruses with differing pathogenesis (eg common cold coronaviruses to SARS-CoV-2) to gain a better understanding of how these viruses infect and how we can intervene. We are again using our platforms to perform genetic and small molecule screens to define new interventions as well as explore mechanisms that may explain distinct pathogenesis.

We have assays in hand to study many different RNA viruses and can hopefully leverage our expertise to identify antivirals active against large numbers of viral families to potentially be one step ahead of any future pandemics.

INNATE IMMUNITY

The first line of defense against pathogens is our innate immune systems. This pathway is characterized by the recognition of foreign invaders through the sensing of non-self antigens. Importantly, these pathways are engaged in the first infected cells and thus are the earliest steps that can alert the organism to infection. Viruses are largely sensed by conserved, germline-encoded pattern recognition receptors which engage downstream signaling pathways and effector mechanisms. We have been exploring the innate immune responses against emerging viruses to identify how these viruses are sensed, what effector pathways are engaged, and how we may boost these pathways for therapeutic interventions.  

Many successful viruses, including SARS-CoV-2, can evade early recognition of classical innate immune sensors which allows the virus to establish early infection. However, pretreatment with interferons can block infection. And thus, we reasoned that there may be additional innate immune agonists that can block infection and we found that cyclic-dinucleotides, or synthetic STING agonists could block infection of SARS-CoV-2 in vitro and in vivo. In contrast, we found that mature neurons respond quite differently to immune agonists. Treatment with interferons does not block Rift valley fever virus infection while we have identified additional agonists that can attenuate infection. We are exploring cell type-specific responses and mechanisms involved.  We are determining how viruses can be restricted by innate immune stimuli in distinct relevant cells to ultimately develop new strategies for interventions.

Diverse antiviral effector pathways can be engaged to attenuate viral infections. We have performed a variety of genetic and biochemical screens to identify these activities. We have found that the ancient cell biological pathway autophagy can restrict some viral infections. Mechanistically, autophagy can selectively target viral components for degradation and we have been exploring how this can control infections. In addition, we have found interesting cross-talk between interferon-induced gene expression and autophagy. Since there are distinct levels of autophagy in different cell types, this may play an important role in setting the basal activity of this antiviral pathway.  

RNA BIOLOGY

These emerging viruses are RNA viruses. Upon infection, viral RNAs are replicated, transcribed, translated, and packaged into new virions. We are interested in exploring the interface between these viral RNAs and the endogenous RNA machinery in host cells. We have used genetics and proteomics to define the roles of RNA binding proteins and RNA decay pathways in the regulation of RNA virus infection. We have found that conserved RNA helicases bind to viral RNAs to block infection. In addition, we have found complex interactions between endogenous decay pathways and viral infection. In some cases, we have found that the decay machinery can directly target viral RNAs for degradation while in other cases we have found that the RNA decay machinery regulates innate immune genes indirectly impacting viral infection. Mechanistic studies are underway to define this important interface. 

In addition, we have begun to explore the role of non-coding RNAs in the regulation of RNA virus infection. There are a large number of non-coding RNAs, with long non-coding RNAs (lncRNAs) as an emerging class of regulatory RNAs. Their role in emerging virus infections is poorly characterized and thus we have been using genetic approaches to define the roles of these genes in arthropod-borne virus infection. We found that one lncRNA, ALPHA, directly binds to chikungunya virus genomic RNA to attenuate infection. We are exploring the roles of additional lncRNAs in RNA virus infection.  

ENTERIC INFECTION

While arthropod-borne viruses are transmitted to humans as blood-borne pathogens when a mosquito takes a blood meal, these viruses are transmitted to the vector orally. Therefore, arboviruses are enteric viruses of insects. We are using a Drosophila model to explore how insects mount a response to these viruses and how the microbiota and microbiota-derived metabolites impact susceptibility to infection. We have identified innate immune pathways that control viral infection systemically as well as those that selectively function in the gut. Moreover, we found that the microbiota provides ligands including cyclic dinucleotides to prime immunity and we are actively exploring this space. 

ANTIVIRALS

There is a clear dearth of antivirals as exemplified by the fact that there are no specific therapeutics approved for most viruses and any arbovirus. The coronavirus pandemic has renewed the globe’s interest in developing antivirals that will be active against related viruses (eg, pan-anti-coronavirus). Nucleoside analogs are the largest class of approved antiviral drugs, and these can be active against divergent viruses because they target the virally encoded RNA-dependent RNA polymerase, which are highly conserved. At the beginning of the pandemic, it was recognized that remdesivir, a nucleoside analog first developed for the ebola virus, was also active against coronaviruses leading to rapid deployment of this drug to treat COVID-19. Unfortunately, remdesivir is not orally bioavailable limiting its use to hospitalized patients and not acutely infected individuals. Since then, molnupiravir, another broadly acting nucleoside analog has been approved.

We set out to determine if we could identify additional antivirals by leveraging our expertise using our cell-based screening platform to identify antivirals active against SARS-CoV-2. We have tested ~20,000 drugs that have been previously developed for those that may also be active against SARS-CoV-2. This has led us to identify a panel of 16 nucleoside analogs with antiviral activity including remdesivir and molnupiravir. We also identified drugs that target nucleoside metabolism and found that inhibiting pyrimidine biosynthesis synergizes with the antiviral activity of remdesivir or molnupiravir suggesting this combination for therapy. We are currently exploring the additional antivirals that we identified in our SARS-CoV-2 screens. Mechanistic studies revealed that 10 drugs block the earliest steps in the infection, viral entry. We are determining how they block viral entry, and whether these may show activity against emerging variants that have increased transmission and spread.  We are screening additional libraries of small molecules to identify new inhibitors. In addition, we are extending our exploration of combinations to identify drugs that could be used together to reduce the likelihood of resistance and increase potency. We are also extending our studies to additional groups of RNA viruses including arboviruses and henipaviruses with the goal of identifying antivirals including nucleoside analogs with potent activity.