Our laboratory has shown that during infection with several negative sense RNA viruses, including respiratory syncytial virus (RSV) and parainfluenza virus, the host antiviral response is primarily triggered by non-standard viral genomes of the copy back (cbVGs) type. cbVGs robustly stimulate the intracellular virus sensor molecules RIG-I and MDA5 to signal for expression of interferons and other pro-inflammatory molecules. We identified a specific RNA motif on a parainfluenza virus (Senday virus; SeV) cbVG that is responsible for its strong immunostimulatory activity (PubMed link). Recently, we identified similar motifs in other respiratory viruses, including RSV and Nipah virus.  The SeV immunostimulatory motif is one of only two immunostimulatory viral RNAs identified to date and it is the strongest known natural stimulators of the antiviral response. Understanding how this motif engages RIG-I and MDA5 could change the understanding of the requirements for robust stimulation of the antiviral response. Current opportunities in this areas aim at answering: How, when and where is this motif exposed to cellular sensors during infection? How does this motif interact with RIG-I and MDA5?  Expertise in RNA biology is ideal. (Updated 12/2025)

We and others have extensively shown that cbVGs alter the course and pathogenesis of viral infections. Fast and strong production of cbVGs generally results in a lower viral load and reduced inflammation, while slow or weak production of cbVGs results in higher viral titers and delayed but robust pathogenic inflammatory responses, both in mice and humans. Our evidence suggests that the speed and amount of cbVGs generated in humans varies independently of the virus, but which host factors modulate cbVG generation is unknown. Projects in this area use several tools including unbiased genetic screens to identify host factors that determine the quality and quantity of cbVG generation in mice and humans.

In addition, we are studying viral factors that influence cbVG generation. In recent work we have identified cbVG generated from rejoining nucleotide one of the viral genome to an internal position close to the 5' of the viral genome (Publication link). These predicted "long cbVGs" are conserved in all viruses we have tested and we are currently investigating their role in generating smaller cbVGs.

Increasing evidence supports the persistence of RNA viruses in different tissues long after the acute infection has been cleared. This evidence includes reports of persistent virus RNA in infections with Ebola virus, Zika virus, measles virus, parainfluenza viruses and respiratory syncytial virus. Persistent viruses are a continue source of virus and are associated with the development of chronic diseases, such as asthma and COPD, after parainfluenza or respiratory syncytial virus infections. It is unknown how these RNA viruses persist and whether there are means of eliminating this reservoir. We have established a mouse model to study the persistence of RNA viruses that are believed to be acute. We have demonstrated that parainfluenza viruses persist leaving footprint in lung epithelial cells and that parainfluenza virus persistence in mice causes chronic asthma-like disease (Publication link) . Current projects investigate the mechanisms behind RNA virus persistence in vivo, follow up on the identification of the cellular reservoir persistent respiratory viruses, test whether cbVGs are responsible for persistence in vivo, and look for the impact of persistence in the upper respiratory tract. In addition, we are investigating the molecular mechanisms leading to the long term maintenance of the virus within cells. 

Non-standard viral genomes are part of the virus ecosystem. Little is known of the impact of non-standard viral genomes on the dynamics of standard virus spread, transmission, or evolution. The ubiquitous presence of non-standard viral genomes in most viral infections and their critical role in initiating host immune responses reveal a puzzling gap in our understanding of the determinants and evolutionary tradeoffs of virus recognition by the host immune system and raise the question: why do viruses retain production of immunostimulatory cbVGs that may ultimately lead to their clearance? We are interested in exploring this question and in addressing how virus, host and cbVGs affect each other. Are cbVGs drivers or regulators of virus evolution? Do different environments within a host affect the virus/cbVG dynamics? Does the immunological status affect viral evolution and cbVG generation?

Unexpectedly, cbVGs localize to different intracellular compartments that the standard viral genome. Efforts to understand the consequences of this distinct intracellular localization led us to discover that the viral polymerase L and its co-factor C are key in guiding parainfluenza viral RNA-containing ribonucleoprotein (RNP) to the microtubule network for transport to the cell surface for virus assembly and budding (Publication link). Understanding the details of the molecular mechanisms behind virus assembly is critical to identify potential antiviral targets. Current work aims at dissecting the molecular details of parainfluenza virus RNP trafficking inside the cells and expand to investigate the assembly and trafficking of RSV RNA from inclusion bodies. 

Henipaviruses are the most dangerous cousins of parainfluenza virus. Infections with Nipah and Hendra virus, although sporadic, are highly lethal to humans. Designing and generating effective antivirals requires detailed understanding of the virus replication process and its weaknesses. Due to a fortuitous accident, we discovered that the polymerase complex of both Nipah and Hendra viruses are promiscuous challenging the long-term paradigm that only the cognate polymerase functions well for replication and no individual components of the replication complex can work with components of another virus (Publication Link). Current work focuses on the mechanism behind the the viral polymerase promiscuity and seeks to develop pan henipa virus antivirals,

A challenge for vaccine development is the absence of safe immunostimulatory molecules to induce protective responses against intracellular pathogens that can evade antibody detection, such as viruses. This type of immune response would ideally be a “type I” immune response including antigen-specific Th1 CD4+ T cells and cytotoxic CD8+ T cells. We have identified replication defective-derived oligonucleotides (DDOs) as potential immunostimulatory molecules able to promote the development of protective type I immunity against viruses. DDOs contain the critical immunostimulatory motif that makes SeV DVGs one of the stronger natural immunostimulants. Our data show that in mice DDOs trigger a type I cellular immune response able to protect from challenge with a highly pathogenic virus when delivered in the context of protein, inactivated virus or mRNA vaccines (Publication link). Currently, we are testing whether DDOs, or similar molecules derived from other viruses, serve as therapeutic agents against cancer.