Our laboratory studies the relationship between a virus and the organism it infects. Our goal is to understand how different components of a virus population, including non-standard viral genomes, affect the infected organism and how this interaction influences the virus evolution and its maintenance in nature. Below is a summary of our current areas of interest and related projects.

Antiviral immunity

Our laboratory has systematically investigated the impact of non-standard viral genomes of the copy back type (cbVGs) on the induction of the antiviral response. We have shown that during infection with many negative sense RNA viruses cbVGs are the primary triggers of the antiviral response through the stimulation of the intracellular virus sensor molecules RIG-I and MDA5. We identified a specific RNA motif on a Sendai virus cbVG that is responsible for its strong immunostimulatory activity. This cbVG is one of the strongest known natural stimulators of the antiviral response. Some of the questions that remain to be addressed are: How, when and where is this motif exposed to cellular sensors during infection? and are there similar strongly stimulatory motifs present in cbVGs from other viruses?

Copy-back viral genomes (cbVGs) and the cell

Non-standard viral genomes are known to exist since the late 1940s. However, many fundamental questions related to their biology and function remain unanswered, including how do they affect the biology and function of the infected cell. Our data revealed unexpected heterogeneity in the content of cbVGs and standard viral genomes in different cells during infection. Some cells have a higher proportion of cbVGs than standard genomes, while others are enriched in standard genomes. In addition, cbVGs interact with the infected cell differently than standard genomes. These distinct interactions result in different cellular responses, including the formation of stress granules, the stimulation of the antiviral response, and cell survival. Remaining open questions in this area are: What determines the establishment of the cbVG-high and cbVG-low phenotypes? Are these phenotypes stable in time? Can cells change from a cbVG-high to a standard genome-high phenotype? Are other physiological processes impacted by cbVGs?

Non-standard viral genomes as part of the virus community

Our laboratory developed powerful bioinformatics tools that allows us to characterize different species of non-standard viral genomes present during infection. With this tool we can now create a catalogue of non-standard viral genomes generated during natural infections and we can begin to investigate their role in determining infection outcome.

Predicting viral disease severity in humans

The respiratory syncytial virus (RSV) infects all children under the age of two and a large number of these children (~3%) are hospitalized with moderate to severe disease. About half of the hospitalized patients have life threatening conditions and/or develop chronic bronchiolitis, asthma or COPD. Currently, there are no means to predict the clinical outcome of RSV infection in order to optimize treatment of patients at high risk of developing severe disease. We found a strong correlation between detection of cbVGs in respiratory secretions from RSV patients and the clinical severity of the disease. Importantly, the kinetics of cbVG generation critically impacts their protective function in humans. Some open questions in this area are: Can we use cbVGs as a disease prognosis tool in humans? Can cbVGs predict disease severity in other viral infections?

Top right: Percentage of cbVG+ and cbVG- pediatric samples. Bottom: Correlation among relative amount of cbVGs and expression of an antiviral gene

Virus dynamics, ecology and evolution

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?

In addition, the impact of different types of non-standard viral genomes and other secondary viral products during infection is unknown, nor is how these viral products affect the ecology of other commensal or pathogenic microorganisms. Projects in this area will answer the following questions: How do cbVGs relate to and collaborate with other viral secondary products? How do they interact with other microbes during infection? Do they have an impact on the ecology and pathogenesis of other viruses, commensal bacteria and/or fungi?

Host determinants of cbVG generation

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 will use exciting and unique tools including respiratory organoids generated from the collaborative cross mice and unbiased genetic screens to identify host factors that determine the quality and quantity of cbVG generation in mice and humans.

RNA virus persistence and impact on chronic lung diseases

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. Available projects in this area will answer the following questions: What are the mechanisms behind RNA virus persistence in vivo? What is the cellular reservoir for the persistence of respiratory viruses? How does a persistent viral infection impact the development of chronic diseases such as asthma? Are cbVGs responsible for persistence in vivo, as it has been observed in vitro?

Vaccines and 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. Available projects in this area will answer the following questions: Can we use DDOs to identify the minimal requirements for effective induction of type I immunity during vaccination? Can we use DDOs to make better vaccines / can we harness them as adjuvants or antivirals? Do DDOs work in larger animals? Can we optimize their safety and delivery?