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Research thematic

 

FROM MOLECULAR MECHANISMS TO PATHOGENESIS OF VIRAL INFECTIONS

To study and combat viral infections, our team employs both fundamental research approaches, focusing on deciphering the molecular mechanisms involved during infection, and applied research to develop new prophylactic and therapeutic treatments. Our research projects can be categorized into two main axes.

 

1. MONONEGAVIRUS AXIS

Many human pathogens, such as the measles virus, mumps virus, rabies virus, and emerging viruses like Ebola and Nipah, are enveloped viruses with a non-segmented, single-stranded RNA genome of negative polarity (order Mononegavirales). We currently lack prophylactic and/or therapeutic treatments for many of these pathogens, highlighting the need to understand how these viruses replicate in order to develop new antiviral approaches.

Fruit bats of the genus Pteropus, found in some French overseas territories, are reservoirs for several henipaviruses, including Nipah virus (NiV), which can be transmitted to humans and regularly causes deadly outbreaks in Southeast Asia and South Asia. For these reasons, this virus poses a pandemic risk and is listed as a priority pathogen by the WHO. We study Nipah virus at the P4 Jean Mérieux laboratory under infectious conditions with in cellula and in vivo experiments.

 

Key Projects

A. Structure and Function of the Viral RNA Synthesis Machinery.

Mononegaviruses use original and sophisticated molecular mechanisms for transcribing and replicating their genome. The RNA synthesis machinery consists of a fully encapsidated genomic RNA within a non-covalent homopolymer of nucleoproteins (N), known as a nucleocapsid, and a polymerase complex comprising two viral proteins: L and P. The L protein possesses all the catalytic activities required for the synthesis of mature mRNA and genome replication. Its cofactor, the P protein, facilitates the recruitment of the complex to the nucleocapsid and the addition of new nucleoproteins during genome replication.

While we have structural and functional information, many questions remain. How do these components assemble to form the RNA synthesis machinery? How does the viral genome access the catalytic site of the polymerase? How are the cap and poly(A) tail added to the mRNAs?...

To gain a comprehensive understanding of the molecular mechanisms at play, we study this molecular machinery through structural approaches (cryo-electron microscopy) and functional assays (in vitro and in cellula reconstitutions of the viral RNA synthesis machinery, recombinant viruses, etc.). Our two primary subjects of study are Nipah virus and vesicular stomatitis virus (VSV), an ideal prototype for examining these mechanisms.

Figure 1. Structure of the components of the RNA synthesis machinery of paramyxoviruses.

 

B. Host-Pathogen Interactions

Throughout evolution, the "arms race" between host cells and their pathogens has led to the development of cellular antiviral mechanisms and viral countermeasures. These diverse and complex interactions are crucial for both the replication and dissemination of the virus as well as its control and elimination by the host.

We decode these molecular mechanisms using molecular and cellular biology approaches (co-immunoprecipitation, reporter gene activation assays, RT-qPCR, flow cytometry, etc.). Our team has specifically elucidated how the non-structural protein W of NiV inhibits the NF-kB signaling pathway (Enchery et al., 2021). Additionally, we have identified cellular sentinel proteins of the innate immune system responsible for detecting NiV RNA (Iampietro et al., 2020). Our group has also demonstrated that the STING signaling pathway, which specializes in detecting pathogenic or degraded DNA, is activated during infections by NiV and measles virus (Iampietro et al., 2021), and deciphered the associated mechanism (Amurri et al., 2024). The basic study of the impact of the STING axis during NiV infections could establish potential targeted therapeutic strategies.

Although asymptomatic in its natural host (fruit bats of the Pteropus genus), NiV infection is highly pathogenic in accidental hosts such as primates. To understand this difference in severity, we conduct comparative studies of host-pathogen interactions and cellular responses to infection in cells derived from natural or accidental hosts.

Figure 2. Mechanisms responsible for STING activation following infection by measles virus and Nipah virus.

 

 

C. Comparative pathogenesis in natural and accidental hosts

The different strains of Nipah virus do not induce symptoms when hosted by bats, yet they are highly pathogenic when encountered by accidental hosts. Infection of primates by the Bangladeshi strain of NiV triggers a severe pulmonary inflammatory response leading to acute respiratory distress, while the Malaysian strain results in equally lethal brain infections. We study the characteristics of this hyperinflammation and the dissemination of the virus within the body to understand the mechanisms responsible for its high pathogenicity. We also compare these mechanisms to the effective defense strategies employed by bats. Gaining a better understanding of these mechanisms could help us develop targeted therapies for humans.

To achieve this, in collaboration with VetAgro Sup, we are establishing a Pteropus aviary to study their immune defense mechanisms. This unique facility will enable us to evaluate the animals' responses in real-time and develop solutions to control viral prevalence in wild populations.

 

Figure 3. Study of the interactions between henipaviruses and their natural and accidental hosts.

 

 

D. Development of antiviral approaches

We conduct preclinical studies to test the efficacy of peptides that block viral entry (through the fusion of the viral and cellular membranes) during respiratory infections caused by measles virus (MeV), Nipah virus (NiV), and SARS-CoV-2. These studies are based on encouraging results obtained in rodent models (hamster model for NiV and transgenic mice for MeV) (Sellin et al., 2006; Mathieu et al., 2018). In this project, we utilize an aerosolization approach for the peptides, representing a novel strategy for administering fusion-inhibiting peptides to protect at-risk populations from respiratory viral infections. 

This project is being conducted in close collaboration with the groups of Anne Moscona and Matteo Porotto at Columbia University in New York, and has already yielded very promising results for a prophylactic treatment against measles (Reynard et al., 2022). Confirming the efficacy of this strategy in non-human primate models will provide the necessary proof of concept to initiate clinical studies. 

The development of these fusion-inhibiting peptide treatments in humans will pave the way for a technological platform to combat infections from MeV and NiV, as well as other viruses that utilize similar entry mechanisms. This technology will then offer a complementary prophylactic approach to vaccination.

In collaboration with the laboratory of Yves Lévy and Sylvain Cardinaud at the Vaccine Research Institute, we have also tested vaccine candidates targeting antigen-presenting cells (Pastor et al., 2024).

Figure 4. Aerosolization of fusion-inhibiting peptides: a new antiviral strategy against respiratory viruses.

 

 

AXIS 2 - SARS-COV-2 AND ENDOGENOUS RETROVIRUS

COVID-19 and its frequent long-term complications (long COVID) continue to pose a major health issue, with at least 65 million patients currently suffering from long COVID worldwide. Due to the significant heterogeneity in patient profiles, there are few biomarkers available to identify high-risk patients who may develop severe forms of COVID-19 and its long-term complications or to guide personalized treatment options. 

Our project aims to analyze the role of human endogenous retroviruses (HERVs), known for their strong pro-inflammatory potential, in the immunopathogenesis of COVID-19 and long COVID, and to identify and evaluate a set of important biomarkers for diagnosis, prognosis, and patient monitoring. Recent data from the consortium have demonstrated that the HERV-W envelope protein is highly expressed in lymphocytes from COVID-19 patients and is correlated with inflammatory markers and respiratory outcomes of the disease (Charvet et al., 2023). These results suggest that HERVs play a role in the pathogenesis of COVID-19.

We are evaluating the biological pathways and functions underlying the association between HERV expression and severe forms of COVID-19 and associated complications. Parameters will be determined to predict the clinical progression of the disease and the exacerbation of symptoms induced by SARS-CoV-2, allowing for a potential grouping of different bio-clinical profiles of patients. The diagnostic and prognostic panels derived from our fundamental research and subsequent evaluations of HERV-associated biomarkers will be assessed to define new indicators for therapeutic strategies based on precision medicine, leading to individualized medical treatment for COVID-19 and long COVID.

Figure 5. Multicenter study of HERV-W envelope activation induced by SARS-CoV-2:
towards personalized treatment for patients with COVID-19 and long COVID.