Emerging respiratory viruses - pathogenesis and countermeasures

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

In any given year, lower respiratory tract infections are the leading cause of infectious disease deaths worldwide, and the fifth most important cause of death overall. The emergence of SARS-CoV-2 and the resulting COVID-19 pandemic highlighted how devastating the effect of emerging respiratory viruses on global public health and economies can be. The COVID-19 pandemic also showed the difficulty of effectively treating severe viral lower respiratory tract infections, once again highlighting that our current understanding of the pathogenesis of viral lower respiratory tract infections is insufficient to drive the development of effective treatments. The main goal of the Molecular Pathogenesis Unit is to contribute to our understanding of the pathogenesis of emerging viruses that cause severe lower respiratory tract disease such as Nipah virus, influenza A virus and coronaviruses on the level of the host and individual cell. Besides studying how these viruses cause respiratory disease, we are also investigating the neurological complications caused by these viruses. Ultimately, our goal is to identify common pathways involved in lower respiratory tract and neurological disease progression and druggable targets within those pathways. Pathogenesis We continued our work to assess the pathogenicity of SARS-CoV-2 variants of concern (VOC) in rhesus macaques, including the Delta, Omicron BA.1, and Omicron BA.2 VOCs. Our data suggest that in rhesus macaques, Delta replicates to higher levels than the other VOCs, whereas Omicron results in a milder disease. These data reflect findings in the human population where Omicron BA.1 and BA.2 caused milder disease than the Delta VOC. We further optimized the procedures to establish and maintain human lung organoids (hLO). These hLO are derived from adult stem cells. We found that these stem cells, although type 2 pneumocyte-like initially, tend to differentiate over time into a more basal cell-like phenotype based on several markers of cell identity. We worked to optimize culture methods to ensure they maintain their alveolar phenotype. We used the hLO from four donors to compare the fitness and pathogenicity of SARS-CoV-2 variants of concern Delta and Omicron, alongside an early clade B isolate. We showed high replicative fitness of Delta, along with severe attenuation of Omicron, demonstrating that hLOs recapitulate observations of SARS-CoV-2 VOC fitness in the clinic and in vivo. We found significant donor-dependent variability in both susceptibility to VOC infection and the host response. We contributed to several clinical studies, including a pathogenesis study in a large autopsy cohort. We showed that SARS-CoV-2 is widely distributed in deceased patients, even among patients who died with asymptomatic to mild COVID-19, and that replication-competent virus is present in multiple pulmonary and extrapulmonary tissues early in infection. MPUs viruses of interest, SARS-CoV-2, Nipah virus and 1918 H1N1 influenza virus can all cause neurological complications. Whereas neurological complication occurred in a small subset of patients with COVID-19 or the Spanish flu, Nipah virus neurological complications contribute equally to the lethality of this virus in humans. The pathogenesis of NiV neurological disease during the acute, convalescent and relapse phase is poorly understood. We are trying to fill that gap in two ways: by studying archived tissue samples from animal experiments and by developing in vitro and in vivo models. Using histologic characterization of African green monkeys infected with Nipah virus, we have shown which cell types are infected, which cell types mount an inflammatory response to infection, and which cells are extravasating into the CNS during infection. We have started to develop a new Syrian hamster model of neurological disease using a combination of Nipah virus inoculation and suboptimal remdesivir treatment to skew the disease in these animals to neurological signs rather than respiratory disease. We have also initiated the development of in vitro models using differentiated neuronal cultures and human cerebral organoids. We have shown that these culture systems are susceptible to infection with Nipah virus. Countermeasures Nipah virus has been identified by the World Health Organization as a major threat to global health for which vaccines urgently need to be developed. We used the vesicular stomatitis virus (VSV)-vectored, live-attenuated vaccine platform to develop and test two vaccine candidates: one expressing the glycoprotein G and one expressing the fusion protein F of Nipah virus. Our vaccine candidates use the FDA- and EMA-approved VSV-EBOV vaccine as a backbone. This vaccine not only has a proven safety record in humans and has been used successfully in several EBOV outbreaks, it also has the advantage of an extremely short time to protection of only 10 days. We tested the protective efficacy of the VSV-EBOV-based Nipah virus vaccines in African green monkeys. We tested the efficacy of both vaccine candidates to protect from lethal challenge with the homologous Nipah virus, genotype Bangladesh, and the heterologous Nipah virus, genotype Malaysia. The VSV-NiVG vaccine induced high neutralizing antibody titers and afforded complete protection from homologous and heterologous challenge. The VSV-NiVF vaccine induced a lower humoral response and afforded complete homologous protection, but only partial heterologous protection (75%). Both vaccines reduced virus shedding from the upper respiratory tract and virus replication in the lungs and central nervous system. Vaccinated animals that survived lethal Nipah virus challenge did not have histologic evidence of persistent Nipah virus replication in the CNS, an important finding since Nipah virus cases in Malaysia have occasionally resulted in lethal encephalitis relapse in survivors. Based on these data, Public Health Vaccines LLC, sponsored by the Coalition of Epidemic Preparedness Innovations, has recently started a phase 1 clinical trial testing the VSV-NiVG vaccine. Remdesivir is an antiviral with broad-spectrum activity against filoviruses, coronaviruses, and paramyxoviruses. With the approval of the use of remdesivir for use in COVID-19 patients, it has become even more interesting to pursue remdesivir as a treatment for other virus infections. Nipah virus is of has an extremely high case fatality rate of 70% and no antivirals are currently approved for use. In a previous study, we showed that remdesivir treatment resulted in 100% survival in African green monkeys infected with a lethal dose of Nipah virus, when treatment was administered 1 day post inoculation. However, disease progression in Nipah virus patients is often very rapid after diagnosis, and 1 dpi treatment initiation likely does not reflect a feasible treatment scenario in patients. Therefore, we tested the efficacy of two different doses of remdesivir (one reflecting the dose used in COVID-19 patients, and one equal to the dose previously used in African green monkeys infected with Nipah virus) when administered on 3 dpi to African green monkeys inoculated with a lethal dose of Nipah virus. Remdesivir treatment initiation on 3 dpi provided partial protection from severe Nipah virus disease that was dose dependent, with 67% of animals in the high dose group surviving the challenge. However, treatment did not prevent clinical disease. Our findings indicate that remdesivir treatment as it is currently used in COVID-19 patients, would be most effective in Nipah virus patients who are still in the early disease stage.