SARS-CoV-2 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. Respiratory viruses keep emerging at a steady pace (e.g. MERS-CoV, enterovirus D68, avian influenza viruses), adding to the burden of respiratory tract infections on global health. In 2019-2020, 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 highlighted the difficulty of effectively treating severe viral lower respiratory tract infections. Major advances have been made in our knowledge of the pathogenic processes involved in severe respiratory disease over the past decade; however, few successful treatments have made their way into the clinic. Although many clinical trials have been performed and are ongoing in COVID-19 patients, very few of those have generated promising results. Even those therapeutics tested with positive outcomes, showed benefits only in a fraction of patients. Thus, it is clear that our current understanding of the pathogenesis of viral lower respiratory tract infections is insufficient to drive the development of effective treatments. Our research has mainly focused on four aspects of COVID-19: animal model development, pathogenesis, support of NIH clinical work, and efficacy of potential antiviral treatments. In terms of animal modeling, we continued our search for a nonhuman primate model that better recapitulates severe COVID-19 in humans by inoculating African green monkeys with SARS-CoV-2. The disease observed in African green monkeys was very similar to that observed in rhesus macaques, with animals showing mild disease with some respiratory signs. Animals shed high levels of virus from the nose and throat and lungs developed mild interstitial pneumonia. This study was designed to not only determine whether African green monkeys develop severe disease after SARS-CoV-2 inoculation, but also to increase our understanding of SARS-CoV-2 pathogenesis. Therefore, we included single-cell RNA sequencing of lungs and mediastinal lymph nodes, showing that SARS-CoV-2 replication in the lungs occurs mainly in pneumocytes, while macrophages drive the inflammatory response. An additional finding in the African green monkey study that was of broad interest to COVID-19 researchers and clinicians, was our finding that genomic RNA (gRNA) levels remain high after inoculation, even in the absence of virus replication. Two control animals were included in this study that were inoculated with inactivated SARS-CoV-2. In these animals, we could detect high levels of gRNA in nose swabs even at 3 days post inoculation; subgenomic RNA (sgRNA) was present in the virus stock used for inoculation but could not be detected in nose swabs, even at 1 day post inoculation. This indicated the great potential value of including sgRNA determination in clinical samples to distinguish long-term RNA shedders from individuals with a long infection (e.g. in immunocompromised patients), as detection of sgRNA would be stronger evidence of recent virus replication. Therefore, these findings resulted in several extensive collaborations with the NIH Clinical Center and clinician-researchers at NIH who we helped to include sgRNA testing in their studies. Finally, we continued our work to test and develop potential SARS-CoV-2 antivirals. We focused on hydroxychloroquine, CR-31-B and a new formulation of remdesivir. Using the rhesus macaque model, we helped to definitively show that hydroxychloroquine is not effective against SARS-CoV-2, a disappointing yet important finding. CR-31-B, an EIF4A inhibitor, also was not effective against SARS-CoV-2 in the K18-hACE2 mouse model. The new remdesivir formulation prevented the development of interstitial pneumonia in rhesus macaque lungs.