SARS-CoV-2 pathogenesis and countermeasures

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications & trials

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 SARS-CoV-2 work consisted of supporting several clinical studies and pathogenesis studies. We continued our work to assess the pathogenicity of SARS-CoV-2 VOC in rhesus macaques, including the Delta, Omicron BA.1, and Omicron BA.2 VOCs. Due to confounding factors in the human population, such as pre-existing immunity, comparing severity of disease caused by different VOCs is challenging. The rhesus macaque model offers the opportunity to study pathogenicity of SARS-CoV-2 VOC in the absence of confounding factors. Clinical scoring in rhesus macaques inoculated with Omicron BA.1 or BA.2 was lower than those inoculated with Delta. Furthermore, inoculated inoculation with the Delta VOC resulted in significantly higher viral loads in nasal swabs, bronchial cytology brush samples, and lung tissue than the D614G, Alpha, Beta, and Omicron BA.1 and BA.2 variants in rhesus macaques, whereas shedding observed in animals inoculated with Omicron BA.1 and BA.2 was similar to the Alpha and Beta VOCs. Cytokines and chemokines were upregulated in nasosorption samples of Delta animals compared to Omicron BA.1 and BA.2 animals. In BAL bronchoalveolar lavage samples, upregulation of cytokines and chemokines was evident on day 2 in Delta and Omicron BA.1 animals, but not in Omicron BA.2 animals. Overall, this these data suggests that in rhesus macaques, Delta replicates to higher levels than the other VOCs, whereas Omicron results in a milder disease. We studied the pathogenicity of SARS-CoV-2 variants of concern (VOC) in human lung organoids (hLO) developed in our laboratory, derived from adult stem cells. We used these hLOs to compare the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, alongside an early clade B isolate containing the D614G mutation in spike. 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. Despite thorough evaluation, we did not observe any evidence of cell death in infected hLOs, suggesting that virus-induced cell death is not epithelial intrinsic. This observation highlights the need for further investigation into the mechanisms of virus-induced pathology in vivo. We utilized hLOs derived from four donors, and we uncovered donor-dependent variability in both susceptibility to VOC infection and the host response. In one hLO donor, we observed enhanced susceptibility to SARS-CoV-2 D614G and Omicron that was associated with a lower level of tonic interferon signaling at baseline in hLOs from one donor. We supported several clinical studies with our standardized SARS-CoV-2 assays. We helped the NIH Clinical Center by performing short-notice, short-turn around testing of patient material in these assays whenever clinically relevant. To investigate the cellular tropism, replication competence, persistence and evolution of SARS-CoV-2 in humans, autopsies were performed on 44 patients who died with COVID-19, with extensive sampling of the central nervous system in 11 of these patients. SARS-CoV-2 was widely distributed, predominantly among patients who died with severe COVID-19, and virus replication was detected in multiple respiratory and non-respiratory tissues, including the brain, early in infection. Our sequence analyses showed significant within-host adaptation of SARS-CoV-2 in different organs. Further, we detected persistent SARS-CoV-2 RNA in multiple anatomic sites, including regions throughout the brain, for up to 230 days following symptom onset. We were the first to isolate infectious virus from the brain, and showed definitively for the first time that SARS-CoV-2 can enter and replicate in the human CNS.Despite extensive distribution of SARS-CoV-2 RNA throughout the body, we observed little evidence of inflammation or direct viral cytopathology outside the respiratory tract. Our data indicate that in some patients SARS-CoV-2 can cause systemic infection and persist in the body for months.