SARS-CoV-2: Pathogenesis and Countermeasure Development

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

(1) Animal model development: We have established the Syrian hamster model for pathogenesis studies and countermeasure development. Following intranasal inoculation of SARS-CoV-2, hamsters consistently developed moderate broncho-interstitial pneumonia, with high viral lung loads and extensive virus shedding. We determined the infectious dose 50 to be only five infectious particles. (Rosenke et al., Emerg Microbes Infect 2020) We determined the ability of SARS-CoV-2 to infect domestic pigs via experimental oral/intranasal/intratracheal inoculation, and to transmit to co-housed nave sentinel pigs. None of the inoculated pigs showed evidence of clinical signs, viral replication or specific antibody responses. Moreover, none of the sentinel pigs displayed markers of SARS-CoV-2 infection. Thus, young pigs are not susceptible to infection. (Meekins et al., Emerg Microbes Infect 2020). We have developed an African green monkey model for assessing SARS-CoV-2 variants. Intranasal Infections with either a contemporary D614G or the UK B.1.1.7 variant caused mild respiratory disease with no significant differences in clinical presentation. Significantly higher levels of viral RNA and infectious virus were found in upper and lower respiratory tract samples and tissues from B.1.1.7 infected animals. Our results indicate that B.1.1.7 infection is associated with increased respiratory replication and shedding but no disease enhancement similar. (Rosenke et al., under review) (2) Antiviral testing: We have established an in vitro drug screening pipeline that will feed promising candidates into in vivo testing using the Syrian hamster model. (Jarvis et al., Antivir Ther 2020). We tested peptide-conjugated morpholino oligomers (PPMO) designed to base-pair with sequence in the 5' terminal region or the leader regulatory sequence region of SARS-CoV-2 genomic RNA for their antiviral efficacy in cell culture. PPMOS were highly efficacious, reducing viral titres by up to 4-6 log10 in cell cultures at 48-72 h post-infection. (Rosenke et al., J Antimicrob Chemother 2021). We assessed the prophylactic/therapeutic efficacy of hydroxychloroquine (HCQ) in two animal disease models. The standard human malaria HCQ prophylaxis and treatment did not significantly benefit clinical outcome nor reduce SARS-CoV-2 replication/shedding in the upper and lower respiratory tract in the Syrian hamster and rhesus macaque disease model. (Rosenke et al., JCI Insight 2020; Funnell et al., Nat Commun 2020). We showed that MK-4482, an orally administered nucleoside analog, inhibits SARS-CoV-2 replication in the Syrian hamster model. The inhibitory effect of MK-4482 on SARS-CoV-2 replication is observed in animals when the drug is administered either beginning 12 h before or 12 h following infection in a high-risk exposure model. These data support the potential utility of MK-4482 to control SARS-CoV-2 infection in humans following high-risk exposure as well as for treatment of COVID-19 patients. (Rosenke et al., Nat Commun 2021). (3) Host response to infection: Severe coronavirus disease 2019 (COVID-19) has been associated with T cell lymphopenia, but no causal effect of T cell deficiency on disease severity has been established. We studied rhesus macaques that were depleted of either CD4+, CD8+, or both T cell subsets prior to infection. Peak virus loads were similar in all groups, but the resolution of virus in the T cell-depleted animals was slightly delayed compared to that in controls. The T cell-depleted groups developed virus-neutralizing antibody responses and class switched to IgG. When reinfected 6 weeks later, the T cell-depleted animals showed anamnestic immune responses characterized by rapid induction of high-titer virus-neutralizing antibodies, faster control of virus loads, and reduced clinical signs. These results indicate that while T cells play a role in the recovery from acute SARS-CoV-2 infections, their depletion does not induce severe disease, and T cells do not account for the natural resistance of rhesus macaques to severe COVID-19. (Hasenkrug et al., mBio 2021). We compared African green monkeys inoculated with infectious SARS-CoV-2 or irradiated, inactivated virus to study the dynamics of virus replication throughout the respiratory tract. Genomic RNA from the animals inoculated with the irradiated virus was found to be highly stable, whereas subgenomic RNA, an indicator of viral replication, was found to degrade quickly. We combined this information with single-cell RNA sequencing of cells isolated from the lung and lung-draining mediastinal lymph nodes. Through detection of reads to the viral genome, we were able to determine that replication of the virus in the lungs appeared to occur mainly in pneumocytes, whereas macrophages drove the inflammatory response. Monocyte-derived macrophages recruited to the lungs, rather than tissue-resident alveolar macrophages, were most likely to be responsible for phagocytosis of infected cells and cellular debris early in infection, with their roles switching during clearance of infection. (Speranza et al., Sci Transl Med 2021). (4) Vaccine development: We have developed repRNA-CoV2S, a stable and highly immunogenic vaccine candidate comprised of an RNA replicon formulated with a novel Lipid InOrganic Nanoparticle (LION) designed to enhance vaccine stability, delivery, and immunogenicity. We have shown that intramuscular injection of LION/repRNA-CoV2S elicited robust anti-SARS-CoV-2 spike protein IgG antibody isotypes indicative of a Type 1 T helper response as well as potent T cell responses in mice. Importantly, a prime-only administration in nonhuman primates elicited antibody responses that potently neutralized SARS-CoV-2 as well as T cell responses indicative of a Type 1 T helper response. (Erasmus et al., Sci Transl Med 2020). We studied the protective activity of an intranasally administered chimpanzee adenovirus-vectored vaccine encoding a pre-fusion stabilized spike (S) protein (ChAd-SARS-CoV-2-S) in non-human primates. Rhesus macaques were immunized with ChAd-Control or ChAd-SARS-CoV-2-S and challenged 1 month later by combined intranasal and intrabronchial routes with SARS-CoV-2. A single intranasal dose of ChAd-SARS-CoV-2-S induces neutralizing antibodies and T cell responses and limits or prevents infection in the upper and lower respiratory tracts after SARS-CoV-2 challenge. (Hassan et al., Cell Rep Med 2021). We further evaluated a DNA vaccine against SARS-CoV-2 in the Syrian hamster model. Hamsters were vaccinated with a DNA-plasmid encoding the SARS-CoV-2 full length spike open reading frame (ORF) before exposure to infectious virus. We tested this vaccine candidate by both intranasal (IN) and intramuscular (IM) routes of administration and complexing with and without an in vivo delivery reagent. Hamsters receiving prime-boost-boost IM-only vaccinations recovered body weight quicker, had decreased lung viral loads, and increased SARS-CoV-2-specific antibody titers compared to control vaccinated animals but, surprisingly, lung pathology was as severe as sham vaccinated controls. The IM/IN combination group showed no efficacy in reducing lung virus titers or pathology. This data demonstrates that in some vaccine contexts, significant antibody responses and decreased viral loads may not be sufficient to prevent lung pathology. (Leventhal et al., Microorganisms 2021). During a regular visit in Mali, our ICER site, in February, we developed and established diagnostic testing for the emerging SARS-CoV-2. At that time Mali did not have any COVID cases, a situation that has changed dramatically. The ICER site (Point G) is now one of 4 national diagnostic centers for COVID testing in Mali.