SARS-CoV-2: Pathogenesis and Countermeasure Development

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

The global public health burden caused by SARS-CoV-2 and its resulting disease, COVID-19, has driven the rapid development of vaccines and treatment options. However, the continued emergence of novel SARS-CoV-2 variants of concern (VOC), which rapidly and globally replace earlier, previously predominant strains, and the diminished efficacy of current vaccines and certain treatments against infection by these VOC has raised concerns. Therefore, additional vaccine and therapeutic approaches are urgently needed. DMTs work had three major objectives: (i) Develop animal disease and infection models and study pathogenesis; (ii) repurpose existing drug compounds and evaluate their therapeutic potential in those animal models; (iii) develop vaccines and perform efficacy testing utilizing those animal models. Animal Models Program Last year, we reported on the establishment of an intranasal Syrian hamster disease model for SARS-CoV-2 recapitulating mild to moderate human COVID-19. SARS-CoV-2 replication in the respiratory tract peaked within days with animals showing mild respiratory disease followed by complete recovery (Rosenke et al., Emerg Microbes Infect 2020). To avoid infection at one key site of virus replication, we followed up with an intramuscular infection model in Syrian hamsters. The model showed similar disease and replication characteristics, but the ID50 was about 3 log10 higher (Rosenke et al., manuscript in preparation). Using the intranasal hamster model, we demonstrated that prior SARS-CoV-2 infection prevents acute disease and lung pathology in reinfected hamsters but not virus replication despite substantial levels of humoral immunity. These findings denoted the potential for transmission through reinfected asymptomatic individuals (Hansen et al., Cell Reports 2022). Throughout this year, we have investigated other animal species as disease/infection models such as young pigs, which were not susceptible to SARS-CoV-2 (Haddock et al., Microorganisms 2022). Squirrel monkeys are also not susceptible to SARS-CoV-2 (Okumura et al., in preparation). We refined the rhesus macaque and established the African green monkey (AGM) model for SARS-CoV-2 infection (Clancy et al., Vet Pathol 2021). Severe COVID-19 has been associated with T cell lymphopenia. Thus, we used the rhesus macaque model and studied SARS-CoV-2 infection following depletion of either CD4+, CD8+, or both T cell subsets prior to infection. The study indicated that while T cells play a role in recovery from acute SARS-CoV-2 infection, 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). To better define pathogenicity of different SARS-CoV-2 VOCs we used the rhesus and AGM models. Intranasal infections of AGMs with either a contemporary D614G SARS-CoV-2 variant or the Alpha VOC caused indistinguishable mild respiratory disease. Significantly higher levels of SARS-CoV-2 replication were found in the respiratory tract from Alpha-infected animals suggesting increased pathogenicity (Rosenke et al., Emerg Microbes Infect 2021). Using the rhesus macaque model we have shown that the Omicron VOC possessed reduced pathogenicity and replication compared to the Delta and other previous VOVs (van Doremalen et al., submitted). Therapeutic Program Early 2020, we started a therapeutic project focusing on repurposing drugs for use against SARS-CoV-2. We established a drug pipeline starting with literature search selecting potential drug candidates (Jarvis et al., Antivir Ther 2020). Next, we used different cell culture systems to define the in vitro efficacy against SARS-CoV-2 and determined the EC50 values of the drugs (Haddock et al., Am J Trop Med Hyg 2021). Finally, we tested promising candidates in the hamster and rhesus macaque model. We could show that despite potent in vitro activity, hydroxychloroquine failed to inhibit SARS-CoV-2 in the hamster and rhesus macaque model (Rosenke et al., JCI Insight 2020; Funnell et al., Nat Commun 2020). Several other drugs showed potent in vitro efficacy with favorable EC50 values, but also failed to protect hamsters against SARS-CoV-2 infection unpublished. We next tested the in vivo efficacy of orally delivered molnupiravir in the hamster model, the lead candidate from in vitro testing. We demonstrated potent inhibitory efficacy of molnupiravir on SARS-CoV-2 replication especially in the lower respiratory tract (Rosenke et al., Nat Commun 2021; Rosenke et al., JCI Insight 2022). This supported the establishment of molnupiravir as a treatment for human COVID cases. Currently, we are testing the in vivo efficacy of molnupiravir against Delta and Omicron in the hamster and rhesus macaque models with the final goal of combination therapy. Vaccine Program In collaboration with the University of Washington and HDT Bio, we established a self-amplifying mRNA vaccine platform based on the alphavirus RNA genome technology to express the SARS-CoV-2 spike protein. For vaccine delivery, we utilized a nanostructured lipid carrier developed by HDT Bio. Initially, we demonstrated that the vaccine candidate was potent in elucidating neutralizing antibody and T cell responses in two animal models (Erasmus et al., Sc Transl Med 2020). Next, we showed that SARS-CoV-2 variant-specific replicating RNA vaccines protected hamsters from disease and pathology and reduced viral shedding following challenge with heterologous VOCs (Hawman et al., eLife 2022). Subsequently, we rapidly developed an Omicron-targeting vaccine and found that mice previously immunized with an ancestral-targeting vaccine failed to elevate neutralizing antibody titers against Omicron following Omicron-targeted boosting. Furthermore, we found that our Omicron-targeted vaccine provides superior protection compared to an ancestral variant-targeted vaccine in hamsters challenged with Omicron. Thus, Omicron-targeted vaccines may provide superior protection against Omicron, but pre-existing immunity and timing of boosting may need to be considered for optimum protection (Hawman et al., eLife 2022). We collaborated with Michael Diamonds group at Washington University on a chimpanzee-adenovirus vectored SARS-CoV-2 vaccine expressing the spike protein. A single intranasal dose of ChAd-SARS-CoV-2-S administered to rhesus macaques induced neutralizing antibodies and T cell responses and limited or prevented infection in the respiratory tracts after SARS-CoV-2 challenge (Hassan et al., Cell Rep Med 2021). The clinical trial of this vaccine is headed by our collaborators at Washington University. We also 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 spike protein. Hamsters receiving prime-boost-boost vaccinations by the intramuscular route only recovered quicker, had decreased lung viral loads, and increased SARS-CoV-2-specific antibody titers compared to control vaccinated animals, but lung pathology was as severe as in controls. Vaccination by the intramuscular/intranasal combination route showed no efficacy in reducing lung virus titers or pathology. This data demonstrated that dependent on vaccine context, significant antibody responses and decreased viral loads may not be sufficient to prevent lung pathology (Leventhal et al., Microorganisms 2021). Field Site Program In February 2020 we established diagnostic testing for the emerging SARS-CoV-2 at our ICER site in Bamako, Mali. At a time, Mali did not report any COVId-19 cases, but the situation changed quickly and the ICER site (Point G) became a key national diagnostic center for COVID testing in Mali. We continued our diagnostic support throughout FY21/22.