A Modified Vaccinia Ankara Vaccine Expressing Spike And Nucleocapsid Protects Rhesus Macaques Against Sars-cov-2 Delta Infection

Nanda Kishore Routhu, Emory University
Sailaja Gangadhara, Emory University
Lilin Lai, Emory University
Meredith E. Davis-Gardner, Emory University
Katharine Floyd, Emory University
Ayalnesh Shiferaw, Emory University
Yannic C. Bartsch, Massachusetts Institute of Technology
Stephanie Fischinger, Massachusetts Institute of Technology
Georges Khoury, Emory University
Sheikh Abdul Rahman, Emory University
Samuel David Stampfer, Emory University
Alexandra Schäfer, The University of North Carolina at Chapel Hill
Sherrie M. Jean, Emory University
Chelsea Wallace, Emory University
Rachelle L. Stammen, Emory University
Jennifer Wood, Emory University
Cohen Joyce, Emory University
Tamas Nagy, University of Georgia
Matthew S. Parsons, Emory University
Lisa Gralinski, The University of North Carolina at Chapel Hill
Pamela A. Kozlowski, LSU Health Sciences Center - New Orleans
Galit Alter, Massachusetts Institute of Technology
Mehul S. Suthar, Emory University
Rama Rao Amara, Emory University


SARS-CoV-2 vaccines should induce broadly cross-reactive humoral and T cell responses to protect against emerging variants of concern (VOCs). Here, we inactivated the furin cleavage site (FCS) of spike expressed by a modified vaccinia Ankara (MVA) virus vaccine (MVA/SdFCS) and found that FCS inactivation markedly increased spike binding to human ACE2. After vaccination of mice, the MVA/SdFCS vaccine induced eightfold higher neutralizing antibodies compared with MVA/S, which expressed spike without FCS inactivation, and protected against the Beta variant. We next added nucleocapsid to the MVA/SdFCS vaccine (MVA/SdFCS-N) and tested its immunogenicity and efficacy via intramuscular (IM), buccal (BU), or sublingual (SL) routes in rhesus macaques. IM vaccination induced spike-specific IgG in serum and mucosae (nose, throat, lung, and rectum) that neutralized the homologous (WA-1/2020) and heterologous VOCs, including Delta, with minimal loss (<2-fold) of activity. IM vaccination also induced both spike- and nucleocapsid-specific CD4 and CD8 T cell responses in the blood. In contrast, the SL and BU vaccinations induced less spike-specific IgG in secretions and lower levels of polyfunctional IgG in serum compared with IM vaccination. After challenge with the SARS-CoV-2 Delta variant, the IM route induced robust protection, the BU route induced moderate protection, and the SL route induced no protection. Vaccine-induced neutralizing and non-neutralizing antibody effector functions positively correlated with protection, but only the effector functions correlated with early protection. Thus, IM vaccination with MVA/SdFCS-N vaccine elicited cross-reactive antibody and T cell responses, protecting against heterologous SARS-CoV-2 VOC more effectively than other routes of vaccination.