Severe-Acute Respiratory-Syndrome-2 (SARS-CoV-2) has caused significant human and economic burden since its appearance in December 2019. Since its emergence, several new variants of concern (VOC) including alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) and omicron (B.1.1.529) lineages have fueled recurring global infection waves. A key player in SARS-CoV-2 viral entry, the Angiotensin Converting Enzyme 2 (ACE2), is predominantly found in the heart, kidneys and lungs. SARS-CoV-2 mutations, particularly in the spike protein, can significantly impact the severity of disease by altering factors such as ACE2 receptor binding affinity, and therefore replication efficiency. In this study, we investigated the differential pathogenesis of SARS-CoV-2 variants using various mouse models to generate insights into the molecular mechanism that governs the severity and transmission dynamics of SARS-CoV-2 in vivo. In the first aim, we compared the pathogenesis and adaptation of SARS-CoV-2 VOC in wild-type laboratory mice. Six-week-old C57BL/6J mice were intranasally infected with SARS-CoV-2 B.1, B.1.1.7, or B.1.351 VOC. Our data show that unlike the B.1 virus, the B.1.1.7 and B.1.351 viruses are capable of infecting C57BL/6 mice and replicating at high concentrations in the lungs. The B.1.351 virus replicated to higher titers in the lungs compared with the B.1.1.7 virus. In addition, robust expression of viral nucleocapsid protein and histopathological changes were detected in the lungs of B.1.351-infected mice. Overall, these data indicate a greater potential for infectivity and adaptation to new hosts by emerging SARS-CoV-2 variants. In the second aim, we evaluated the effects of differential qualitative and quantitative expression of ACE2 on SARS-CoV-2 pathogenesis using various mouse models. We infected transgenic mice expressing (1) both mouse and human ACE2 (K18-hACE2); (2) only mouse ACE2 (C57BL/6) and (3) a transgenic novel mouse model which exclusively expresses only human ACE2 (hACE2-KI). hACE2-KI mice are a new animal model developed by Envigo using the CRISPR/Cas9 technology to replace the mACE2 with human ACE-2 (hACE2). Six-week-old mice from each group were intranasally infected with 105 PFU of SARS-CoV-2 B.1 or B.1.351 viruses. Overall, the hACE2-KI mice were less susceptible compared to K18-hACE2 mice and more susceptible compared to C57BL/6J mice to SARS-CoV-2 infection. The presence of hACE2 is necessary for the replication of SARS-CoV-2 B.1 in mice, however, with the presence of mACE2, there is increased viral infection and therefore mortality. In the third aim, we analyzed the protective efficacy of a multi-antigen viral-vectored vaccine (GEO-CM02) against SARS-CoV-2 and VOC using our pre-clinical mouse model. First generation vaccines based on the spike (S) protein induced neutralizing antibodies that provided significant levels of protection against the initial variants. However, vaccine efficacy was disrupted by emerging variants that contributed to neutralizing antibody evasion. GeoVax has designed a multiantigen SARS-CoV-2 vaccine that expresses S, membrane (M), and envelope (E) antigens, designated GEO-CM02. GEO-CM02 vaccine efficacy studies in the lethal K18-hACE2 mouse model demonstrated complete protection with a single dose against the original B.1 virus and B.1.1.529 variant. Animals were fully protected prior to the detection of neutralizing antibodies, the widely accepted as the correlation of protection, likely indicating a critical T-cell contribution. Both single and two-dose GEO-CM02 vaccination elicited high levels of neutralizing antibodies, effectively controlled lung viral burden, reduced viral load in the lung, brain, and olfactory bulb and reduced inflammatory cytokines and chemokines in the lungs. These data indicate that vaccination with the multi-antigen GEO-CM02 vaccine can protect against severe disease and death induced by SARS-CoV-2 and its variants in a highly relevant pre-clinical model.