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COVID-19 Vaccine Research at Penn Medicine: Searching for COVID Immunity


The field of vaccine research is vast, intricately complex, and fluid. This article offers a review of a few of the early research efforts at the Perelman School of Medicine now informing the ongoing clinical development programs for potential SARS-CoV-2 vaccines. This blog post is not a definitive review of current vaccine research (for this, we recommend other sources [1, 2]) nor is it intended to offer clinical or practical guidance or definitive conclusions.

Researchers at the Perelman School of Medicine at the University of Pennsylvania are contributing to a better understanding of the morphology and pathology of SARS-CoV-2 in the effort to develop a safe and efficacious vaccine.

Of the seven coronaviruses known to infect humans, SARS-CoV-2 is perhaps the most highly infectious. Fortunately, the composition of the virus is relatively well understood. The complete genome for SARS-CoV-2 was sequenced within six weeks of the first reports of the outbreak in Guangdong China. Its structure has since been elucidated by Susan R. Weiss, PhD, at the Penn's Center of Research for Coronaviruses and Other Emerging Pathogens, among others.

SARS-CoV2 structure demonstrating capsid proteins S, N, M, and E

Structure of SARS-CoV-2

The SARS-CoV-2 virus consists of four structural proteins: 

  • S (spike);
  • E (envelope) surrounds the nucleocapsid;
  • M (membrane) surrounds the nucleocapsid; and
  • N protein, or nucleocapsid, which holds the viral RNA. 

Following infection with SARS-CoV-2, the S and N proteins are the major antigenic targets for antibodies, (e.g., IgG, IgM, IgA).

SARS-CoV-2 Protein Interactions

The S glycoprotein is prominent in the induction of host immune responses. Located on the surface of the virus, S is the mediator for cell invasion. The protein has two subunits: S1, which holds the receptor binding domain (RBD); and S2, which contains the peptide responsible for fusion between the viral envelope and the host cell membrane.

Studies suggest that the S1 subunit is responsible for the virus’ binding affinity and tropism for angiotensin converting enzyme 2 (ACE2), which serves as the entry receptor for SARS-CoV-2 in the respiratory epithelia. Antigenic peptides have been identified on both the S1 and S2 subunits.

Typically, individuals infected with SARS-CoV-2-develop IgM, IgG, and IgA antibodies against the N- and S-proteins between one and two weeks after  symptoms appear. Part of the adaptive immune system, nAbs are produced by mature B cells primed by CD4+ helper T cells. The antibodies bind at antigens to block their interaction with the host cell. Activated B and T helper cells (CD4, CD8) are essential to the humoral immune memory response, and are thus a target for vaccine development.

From a purely mechanical perspective, anything that interferes with binding or fusion at the S protein would be expected to inactivate the virus. Not surprisingly, many of the vaccines in development are targeting the S protein to block its binding potential via specific viral nAbs. Other seek to interfere with viral replication.

The N Protein: A Target for Vaccines—And a Conundrum

In animal studies, the SARS-CoV N protein has been shown to generate coronavirus-specific CD8+ T cells, and in other coronaviruses, these cells have been shown to offer immunogenic protection. At least two studies of a vaccine employing DNA encoding the N protein of SARS-CoV have reportedly elicited SARS-CoV N-specific humoral and CD8+ T-cell responses in mice.

However, versus SARS-CoV-2, the N protein presents a conundrum. While it has been found to be highly immunogenic, it has been reported that antibodies against the N protein of SARS-CoV-2 do not provide immunity to infection. Moreover, at least one report suggests N protein-induced pathogenesis, a source concern for N protein-derived vaccines. Notwithstanding, at least one N protein-based SARS-CoV2 vaccine is in development.

Ongoing COVID-19 Vaccine Studies at the University of Pennsylvania

The development of a successful vaccine is premised on the discovery of a viable means to neutralize the virus, and the production of an efficacious and sustained immunity thereafter. It is presumed that a successful vaccine will be durable, generally available and safe.

As of today, according to the Milken Institute, there are 203 vaccines in development for COVID-19.

25 of these vaccines are in human studies. These include inactivated and live attenuated approaches; protein subunit and virus-like particles; DNA or RNA-based vaccines; replicating and non-replicating viral vectors (placing a viral gene into a different virus) and unique approaches, such as chimeric and self-assembling vaccines.

The efforts of researchers at the Center of Research for Coronaviruses and Other Emerging Pathogens as well as a number of affiliated laboratories at the Perelman School of Medicine are directed at the development of mRNA and DNA vaccines for SARS-CoV-2, as well as the evaluation of neutralizing antibodies, complement-fixing antibodies and humoral immune responses, and the characterization of both the pathogenicity of the virus and infectious responses to it.

Recent research from colleagues at the Perelman School and Penn Medicine include:

Maris, et al, have created a comprehensive immunogenicity map of the SARS-CoV-2 virus to propose sixty-five 33-mer peptide sequences with the potential to generate B and T cell epitopes from a diverse sampling of viral domains across all SARS CoV-2 genes.

The peptides are predicted to activate CD4 and CD8 T cells, are highly dissimilar from the self-proteome, are conserved across 15 related coronaviruses, and are expected to drive long-term immunity in the majority of the population.

The authors anticipate that the highest scoring peptides will result in safe and immunogenic T cell epitopes; the B cell epitopes, they conclude, should be evaluated for safety and efficacy using previously reported methods.

SARS-CoV-2 mRNA-based vaccines are among the most promising vaccine candidates against COVID-19, though no mRNA vaccines for humans have been licensed to date.

In this study, Pardi, et al, evaluated two nucleoside-modified mRNA vaccines after a single injection in BALB/c mice. One candidate encoded the full length S protein with deleted furin cleavage site (at the S2 subunit); the other encoded the S protein receptor binding domain (RBD) in the S1 subunit.

The authors demonstrated that both vaccines induced potent T and B cell immune responses in the spleen and lung, and both elicited high levels of CD4+ and CD8+ immune response cytokines  and the generation of antigen-specific memory B cells.

DNA-based vaccines work by inserting a genetically engineered viral gene into DNA molecules (plasmids) to build viral proteins that the immune system recognizes as foreign, triggering an innate immune response to disease. DNA vaccine have not yet been approved for human use.

A team at the Wistar Institute led by David B. Weiner, PhD, has engineered a synthetic DNA-based vaccine candidate (INO-4800). Developed by generate a highly optimized DNA sequence encoding the SARS-CoV-2 spike protein, the vaccine demonstrated robust expression of S protein in vitro. In small animal studies of INO-4800, T cell responses were observed as well as blocking of ACE2/SARS-CoV-2 S protein interaction and the elicitation of neutralizing IgG antibodies bound to S protein antigens in the S1 and S2 subunits and RBD.

The vaccine is now in Phase 1 testing in humans.

A team at the Perelman School led by E. John Wherry, PhD, has identified patient immunotype profiles that may have implications for vaccine design or application. The team used high dimensional cytometry to compare B and T cell populations from COVID-19 patients to those of healthy and recovered individuals.

This approach resulted in several key findings, including heterogeneity of immune response as a defining feature of COVID-19 in hospitalized patients. Many COVID-19 patients displayed robust CD8 T cell and/or CD4 T cell activation and proliferation and PB responses, though a considerable subgroup of patients (~20%) had minimal detectable response compared to controls.

Following deep immune profiling, three “immunotypes” associated with poor clinical trajectories versus improving health were identified. A exemplar of heterogeneity, these immunotypes ranged from patients with robust activation and proliferation of CD4 T cells to those largely lacking detectable lymphocyte response to infection, suggesting a failure of immune activation.

The authors conclude that these findings may have implications for the design of therapeutics and vaccines for COVID-19.

For more information about vaccine studies and development at the Perelman School of Medicine, visit the Penn Center for Research on Coronavirus and Other Emerging Pathogens.

Additional Penn Resources on COVID-19 Vaccines

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The Penn Physician Blog is a resource for health care professionals featuring Penn Medicine physicians and their research, innovations, programs and events. 

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