Design and Characterization of a Computationally Optimized Broadly Reactive Hemagglutinin Vaccine for H1N1 Influenza Viruses

Abstract

One of the challenges of developing influenza A vaccines is the diversity of antigenically distinct isolates. Previously, a novel hemagglutinin (HA) for H5N1 influenza was derived from a methodology termed computationally optimized broadly reactive antigen (COBRA). This COBRA HA elicited a broad antibody response against H5N1 isolates from different clades. We now report the development and characterization of a COBRA-based vaccine for both seasonal and pandemic H1N1 influenza virus isolates. Nine prototype H1N1 COBRA HA proteins were developed and tested in mice using a virus-like particle (VLP) format for the elicitation of broadly reactive, functional antibody responses and protection against viral challenge. These candidates were designed to recognize H1N1 viruses isolated within the last 30 years. In addition, several COBRA candidates were designed based on sequences of H1N1 viruses spanning the past 100 years, including modern pandemic H1N1 isolates. Four of the 9 H1N1 COBRA HA proteins (X1, X3, X6, and P1) had the broadest hemagglutination inhibition (HAI) activity against a panel of 17 H1N1 viruses. These vaccines were used in cocktails or prime-boost combinations. The most effective regimens that both elicited the broadest HAI response and protected mice against a pandemic H1N1 challenge were vaccines that contained the P1 COBRA VLP and either the X3 or X6 COBRA VLP vaccine. These mice had little or no detectable viral replication, comparable to that observed with a matched licensed vaccine. This is the first report describing a COBRA-based HA vaccine strategy that elicits a universal, broadly reactive, protective response against seasonal and pandemic H1N1 isolates. IMPORTANCEUniversal influenza vaccine approaches have the potential to be paradigm shifting for the influenza vaccine field, with the goal of replacing the current standard of care with broadly cross-protective vaccines. We have used COBRA technology to develop an HA head-based strategy that elicits antibodies against many H1 strains that have undergone genetic drift and has potential as a "subtype universal" vaccine. Nine HA COBRA candidates were developed, and these vaccines were used alone, in cocktails or in prime-boost combinations. The most effective regimens elicited the broadest hemagglutination inhibition (HAI) response against a panel of H1N1 viruses isolated over the past 100 years. This is the first report describing a COBRA-based HA vaccine strategy that elicits a broadly reactive response against seasonal and pandemic H1N1 isolates. Influenza vaccine efficacy is constantly undermined by antigenic variation in the circulating viral strains, particularly in the hemagglutinin (HA) and neuraminidase (NA) proteins. Current influenza vaccination strategies rely on changing the HA and NA components of the annual human influenza vaccine to ensure that they antigenically match circulating influenza strains (1, 2). Developing an influenza vaccine that is capable of providing broad and long-lasting protective antibody responses r...

Respiratory virus-induced heterologous immunity

“…Seasonal and pandemic-derived H1N1 COBRA HAs with the broadest HAI activity were inoculated into mice, using virus-like particles (VLP). Vaccination induced broadly-reactive antibodies and protected mice from A(H1N1)pdm09 challenge [69].…”

Synthetic biology for bioengineering virus‐like particle vaccines

“…(b) VLPs can be engineered to offer broader immunogenicity, improved immunogenicity, or enhanced stability. Broadly immunogenic VLPs can be obtained by displaying multiple antigenically distinct epitopes (Pushko et al, ; Schwartzman et al, ), highly conserved epitopes (Krammer, ; Wiersma et al, ), or computationally optimized epitopes (Carter et al, ) within a single VLP. Improving VLP immunogenicity can be achieved by incorporating immunomodulatory agents, such as dendritic cells targeting antibodies into particles structure (Rosenthal et al, ).…”

“…The AntigenDB (http://www.imtech.res.in/raghava/antigendb/) stores sequences, structures, origins, and epitopes of pathogen antigens (Ansari, Flower, & Raghava, ). The Computationally Optimized Broadly Reactive Antigen (COBRA) methodology was recently developed to overcome the challenges associated with antigenic diversity in influenza subtypes (Carter et al, ). This in silico approach, which uses consensus building to generate a number of antigen candidates termed COBRA antigens, was used to identify HA antigens that were broadly protective against H1N1 strains.…”

“…These broadly reactive antigens, which are located within the membrane proximal stalk domain of the hemagglutinin protein have been inserted into VLPs and demonstrate success as vaccines candidates (Ben‐Yedidia, ; Krammer, ; Wiersma, Rimmelzwaan, & de Vries, ). Broad protection is also possible through the simultaneous display of multiple, antigenically distinct (Prabakaran et al, ; Pushko et al, ; Schwartzman et al, ), or chimeric (Carter et al, ) HA antigens from different influenza subtypes within the same VLP.…”

Influenza A Virus Antibodies with Antibody-Dependent Cellular Cytotoxicity Function

“…Therefore, the ultimate goal is to develop a universal vaccine that could confer long-lasting protection against multiple influenza strains, including the drifted seasonal influenza viruses and antigenically distinct viruses. Several approaches are employed to achieve that goal, such as stalk-based immunogen [10], chimeric HA immunogen strategies [11] and computationally optimized broadly reactive antigen (COBRA)-based vaccines [12,13]. Elicitation of antibodies exhibiting ADCC activities also contributes to the design of universal vaccines, which are thought to confer broad-spectrum protection [14].…”