Advanced Drug Delivery Reviews 170 (2021) 113–141 Contents lists available at ScienceDirect Advanced Drug Delivery Reviews journal homepage: www.elsevier.com/locate/addr Advances in gene-based vaccine platforms to address the COVID-19 pandemic Deborah Pushparajah a,1, Salma Jimenez a,c,1,ShirleyWonga,HibahAlattasa, Nafiseh Nafissi b, Roderick A. Slavcev a,b,c,⁎ a School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada b Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada c Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada article info abstract Article history: The novel betacoronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has spread across Received 1 October 2020 the globe at an unprecedented rate since its first emergence in Wuhan City, China in December 2019. Scientific Received in revised form 23 December 2020 communities around the world have been rigorously working to develop a potent vaccine to combat COVID-19 Accepted 1 January 2021 (coronavirus disease 2019), employing conventional and novel vaccine strategies. Gene-based vaccine platforms Available online 7 January 2021 based on viral vectors, DNA, and RNA, have shown promising results encompassing both humoral and cell-mediated immune responses in previous studies, supporting their implementation for COVID-19 vaccine de- Keywords: Coronavirus velopment. In fact, the U.S. Food and Drug Administration (FDA) recently authorized the emergency use of two COVID-19 RNA-based COVID-19 vaccines. We review current gene-based vaccine candidates proceeding through clinical SARS-CoV-2 trials, including their antigenic targets, delivery vehicles, and route of administration. Important features of pre- Vaccines vious gene-based vaccine developments against other infectious diseases are discussed in guiding the design and DNA vaccines development of effective vaccines against COVID-19 and future derivatives. RNA vaccines ©2021ElsevierB.V.Allrightsreserved. Replicative viral vaccines Non-replicative viral vaccines Contents 1. Introduction............................................................... 114 2. COVID-19vaccinetargets......................................................... 115 2.1. Optimalantigenselection..................................................... 115 2.2. COVID-19immunogenictargets.................................................. 115 2.3. AminoacidsequencealignmentofstructuralproteinsfromCoronavirus................................ 116 3. Novelgene-basedvaccineplatforms.................................................... 116 3.1. Viralvectorvaccines........................................................ 116 3.2. Nucleicacidvaccines....................................................... 117 4. Gene-basedvaccineadministration.................................................... 118 4.1. Routeofadministration...................................................... 118 4.1.1. Mucosalvaccination.................................................... 118 4.1.2. Parenteralvaccination................................................... 118 Abbreviations: a.a, amino acid; AAV, adeno-associated virus; ACE2, angiotensin converting enzyme 2; ADE, antibody dependent enhancement; BGH, bovine growth hormone; ChAd, chimpanzee adenovirus; COVID-19, coronavirus disease 2019; CMV, cytomegalovirus; DPP4, dipeptidyl peptidase 4; E, envelope; EP, electroporation; GBV, gene-based vaccine; GP, gly- coprotein; GC, guanine-cytosine; HA, hemagglutinin; HAI, hemagglutinin inhibition; IFN, interferon; IIV, inactivated influenza virus vaccine; IL, interleukin; LNP, lipid nanoparticle; Lunar, lipid-enabled and unlocked nucleomonomer agent modified RNA; M, membrane; MIV, monovalent inactivated virus; MERS-CoV, Middle East respiratory syndrome coronavirus; MV, mea- sles virus; MVA, modified vaccinia virus Ankara; N, nucleocapsid; OGN, oligodeoxynucleotide; ORF, open reading frame; polyA, polyadenylation; RSV, respiratory syncytial virus; saRNA, self-amplifying RNA; SARS-CoV, severe acute respiratory syndrome coronavirus; SARS-CoV-2, severe acute respiratory syndrome 2; SLE, systemic lupus erythematosus; S, spike; RBD, re- ceptor binding domain; Th, T helper; TLR, toll-like receptor; TNF, tumor necrosis factor; tPA, tissue plasminogen activator; VSV, vesicular stomatitis virus; WNV, West Nile virus. ⁎ Corresponding author at: School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener ON, N2G 1C5, Canada. E-mail address: [email protected] (R.A. Slavcev). 1 Deborah Pushparajah and Salma Jimenez equally contributed to this work. https://doi.org/10.1016/j.addr.2021.01.003 0169-409X/© 2021 Elsevier B.V. All rights reserved. D. Pushparajah, S. Jimenez, S. Wong et al. Advanced Drug Delivery Reviews 170 (2021) 113–141 4.2. Noveldeliverytools........................................................ 119 5. Immunityandsafetyofpreviousgene-basedvaccines............................................ 119 5.1. Previousviralvectorvaccineimmunityandsafety.......................................... 119 5.1.1. Non-replicativeviralvectorvaccines............................................ 119 5.1.2. Replicativeviralvectorvaccines.............................................. 122 5.2. PreviousDNAvaccineimmunityandsafety............................................. 123 5.3. PreviousRNAvaccineimmunityandsafety............................................. 123 6. COVID-19gene-basedvaccines...................................................... 124 6.1. Viralvectorvaccines........................................................ 124 6.2. DNAvaccines........................................................... 126 6.3. RNAvaccines........................................................... 126 7. Adjuvantadministration......................................................... 130 8. Immuneenhancementofgene-basedvaccines............................................... 132 8.1. Antibodydependentenhancement................................................. 132 8.2. Th2immunopathology....................................................... 132 9. Conclusions............................................................... 133 Acknowledgements.............................................................. 133 References.................................................................. 133 1. Introduction infection rates, longer incubation periods, and increased levels of asymptomatic transmission [5]. The 2019 novel coronavirus outbreak (COVID-19), caused by the As of December 2020, WHO reports 215 COVID-19 vaccine candi- severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) corona- dates in development [6]. Of these, 52 are undergoing clinical evaluation virus, was declared a global pandemic on March 11, 2020 by the World and 163 are still in preclinical development. These candidates encom- Health Organization (WHO) and has since imparted significant morbid- pass a diverse selection of vaccine platforms: protein-based (subunit ity and fatalities as governing bodies scramble to mitigate looming eco- and virus-like particle), virus-based (live attenuated and inactivated), nomic fallout. As of December 2020, this highly transmissible virus has and novel gene delivery strategies such as nucleic acid (DNA and already infected over 65 million worldwide, resulting in more than 1.5 RNA), and viral vector (replicative and non-replicative) (Fig. 1). Con- million deaths [1]. Born out of mutation, SARS-CoV-2 will continue to ventional strategies, such as inactivated viral, live attenuated viral, and drift as a response to evolutionary pressures, and as the outbreak con- protein subunit vaccines have demonstrated successful outcomes in tinues, it will spread and kill indiscriminately. The need for protective the past, but tend to confer complications with safety, limited cross- solutions and, in particular, a safe and effective vaccine is of highest pri- protection and immunogenicity [7]. Novel vaccine platforms include ority and paramount urgency. virus-like particles, viral vectors, and nucleic acid vaccines [8]. Gene- As a member of the Coronavirdae family, SARS-CoV-2 is classified as a based vaccines (GBVs), including both viral vectors and nucleic acid vac- betacoronavirus which is characterized by having a single-stranded, cines, genetically encode an antigen to be delivered. They depend on the positive-sense, enveloped RNA genome varying from 26.5 to 31.7 kb successful expression of delivered gene cassettes to peptide antigen(s), in size [2]. The virus is one of six human transmissible coronaviruses dis- which must then be presented to immune cells to stimulate an immune covered to date [3]. COVID-19 presents similar features and symptoms response. Viral vector vaccines have previously been approved by to previous outbreaks of related betacoronaviruses: severe acute respi- health authorities [9]. The first two RNA-based vaccines against ratory syndrome coronavirus (SARS-CoV) and Middle East respiratory COVID-19 were recently approved by the U.S. FDA for emergency use syndrome coronavirus (MERS-CoV), which emerged in 2002 and [10,11,12]. This renders DNA-based vaccines as the only completely un- 2012, respectively [4,5]. Although these viruses share considerable tested therapeutic vaccine approach for human application [13]. sequence similarity, SARS-CoV-2 has thus far demonstrated higher Heightened interest in the development of GBVs is attributed to some protein subunit (71) gene-based (98) non-replicating viral