Canadian Journal of Microbiology Frontrunners in the race to develop a SARS-CoV-2 vaccine Journal: Canadian Journal of Microbiology Manuscript ID cjm-2020-0465.R1 Manuscript Type: Review Date Submitted by the 16-Nov-2020 Author: Complete List of Authors: Russell, Raquel; University of Manitoba, Department of Microbiology Pelka, Peter; University of Manitoba, Department of Microbiology Mark, Brian; University of Manitoba, Department of Microbiology Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, Keyword: COVID-19,Draft vaccine development Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : © The Author(s) or their Institution(s) Page 1 of 91 Canadian Journal of Microbiology 1 2 3 Frontrunners in the race to develop a SARS-CoV-2 vaccine 4 5 Authors: Raquel L. Russell, Peter Pelka, Brian L. Mark 6 7 Affiliations: Department of Microbiology,Draft University of Manitoba, Winnipeg, 8 Manitoba, Canada, R3T2N2 9 10 Correspondence: Brian L. Mark, Ph.D., 11 email: [email protected] 12 tel: 1-204-480-1430 13 14 15 16 17 1 © The Author(s) or their Institution(s) Canadian Journal of Microbiology Page 2 of 91 1 Abstract 2 Numerous studies continue to be published on the COVID-19 pandemic that is being 3 caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Given the 4 rapidly evolving global response to SARS-CoV-2, here we primarily review the leading COVID- 5 19 vaccine strategies that are currently in Phase III clinical trials. Non-replicating viral vector 6 strategies, inactivated virus, recombinant protein subunit vaccines, and nucleic acid vaccine 7 platforms are all being pursued in an effort to combat the infection. Preclinical and clinal trial 8 results of these efforts are examined as well as the characteristics of each vaccine strategy from 9 the humoral and cellular immune responses they stimulate, effects of any adjuvants used, and the 10 potential risks associated with immunizationDraft such as antibody dependent enhancement (ADE). A 11 number of promising advancements have been made toward the development of multiple vaccine 12 candidates. Preliminary data now emerging from phase III clinical trials show encouraging 13 results for the protective efficacy and safety of at least three frontrunning candidates. There is 14 hope that one or more will emerge as potent weapons to protect against SARS-CoV-2. 15 16 Keywords: Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, COVID-19, 17 vaccine development 18 19 20 21 2 © The Author(s) or their Institution(s) Page 3 of 91 Canadian Journal of Microbiology 1 Introduction 2 The first cases of a viral pneumonia of unknown cause were reported in December 2019 3 in Wuhan, China (Huang et al. 2020). Case numbers grew quickly, and the virus spread across 4 numerous borders, prompting the World Health Organization to declare a pandemic in March of 5 2020. In the early stages of the outbreak, electron micrographs of the virus revealed 6 characteristics consistent with coronaviruses, including enveloped, spherical-like particles 7 covered in spikes that resembled a solar corona (Gorbalenya et al. 2020). Sequencing of the full- 8 length viral genome from patient isolates confirmed it to be a coronavirus with remarkable 9 similarity (~79% nucleic acid identify) to the coronavirus that caused the Severe Acute 10 Respiratory Syndrome Coronavirus (SARS-CoV-1)Draft pandemic of 2003 (Kim et al. 2020b). Given 11 its similarity to SARS-CoV-1, the current coronavirus is referred to as SARS-CoV-2 and only a 12 handful of countries appear to have been spared from the virus (although cases could have been 13 missed). As of November 2, 2020, more than 46 million COVID-19 cases have been reported 14 worldwide and over 1.2 million related deaths have occurred (Gardner n.d.). Most infected 15 individuals experience mild or moderate symptoms, but up to 20% of cases can be severe (Chen 16 et al. 2020). Common symptoms include cough, shortness of breath, fatigue, and fever, but can 17 progress into a critical condition known as acute respiratory distress syndrome (ARDS) (Huang 18 et al. 2020). Risk for severe disease increases with age and comorbidities such as hypertension, 19 obesity and diabetes (Richardson et al. 2020). It has been reported that SARS-CoV-2 is 20 effective at evading and crippling both innate and acquired immune responses (Zhang et al. 21 2020a; Qin et al. 2020). Similar to other coronaviruses, SARS-CoV-2 appears able to supress 22 interferon (IFN) induction and signaling (Cameron et al. 2012; Hadjadj et al. 2020), which is 23 critical to innate antiviral response and their suppression drives infection and disease 3 © The Author(s) or their Institution(s) Canadian Journal of Microbiology Page 4 of 91 1 progression. Another complication associated with SARS-CoV-2 is development of a “cytokine 2 storm” associated with severe COVID-19, causing ARDS likely due to, in part, a dysregulated 3 IFN-I response (Channappanavar et al. 2016; Hadjadj et al. 2020). Previously, animal models of 4 SARS-CoV-1 and MERS coronavirus infections have shown that a lack of an early IFN-I 5 response correlates with disease severity (Channappanavar et al. 2016, 2019). Blocked IFN 6 signalling with SARS-CoV-2 may boost inflammatory pathways leading to the secretion of large 7 amounts of cytokine interleukins (IL-6, IL-8, IL-1β) (Gong et al. 2020). The release of these 8 cytokines triggers pro-inflammatory responses such as fever, neutrophil recruitment, and 9 monocyte activation. Lymphopenia has also been noted in moderate and severe cases of COVID- 10 19 (Tan et al. 2020). Draft 11 Coronavirus Biology 12 Betacoronaviruses and alphacoronaviruses are mammal infecting genera of the 13 Coronaviridae family within the order Nidovirales (Roper and Rehm 2009; Gorbalenya et al. 14 2020). With the emergence of SARS-CoV-2, there are now seven known human coronaviruses, 15 all of which cause disease (Graham et al. 2013). Some of these coronaviruses are commonly 16 encountered, such as the α-coronaviruses HCoV-229E and HCoV-NL63, and β-coronaviruses 17 HCoV-OC43 and HCoV-HKU1, which cause minor and seasonal respiratory infections 18 (Hendley et al. 1972; van der Hoek et al. 2004; Woo et al. 2005). However, the three most recent 19 coronaviruses to have emerged are capable of causing severe disease and include SARS-CoV-1, 20 MERS-CoV, and now SARS-CoV-2. They are all β-coronaviruses and SARS-CoV-2 shares 21 roughly 79% and 50% whole genome sequence similarity to SARS-CoV-1 and MERS-CoV 22 respectively (Lu et al. 2020). 4 © The Author(s) or their Institution(s) Page 5 of 91 Canadian Journal of Microbiology 1 Coronaviruses are enveloped viruses that share a large (~30 kb) single-stranded positive 2 sense RNA genome (Fehr and Perlman 2015). The SARS-CoV-2 genome contains two main 3 open reading frames (ORFs), ORF1a and ORF1b, expressing polyproteins pp1a and pp1b 4 respectively. During translation, ribosomes can switch from ORF1a to ORF1b by a -1 frameshift 5 upon encountering a slippery sequence (Maier et al. 2015). The translated polyproteins both 6 consist of non-structural proteins (nsps), with pp1a containing nsps 1-11 and pp1b containing 7 nsps 1-16 (Maier et al. 2015). To create singular nsps, the polyproteins are cut at specific sites by 8 two enzymes: main protease (Mpro, also known as 3CLpro) and papain-like protease (PLpro) 9 (Hegyi and Ziebuhr 2002; Maier et al. 2015). These proteases are resident within nsp3 and nsp5, 10 respectively, and autocatalytically cleave the viral polyproteins into functional nsp units. Many 11 of the nsps produced come together to formDraft the replicase-transcriptase complex (RTC) that 12 allows for RNA replication and sub-genomic RNA transcription (Maier et al. 2015). Nsp12 13 contains the RNA dependent RNA polymerase domain, while nsp14 contains the 14 exoribonuclease domain that is important for replication accuracy (Maier et al. 2015). Viral RNA 15 produced by the RTC includes genomic and sub-genomic RNAs and both are positive sense 16 strands made from negative sense strand intermediates, also referred to as antigenomes (Maier et 17 al. 2015). Sub-genomic RNA acts as mRNA for structural and accessory gene translation. The 18 functions of accessory proteins are still relatively unknown for SARS-CoV-2, but they may be 19 involved in innate immune response suppression similar to SARS-CoV-1 (Kopecky-Bromberg et 20 al. 2007). Sub-genomic RNAs are read by host ribosomes to create the viral structural spike (S), 21 matrix (M), envelope (E), and nucleocapsid (N) proteins (Fehr and Perlman 2015). The S, E, and 22 M proteins are translated and sent to the endoplasmic reticulum where they follow a secretory 23 pathway into an endoplasmic reticulum- Golgi intermediate compartment (Maier et al. 2015). 5 © The Author(s) or their Institution(s) Canadian Journal of Microbiology Page 6 of 91 1 This is where virion maturation takes place, as genomic RNA encapsidated in N protein 2 combines with the other structural proteins. 3 Currently, vaccine development for COVID-19 has focused predominantly on the S 4 protein of SARS-CoV-2 (Fig 1). The S protein facilitates viral entry into the cell through 5 engagement of the human angiotensin-converting enzyme 2 (hACE2) receptor and since it is 6 located on the virion surface, it is vulnerable to a humoral (antibody) immune response and is 7 thus a promising immunogen for vaccine development (Wang et al. 2020b). The human S protein 8 receptor, hACE2, is expressed on various tissues throughout the body and is highly expressed on 9 small intestinal epithelial cells and lung alveolar epithelial cells (Hamming et al.