key: cord-0708142-m4ke02fw authors: de Queiroz, Nina Marí G.P.; Marinho, Fabio V.; Chagas, Marcelo A.; Leite, Luciana C.C.; Homan, E. Jane; de Magalhães, Mariana T.Q.; Oliveira, Sergio C. title: Vaccines for COVID-19: perspectives from nucleic acid vaccines to BCG as delivery vector system date: 2020-09-19 journal: Microbes Infect DOI: 10.1016/j.micinf.2020.09.004 sha: 2f2e3d77eca39e606d45eeb6a124f2cad91300f0 doc_id: 708142 cord_uid: m4ke02fw This article discusses standard and new disruptive strategies in the race to develop an anti-COVID-19 vaccine. We also included new bioinformatic data from our group mapping immunodominant epitopes and structural analysis of the spike protein. Another innovative approach reviewed here is the use of BCG vaccine as priming strategy and/or delivery system expressing SARS-CoV-2 antigens. The pandemic Coronavirus Disease 2019 (COVID-19) is the third global threat 24 mediated by betacoronaviruses within this century. These enveloped viruses were thought to be 25 restricted to animals until the first outbreak in 2002, where Severe Acute Respiratory Syndrome 26 Coronavirus (SARS-CoV) infected around 8,000 people reaching a fatality ratio of 9.6% [1] . 27 Again in 2012, Middle East Respiratory Coronavirus (MERS-CoV) was the cause of an 28 endemic in Middle Eastern countries, affecting almost 2,500 people with approximately 35% of 29 fatality ratio and outbreaks outside the region [1] . Less than a decade later, SARS-CoV-2 30 spread COVID-19 worldwide, so far with more than 18,847,261 confirmed cases and 708,469 31 deaths (data updated on 08/06/2020, available at Johns Hopkins Coronavirus Resource Center, 32 https://coronavirus.jhu.edu/map.html). Currently, the only way to deal with this disease is 33 through supportive care to treat the symptoms and mandatory isolation to slow down the 34 transmission, that includes even those not affected. The course of COVID-19 and other 35 coronaviruses diseases outbreaks can overload worldwide health systems and have severe 36 implications in lives lost and economics, underscoring the need for effective vaccines. 37 proteins are cleaved into two subunits: (a) receptor binding subunit, S1, and (b) membrane 190 fusion subunit, S2. It uses the N-terminal region as a signal sequence to access the endoplasmic 191 reticulum of cells and this region is highly N-glycosylated. The S1 subunit of S protein has a 192 receptor binding domain (RBD) composed of a central subdomain (core) and a connection 193 motif for the receptor. The central subdomain has 5 beta antiparallel sheets, connected by 194 alpha-helices, and stabilized by 3 disulfide bridges. The protein's S2 subunit is also similar to 195 that of SARS-CoV and is responsible for the fusion of membranes from severe conformational 196 changes [69, 59, 70] . S2 has two regions of heptad repeats (HR). During the fusion process, S2 197 dissociates from S1 and the HR1 and HR2 regions and form a 6-helix bundle (6-HB) structure, 198 exposing a hydrophobic fusion peptide inserted in the host membrane and allowing the 199 membrane to approach the virus for fusion. 200 Recent experimental data support biophysical and structural evidence that the glycosylated 201 S protein of SARS-CoV-2 binds to the ACE2 receptor with greater affinity than that of 202 SARS-CoV [12] . Hence, the atomic level understanding of these interactions is important for 203 the structural and biophysical elucidation of the initial virus infection process in human cells. 204 By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in 205 the immunogenic structural proteins of SARS-CoV, many authors identified a set of B cell and 206 T cell epitopes derived from the spike and the nucleocapsid proteins that map identically to 207 SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among 208 the 120 available SARS-CoV-2 sequences (as of February 2020), immune targeting of these 209 epitopes may potentially offer protection against this novel virus. These results provide a 210 the SARS-CoV-2 S RBD protein receptor and ACE2 [73] . We performed molecular dynamic 224 simulations of the complexes. The major amino acids involved in the binding identified by 225 interaction analysis after simulations, include the Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 226 34 amino acid residues of the ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 227 417 residues in the SARS-CoV-2 S protein RBD. By locating these amino acid residues, the 228 authors propose that blockers can be designed to inhibit binding and interrupt the entry of the 229 SARS-CoV-2 virus into host cells (Fig. 3) . 230 By using a computational approach, the RBD region of the SARS-CoV-2 S protein was 231 explored to identify various immunodominant epitopes for the development of diagnostics and 232 vaccines. B cell linear epitope probability and MHC binding affinity were determined for all 233 sequential peptides with a single amino acid displacement by our group, using an updated 234 version of methods previously described [74] . The results obtained here could also help us to 235 understand the SARS-CoV-2 surface protein response towards T-and B-cells. Mapping of 236 predicted B and T cell epitopes indicates that the most probable B cell epitopes are located 237 throughout the RBD region of Spike protein (Fig. 4) . In the region of amino acids 450-525 there 238 are also two regions where sequential 15-mers are predicted to have high affinity binding for 239 many human MHC II DRB alleles. Within the region of amino acids 475-500 there is also 240 a region of sequential 9-mers predicted to bind to multiple MHC class I alleles. This indicates 241 that the RBD region of Spike from SARS-CoV-2 is most likely to elicit a strong antibody 242 response due to the number of B cell epitopes with associated T cell help predicted and may 243 also elicit CTLs. 244 propose to test BCG vaccination in health professionals naturally exposed to COVID-19 401 infection to determine whether heterologous protection exists or not. The heterologous effect of 402 BCG vaccination remains a vast field for research. 403 Our group is working in collaboration with national and international institutes to 404 develop a new vaccine strategy using rBCG to express the immunodominant epitopes in the 405 RBD region of the S protein from SARS-CoV-2 (Fig. 4) that can lead to immune system 406 activation synergistically with BCG recognition. In addition, another interesting strategy would 407 be to use a BCG vector to express other agonists that activate important innate immunity 408 pathways involving type I IFN, which play an important role in the anti-viral response and in 409 the recruitment of lymphocytes [140] [141] [142] . The concern that people already vaccinated with 410 BCG could mount an immune response against the vector, preventing it from delivering the 411 spike protein antigen into human, does not seem to be relevant given the satisfactory results 412 with other studies involving rBCG persistence in the host. Another concern involves the release 413 of IL-6 and other inflammatory cytokines that could aggravate COVID-19 pathology. During SARS-CoV-2 infection, immune responses are believed to be essential for viral 427 infection clearance and immunological memory. However, they also cause collateral damage to 428 the lung tissue that can be detrimental and even fatal in some cases. This is a comprehensive 429 review that has focused on host immune responses to SARS-CoV-2 infection, potential epitope 430 targets for vaccine development and different vaccine strategies from live viral vectors, 431 protein-based vaccines, nucleic acid vaccines and the use of BCG as potential delivery system 432 to boost antiviral response via trained immunity. Additionally, we added original data on 433 prediction of B cell and T cell epitopes on RBD region of spike protein, structural comparison 434 analysis between the SARS-CoV-2, SARS-CoV and MERS CoV S proteins and interaction of 435 SARS-CoV-2 RBD with ACE2 receptor. Here, we discussed the hypothesis that BCG 436 vaccination might be a potent preventive measure against SARS-CoV-2 infection and/or may 437 reduce COVID-19 disease severity. One critical vaccine target is to raise antibodies directed to 438 the SARS-CoV-2 spike protein and its receptor-binding domain, the component required for 439 virus binding to its host cell entry receptor ACE2. Given the immediate threat of the 440 SARS-CoV-2 pandemic, vaccine trials should be designed and started as pragmatic studies 441 with feasible primary end points that can be performed rapidly and that could provide results 442 a short period. Due to limitations in vaccine development, randomized controlled trials are 443 needed to provide the highest quality proof that these vaccines can protect against COVID-19. 444 Additionally, we must also recognize that there are potential safety issues that could slow the 445 clinical development path and testing. Since, there is a desperately urgent need to develop 446 strategies to restrain SARS-CoV-2 and limit the pandemic, worldwide efforts are gathered to 447 move forward with all these vaccine candidates already in clinical testing and development. 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