Basic Coronavirus biology and vaccines for COVID-19
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Two mRNA vaccines based on the spike protein S have been authorized by the Food and Drug Administration. Antibody-based diagnostic test detect antibodies developed against protein S. Mutations in the genome of SARS-CoV-2 might compromise the precision of diagnostic tests and the efficacy of vaccines and antiviral drugs. We recently profiled genomic variation in human coronaviruses SARS[1]CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). As in all species of the genus Betacoronavirus, the genome is hyper variable, and mutations are not random. The most variable cistron codes for the spike S protein. Hyper variation in protein S has the potential to affect the efficacy of vaccines, the reliability of antibody-based diagnostic test, and predicts potential for repeated SARS-CoV-2 infections. Here we review the basics of coronavirus biology and genomic variation, and link them to diagnostic tests, vaccines, and antiviral drugs.
Keywords
Full Text:
PDFReferences
Amanat F and Krammer F. 2020. SARS-CoV-2 Vaccines: Status Report. Immunity 52(4): 583-589. https://doi.org/10.1016/j.immuni.2020.03.007
Baum A, Fulton BO, Wloga E, Copin R, Pascal KE, Russo V, Giordano S, Lanza K, Negron N, Ni M, Wei Y, Atwal GS, Murphy AJ, Stahl N, Yancopoulos GD and Kyratsous CA. 2020. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369(6506): 1014-1018. https://doi.org/10.1126/science.abd0831
Becerra-Flores M and Cardozo T. 2020. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. International Journal of Clinical Practice 74(8): e13525. https://doi.org/10.1111/ijcp.13525
Brian DA and Baric RS. 2005. Coronavirus genome structure and replication. Current Topics and Microbiology Immunology 287: 1-30. https://doi.org/10.1007/3-540-26765-4_1
Brochot E, Demey B, Touzé A, Belouzard S, Dubuisson J, Schmit J-L, Duverlie G, Francois C, Castelain S and Helle F. 2020. Anti-spike, Anti-nucleocapsid and Neutralizing Antibodies in SARS-CoV-2 Inpatients and Asymptomatic carriers. Frontiers in Microbiology. 24 p. https://doi.org/10.3389/fmicb.2020.584251
Cagliani R, Forni D, Clerici M and Sironi M. 2020. Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Virology 94: e00411-00420. https://doi.org/10.1128/JVI.00411-20
Cai Y, Zhang J, Xiao T, Peng H, Sterling SM, Walsh RM, Rawson S, Rits-Volloc, S and Chen B. 2020. Distinct conformational states of SARS-CoV-2 spike protein. Science 369(6511) 1586-1592. https://doi.org/10.1126/science.abd4251
Cantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, van der Meer F, Kallio K, Kaya T, Anastasina M, Smura T, Levanov L, Szirovicza L, Tobi A, Kallio-Kokko H, Österlund P, Joensuu M, Meunier FA, Butcher SJ, Winkler MS, Mollenhauer B, Helenius A, Gokce O, Teesalu T, Hepojoki J, Vapalahti O, Stadelmann C, Balistreri G and Simons M. 2020. Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 370(6518): 856-860. https://doi.org/10.1126/science.abd2985
Charon J, Barra A, Walter J, Millot P, Hebrard E, Moury B and Michon T. 2018. First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process. Molecular Biology and Evolution 35(1): 38-49. https://doi.org/10.1093/molbev/msx249.
Corbett KS, Edwards DK, Leist SR, Abiona OM, Boyoglu-Barnum S, Gillespie RA, Himansu S, Schäfer A, Ziwawo CT, DiPiazza AT, Dinnon KH, Elbashir SM, Shaw CA, Woods A, Fritch EJ, Martinez DR, Bock KW, Minai M, Nagata BM, Hutchinson GB, Wu K, Henry C, Bahl K, Garcia-Dominguez D, Ma L, Renzi I, Kong W-P, Schmidt SD, Wang L, Zhang Y, Phung E, Chang LA, Loomis RJ, Altaras NE, Narayanan E, Metkar M, Presnyak V, Liu C, Louder MK, Shi W, Leung K, Yang ES, West A, Gully KL, Stevens LJ, Wang N, Wrapp D, Doria-Rose NA, Stewart-Jones G, Bennett H, Alvarado GS, Nason MC, Ruckwardt TJ, McLellan JS, Denison MR, Chappell JD, Moore IN, Morabito KM, Mascola JR, Baric RS, Carfi A and Graham BS. 2020. SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Nature 586: 567-571. https://doi.org/10.1038/s41586-020-2622-0
Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG and Decroly E. 2020. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Research 176: 104742. https://doi.org/10.1016/j.antiviral.2020.104742
Cui J, Li F and Shi ZL. 2019. Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology 17: 181-192. https://www.nature.com/articles/s41579-018-0118-9
Dearlove B, Lewitus E, Bai H, Li Y, Reeves DB, Joyce MG, Scott PT, Amare MF, Vasan S, Michael NL, Modjarrad K and Rolland M. 2020. A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proceedings of the National Academy of Sciences 117(38): 23652-23662. https://doi.org/10.1073/pnas.2008281117
Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M, Corbet-Detig R, Kent WJ, Haussler D and Haeussler M. 2020. The UCSC SARS-CoV-2 Genome Browser. Nature Genetics 52: 991-998. https://www.nature.com/articles/s41588-020-0700-8
Forster P, Forster L, Renfrew C and Forster M. 2020. Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Sciences 117(17): 9241-9243. https://doi.org/10.1073/pnas.2004999117
Gallagher TM and Buchmeier MJ. 2001. Coronavirus spike proteins in viral entry and pathogenesis. Virology 279(2): 371-374. https://doi.org/10.1006/viro.2000.0757
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T and Neher RA. 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34(23): 4121-4123. https://doi.org/10.1093/bioinformatics/bty407
Hebrard E, Bessin Y, Michon T, Longhi S, Uversky VN, Delalande F, Van Dorsselaer A, Romero P, Walter J, Declerck N and Fargette D. 2009. Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses. Virology Journal 6: 23. https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-6-23
Holland LA, Kaelin EA, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, and Lim ES. 2020. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020). Journal Virology 94(14): JVI.00711-00720. https://doi.org/10.1128/JVI.00711-20
Jary A, Leducq V, Malet I, Marot S, Klement-Frutos E, Teyssou E, Soulié C, Abdi B, Wirden M, Pourcher V, Caumes E, Calvez V, Burrel S, Marcelin A-G and Boutolleau D. 2020. Evolution of viral quasispecies during SARS-CoV-2 infection. Clinical Microbiology and Infection 26(11):1560.e1-1560.e4. https://doi.org/10.1016/j.cmi.2020.07.032
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, Angyal A, Brown RL, Carrilero L, Green LR, Groves DC, Johnson KJ, Keeley AJ, Lindsey BB, Parsons PJ, Raza M, Rowland-Jones S, Smith N, Tucker RM, Wang D, Wyles MD, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO and Montefiori DC. 2020. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 182(4): 812-827.e819. https://doi.org/10.1016/j.cell.2020.06.043
Kuo L, Godeke GJ, Raamsman MJ, Masters PS and Rottier PJ. 2000. Retargeting of coronavirus by substitution of the spike glycoprotein ectodomain: crossing the host cell species barrier. Journal Virology 74(3): 1393-1406. https://doi.org/10.1128/jvi.74.3.1393-1406.2000
Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, Zhang Q, Shi X, Wang Q, Zhang L and Wang X. 2020. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581: 215-220. https://www.nature.com/articles/s41586-020-2180-5
LaTourrette K, Holste NM, Rodriguez-Peña R, Arruda-Leme R and García-Ruiz H. 2021. Genome-wide variation in betacoronaviruses. Journal of Virology 95(15): e0049621. https://www.ncbi.nlm.nih.gov/pubmed/34037417.
Lauring AS and Andino R. 2010. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 6: e1001005. https://doi.org/10.1371/journal.ppat.1001005
Li CK-f, Wu H, Yan H, Ma S, Wang L, Zhang M, Tang X, Temperton NJ, Weiss RA, Brenchley JM, Douek DC, Mongkolsapaya J, Tran B-H, Lin C-lS, Screaton GR, Hou J-l, McMichael AJ and Xu X-N. 2008. T cell responses to whole SARS coronavirus in humans. The Journal of Immunology 181(8): 5490-5500. https://doi.org/10.4049/jimmunol.181.8.5490
Li F. 2013. Receptor recognition and cross-species infections of SARS coronavirus. Antiviral Research 100(1): 246-254. https://doi.org/10.1016/j.antiviral.2013.08.014
Li F. 2016. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annual Review of Virology 3: 237-261. https://doi.org/10.1146/annurev-virology-110615-042301
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo H-C, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou C-W, Javanmardi K, Finkelstein IJ and Musser J. 2020. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020.2009.2022.20199125. https://doi.org/10.1128/mBio.02707-20
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W and Tan W. 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet 395(10224): 565-574. https://doi.org/10.1016/S0140-6736(20)30251-8
Millet JK, and Whittaker GR. 2015. Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis. Virus Research 202: 120-134. https://doi.org/10.1016/j.virusres.2014.11.021
Muth D, Corman VM, Roth H, Binger T, Dijkman R, Gottula LT, Gloza-Rausch F, Balboni A, Battilani M, Rihtaric D, Toplak I, Ameneiros RS, Pfeifer A, Thiel V, Drexler JF, Muller MA and Drosten C. 2018. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission. Scientific Report 8: 15177. https://doi.org/10.1038/s41598-018-33487-8
Nigam D and Garcia-Ruiz H. 2020. Variation Profile of the Orthotospovirus Genome. Pathogens 9(7): 521. https://doi.org/10.3390/pathogens9070521
Noy-Porat T, Makdasi E, Alcalay R, Mechaly A, Levy Y, Bercovich-Kinori A, Zauberman A, Tamir H, Yahalom-Ronen Y, Israeli Ma, Epstein E, Achdout H, Melamed S, Chitlaru T, Weiss S, Peretz E, Rosen O, Paran N, Yitzhaki S, Shapira SC, Israely T, Mazor O and Rosenfeld R. 2020. A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes. Nature Communications 11: 4303. https://www.nature.com/articles/s41467-020-18159-4
Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S, Finkelstein DB, Xu X, Wang J, Ma J, Fan Y, Rakestraw KM, Webster RG, Hoffmann E, Krauss S, Zheng J, Zhang Z and Naeve CW. 2006. Large-Scale Sequence Analysis of Avian Influenza Isolates. Science 311(5767): 1576-1580. https://doi.org/10.1126/science.1121586
Pardi N, Hogan MJ, Porter FW and Weissman D. 2018. mRNA vaccines — a new era in vaccinology. Nature Reviews Drug Discovery 17: 261-279. https://www.nature.com/articles/nrd.2017.243
Phan T. 2020a. Genetic diversity and evolution of SARS-CoV-2. Infection, Genetics and Evolution 81: 104260. https://doi.org/10.1016/j.meegid.2020.104260
Phan T. 2020b. Novel coronavirus: From discovery to clinical diagnostics. Infection, Genetics and Evolution 79: 104211. https://doi.org/10.1016/j.meegid.2020.104211
Rantalainen KI, Eskelin K, Tompa P, and Mäkinen K. 2011. Structural flexibility allows the functional diversity of potyvirus genome-linked protein VPg. Journal of virology 85: 2449-2457. https://jvi.asm.org/content/85/5/2449
Sanjuán R and Domingo-Calap P. 2016. Mechanisms of viral mutation. Cellular and Molecular Life Sciences 73(23): 4433-4448. https://doi.org/10.1007/s00018-016-2299-6
Taboada B, Vazquez-Perez JA, Muñoz-Medina JE, Ramos-Cervantes P, Escalera-Zamudio M, Boukadida C, Sanchez-Flores A, Isa P, Mendieta-Condado E, Martínez-Orozco JA, Becerril-Vargas E, Salas-Hernández J, Grande R, González-Torres C, Gaytán-Cervantes FJ, Vazquez G, Pulido F, Araiza-Rodríguez A, Garcés-Ayala F, González-Bonilla CR, Grajales-Muñiz C, Borja-Aburto VH, Barrera-Badillo G, López S, Hernández-Rivas L, Perez-Padilla R, López-Martínez I, Ávila-Ríos S, Ruiz-Palacios G, Ramírez-González JE and Arias CF. 2020. Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico. Journal of Virology 94(1(): e01056-01020. https://doi.org/10.1128/JVI.01056-20
Tillett RL, Sevinsky JR, Hartley PD, Kerwin H, Crawford N, Gorzalski A, Laverdure C, Verma SC, Rossetto CC, Jackson D, Farrell MJ, Van Hooser S and Pandori M. 2020. Genomic evidence for reinfection with SARS-CoV-2: a case study. The Lancet Infectious Diseases 21(1): 52-58. https://doi.org/10.1016/S1473-3099(20)30764-7
van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, Ortiz AT and Balloux F. 2020. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics and Evolution 83: 104351. https://doi.org/10.1016/j.meegid.2020.104351
Volz EM, Hill V, McCrone JT, Price A, Jorgensen D, Toole A, Southgate JA, Johnson R, Jackson B, Nascimento FF, Rey SM, Nicholls SM, Colquhoun RM, da Silva Filipe A, Shepherd JG, Pascall DJ, Shah R, Jesudason N, Li K, Jarrett R, Pacchiarini N, Bull M, Geidelberg L, Siveroni I, Goodfellow IG, Loman NJ, Pybus O, Robertson DL, Thomson EC, Rambaut A and Connor TR. 2020. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity 184(1): 64-75. https://doi.org/10.1016/j.cell.2020.11.020
Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT and Veesler D. 2020. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 181(2): 281-292.e6. https://doi.org/10.1016/j.cell.2020.02.058
Wan Y, Shang J, Graham R, Baric RS and Li F. 2020. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. Journal of Virology 94(7): e00127-00120. https://doi.org/10.1128/JVI.00127-20
Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS and McLellan JS. 2020a. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367(6483): 1260-1263. https://doi.org/10.1126/science.abb2507
Wrapp D, De Vlieger D, Corbett KS, Torres GM, Wang N, Van Breedam W, Roose K, van Schie L, Team V-CC-R, Hoffmann M, Pohlmann S, Graham BS, Callewaert N, Schepens B, Saelens X and McLellan JS. 2020b. Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies. Cell 181(5): 1004-1015.e15. https://doi.org/10.1016/j.cell.2020.04.031
Xia S, Liu M, Wang C, Xu W, Lan Q, Feng S, Qi F, Bao L, Du L, Liu S, Qin C, Sun F, Shi Z, Zhu Y, Jiang S and Lu L. 2020. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Research 30: 343-355. https://www.nature.com/articles/s41422-020-0305-x
Yan R, Zhang Y, Li Y, Xia L, Guo Y and Zhou Q. 2020. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 367(6485): 1444-1448. https://doi.org/10.1126/science.abb2762
Yuan M, Wu NC, Zhu X, Lee C-CD, So RTY, Lv H, Mok CKP, and Wilson IA. 2020. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science 368(6491): 630-633. https://doi.org/10.1126/science.abb7269
Zhai X, Sun J, Yan Z, Zhang J, Zhao J, Zhao Z, Gao Q, He W-T, Veit M and Su S. 2020. Comparison of Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Binding to ACE2 Receptors from Human, Pets, Farm Animals, and Putative Intermediate Hosts. Journal of Virology 94: e00831-00820. https://doi.org/10.1128/JVI.00831-20
Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y and Shi W. 2020. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Current Biology 30(11): 2196-2203 e2193. https://doi.org/10.1016/j.cub.2020.05.023
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus I and Research T. 2020. A Novel Coronavirus from Patients with Pneumonia in China, 2019. The New England Journal of Medicine 382: 727-733. https://doi.org/10.1056/NEJMoa2001017
Zhu Z, Chakraborti S, He Y, Roberts A, Sheahan T, Xiao X, Hensley LE, Prabakaran P, Rockx B, Sidorov IA, Corti D, Vogel L, Feng Y, Kim JO, Wang LF, Baric R, Lanzavecchia A, Curtis KM, Nabel GJ, Subbarao K, Jiang S and Dimitrov DS. 2007. Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceeding of the National Academy of Sciences of United States of America 104(29): 12123-12128. https://doi.org/10.1073/pnas.0701000104
DOI: http://dx.doi.org/10.18781/R.MEX.FIT.2021-1
Refbacks
- There are currently no refbacks.