Emerging coronaviruses: Genome structure, replication, and pathogenesis

Yu Chen, Qianyun Liu, Deyin Guo, Yu Chen, Qianyun Liu, Deyin Guo

Abstract

The recent emergence of a novel coronavirus (2019-nCoV), which is causing an outbreak of unusual viral pneumonia in patients in Wuhan, a central city in China, is another warning of the risk of CoVs posed to public health. In this minireview, we provide a brief introduction of the general features of CoVs and describe diseases caused by different CoVs in humans and animals. This review will help understand the biology and potential risk of CoVs that exist in richness in wildlife such as bats.

Keywords: coronavirus; epidemiology; pathogenesis; respiratory tract; virus classification; zoonoses.

© 2020 Wiley Periodicals, Inc.

Figures

Figure 1
Figure 1
The genomic structure and phylogenetic tree of coronaviruses. A, The phylogenetic tree of representative CoVs, with the new coronavirus 2019‐nCoV highlighted in red. B, The genome structure of four genera of coronaviruses. Pp1a and pp1b represent the two long polypeptides that are processed into 16 nonstructural proteins. S, E, M, and N indicate the four structural proteins spike, envelope, membrane, and nucleocapsid. 2019‐nCoV, 2019 novel coronavirus; CoVs, coronavirus; HE, hemagglutinin‐esterase. Viral names: HKU, coronaviruses identified by Hong Kong University; HCoV, human coronavirus; IBV, infectious bronchitis virus; MHV, murine hepatitis virus; TGEV, transmissible gastroenteritis virus

References

    1. Wang LF, Shi Z, Zhang S, Field H, Daszak P, Eaton B. Review of bats and SARS. Emerg Infect Dis. 2006;12(12):1834‐1840.
    1. Ge XY, Li JL, Yang XL, et al. Isolation and characterization of a bat SARS‐like coronavirus that uses the ACE2 receptor. Nature. 2013;503(7477):535‐538.
    1. Chen Y, Guo D. Molecular mechanisms of coronavirus RNA capping and methylation. Virol Sin. 2016;31(1):3‐11.
    1. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17(3):181‐192.
    1. Cauchemez S, Van Kerkhove MD, Riley S, Donnelly CA, Fraser C, Ferguson NM. Transmission scenarios for Middle East respiratory syndrome coronavirus (MERS‐CoV) and how to tell them apart. Euro Surveill. 2013;18(24):pii: 20503.
    1. Snijder EJ, van der Meer Y, Zevenhoven‐Dobbe J, et al. Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex. J Virol. 2006;80(12):5927‐5940.
    1. Hussain S, Pan J, Chen Y, et al. Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus. J Virol. 2005;79(9):5288‐5295.
    1. Sawicki SG, Sawicki DL, Siddell SG. A contemporary view of coronavirus transcription. J Virol. 2007;81(1):20‐29.
    1. Perlman S, Netland J. Coronaviruses post‐SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7(6):439‐450.
    1. Masters PS. The molecular biology of coronaviruses. Adv Virus Res. 2006;66:193‐292.
    1. Ziebuhr J, Snijder EJ, Gorbalenya AE. Virus‐encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol. 2000;81(Pt 4):853‐879.
    1. Eckerle LD, Becker MM, Halpin RA, et al. Infidelity of SARS‐CoV Nsp14‐exonuclease mutant virus replication is revealed by complete genome sequencing. PLOS Pathog. 2010;6(5):e1000896.
    1. Ogando NS, Ferron F, Decroly E, Canard B, Posthuma CC, Snijder EJ. The curious case of the nidovirus exoribonuclease: its role in RNA synthesis and replication fidelity. Front Microbiol. 2019;10:1813.
    1. Smith EC, Blanc H, Vignuzzi M, Denison MR. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLOS Pathog. 2013;9(8):e1003565.
    1. Huang C, Lokugamage KG, Rozovics JM, Narayanan K, Semler BL, Makino S. SARS coronavirus nsp1 protein induces template‐dependent endonucleolytic cleavage of mRNAs: viral mRNAs are resistant to nsp1‐induced RNA cleavage. PLOS Pathog. 2011;7(12):e1002433.
    1. Tanaka T, Kamitani W, DeDiego ML, Enjuanes L, Matsuura Y. Severe acute respiratory syndrome coronavirus nsp1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA. J Virol. 2012;86(20):11128‐11137.
    1. Graham RL, Sims AC, Brockway SM, Baric RS, Denison MR. The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication. J Virol. 2005;79(21):13399‐13411.
    1. Gadlage MJ, Graham RL, Denison MR. Murine coronaviruses encoding nsp2 at different genomic loci have altered replication, protein expression, and localization. J Virol. 2008;82(23):11964‐11969.
    1. Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: structures and functions of a large multi‐domain protein. Antiviral Res. 2018;149:58‐74.
    1. Serrano P, Johnson MA, Chatterjee A, et al. Nuclear magnetic resonance structure of the nucleic acid‐binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3. J Virol. 2009;83(24):12998‐13008.
    1. Beachboard DC, Anderson‐Daniels JM, Denison MR. Mutations across murine hepatitis virus nsp4 alter virus fitness and membrane modifications. J Virol. 2015;89(4):2080‐2089.
    1. Gadlage MJ, Sparks JS, Beachboard DC, et al. Murine hepatitis virus nonstructural protein 4 regulates virus‐induced membrane modifications and replication complex function. J Virol. 2010;84(1):280‐290.
    1. Stobart CC, Sexton NR, Munjal H, et al. Chimeric exchange of coronavirus nsp5 proteases (3CLpro) identifies common and divergent regulatory determinants of protease activity. J Virol. 2013;87(23):12611‐12618.
    1. Zhu X, Fang L, Wang D, et al. Porcine deltacoronavirus nsp5 inhibits interferon‐beta production through the cleavage of NEMO. Virology. 2017;502:33‐38.
    1. Zhu X, Wang D, Zhou J, et al. Porcine deltacoronavirus nsp5 antagonizes type I interferon signaling by cleaving STAT2. J Virol. 2017;91(10):pii: e00003‐17.
    1. Angelini MM, Akhlaghpour M, Neuman BW, Buchmeier MJ. Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double‐membrane vesicles. mBio. 2013;4(4):pii: e00524‐13.
    1. Cottam EM, Whelband MC, Wileman T. Coronavirus NSP6 restricts autophagosome expansion. Autophagy. 2014;10(8):1426‐1441.
    1. Kirchdoerfer RN, Ward AB. Structure of the SARS‐CoV nsp12 polymerase bound to nsp7 and nsp8 co‐factors. Nat Commun. 2019;10(1):2342.
    1. Zhai Y, Sun F, Li X, et al. Insights into SARS‐CoV transcription and replication from the structure of the nsp7‐nsp8 hexadecamer. Nat Struct Mol Biol. 2005;12(11):980‐986.
    1. te Velthuis AJ, van den Worm SH, Snijder EJ. The SARS‐coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension. Nucleic Acids Res. 2012;40(4):1737‐1747.
    1. Egloff MP, Ferron F, Campanacci V, et al. The severe acute respiratory syndrome‐coronavirus replicative protein nsp9 is a single‐stranded RNA‐binding subunit unique in the RNA virus world. Proc Natl Acad Sci USA. 2004;101(11):3792‐3796.
    1. Zeng Z, Deng F, Shi K, et al. Dimerization of coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity. J Virol. 2018;92(17):e00692‐18.
    1. Bouvet M, Lugari A, Posthuma CC, et al. Coronavirus Nsp10, a critical co‐factor for activation of multiple replicative enzymes. J Biol Chem. 2014;289(37):25783‐25796.
    1. Chen Y, Su C, Ke M, et al. Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′‐O‐methylation by nsp16/nsp10 protein complex. PLOS Pathog. 2011;7(10):e1002294.
    1. Decroly E, Debarnot C, Ferron F, et al. Crystal structure and functional analysis of the SARS‐coronavirus RNA cap 2′‐O‐methyltransferase nsp10/nsp16 complex. PLOS Pathog. 2011;7(5):e1002059.
    1. Ma Y, Wu L, Shaw N, et al. Structural basis and functional analysis of the SARS coronavirus nsp14‐nsp10 complex. Proc Natl Acad Sci USA. 2015;112(30):9436‐9441.
    1. Fang SG, Shen H, Wang J, Tay FPL, Liu DX. Proteolytic processing of polyproteins 1a and 1ab between non‐structural proteins 10 and 11/12 of coronavirus infectious bronchitis virus is dispensable for viral replication in cultured cells. Virology. 2008;379(2):175‐180.
    1. Ahn DG, Choi JK, Taylor DR, Oh JW. Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA‐dependent RNA polymerase capable of copying viral RNA templates. Arch Virol. 2012;157(11):2095‐2104.
    1. te Velthuis AJW, Arnold JJ, Cameron CE, van den Worm SHE, Snijder EJ. The RNA polymerase activity of SARS‐coronavirus nsp12 is primer dependent. Nucleic Acids Res. 2010;38(1):203‐214.
    1. Adedeji AO, Lazarus H. Biochemical characterization of Middle East respiratory syndrome coronavirus helicase. mSphere. 2016;1:5.
    1. Hao W, Wojdyla JA, Zhao R, et al. Crystal structure of Middle East respiratory syndrome coronavirus helicase. PLOS Pathog. 2017;13(6):e1006474.
    1. Jia Z, Yan L, Ren Z, et al. Delicate structural coordination of the severe acute respiratory syndrome coronavirus Nsp13 upon ATP hydrolysis. Nucleic Acids Res. 2019;47(12):6538‐6550.
    1. Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E. RNA 3′‐end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex. Proc Natl Acad Sci USA. 2012;109(24):9372‐9377.
    1. Chen Y, Cai H, Pan J, et al. Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase. Proc Natl Acad Sci USA. 2009;106(9):3484‐3489.
    1. Minskaia E, Hertzig T, Gorbalenya AE, et al. Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc Natl Acad Sci USA. 2006;103(13):5108‐5113.
    1. Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kao CC. RNA recognition and cleavage by the SARS coronavirus endoribonuclease. J Mol Biol. 2006;361(2):243‐256.
    1. Deng X, Hackbart M, Mettelman RC, et al. Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages. Proc Natl Acad Sci USA. 2017;114(21):E4251‐E4260.
    1. Zhang L, Li L, Yan L, et al. Structural and biochemical characterization of endoribonuclease Nsp15 encoded by middle east respiratory syndrome coronavirus. J Virol. 2018;92(22):pii: e00893‐18.
    1. Shi P, Su Y, Li R, Liang Z, Dong S, Huang J. PEDV nsp16 negatively regulates innate immunity to promote viral proliferation. Virus Res. 2019;265:57‐66.
    1. Beniac DR, Andonov A, Grudeski E, Booth TF. Architecture of the SARS coronavirus prefusion spike. Nat Struct Mol Biol. 2006;13(8):751‐752.
    1. Delmas B, Laude H. Assembly of coronavirus spike protein into trimers and its role in epitope expression. J Virol. 1990;64(11):5367‐5375.
    1. Nal B. Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E. J Gen Virol. 2005;86(Pt 5):1423‐1434.
    1. Neuman BW, Kiss G, Kunding AH, et al. A structural analysis of M protein in coronavirus assembly and morphology. J Struct Biol. 2011;174(1):11‐22.
    1. DeDiego ML, Alvarez E, Almazan F, et al. A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo. J Virol. 2007;81(4):1701‐1713.
    1. Nieto‐Torres JL, DeDiego ML, Verdiá‐Báguena C, et al. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLOS Pathog. 2014;10(5):e1004077.
    1. Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015;1282:1‐23.
    1. Chang C, Sue SC, Yu T, et al. Modular organization of SARS coronavirus nucleocapsid protein. J Biomed Sci. 2006;13(1):59‐72.
    1. Hurst KR, Koetzner CA, Masters PS. Identification of in vivo‐interacting domains of the murine coronavirus nucleocapsid protein. J Virol. 2009;83(14):7221‐7234.
    1. Cui L, Wang H, Ji Y, et al. The nucleocapsid protein of coronaviruses acts as a viral suppressor of RNA silencing in mammalian cells. J Virol. 2015;89(17):9029‐9043.
    1. Woo PCY, Lau SKP, Lam CSF, et al. Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86(7):3995‐4008.
    1. Su S, Wong G, Shi W, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24(6):490‐502.
    1. Zhou P, Fan H, Lan T, et al. Fatal swine acute diarrhoea syndrome caused by an HKU2‐related coronavirus of bat origin. Nature. 2018;556(7700):255‐258.
    1. Simas PVM, Barnabé ACS, Durães‐Carvalho R, et al. Bat coronavirus in Brazil related to appalachian ridge and porcine epidemic diarrhea viruses. Emerg Infect Dis. 2015;21(4):729‐731.
    1. Cinatl J, Morgenstern B, Bauer G, Chandra P, Rabenau H, Doerr H. Treatment of SARS with human interferons. Lancet. 2003;362(9380):293‐294.
    1. Chan JFW, Chan KH, Kao RYT, et al. Broad‐spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus. J Infect. 2013;67(6):606‐616.
    1. Cheng KW, Cheng SC, Chen WY, et al. Thiopurine analogs and mycophenolic acid synergistically inhibit the papain‐like protease of Middle East respiratory syndrome coronavirus. Antiviral Res. 2015;115:9‐16.
    1. Wang Y, Sun Y, Wu A, et al. Coronavirus nsp10/nsp16 methyltransferase can be targeted by nsp10‐derived peptide in vitro and in vivo to reduce replication and pathogenesis. J Virol. 2015;89(16):8416‐8427.
    1. Mair‐Jenkins J, Saavedra‐Campos M, Baillie JK, et al. The effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta‐analysis. J Infect Dis. 2015;211(1):80‐90.
    1. Graham RL, Donaldson EF, Baric RS. A decade after SARS: strategies for controlling emerging coronaviruses. Nat Rev Microbiol. 2013;11(12):836‐848.
    1. de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016;14(8):523‐534.

Source: PubMed

Sponzoři a spolupracovníci

Zdravotní podmínky

Drogové intervence

3
Předplatit