THEVIRUSES. Recent volumes in the series: Series Editors HEINZ FRAENKEL-CONRAT, University 01 California Berkeley, California

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2 The Coronaviridae

3 THEVIRUSES Series Editors HEINZ FRAENKEL-CONRAT, University 01 California Berkeley, California ROBERT R. WAGNER, University 01 Virginia School 01 Medicine Charlottesville, Virginia THE VIRUSES: Catalogue, Characterization, and Classification Heinz Fraenkel-Conrat Recent volumes in the series: THE ARENA VIRIDAE Edited by Maria S. Salvato THE BACTERIOPHAGES Volumes 1 and 2 Edited by Richard Calendar THE CORONA VIRIDAE Edited by Stuart G. Siddell THE HERPESVIRUSES Volumes 1-3 Edited by Bernard Roizman Volume 4 Edited by Bernard Roizman and Carlos Lopez THE INFLUENZA VIRUSES Edited by Robert M. Krug THE PAPOVAVIRIDAE Volume 1 Edited by Norman P. Salzman Volume 2 Edited by Norman P. Salzman and Peter M. Howley THE PARAMYXOVIRUSES Edited by David W. Kingsbury THE PARVOVIRUSES Edited by Kenneth 1. Berns THE PLANT VIRUSES Volume 1 Edited by R. 1. B. Francki Volume 2 Edited by M. H. V. Van Regenmortel and Heinz Fraenkel-Conrat Volume 3 Edited by Renate Koenig Volume 4 Edited by R. G. Milne THE REOVIRIDAE Edited by Wolfgang K. Joklik THE RETROVIRIDAE Volumes 1-4 Edited by Jay A. Levy THE RHABDOVIRUSES Edited by Robert R. Wagner THE TOGA VIRIDAE AND FLAVIVIRIDAE Edited by Sondra Schlesinger and Milton J. Schlesinger THE VIROIDS Edited by T. O. Diener

4 The Coronaviridae Edited by STUART G. SIDDELL Institute of Virology University of Würzburg Würzburg, Germany Springer Science+Business Media, LLC

5 Llbrary of Congress Cataloglng-ln-Publlcatlon Data The eoronaviridae I edited by Stuart G. Siddell. p. em. -- <rhe viruses) Ineludes bibliographieal referenees and index. 1. Coronaviruses. 2. Coronavirus infeetions. I. Siddell. S. II. Series. [DNLM, 1. Coronaviridae. 2. Coronaviridae Infeetions. QW C8 C J QR39!t. C ' de20 DNLM/DLC for Llbrary of Congress CIP ISBN ISBN (ebook) DOI / Springer Science+Business Media New York Original1y pub1ished by Plenum Press, New York in Softcover reprint ofthe hardcover 1st edition All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher

6 Contributors Robert Anderson, Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, B3H 4H7 Canada David A. Brian, Department of Microbiology, University of Tennessee, Knoxville, Tennessee I. Brierley, Virology Division, Department of Pathology, Cambridge University, Cambridge CB2 IQP, England T. D. K. Brown, Virology Division, Department of Pathology, Cambridge University, Cambridge CB2 IQP, England David Cavanagh, Institute for Animal Health, Division of Molecular Biology, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN, England Susan R. Compton, Section of Comparative Medicine, Yale University, New Haven, Connecticut Jane K. A. Cook, Intervet UK Ltd., Huntingdon, Cambridgeshire PEl7 2BQ, England Samuel Dales, Cytobiology Group, Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, N6A SCI Canada Raoul J. de Groot, Virology Division, Department of Infectious Diseases and Immunology, University of Utrecht, 3584 CL Utrecht, The Netherlands Luis Enjuanes, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Auton6ma, Cantoblanco, Madrid, Spain David J. Garwes, Ministry of Agriculture, Fisheries & Food, London SWIP 3JR, England Brenda G. Hogue, Department of Microbiology and Immunology, Division of Molecular Virology, Baylor College of Medicine, Houston, Texas Kathryn V. Holmes, Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland Marian C. Horzinek, Virology Division, Department of Infectious Diseases and Immunology, University of Utrecht, 3584 CL Utrecht, The Netherlands Thomas E. Kienzle, John L. McClellan Memorial Veterans Administration Medical Research Service, Litde Rock, Arkansas 72205; present address: Department of Ophthalmology, Baylor College of Medicine, Houston, Texas v

7 vi CONTRIBUTORS Marion Koopmans, Virology Section, National Institute of Public Health and Environmental Protection, 3720 BA Bilthoven, The Netherlands Hubert Laude, Laboratoire de Virologie et Immunologie Moleculaires, INRA, Centre de Recherches de Jouy-en-Josas, Jouy-en-Josas, France Willem Luytjes, Department of Virology, Institute of Medical Microbiology, Leiden University, 2300 AH Leiden, The Netherlands Paul S. Masters, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York A. P. A. Moekett, Intervet, Inc., Millsboro, Delaware Steven H. Myint, Department of Microbiology, University of Leicester, Leicester LEI 9HN, England Peter J. M. Rottier, Institute of Virology, Departme~t of Infectious Diseases and Immunology, University of Utrecht, 3584 CL Utrecht, The Netherlands Stuart G. Siddell, Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany Erie J. Snijder, Department of Virology, Institute of Medical Microbiology, Leiden University, 2300 AH Leiden, The Netherlands Willy J. M. Spaan, Department of Virology, Institute of Medical Microbiology, Leiden University, 2300 AH Leiden, The Netherlands Robbert G. van der Most, Department of Virology, Institute of Medical Microbiology, Leiden University, 2300 AH Leiden, The Netherlands Bernard A. M. Van der Zeijst, Institute of Infectious Diseases and Immunology, School of Veterinary Medicine, University of Utrecht, 3508 TD Utrecht, The N etherlands

8 Preface Coronaviruses were recognized as a group of enveloped, RNA viruses in 1968 and accepted by the International Committee on the Taxonomy of Viruses as a separate family, the Coronaviridae, in By 1978, it had become evident that the coronavirus genomic RNA was infectious (i.e., positive strand), and by 1983, at least the framework of the coronavirus replication strategy had been perceived. Subsequently, with the application of recombinant DNA techniques, there have been remarkable advances in our understanding of the molecular biology of coronaviruses, and a mass of structural data concerning coronavirus genomes, mrnas, and pro teins now exists. More recently, attention has been focused on the role of essential and accessory gene products in the coronavirus replication cyde and a molecular analysis of the structure-function relationships of coronavirus proteins. Nevertheless, there are still large gaps in our knowledge, for instance, in areas such as the genesis of coronavirus subgenomic mrnas or the function of the coronavirus RNA-dependent RNA polymerase. The diseases caused by coronaviruses have been known for much longer than the agents themselves. Possibly the first coronavirus-related disease to be recorded was feline infectious peritonitis, as early as The diseases associated with infectious bronchitis virus, transmissible gastroenteritis virus, and murine hepatitis virus were all well known before However, it was only the realization in the late 1960s that a coronavirus was responsible for a human disease, the common cold, that brought these virus es to the attention of academic virologists. The advances of the last few years, for example, in the molecular analysis of coronavirus protein immunogenicity or the identification of coronavirus receptors, have undoubtedly given an impetus to studies on coronavirus pathogenesis. At the same time, however, they have also begun to reveal the complexities of the coronavirus-host relationship. In parallel with the studies on coronaviruses, re cent insights into the genome organization, replication strategy, and nudeotide sequences of two other groups of viruses, the toroviruses and the arteriviruses, have led to the idea of a "coronaviruslike" superfamily. This idea, which is based essentially on a molecular view of evolution, led, in 1992, to the indusion of the toroviruses as a second genus in the Coronaviridae. The question of how the evolutionary vii

9 viii PREFACE links between the Coronaviridae and the arteriviruses should be reflected in their taxonomie status is still open to discussion. This volume consists essentially of two parts. The first 12 chapters discuss the molecular aspects of coronavirus and torovirus biology. First, the unique features of coronavirus replication, including the genome organization, transcription, and translation strategies, and the importance of RNA recombination are reviewed. This is followed by a chapter on coronavirus receptors. Then each of the virus structural and nonstructural pro teins is described in detail. FinaIly, the molecular biology of toroviruses and the idea of a "coronaviruslike" superfamily is discussed. In the second part of the volume, which consists of seven chapters, selected biological aspects of the most important coronavirus and torovirus infections are covered. These range from the experimental study of murine coronavirus infections to the problems of coronavirus infection in poultry and swine. I hope that this volume will be useful to both academic researchers and their students, as weil as clinicians and veterinarians with an interest in coronavirus-related diseases. I would like to thank the contributors, the staff of Plenum Press, and my wife for their patience during the preparation of this volume. University 01 Würz burg Würz burg, Germany Stuart G. Siddell

10 Contents Chapter 1 The Coronaviridae: An Introduction Stuart G. Siddell I. Introduction Classification A. Serological Relationships... 3 B. Sequence Relationships... 5 III. Genome Organization... 6 IV. Morphology and Physicochemical Properties... 8 V. Conclusion... 9 VI. References Chapter 2 Coronavirus Replication, Transcription, and RNA Recombination Robbert G. van der Most and Willy J. M. Spaan I. Introduction Replication Transcription A. Introduction B. Negative-Stranded RNAs C. Leader-Primed Transcription D. The Intergenie Promoter Sequence E. The Control of Subgenomic mrna Abundance F. Heterogeneity of Subgenomic mrnas IV. RNA Recombination V. References ix

11 x CONTENTS Chapter 3 Coronavirus Gene Expression: Genome Organization and Protein Synthesis Willem Luytjes I. Introduction A. General Genome Structure B. General Translation Strategy II. Coronavirus Genome: Coding Assignments and Translation Strategy of Conserved Genes A. The Polymerase (POL) Coding Region B. The Large-Surface (S) Pro tein Gene C. The Small-Membrane (sm) Pro tein Gene D. The Membrane (M) Protein Gene E. The Nucleocapsid (N) Protein Gene III. Coronavirus Genome: Coding Assignments and Expression of Nonconserved Genes A. ORFs between the POL and S Genes: Region I B. ORFs between the Sand sm Genes: Region II C. ORFs between the M and N Genes: Region III D. ORFs Downstream of the N Gene: Region IV IV. Conclusion V. References Chapter 4 Coronavirus Receptors Kathryn V. Holmes and Susan R. Compton I. Coronavirus Species and Tissue Tropisms II. Coronavirus Envelope Glycoproteins That Interact with Receptors III. Coronavirus Binding and Penetration IV. Carcinoembryonic Antigen-Related Receptors for MHV V. Aminopeptidase N Receptors for TGEV and HCV-229E VI. Carbohydrate Receptors for Coronaviruses VII. References Chapter 5 The Coronavirus Surface Glycoprotein David Cavanagh I. Physicochemical Properties A. Electron Microscope Observations B. Sedimentation Characteristics

12 CONTENTS xi C. Electrophoretic Analysis H. Primary Structure A. Overall Features B. Specific Features III. Structural and Antigenic Variation of S A. S Protein Is a Major Inducer of Neutralizing Antibody B. Location of Antigenie Sites IV. Induction of Protective Immunity V. Biological Functions A. Primary Attachment to Cells B. Membrane Fusion VI. Role of S in Pathogenicity VII. References Chapter 6 The Coronavirus Membrane Glycoprotein Peter r M. Rottier I. Introduction Physicochemical Properties A. Covalent Modifications B. Solubility III. Protein Structure A. Primary Structure B. Membrane Topology IV. Assembly in the Endoplasmic Reticulum V. Intracellular Transport and Maturation A. Transport and Processing in Coronavirus-Infected Cells B. Transport of the Expressed M Protein VI. Biological Functions A. Role of M in Coronavirus Budding B. Induction of Immunological Responses VII. Summary and Perspectives VIII. References Chapter 7 The Coronavirus Nucleocapsid Protein Hubert Laude and Paul S. Masters I. Introduction Coronavirus Ribonucleoprotein III. N Pro tein Structure IV. Synthesis of N Protein and Nucleocapsid Formation V. N Phosphorylation

13 xii CONTENTS VI. N Protein Binding to RNA VII. N-N and N-M Protein Interactions VIII. Potential Role of N Protein in RNA Synthesis IX. Antigenic Properties X. Conclusion XI. References Chapter 8 The Coronavirus Hemagglutinin Esterase Glycoprotein David A. Brian, Brenda G. Hogue, and Thomas E. Kienzle I. Discovery of the Hemagg1utinin Esterase Pro tein Deduced Amino Acid Sequence and Properties of the Bovine Coronavirus Hemagg1utinin Esterase Pro tein III. Comparison of the HEs of the BCY, HCV-OC43, MHV, and Influenza C Virus IV. Model of the BCV HE on the Virion V. Hemagglutinating Activity and Its Possible Role in Vivo VI. Esterase Activity and Its Possible Role in Vivo VII. Conc1uding Remarks VIII. References Chapter 9 The Small-Membrane Protein Stuart G. Siddell I. Introduction 11. Structure Expression.... IV. In Vitra Studies.... A. MHV mrna B. IBV mrna V. In Vivo Studies.... VI. Function.... VII. References Chapter 10 The Coronavirus Nonstructural Proteins T. D. K. Brawn and 1. Brierly I. Introduction Products of mrnai "

14 CONTENTS xiii A. Sequence Analysis of the Unique Regions of mrna Is 192 B. Expression of the la and Ib ORFs in Vitra C. Detection of the Products of mrna 1 in Vivo III. Putative Nonstructural ORFs Present in the Subgenomic RNAs of MHV A. mrna B. mrna C. mrna IV. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of BCV A. mrna B. mrna C. mrnas 5 and V. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of HCV-OC A. The 5 ORF B. The 5-1 ORF VI. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of TGEV and PRCV A. mrna B. mrna VII. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of FIPV and FECV A. mrna VIII. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of CCV A. mrna IX. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of HCV 22ge A. mrna B. mrna X. Putative Nonstructural Polypeptide ORFs Present in the Subgenomic RNAs of IBV A. mrna B. mrna XI. Conclusion XII. References Chapter 11 The Molecular Biology of Toroviruses Brie J. Sni;der and Marian C. Horzinek I. Introduction The Torovirion III. The Torovirus Genome IV. Berne Virus Transcription and Translation