(BQ) Part 1 book Principles and practice of clinical virology has contents: Diagnostic approaches, emerging virus infections, varicella zoster, hepatitis viruses, epstein–barr virus, viruses other than rotaviruses associated with acute diarrhoeal disease,... and other contents.
Principles and Practice of Clinical Virology SIXTH EDITION Principles and Practice of Clinical Virology, Sixth Edition © 2009 John Wiley & Sons Ltd ISBN: 978-0-470-51799-4 Edited by A J Zuckerman, J E Banatvala, B D Schoub, P D Griffiths and P Mortimer Principles and Practice of Clinical Virology SIXTH EDITION Edited by Arie J Zuckerman UCL Medical School, London, UK Jangu E Banatvala Guy’s, King’s and St Thomas’ School of Medicine, London, UK Barry D Schoub National Institute of Virology, Sandringham, South Africa Paul D Griffiths UCL Medical School, London, UK Philip Mortimer Health Protection Agency, London, UK A John Wiley & Sons, Ltd., Publication This edition first published 2009 © 2009 John Wiley & Sons Ltd Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical and Medical business with Blackwell Publishing Registered office: John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Other Editorial Offices 9600 Garsington Road, Oxford, OX4 2DQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988 All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic books Designations used by companies to distinguish their products are often claimed as trademarks All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners The publisher is not associated with any product or vendor mentioned in this book This publication is designed to provide accurate and authoritative information in regard to the subject matter covered It is sold on the understanding that the publisher is not engaged in rendering professional services If professional advice or other expert assistance is required, the services of a competent professional should be sought The contents of this work are intended to further general scientific research, understanding, and discussion only and are not intended and should not be relied upon as recommending or promoting a specific method, diagnosis, or treatment by physicians for any particular patient The publisher and the author make no representations or warranties with respect to the accuracy or completeness of the contents of this work and specifically disclaim all warranties, including without limitation any implied warranties of fitness for a particular purpose In view of ongoing research, equipment modifications, changes in governmental regulations, and the constant flow of information relating to the use of medicines, equipment, and devices, the reader is urged to review and evaluate the information provided in the package insert or instructions for each medicine, equipment, or device for, among other things, any changes in the instructions or indication of usage and for added warnings and precautions Readers should consult with a specialist where appropriate The fact that an organization or Website is referred to in this work as a citation and/or a potential source of further information does not mean that the author or the publisher endorses the information the organization or Website may provide or recommendations it may make Further, readers should be aware that Internet Websites listed in this work may have changed or disappeared between when this work was written and when it is read No warranty may be created or extended by any promotional statements for this work Neither the publisher nor the author shall be liable for any damages arising herefrom Library of Congress Cataloging-in-Publication Data: Principles and practice of clinical virology / edited by Arie J Zuckerman [et al.] – 6th ed p ; cm Includes bibliographical references and index ISBN 978-0-470-51799-4 Virus diseases Medical virology I Zuckerman, Arie J [DNLM: Virus Diseases WC 500 P957 2008] RC114.5.P66 2008 616.9 101—dc22 2008040268 A catalogue record for this book is available from the British Library ISBN: 978-0-470-51799-4 Typeset in 9/11 Times Roman by Laserwords Private Limited, Chennai, India Printed in Singapore by Fabulous Printers Pte Ltd First Impression 2009 Contents List of Contributors Preface xi xiii Past, Present and Future of Clinical Virology: An Overview Diagnostic Approaches Katie Jeffery and Emma Aarons xv Introduction Electron Microscopy Histology/Cytology Virus Isolation Serology Molecular Amplification Techniques Recommended Diagnostic Investigations 20 Future Trends 22 Viral Transmission: Infection Acquired by the Blood-borne Route 29 Will Irving Introduction 29 Prevention of Exposure through Infection Control 30 Prevention of Infection through Specific Pre- and Post-exposure Policies 30 Patient-to-patient Transmission 30 Patient-to-HCW Transmission 32 HCW-to-patient Transmission 36 Viral Transmission: Infection Acquired by All Other Routes (Respiratory, Eye–Nose–Mouth, Inoculation and Faeco-orally) 43 Philip Rice Introduction 43 Measles, Mumps and Rubella 44 Cytomegalovirus 47 Varicella Zoster Virus 48 Herpes Simplex Virus 53 Noroviruses 54 Rotavirus 56 Parvovirus B19 56 Respiratory Viruses 58 Emerging Virus Infections Brian W.J Mahy Introduction 69 Factors Contributing to Emergence Future Directions 77 69 69 Vaccinology Francis E Andre and Hugues H Bogaerts 81 Introduction 81 Burden of Viral Diseases and their Reproductive Rates 82 The Immune System and its Role in Natural and Artificially-induced Immunity 83 Discovery of Protective Antigens in Pathogens 85 Presentation of Protective Antigens through Vaccines and Types of Vaccine 86 Research and Development on Vaccines and their Commercial Introduction 86 Social Marketing of Introduced Vaccines 88 Planning and Implementation of Vaccination Programmes 89 Surveillance of Disease Incidence and Adverse Events Before and After Implementation of Vaccination 89 Rectification of Publicized Falsehoods and Maintenance of Vaccination Coverage 89 Viral Vaccines on the Horizon and the Roadblocks to Future Vaccine Development 90 Closing Comments 91 Herpes Simplex Virus Type and Type Marianne Forsgren and Paul E Klapper Morphology 95 Replication 97 Epidemiology 103 Viral Diagnosis 105 Antiviral Chemotherapy 108 95 vi Contents Clinical Features, Diagnosis and Management Concluding Remarks 128 Varicella Zoster Judith Breuer 112 133 Introduction 133 The Virus 133 Epidemiology 142 Clinical Features 143 Diagnosis of VZV Infection 148 Treatment 151 Prevention 153 Cytomegalovirus Paul D Griffiths 12 Hepatitis Viruses 273 Tim J Harrison, Geoffrey M Dusheiko and Arie J Zuckerman 161 Introduction 161 The Virus 161 Epidemiology 166 Routes of Infection 167 Pathogenesis 168 Clinical Features 173 Diagnosis 175 Management 180 Prevention 183 Treatment 185 Introduction Hepatitis A Hepatitis E Hepatitis B Hepatitis D Hepatitis C 273 275 280 282 307 309 13 GB Virus C (GBV-C) and Torque Teno Virus (TTV) 321 Shigeo Hino Introduction 321 GB Virus C (GBV-C) 321 Torque Teno Virus (TTV) 325 Epstein–Barr Virus Tanzina Haque and Dorothy H Crawford Introduction 199 The Virus 199 Epidemiology 204 EBV-associated Diseases 205 EBV Infection in the Immunocompromized Host Vaccine Development 218 Worldwide Distribution of KSHV in the General Population 247 Transmission 249 Clinical Manifestations 251 Pathogenesis 254 Diagnostic Assays 261 Antiviral Therapy 263 199 215 10 Roseoloviruses: Human Herpesviruses 6A, 6B and 223 Katherine N Ward and Duncan A Clark Introduction 223 Biology of the Viruses 223 Epidemiology and Pathogenesis 228 Disease Associations 231 Laboratory Diagnosis 236 Antiviral Therapy 240 Concluding Remarks 240 11 Kaposi’s Sarcoma-associated Herpesvirus (Human Herpesvirus 8) 245 Cornelia Henke-Gendo, Abel Viejo-Borbolla and Thomas F Schulz Introduction 245 Origin and Evolution of KSHV 245 14 Rotaviruses Ulrich Desselberger and Jim Gray 337 Introduction 337 Rotavirus Structure, Genome and Gene–Protein Assignment 337 Classification 337 Replication 338 Pathogenesis 342 Immune Responses and Correlates of Protection 343 Illness, Diagnosis and Treatment 343 Epidemiology 344 Vaccine Development 345 15 Viruses other than Rotaviruses Associated with Acute Diarrhoeal Disease 355 Jim Gray and Ulrich Desselberger Introduction 355 Enteric Adenoviruses 357 Noroviruses and Sapoviruses (Human Caliciviruses) 358 Astroviruses 363 Gastrointestinal Viruses Not Regularly Associated with Acute Diarrhoeal Disease 364 16 Influenza Maria Zambon and Chris W Potter 373 Contents Other Clinical Manifestations 477 Diagnosis 477 Treatment 481 Prevention 482 Future Prospects 483 Introduction 373 Viral Variation 380 Virus Classification 384 Pathogenesis 385 Clinical Features 388 Diagnosis of Infection 391 Treatment and Prevention 396 17 Parainfluenza Viruses 409 Stelios Psarras, Nikolaos G Papadopoulos and Sebastian L Johnston Introduction 409 Taxonomy 409 Structure and Physical Properties 410 Receptors, Virus Entry and Host Range 411 Replication 414 Viral Transmission, Incubation and Shedding 416 Pathogenesis 417 Antigenicity and Immunity 418 Epidemiology 420 Clinical Features 423 Diagnosis 425 Prevention 428 Treatment 429 18 Respiratory Syncytial Virus Caroline Breese Hall vii Introduction 463 Description and Characteristics of the Virus 464 Pathogenesis 468 Immune Response 469 Epidemiology 470 Clinical Features 471 Respiratory Infections 471 Ocular Infections 474 Gastrointestinal Infections 475 Haemorrhagic Cystitis 475 Adenoviruses Infections in Immunocompromized Patients 475 Introduction 489 Taxonomy 489 Physical Properties 492 Incubation and Transmission 492 Host Range 493 Pathogenesis 493 Immunity 495 Epidemiology 496 Clinical Features 497 Diagnosis 498 Prevention and Treatment 500 21 Coronaviruses and Toroviruses J.S Malik Peiris and L.L.M Poon 441 Introduction 441 The Virus 441 Epidemiology 442 Pathogenesis 444 Immunity 445 Clinical Features 446 Diagnosis 450 Management 452 Prevention 453 19 Adenoviruses Marcela Echavarr´ıa 20 Rhinoviruses 489 Nikolaos G Papadopoulos, Maria Xatzipsalti and Sebastian L Johnston 511 Introduction 511 The Viruses 511 Initiation of Infection and Pathogenesis 517 Epidemiology 519 Clinical Features 520 Diagnosis 523 RT-PCR 524 Prophylaxis: Active and Passive Immunization 525 Therapy 526 Acknowledgements 526 22 Measles Virus 533 Sibylle Schneider-Schaulies and Volker ter Meulen 463 Introduction 533 The Virus 533 Virus Morphology 535 Genome Structure 535 MV Protein Functions 536 The Replication Cycle 538 Biological Properties of the Measles Virus 540 Epidemiology and Relatedness of Different Virus Isolates 541 Clinical Manifestations 542 The Pathogenesis of Measles and its Complications 545 Diagnosis 551 Management 552 Prevention 552 viii Contents 23 Rubella 561 Jennifer M Best, Joseph P Icenogle and David W.G Brown Historical Introduction 561 The Virus 562 Postnatally Acquired Infection 565 Congenitally Acquired Infection 569 Laboratory Techniques and Diagnosis 576 Prevention—Rubella Vaccination 580 24 Mumps Pauli Leinikki 593 Introduction 593 The Virus 593 Pathogenesis 595 Clinical Picture 595 Laboratory Diagnosis 597 Epidemiology and Control 598 25 Enteroviruses Philip D Minor and Peter Muir 601 Introduction 601 The Viruses 601 Pathobiological and Clinical Aspects of Human Enteroviruses 608 Laboratory Diagnosis of Enterovirus Infections 615 Prevention and Treatment of Enterovirus Infections 617 Future Prospects 620 26 Poxviruses Peter B Jahrling 625 Introduction 625 Virus Characteristics 625 Clinical Aspects of Orthopoxvirus Infections 627 Diagnosis 632 Medical Management 634 Other Poxviruses Infecting Humans 635 Diagnosis 637 27 Alphaviruses Graham Lloyd 643 Introduction 643 The Virus 643 Spectrum of Diseases Caused by Alphaviruses 647 Diagnosis of Alphavirus Infections 647 Management and Prevention 647 Alphaviruses Associated with Fevers and Polyarthritis 648 Alphaviruses Associated with Encephalitis 656 Other Alphaviruses 661 28 Flaviviruses Barry D Schoub and Marietjie Venter 669 Introduction 669 Properties of the Virus 670 Yellow Fever 672 Other Members of the ‘Unassigned’ Subgroup of Flaviviruses 678 Dengue 679 Zika 684 Japanese Encephalitis 684 St Louis Encephalitis 687 West Nile Virus 688 Murray Valley Encephalitis 690 Tick-borne Encephalitis 691 Omsk Haemorrhagic Fever 694 Kyasanur Forest Disease 694 Powassan Virus 695 29 Bunyaviridae Robert Swanepoel and Felicity J Burt Introduction 699 The Virus 700 Laboratory Diagnosis 703 Genus Orthobunyavirus 706 Genus Phlebovirus 711 Genus Nairovirus 717 Genus Hantavirus 721 Bunyaviruses Unassigned to Genus 699 726 30 Arenaviruses Colin R Howard 733 Introduction 733 Ultrastructure of Arenaviruses and Infected Cells 735 Chemical Composition 737 Replication 739 Diagnosis of Human Arenavirus Infections 740 Antigenic Relationships 741 Clinical and Pathological Aspects 741 Persistent Infection 743 Pathology of Arenavirus Infections: General Features 744 Other Arenavirus Infections 750 Summary 751 31 Filoviruses Susan P Fisher-Hoch Introduction 755 Epidemiology 756 Ecology 761 Transmission and Risk Factors Clinical Spectrum 763 763 755 Contents Laboratory Diagnosis 764 Patient Management 765 Past Infection and Persistence 766 Virology 766 Animal Models 767 Serological Studies 768 Pathogenesis and Immunology 768 Control 769 Perspective 770 32 Rabies and Other Lyssavirus Infections Mary J Warrell Polyomavirus-specific Immune Response 845 Treatment of Polyomavirus-associated Diseases 847 Acknowledgements 848 35 Human Parvoviruses Kevin E Brown 777 Introduction 777 History 777 Classification 778 Virus Structure 778 Replication 780 Inactivation of Virus and Stability of Vaccine Antigen 781 Epizootiology and Epidemiology 781 Incidence of Human Rabies 783 Pathogenesis 783 Immunology 785 Routes of Infection 786 Clinical Features of Rabies in Animals 787 Clinical Features in Humans 787 Diagnosis 794 Management of Human Rabies 796 Pathology 796 Human Rabies Prophylaxis 797 Control of Animal Rabies 800 33 Papillomaviruses Dennis McCance 853 Introduction 853 Human Parvovirus B19 (B19V) 854 Pathogenesis 856 Epidemiology 858 Clinical Features 859 Laboratory Diagnosis 863 Treatment and Prevention 865 36 Human Retroviruses Robin A Weiss 869 Introduction 869 Retrovirus Replication and Genomes 869 Taxonomy 870 Human and Zoonotic Retrovirus Infections 870 Retroviral Vectors 872 37 The Human T-lymphotropic Viruses Graham P Taylor 807 Introduction 807 Classification 807 Physical and Chemical Properties 807 Serology 811 Viral Replication 811 Natural History of HPV Infections 812 Pathogenesis 813 Diagnosis 817 Treatment 818 Vaccination 819 34 The Human Polyomaviruses Kristina Dăorries ix 875 Introduction 875 History 875 The Virus 876 Diagnosis 879 Viral Variation 880 Epidemiology 881 Transmission 883 HTLV-associated Disease 884 Pathogenesis 886 Treatment 889 Prevention of Disease 891 HIV and HTLV Co-infection 891 38 Human Immunodeficiency Viruses 897 Deenan Pillay, Anna Maria Geretti and Robin A Weiss 823 Classification and Detection 823 Virion Structure and Composition 823 Virus Life Cycle 823 State of Human Polyomavirus Infection 833 Diagnostic Evaluation of Polyomavirus-associated Disease 843 Introduction and Classification 897 Epidemiology 899 Replication 900 Host Genetic Determinants for HIV/AIDS 903 Viral Dynamics and Pathogenesis 903 Immune Responses 905 The Laboratory Diagnosis of HIV Infection 906 The Natural History of HIV Infection and Its Clinical Manifestations 909 x Contents Antiretroviral Therapy—A Historical Perspective 916 Monitoring of Antiretroviral Therapy and Resistance 917 Antiretroviral Drug Classes 921 Transmission of Drug Resistance 929 Prevention 929 Vaccines 932 39 Human Prion Diseases John Collinge Introduction to Prions and Historical Perspective 939 Structural Biology of Prions 940 Normal Cellular Function of PrP 943 Prion Strains 943 Neuronal Cell Death in Prion Disease 945 The ‘Species Barrier’ 945 Pathogenesis 946 Animal Prion Diseases 947 Aetiology and Epidemiology of Human Prion Disease 948 Clinical Features and Diagnosis 949 Molecular Diagnosis of Prion Disease 959 Pre-symptomatic and Antenatal Testing 960 Prevention and Public Health Management 960 Prognosis and Treatment 961 Concluding Remarks 962 Useful Websites 962 939 Index 969 Coronaviruses and Toroviruses Antigenic Structure Virus-neutralizing and haemagglutination-inhibiting antibodies are induced by both the S and HE proteins of coronaviruses and toroviruses and some antibodies against the coronavirus M protein neutralize virus in the presence of complement Epitope mapping of coronaviruses has been done mostly for S protein and has shown that virus-neutralizing epitopes are formed largely by the N-terminal S1 half of the protein, which has much greater amino acid sequence variation (Siddell, 1995) Removal of glycans from the S protein of IBV greatly diminished the binding of virus-neutralizing monoclonal antibodies The S protein has been shown to be a major inducer of protective immunity (Buchholz et al., 2004) although the other structural proteins, particularly the nucleocapsid protein, contribute to cell-mediated protection In the case of feline infectious peritonitis virus (FIPV), the immune response to S protein is believed to exacerbate the disease FIPV attached to anti-S antibody remains infectious and is more readily taken up by macrophages (antibody-dependent enhancement), within which FIPV replicates (de Groot and Horzinek, 1995) Similar antibody-dependent enhancement has not been reported for human coronaviruses, although there is a report that SARS-CoV spike-bearing viral pseudotypes can enter human B cell lines that lack the virus receptor angiotensin-converting enzyme (ACE2) via FcγRII in the presence of antibody (Kam et al., 2007) and one needs to be alert to this possibility Immune electron microscopy has revealed relationships between the toroviruses of humans, equines and bovines Much remains to be done to establish the extent of variation among human toroviruses INITIATION OF INFECTION AND PATHOGENESIS Cell Attachment Proteins The S protein serves to attach the virus to cells The extent to which the HE protein, when present, is also responsible for cell attachment is not clear The HE proteins, in contrast to the S proteins, of both coronaviruses and toroviruses are not required for replication in vitro (Popova and Zhang, 2002) Amino acids 417–547 of the HCoV-229E S protein were required for binding to its cell receptor and the receptor-binding motif of SARS-CoV’s S protein has been mapped to the amino acid residues 424–494 (Li et al., 2005b; Wentworth and Holmes, 2007) The role of S protein as a determinant of host cell range has been demonstrated using recombinant coronaviruses 517 expressing heterologous S proteins For example, MHV expressing the feline coronavirus (FCoV) S protein was able to successfully infect and replicate in feline cells previously refractory to MHV infection It is the S1 part of S protein that determines receptor specificity Experiments with recombinant MHVs showed that the extent of replication of the virus, and the degree of hepatitis in the liver, was determined largely by the S protein Gallagher and Buchmeier (2001) have reviewed virus entry and pathogenesis for MHV Cell Receptors for Coronaviruses The specificity of virus attachment to host cells can be a major factor in determining host range, tissue tropism and hence pathogenesis Three cellular proteins – aminopeptidase N (APN), carcinoembryonic antigen cell adhesion molecule (CEACAM-1) and ACE2 – have been identified as the principal receptors for binding group and coronaviruses The transfer of coronavirus receptors from susceptible cells to other cells can render the latter susceptible to infection (Wentworth and Holmes, 2007) Human APN has been identified as the receptor for HCoV-229E This protein is a metalloprotease located on the surface of epithelial cells, including those of the intestine, lung and kidney Human cells that were not susceptible to canine coronavirus (CCoV) or FCoV became susceptible when transfected with a human/canine chimaera of APN The critical, C-terminal domain was formed by amino acids 643–841 of the canine APN When amino acids 255–348 of porcine APN were replaced by amino acids 260–353 of human APN, the resulting chimeric protein was able to function as a receptor for HCoV-229E Thus different parts of APN molecules may function as receptors for most group coronaviruses Expression of feline APN in rodent cells rendered the cells susceptible not only to FCoV but also to HCoV-229E, CCoV and TGEV Previous work had shown, however, that human APN would bind HCoV-229E but not TGEV, while porcine APN would bind TGEV but not human coronavirus (HCoV) Surprisingly, HCoV-NL63, also a human group coronavirus, uses ACE2 for receptor binding (Hofmann et al., 2005) Much less work has been done on receptors for group 2a human coronaviruses The cellular receptor for MHV (a group 2a coronavirus, like HCoV-OC43), is a member of the CEA family of glycoproteins in the immunoglobulin superfamily (Lai and Cavanagh, 1997) CEACAM-1, is a 424-amino-acid glycoprotein with four immunoglobulin-like domains A soluble form of this protein has been crystallized and its atomic structure has been deduced (Tan et al., 2002) The immunoglobulin-loop of human CEACAM-1 confers virus-binding specificity Different isoforms of 518 Principles and Practice of Clinical Virology, Sixth Edition murine CEACAM-1 protein exist These have extensive differences in the N-terminal immunoglobulin-like domain to which MHV binds and so bind MHV to different extents Amino acids 38–43 were key elements for binding MHV and for virus-induced membrane fusion (Rao et al., 1997) When a persistent infection of MHV was established in murine 17 Cl cells, which express very low levels of the CEACAM-1 receptor, there was selection of mutant MHVs that were better able to use other molecules as receptors (Schickli et al., 1997) Human ACE2, an 805-amino-acid glycoprotein, is the primary receptor for SARS-CoV and HCoV-NL63 It is a carboxypeptidase which cleaves angiotensin II to angiotensin-(1-7) In addition to playing a role in regulating the blood pressure and cardiovascular and renal function, the renin–angiotensin system is believed to modulate acute lung injury The crystal structure of the protein complex comprising the human ACE2 and SARS-CoV receptor-binding domain has been elucidated The adaptation of the SARS-CoV-like civet virus to humans was associated with key changes in the spike protein which enhance binding to the ACE2 receptor In comparison to the human SARS-CoV, the civet SARS-CoV-like virus spike has two amino acid substitutions in the spike (N479K; T487S) that adversely affect its interaction with human ACE2 (Li et al., 2005b) Similarly, the civet-like virus that re-emerged to infect humans in late 2003 also had the T487S amino acid substitution and an additional change at L472P compared with human SARS-CoV and this probably contributed to its poor pathogenicity and transmissibility in humans Thus a small number of spike mutations may be critical for facilitating efficient interspecies transmission The spike of the SARS-like coronavirus found in bats is markedly different in this region and will not bind human ACE2 Apart from ACE2, other cellular proteins such as DC-SIGN, L-SIGN and L-SECtin are also able to facilitate virus binding of some coronaviruses (Wentworth and Holmes, 2007) The expression of L-SIGN in cells lacking ACE2 expression allows SARS-CoV binding but not virus replication It is thus a binding receptor rather than a functional receptor for SARS-CoV Involvement of Glycans on Receptors The S protein of some coronaviruses and the HE protein of group 2a coronaviruses bind to sialoglycoconjugates on cell surfaces and these interactions may also be relevant for virus entry and tissue tropism Attachment of coronaviruses might be a two-step process Primary attachment might be mediated by a first receptor, for example, N-acetyl-9-O-acetylneuraminic acid (Neu5, 9Ac2 ) for some coronaviruses, a second receptor for example, APN or CEACAM-1 proteins, bringing the virus and cell membranes closer together for subsequent membrane fusion Some receptors might fulfil both functions for some coronaviruses Both the S and HE proteins of bovine coronavirus (BCoV) bind to cell surface components, an important one being the glycan component Neu5, 9Ac2 This residue acts as a receptor not only on erythrocytes but also on susceptible cell cultures (Schultze and Herrler, 1992) The S protein binds more efficiently than HE to Neu5,9Ac2 and it has been proposed that the BoCV S protein is responsible for the primary attachment to cells HE proteins from different group 2a coronaviruses have different specificities to bind or cleave sialoglycoconjugates For instance, the HE protein of HCoV-OC43 prefers to bind to Neu5,9Ac2 and it is also a sialate-4-O-acetylesterase Thus by contributing to both binding and removal of the virus from the cell surface, the HE protein may help virus release as well as virus entry Host Range of Coronaviruses Interspecies transmission of coronaviruses is well recognized in animals The closely related group coronaviruses, porcine transmissible gastroenteritis virus, canine and FCoV can infect pigs with some disease expression BCoV can naturally infect dogs and humans and even cause disease in avian hosts The HCoV-OC43 has >99% amino acid identity in its S and HE proteins with the corresponding proteins of BCoV A recently discovered respiratory CCoV is a group coronavirus, the S protein of which had 96 and 95% amino acid identity with that of BCoV and HCoV-OC43, respectively Cross-infection by these viruses has not been studied but a broad host range for them is a possibility (Saif, 2006) Coronaviruses can undergo dramatic changes in virulence and tissue tropism Porcine enteric transmissible gastroenteritis virus caused a highly virulent disease in pigs A spontaneously occurring spike gene deletion mutation led to the emergence of a virus (porcine respiratory coronavirus) with a tropism for the respiratory tract and reduced virulence in pigs These changes in the spike were responsible for the altered tissue tropism (Ballesteros et al., 1997) Interestingly these deletion mutants arose independently in Europe and North America as these viruses have differences in the size of the spike deletion Thus it is no surprise that a civet SARS-like virus was able to establish itself and to transmit and cause disease in humans In addition to the changes in the civet virus spike that led to a dramatic change, the binding affinity for the human ACE2 receptor also altered Another striking difference observed in human SARS-CoV is a 29-nucleotide deletion which interrupts the ORF8ab of the civet virus Coronaviruses and Toroviruses (Guan et al., 2003) The biological significance of this deletion is still unclear Fusion Processes The S protein of coronavirus is a class fusion protein The fusion processes for coronavirus viral entry is not completely understood During the fusion, the S protein undergoes a series of conformational changes The binding of S to the receptor could induce the separation of S1 from S2, and alter the conformation of S1, generating alternative disulfide linkages within S1 The fusion peptide in the S2 region is then exposed to host cell membrane This is followed by a series of conformational changes of the S2 protein and the hydrophobic heptad repeat regions (i.e HR1 and HR2) in the S2 domains of the trimeric complex to form a six-helical bundle at the final stages of fusion It is believed that a small region rich in tyrosine and tryptophan residues before the transmembrane domain of S2 may help to destabilize lipid bilayers, thereby leading to pore formation and membrane fusion (Wentworth and Holmes, 2007) EPIDEMIOLOGY Seroepidemiology indicates that antibodies to 229E and OC43 appear early in life and are ubiquitous by adulthood (McIntosh et al., 1970) Limited data based on enzyme-linked immunosorbent assay (ELISA)-based assays using portions of the recombinant nucleocapsid and pseudotyped virus expressing the NL63 spike protein suggest that the same is true of NL63 (Hofmann et al., 2005; Shao et al., 2007) There is limited seroepidemiology data on HKU1 as this virus still cannot be cultivated efficiently Preliminary ELISA assays using recombinant HKU1 nucleocapsid protein showed evidence of seroconversion in patients with HKU1 disease but a low (2%) seroprevalence in the community (Woo et al., 2005a) Community studies have shown that the incidence of, for example, coronavirus 299E infections may vary from year to year from as low as 1% to as high as 34% (Hamre and Beem, 1972) Coronaviruses appear to have a winter–spring seasonality in temperate regions In subtropical Hong Kong, the seasonality appears to be similar except that NL63 may be found in early summer and autumn (Chiu et al., 2005; Lau et al., 2006) Unlike many other respiratory viral infections, all age groups appear to be uniformly infected with HCoVs Reinfection of individuals with the same HCoV serotype often occurs within months of the first infection, suggesting that even homologous protection is short-lived Available data suggest that antibodies to one HCoV group may not be protective against infection with viruses from the other HCoV group 519 Severe Acute Respiratory Syndrome SARS emerged as a pneumonic respiratory disease in Guangdong Province, China in November 2002 and within weeks had spread to affect about 8000 patients in 29 countries across five continents, associated with an overall fatality rate of 9.6% (Peiris et al., 2007) A novel coronavirus, SARS-CoV was identified as the aetiological agent (Drosten et al., 2003; Ksiazek et al., 2003; Peiris et al., 2003b) The lack of antibody to SARS-CoV in asymptomatic healthy people in the community suggested that it was a disease that emerged from an animal reservoir (Ksiazek et al., 2003; Peiris et al., 2003b) The earliest human cases of SARS in late 2002 had epidemiological links with live animal markets (Xu et al., 2004) A virus closely related (99.8% nucleotide identity) to SARS-CoV was detected in palm civets (Paguma larvata) and other small mammal markets in southern China where live game animals are sold as exotic foods for human consumption (Guan et al., 2003) Humans working in these markets had high prevalence of antibody to SARS-CoV although they had no history of a SARS-like disease, suggesting that they had been infected with the less pathogenic precursor SARS-CoV-like virus Furthermore, when SARS re-emerged to infect humans in Guangdong in late 2003 and early 2004, the virus was more closely related to the civet-like virus rather than to the human adapted virus that spread worldwide in mid 2003 It was of low pathogenicity and failed to transmit from human to human (Liang et al., 2004), probably as a consequence of the poor affinity of the virus–receptor interaction (see above) Thus it is likely that these animal markets were the interface which allowed the precursor virus to adapt and amplify in animals such as civets and infect humans However, civets were not the natural reservoir A SARS-like coronavirus has been found in wild caught bats (Rhinolophus spp.) and these appear to be the natural reservoir from which SARS-CoV emerged (Lau et al., 2005; Li et al., 2005a) The nucleotide identity between the bat precursor virus and human SARS-CoV is only around 90% and this precursor virus had to undergo significant adaptation before becoming efficiently transmissible in humans As bats, civets and a range of other animal species are sold for human consumption within the markets of Guangdong, this provided the ideal milieu for such adaptation to occur (Peiris et al., 2007) While many SARS patients did not transmit infection at all, a few patients accounted for a disproportionately large number of secondary cases, the so-called ‘super-spreading incidents’ Although host factors may have played a role in these super-spreading events, in many instances it was a combination of host factors and environmental circumstances that facilitated transmission Overall, the basic reproduction number of SARS was estimated to 520 Principles and Practice of Clinical Virology, Sixth Edition be approximately 2–4 (Lipsitch et al., 2003; Riley et al., 2003) Respiratory droplets were believed to be the major vehicle of transmission and the use of effective droplet precautions did protect healthcare workers (Seto et al., 2003) However, true air-borne transmission probably did occur in some instances through the use of aerosol-generating procedures such as intubation, suction, high-flow oxygen therapy and the use of nebulizers Infectious virus was also present in faeces (Peiris et al., 2003b) and the largest super-spreading incident at Amoy Gardens in Hong Kong which led to over 300 cases is believed to have occurred through aerosolization of infected faeces in the sewage system in a high-rise apartment (Yu et al., 2004) SARS-CoV retains viability for much longer periods than 229E, suggesting that fomites may also be an important means of virus transmission (Rabenau et al., 2005) Unlike many other respiratory viral infections, relatively little SARS transmission occurred early (first five days) in the illness (Lipsitch et al., 2003) This was probably related to the low viral load in the upper respiratory tract (and faeces) early in the illness with a peak of viral load at around day 10 of disease (Peiris et al., 2003a) These disease characteristics probably contributed to the dramatic spread in the hospital setting (by which time patients were highly contagious) and the relatively lower transmission within the family setting Healthcare workers comprised 21% of all cases (Peiris et al., 2007) Another unusual feature of SARS was that asymptomatic infections was uncommon (Leung et al., 2004b) The absence of large number of asymptomatic transmitters of the disease and the limited transmission in the first five days of illness were fortuitous features of this disease that allowed its successful containment through the application of public health measures such as case detection and isolation It is relevant to consider whether SARS may return Since the interruption of the major global outbreak in July 2003, there is no evidence of continued circulation of the human-adapted SARS-CoV in humans or animals However, this virus exists in laboratories and there were three laboratory infections in 2003 and 2004, in one instance, leading to transmission in the community Fortunately, these outbreaks were successfully contained The SARS-CoV-like civet virus led to four new cases in December 2003 and January 2004, many of whom had a history of contact with the animal market trade, but these civet SARS-CoV were not well adapted to efficient human transmission (see above) The sale of civets in big animal markets in southern China was subsequently banned While it is possible that an illegal trade continues, this will probably not provide the same opportunities for interspecies transmission and sustained circulation of virus as may happen in the large organized animal market setting The original precursor virus still exists in bats and it is conceivable that it may re-emerge, again re-adapt to human transmission and lead to human outbreaks (Peiris et al., 2007) CLINICAL FEATURES Association of human disease with coronavirus 229E and OC43 has been conclusively established by infecting human volunteers with cultured virus and documenting ‘common cold‘-like symptoms in association with virus replication in the upper respiratory tract (Bradburne et al., 1967; Hamre and Procknow, 1966) thereby fulfilling Koch’s postulates These studies also established that the incubation period was around two days with peak symptoms occurring at three to four days Virus was detectable in the respiratory tract around the time of symptom onset and continued to be detectable for around five days Coronaviruses (229E and OC43) account for approximately 25% of common colds and are second only to rhinoviruses as the causative agent (Makela et al., 1998) The symptoms are those of a nasal discharge, mild sore throat, sneezing, general malaise, perhaps with headache and lasts for an average of six to seven days Fever and coughing may be exhibited in 10 and 20% of cases, respectively No difference is observed between 229E and OC43 strains in the pathology of infection Generally symptoms are indistinguishable from those of colds caused by rhinoviruses Subclinical or very mild infections are common HCoVs were found in 10% of children with otitis media with effusion, respiratory syncytial virus being associated with approximately 30% of cases (Pitkaranta et al., 1998) Ethical considerations have precluded human volunteer studies being done with the more recently discovered coronaviruses NL63 and HKU1 or for SARS-CoV Thus disease association has been indirect, by detecting the virus in the respiratory tract in association with disease The aetiological link has been conclusive with SARS where the virus and seroconversion to it was almost exclusively associated with clinical disease and there was minimal asymptomatic infection (see above) Furthermore, the virus was demonstrated at the site of pathology, viz lung and gastrointestinal tracts (Nicholls et al., 2006; Peiris et al., 2003b) Experimental transmission of the virus to cynomolgous macaques led to SARS-like lung pathology (Fouchier et al., 2003) Taken together, these findings satisfy Koch’s postulates for an association of a pathogen and disease However, in the case of NL63 Coronaviruses and Toroviruses and HKU1, the association with human disease depends on the virus being more frequently found in the respiratory tract of patients with disease than in matched controls While detection of these viruses in association with respiratory disease has been observed in many studies worldwide, fewer studies have compared these data with concurrent age-matched controls These viruses (and also HCoV-229E or HCoV-OC43) can occasionally be found in ‘healthy‘ controls and furthermore, finding multiple respiratory viruses in patients with disease makes it difficult to establish the contribution of each one to the illness (van der Hoek, 2007) Unlike SARS-CoV, neither of these viruses has relevant animal models that can be used to fulfil Koch’s postulates In studies that have used a control group for comparison, 229E and OC43 were associated with 11% of children with acute respiratory tract disease compared with 0.37% of controls (P < 0.01), confirming the data from volunteer studies (van Elden et al., 2004) NL63 and HKU1 were not sought in this study In patients aged 60 years or older, 229E and OC43 were found in 17% of 107 elderly subjects with acute respiratory disease and only 2% of controls Rhinovirus was more commonly detected (32% of patients and 2% of controls) while influenza was less common (7% of cases and 0% controls) (Graat et al., 2003) In a study of children and young adults, 229E and OC43 were detected in both patients (3.6% of flu-like illness; 7.7% of other respiratory illness) and in controls (3.9%) and there was no statistically significant association with disease (van Gageldonk-Lafeber et al., 2005) Coronaviruses have also been associated with exacerbations of wheezing in asthmatic children (McIntosh et al., 1973) Coronavirus was detected in approximately 5% of children (Freymuth et al., 1999) and 22% of adults hospitalized because of asthma (Atmar et al., 1998) Allergic patients with a common cold, associated with a number of viruses, including HCoVs (25%), had prolonged nasal eosinophil influx (van Benten et al., 2001) Whether that would increase the risk of subsequent allergen-induced hypersensitivity reactions is not known An experimental model has been established for viral wheeze, involving volunteers (some atopic, others not) with and without a history of viral wheeze (McKean et al., 2001) Over half developed colds after inoculation with HCoV-229E The viral wheezers reported more upper respiratory tract symptoms than controls Over half of the wheezers, but none of the controls, reported lower respiratory tract symptoms (wheeze, chest tightness and shortness of breath) NL63 has been found significantly more often in patients with croup than in controls (17% vs 4%) and appeared to be an even more important cause of this disease than parainfluenza virus (van der Hoek et al., 2005) 521 However, studies of cases and controls for association of NL63 with other features of acute respiratory disease have been inconclusive (Boivin et al., 2005; Dare et al., 2007) An alternative, but less definitive approach of establishing disease associations is to identify patients with the virus of interest without any other relevant respiratory pathogen NL63 was detected as the sole pathogen in 0.4–9.3% of patients with respiratory infection and HKU1 in between 0.3 and 4.4% of patients (van der Hoek, 2007) The symptoms found in patients with NL63 alone included fever, cough, rhinorrhoea, pharyngitits, croup, bronchiolitis, pneumonia and febrile seizures Some patients had underlying disease A association of NL63 with Kawasaki disease has not been confirmed HKU1 was associated with a similar spectrum of disease as seen with NL63 although it was not associated with croup Febrile seizures were more common in HKU1 infected patients that those with OC43 (Woo et al., 2005b) Between 50 and 80% of patients had underlying diseases (van der Hoek, 2007) In hospitalized patients, 229E, OC43, NL63 and HKU1 have all been found in upper as well as lower respiratory tract disease, especially in children (Arden et al., 2005; Boivin et al., 2005; Chiu et al., 2005; Sloots et al., 2006; Woo et al., 2005b) These coronaviruses have also been detected in bronchoalveolar lavages of immunocompromised and noncompromised adults, providing additional evidence of their pathogenic potential in the lower respiratory tract (Garbino et al., 2006) Follow-up bronchoalveolar lavage specimens were available from some patients and these were often negative, indicating that the virus was temporally associated with the clinical symptoms HKU1 has also been detected in respiratory specimens from patients with diarrhoeal symptoms and in stool specimens in association with fever, otitis and convulsions (Vabret et al., 2006) Thus, it is possible that, as with SARS, HKU1 may lead to disseminated disease Coronaviruses have been associated with nosocomial outbreaks of disease in children in neonatal units and in premature babies (Esper et al., 2005; Sizun et al., 1995) Neonates with coronavirus infections had bradycardia, apnoea, hypoxaemia, fever or abdominal distention Chest X-ray revealed diffuse infiltrates As with influenza and respiratory syncytial virus, coronaviruses are also associated with respiratory illness in the elderly (Falsey et al., 2002;Walsh et al., 1999) Severe Acute Respiratory Syndrome The incubation period of SARS is estimated to be 2–14 days SARS typically presents as fever, myalgia, malaise, chills or rigour and fever of acute onset leading in some patients to a rapidly progressing viral pneumonia A dry cough is common but rhinorrhoea and sore throat are 522 Principles and Practice of Clinical Virology, Sixth Edition less prominent Watery diarrhoea was reported in a proportion of patients Radiological abnormalities were seen in >60% of cases at presentation Typically the chest radiograph showed ground glass opacities, and focal consolidation over the periphery and subpleural regions of the lower zones of the lung One or both lungs may be involved and the radiological changes may shift location High-resolution computed tomography (CT) scanning allowed detection of abnormalities in a proportion of patients with initially unremarkable chest radiographs While approximately one-third of patients improved, with defervescence and resolution of the radiographic changes, others progressed to develop increasing shortness of breath, tachypnoea and oxygen desaturation Extrapulmonary manifestations included hepatic dysfunction, a marked lymphopenia involving both B and T cells (CD4 and CD8 subsets) and NK cells and less commonly, central nervous system (CNS) manifestations (Cheng et al., 2007; Peiris et al., 2003c, 2007) About 20–30% of patients required management in intensive care and many of them needed mechanical ventilation The terminal events were severe respiratory failure associated with acute respiratory distress syndrome and multiple organ failure The overall case fatality rate was 9.6% The clinical features of SARS were not pathognomonic and a contact history and virological evidence of infection were important in establishing the diagnosis The occurrence of clusters of cases of a rapidly progressing pneumonia in a family or hospital setting was suggestive of the disease The severity of illness and increasing case fatality was associated with increasing age and presence of other co-morbidities A higher viral load in nasopharynx and serum early in the disease was an independent risk factor for mortality (Chu et al., 2004b) Children had a milder disease course (Leung et al., 2004a) The elderly may present atypically without fever or respiratory symptoms and failure to recognize such atypical presentations led to catastrophic nosocomial outbreaks (Chow et al., 2004) Residual impairment of lung function persists into late convalescence including restrictive lung function abnormalities due to lung fibrosis, impairment in diffusion capacity, muscle weakness, and reduced exercise capacity Psychological sequelae including depression and post-traumatic stress have been reported in survivors (Cheng et al., 2007) Coronaviruses and Toroviruses Associated with the Human Enteric Tract Coronavirus-like (non-SARS) viruses have been isolated from faecal specimens from humans (Duckmanton et al., 1997) Some of these viruses were isolated from infants with necrotizing enterocolitis, patients with nonbacterial gastroenteritis and from homosexual men with diarrhoea who were symptomatic and seropositive for human immunodeficiency virus Some isolates were shown to be serologically related to OC43 The discovery that a protein found in enterocytes functions as a receptor for HCoV-229E strengthens the likelihood that coronaviruses might replicate in the human alimentary tract Evidence has increased that toroviruses are associated with gastroenteritis in humans In a case–control study of children, an antigen-capture ELISA revealed torovirus in stools from 27% (9/33) of children with acute diarrhoea, 27% (11/41) with persistent diarrhoea and none in controls (Koopmans et al., 1997) Enteroaggregative Escherichia coli was commonly found in assocation with the torovirus In another childhood study electron microscopy revealed a torovirus incidence of 35% (72/206) and 15% in gastroenteritis cases and controls, respectively (Jamieson et al., 1998) Those infected with torovirus were more frequently immunocompromised (43 vs 16%) and nosocomially infected (58 vs 31%); experienced less vomiting (47 vs 68%); had more bloody diarrhoea (11 vs 2%) Coronaviruses in the Central Nervous System Multiple sclerosis (MS) is a chronic disease of the CNS involving multifocal regions of inflammation and myelin destruction Coronaviruses are one of the many infectious agents that have been proposed as causes for triggering MS and associated with demyelination in humans and rodents (Stohlman and Hinton, 2001) Coronavirus RNA and evidence of virus replication have been detected in the brains of humans and many human neural cell lines have been shown to support the replication of both OC43 and 229E types of HCoV Murine hepatitis virus infection in mice and rats has long been a model for coronavirus-induced demyelination, although the exact mechanism(s) by which MHV induces demyelination and the role of the immune system in the pathology is not known Inflammatory mediators, for example, interleukin 1β, tumour necrosis factor, IL-6 and an MHV-induced immune response that cross-reacts with myelin proteins, have been proposed as possible mechanisms Peripheral cross-reactive T-cell clones recognizing both HCoV and a myelin antigen have been detected in MS patients It has also been hypothesized that HCoV RNA might sometimes lead to a low level of viral protein synthesis that could be involved in the stimulation of immune responses within the CNS, exacerbating the effect of coronaviral infection in MS patients (Arbour et al., 2000) Persistent OPC43 and 229E infections have been established in some human neural cell lines Coronaviruses and Toroviruses Pathology and Pathogenesis There are limited pathology data from patients infected with the non-SARS human coronaviruses because they have been generally mild and those rare instances of fatal disease have not been investigated at autopsy There is a report of electron microscopic changes in the nasal mucosa of a child with coronavirus infection There was minimal cytopathology but evidence of active virus replication with virus particles seen within cytoplasmic vesicles and the Golgi apparatus (Afzelius, 1994) Severe Acute Respitatory Syndrome Although the major adverse pathology was on the respiratory tract, SARS was a disseminated infection with virus being isolated from the upper respiratory tract, the lungs, faeces and urine (Chan et al., 2004) and with reverse transcription polymerase chain reaction (RT-PCR) evidence of viral RNA in the plasma and serum (Ng et al., 2003) Viral RNA has also been detected in the lymph nodes, spleen, liver, heart, kidey and skeletal muscle (Farcas et al., 2005) Autopsy findings in the patients who died in the first 10 days of illness revealed diffuse alveolar damage, air-space oedema, desquamation of pneumocytes, inflammatory infiltrate and hyaline membrane formation (Franks et al., 2003; Nicholls et al., 2003) Virus antigen was detectable by immunohistochemistry in alveolar epithelial cells and also in macrophages and bronchial epithelium within the first 10 days of illness but rarely after that (Nicholls et al., 2006) This correlates with in vitro studies showing that SARS-CoV replicates in differentiated type alveolar epithelium and in ciliated cells in primary human airway epithelium but not in undifferentiated alveolar epithelial cell lines such as A549 (Mossel et al., 2007; Sims et al., 2005) Intestinal epithelial cells had viral particles demonstrable by electron microscopy with no obvious cytopathology and this is consistent with the watery diarrhoea observed clinically (Leung et al., 2003) Patients with SARS had high serum levels of a range of pro-inflammatory chemokines (IL-8, CCL2, CXCL10) and cytokines (IL-1, IL-6) (Wong et al., 2004) and these same immune mediators were elicited from virus-infected macrophages in vitro (Cheung et al., 2005) It is not clear whether these mediators are a reflection of the severe tissue damage or are contributing to the exacerbation of pathology induced by the virus Genetic polymorphisms associated with susceptibility to SARS have been identified Two independent studies have reported an increased susceptibility to SARS associated with low serum levels of mannose-binding lectin (MBL) and that MBL neutralizes the infectivity 523 of SARS-CoV in vitro (Ip et al., 2005; Zhang et al., 2005) Although other genetic polymorphisms have also been reported to be associated with SARS (HLA-B*4601; HLA-B*0707, ICAM-3, CLEC4M), they have not been independently confirmed DIAGNOSIS Diagnosis of HCoV infections was not routinely done in most diagnostic virus laboratories in the past because these viruses are not readily culturable in vitro and well-standardized reagents for immunological detection were not available Antigen-capture ELISAs have been used to detect HCoV antigens in nasal and throat swabs, and nasopharyngeal aspirates, and to detect HTVs in stools (Koopmans et al., 1997) Furthermore, the human coronaviruses 229E and OC43 were considered nothing more than the cause of the ‘common cold‘ The discovery of SARS and other novel human coronaviruses, the realization that human coronaviruses can cause clinically significant disease and the more widespread use of PCR or molecular diagnostics in clinical virology laboratories is leading to a reassessment The specimens for diagnosis of coronavirus infections are typically respiratory specimens (nasopharyngeal aspirates, nasopharyngeal swabs, throat and nose swabs and, when available, bronchoalveolar lavages) and paired sera for seroconversion when appropriate In the case of SARS, viral RNA was also detectable in faecal specimens and in serum HKU1 has also been detected by RT-PCR in faeces It is notable that the discovery of a novel coronavirus as the cause of SARS relied heavily on the classical virological techniques of virus isolation and electron microscopy, subsequently followed by molecular diagnostics and genome sequencing (Drosten et al., 2003; Ksiazek et al., 2003; Peiris et al., 2003b) The use of virus detection microarrays also independently identified the cell culture isolate as a coronavirus (Wang et al., 2003) Initial partial sequence information was obtained using random primer-based RT-PCR (Drosten et al., 2003; Peiris et al., 2003b) and by consensus primer RT-PCR methods (Ksiazek et al., 2003) The discovery of the new human coronavirus NL63 was achieved by virus isolation followed by a novel approach VIDISCA (virus discovery based on cDNA-AFLP) to identify the virus isolate by deriving fragments of genetic sequence (van der Hoek et al., 2004) HKU1 and novel bat coronaviruses were discovered using consensus primer RT-PCR methods (Poon et al., 2005a; Woo et al., 2005a) Virus detection microarrays are likely to be a strategy of the future (Kistler et al., 2007) 524 Principles and Practice of Clinical Virology, Sixth Edition Virus Isolation HCoV-OC43 and related strains were considerably more difficult to propagate in cell culture than HCoV-229E-related strains and required the use of organ cultures, hence the letters ‘OC’ Now, however, cell lines are available for the propagation of both laboratory-adapted HCoV types, although primary isolation remains difficult 229E and related strains can be isolated in roller culture monolayers of human embryonic lung fibroblasts such as W138 and MRC5 cells and the human embryonic intestinal fibroblast cell MA177 In virus-positive cultures, a gradual cytopathic effect consisting of small, granular, round cells appears throughout the monolayers, especially around the periphery of the monolayers However, cell sheets are rarely destroyed completely on initial isolation (Myint, 1995) Vero E6 cells and fetal rhesus kidney cells have been used for the isolation of SARS-CoV (Drosten et al., 2003; Ksiazek et al., 2003; Peiris et al., 2003b) Passage of SARS-CoV in cells leads to the emergence of amino acid substitutions in the spike and M genes related to adaptation to the host cells (Poon et al., 2005b) HCoV-NL63 can be cultured in tertiary monkey kidney cells and in LLC-MK2 cells HCoV-HKU1 is difficult to grow but has been isolated in HuH7 cells (Vabret et al., 2006) Human torovirus has not been grown in vitro in ice cold acetone or virus neutralization tests were used for detecting seroconversion to SARS-CoV and for seroepidemiological studies Neutralizing antibodies against SARS-CoV peak at around four months after disease onset and decline gradually thereafter Around 16% of survivors had undetectable levels of neutralizing antibody three years later (Cao et al., 2007) There may be cross-reactions in other serological tests For instance, immunofluorescent antibody responses to SARS-CoV appear to be associated with anamnestic responses to other human coronaviruses (OC43, 229E) although the converse was not true, possibly because there was no prior immunological memory to SARS-CoV to give rise to the anamnestic responses (Chan et al., 2005) ELISA assays using recombinant nucleocapsid antigens have been described, but positive results must be confirmed by immunofluorescence or microneutralization tests (Woo et al., 2004) HTV purified from the stool of a patient was used in an haemagglutination-inhibition assay to detect antibodies to HTV in nosocomial cases of gastroenteritis; acute and convalescent sera were examined, revealing rises in antibody titres (Jamieson et al., 1998) Bovine antisera to BTV cross-reacted with the human toroviruses, showing that BTV antisera could be used for human diagnostic purposes Human convalescent HTV serum reacted with the HE protein of BTV in western blots Electron Microscopy Electron microscopy is not routinely used for diagnosis of HCoV causing respiratory disease although it has been sometimes been used to detect HCoVs in epithelial cells shed from the nasopharynx of patients after attempted isolation in cell culture (229E strains, SARS-CoV) and organ culture (OC43 type) Immune electron microscopy has been used with convalescent sera from patients Enteric HCoVs and HTVs have also been sought in faeces using electron and immune electron microscopy (Duckmanton et al., 1997) The two types of virus are of similar size HTVs are pleomorphic, sometimes exhibiting a torus (doughnut) appearance and an irregular rod shape The spikes of coronaviruses, and possibly of toroviruses, are not always clearly revealed by negative staining Thus the two viruses can be confused if electron microscopy alone is used; corroborative evidence is required (Cornelissen et al., 1998) Serology Complement fixation, enzyme immunoassay, immunofluorescence or neutralization tests have been used for serodiagnosis of coronaviruses (Myint, 1995) Immunofluorescence tests on virus-infected cells fixed RT-PCR RT-PCR assays are increasingly used for the diagnosis of respiratory viruses, including coronaviruses (Vabret et al., 2001) Given the limited sequence data available on 229E and OC43, as well as prototype viruses isolated many years ago, it is possible that the incidence of these viruses is underestimated through primers not detecting variant strains This situation will improve with the availability of more virus sequence data The design of consensus primers that potentially detect viruses within the coronavirus genus has been useful in our hands Modifications based on the primers reported by Ksiazek (Ksiazek et al., 2003; Stephensen et al., 1999) targeted at ORF1b appear to perform well, although they are not as sensitive as virus-specific primers for directly detecting HCoV in clinical specimens (Chiu et al., 2005; Poon et al., 2005a) The application of PCR technology for the detection of HTVs awaits gene sequence data Microarray Analysis Viral microarrays that detect a wide range of known and unknown viral pathogens are being used to identify Coronaviruses and Toroviruses pathogens in clinical specimens These are providing a better insight into the global viral flora present in health and disease and also leading to the detection of novel pathogens (Kistler et al., 2007; Quan et al., 2007; Wang et al., 2002) However, as with PCR-based methods, it is important to have relevant age-matched controls in these studies to be able to interpret the clinical significance of such findings PROPHYLAXIS: ACTIVE AND PASSIVE IMMUNIZATION Active Immunization There are no vaccines for the group and HCoVs, but following the SARS outbreak in 2003 there has been interest in developing a vaccine for SARS There have been coronavirus vaccines for veterinary use, but they have had limited success and it is perhaps relevant to learn from the successes and limitation of these veterinary vaccines They have been developed against three group coronaviruses – TGEV, FCoV and CCoV – and the group coronavirus IBV With the possible exception of IBV vaccines, the coronavirus vaccines have been only marginally effective in the field (Saif, 2005)) Live vaccines have been more effective than killed vaccines for TGEV in pigs and IBV in chickens Serum neutralizing antibodies generally fail to correlate with protection but immunoglobulin A (IgA) antibody in the colostrum is a better correlate of protection against TGEV For TGEV and IBV, priming with a live attenuated vaccine and boosting with a killed vaccine led to increased mucosal immunity Vaccinating cats with FCoV vaccines actually led to enhanced disease with the antibody to the spike leading to immunopathology (Olsen, 1993) Vaccines for IBV in chicken are widely used but antigenic variability of the virus poses a challenge because cross-immunity is generally poor (Cavanagh and Naqi, 2003) Work towards a vaccine for SARS has been reviewed (Cheng et al., 2007; Gillim-Ross and Subbarao, 2006) Experimental challenge studies in mice immunized with DNA vaccines and the use of adoptive transfer and T-cell deletion established that antibodies rather than T cells are the key effectors of vaccine-mediated immune protection (Subbarao et al., 2004) A range of vaccine strategies including the use of inactivated whole virus vaccines, subunit vaccines (including baculovirus-expressed S1 subdomain, trimeric spike protein expressed in mammalian cells), DNA vaccines expressing the spike, the N, M or E proteins, vectored vaccines based on modified vaccinia Ankara (MVA) virus, vesicular stomatitis virus, parainfluenza type or adenovirus vectors, have been 525 evaluated An attenuated parainfluenza virus vector individually expressing SARS-CoV spike, E, M and N proteins showed that only the recombinants expressing spike protein were effective in inducing neutralizing antibodies and protecting hamsters from experimental challenge (Buchholz et al., 2004) Induction of neutralizing antibody responses and, where relevant, T cell responses, were measured Some of these experimental vaccines have been evaluated in experimental animal models with challenge using infectious SARS-CoV Experimental challenge of vaccinated animals did not convincingly reveal evidence of immune-mediated disease enhancement, as has been seen with FCoV As SARS is no longer circulating in the human population, there has been little incentive to take these experimental vaccines to human clinical trials These vaccines have all been prepared using the human SARS-CoV However, it is likely that a re-emergent SARS will arise from re-adaptation of a precursor virus from the animal reservoir As none of these bat or civet SARS-like CoVs can be cultured in vitro, cross-protection of these vaccines against the wild-type animal precursor viruses has not been tested However, reverse genetics has allowed the reconstruction of animal (civet-like) SARS-CoV and these viruses are less efficiently neutralized by human convalescent antisera to SARS-CoV ( (Rockx et al., 2007) This possibly reflects that fact that, while the receptor-binding domain is the major SARS-CoV neutralization determinant (Yi et al., 2005), the SARS-CoV from civets does not efficiently bind the human ACE2 receptor This raises questions whether a vaccine developed against the human SARS-CoV will be effective in protection against a future re-emergent animal SARS-like CoV More recently, human monoclonals that neutralize both SARS-CoV as well as GD03 and civet viruses SZ3 and SZ16 have been reported (Zhu et al., 2007) While this provides evidence of the existence of antibody paratopes that will cross-neutralize both human and closely related animal precursors, this does not imply that many of the vaccine strategies used hitherto will predominantly induce antibody to such conserved protective epitopes Passive Immunization Passive immunization with human monoclonal antibodies to the SARS-CoV spike protein have been successful in protecting mice and ferrets from challenge with SARS-CoV (ter Meulen et al., 2004) While some of these monoclonal antibodies failed to cross-neutralize closely related animal viruses, antibodies that cross-neutralize SARS-CoV and strains of civet origin are now available and protect mice from challenge with reconstructed viruses with spike protein that represents both human and 526 Principles and Practice of Clinical Virology, Sixth Edition civet viruses (Rockx et al., 2007, 2008) Pools of such antibodies have promise for passive immunization and also perhaps for immunotherapy of patients with SARS-like disease THERAPY Notwithstanding research in this area, antiviral drugs are not currently in use for control of the ‘common cold’ or other respiratory manifestations caused by HCoVs SARS was a severe pneumonia caused by what was initially an unknown pathogen and the global spread of the disease was contained in a relatively short period of time As such, there are no controlled clinical trial data on which to base treatment recommendations Clinical management of SARS is primarily supportive care Since SARS has no pathognomonic features and presents as a community-acquired pneumonia, appropriate antimicrobial coverage should be given until the diagnosis of SARS is virologically confirmed, at which point antimicrobials could be stopped unless there is reason to suspect secondary bacterial complications Initially, given the lack of knowledge of the causative virus or its antiviral susceptibility, ribavirin was used as a broad-spectrum antiviral therapeutic option for SARS Subsequently there were contradictory results on the in vitro antiviral susceptibility of SARS-CoV to ribavirin (Morgenstern et al., 2005; Tan et al., 2004) The discrepant findings may be related to the cell lines used (Vero, Caco-2, pig kidney cells) Interferon (IFN)-αn1, IFN-αn3, leukocytic iIFN and IFN-β have evidence of antiviral effect in vitro The HIV protease inhibitor nelfinovir and a number of other compounds, including glycyrrhizin, baicalin and chloroquine, ACE2 analogues, antiviral peptides targeting the heptad repeat region of the S2 subunit of the spike protein and small interfering RNA (siRNA) have been shown to have antiviral effects in vitro (reviewed in (Cheng et al., 2007; Haagmans and Osterhaus, 2006) Some of these compounds have been tested in experimentally infected animals Pegylated IFN-α significantly reduced lung virus titres in cynomolgus macaques (Haagmans et al., 2004) Interferon-αBD at higher doses and the IFN inducer Ampligen (poly(I):poly(C)) inhibited virus replication in BALB/c mice but nelfinavir, chloroquine and ribavirin did not (Barnard et al., 2006a, 2006b) Clinical data have suggested that the use of the recombinant consensus IFN-α preparation alfacon-1 together with corticosteroids (Loutfy et al., 2003) and that the use of the protease inhibitor nelfinovir/lopinavir together with ribavirin (Chu et al., 2004a) appears to improve clinical outcome compared to historical controls Passive immunotherapy with convalescent plasma containing high neutralizing antibody titres to SARS-CoV was used in some patients with no adverse effects and perhaps some clinical benefit in comparison to historical controls (Cheng et al., 2005) However, these were not controlled clinical trials and the use of historical controls may be misleading Immunomodulators including corticosteroid therapy were used in patients with SARS in view of their previous use in acute respiratory distress syndrome There is, however, no documented evidence of clinical benefit and they may increase viral load in the plasma (Lee et al., 2004) and increase the risk of adverse effects, including avascular necrosis of bone In summary, the IFNs appear to be the only class of antiviral agents that has evidence of in vitro activity and efficacy in experimental animal models ACKNOWLEDGEMENTS We acknowledge the contribution of Dr David Cavanagh whose chapter in the previous edition of this book formed the basis of the present revision and update We acknowledge research funding from the National Institutes of Health (NIAID contract HHSN266200700005C) and through a Special Research Achievement Award from The University of Hong Kong to JSMP REFERENCES Afzelius, B.A (1994) Ultrastructure of human nasal epithelium during an episode of coronavirus infection Virchows Archiv , 424, 295–300 Arbour, N., Day, R., Newcombe, J and Talbot, P.J (2000) Neuroinvasion by human respiratory coronaviruses Journal of Virology, 74, 8913–21 Arden, K.E., Nissen, M.D., Sloots, T.P and Mackay, I.M (2005) New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Journal of Medical Virology, 75, 455–62 Atmar, R.L., Guy, E., Guntupalli, K.K et al (1998) Respiratory tract viral infections in inner-city asthmatic adults Archives of Internal Medicine, 158, 2453–59 Ballesteros, M.L., Sanchez, C.M and Enjuanes, L (1997) Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism Virology, 227, 378–88 Barnard, D.L., Day, C.W., Bailey, K et al (2006a) Evaluation of immunomodulators, interferons and known in vitro SARS-coV inhibitors for inhibition of SARS-coV replication in BALB/c mice Antiviral Chemistry and Chemotherapy, 17, 275–84 Coronaviruses and Toroviruses Barnard, D.L., Day, C.W., Bailey, K et al (2006b) Enhancement of the infectivity of SARS-CoV in BALB/c mice by IMP dehydrogenase inhibitors, including ribavirin Antiviral Research, 71, 53–63 Beards, G.M., Hall, C., Green, J et al (1984) An enveloped virus in stools of children and adults with gastroenteritis that resembles the Breda virus of calves Lancet , 1, 1050–52 Beaudette, F.R and Hudson, C.B (1937) Cultivation of the virus of infectious bronchitis Journal of the American Veterinary Medical Association, 90, 51–60 van Benten, I.J., KleinJan, A., Neijens, H.J et al (2001) Prolonged nasal eosinophilia in allergic patients after common cold Allergy, 56, 949–56 Boivin, G., Baz, M., Cote, S et al (2005) Infections by human coronavirus-NL in hospitalized children The Pediatric Infectious Disease Journal , 24, 1045–48 Bradburne, A.F., Bynoe, M.L and Tyrrell, D.A (1967) Effects of a ‘new’ human respiratory virus in volunteers British Medical Journal , 3, 767–69 Buchholz, U.J., Bukreyev, A., Yang, L et al (2004) Contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity Proceedings of the National Academy of Sciences of the United States of America, 101, 9804–809 Cao, W.C., Liu, W., Zhang, P.H et al (2007) Disappearance of antibodies to SARS-associated coronavirus after recovery The New England Journal of Medicine, 357, 1162–63 Cavanagh, D and Naqi, S (2003) Infectious bronchitis, in Diseases of Poultry, 11th edn (eds Y.M Saif, H.J Barnes J.R Glisson et al.), Iowa State Press, Iowa, pp 101–19 Chan, K.H., Poon, L.L., Cheng, V.C et al (2004) Detection of SARS coronavirus in patients with suspected SARS Emerging Infectious Diseases, 10, 294–99 Chan, K.H., Cheng, V.C., Woo, P.C et al (2005) Serological responses in patients with severe acute respiratory syndrome coronavirus infection and cross-reactivity with human coronaviruses 229E, OC43, and NL63 Clinical and Diagnostic Laboratory Immunology, 12, 1317–21 Cheng, V.C., Lau, S.K., Woo, P.C and Yuen, K.Y (2007) Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection Clinical Microbiology Reviews, 20, 660–94 Cheng, Y., Wong, R., Soo, Y.O et al (2005) Use of convalescent plasma therapy in SARS patients in Hong Kong European Journal of Clinical Microbiology and Infectious Diseases, 24, 44–46 Cheung, C.Y., Poon, L.L., Ng, I.H et al (2005) Cytokine responses in severe acute respiratory syndrome 527 coronavirus-infected macrophages in vitro: possible relevance to pathogenesis Journal of Virology, 79, 7819–26 Chiu, S.S., Chan, K.H., Chu, K.W et al (2005) Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong, China Clinical Infectious Diseases, 40, 1721–29 Chow, K.Y., Lee, C.E., Ling, M.L et al (2004) Outbreak of severe acute respiratory syndrome in a tertiary hospital in Singapore, linked to an index patient with atypical presentation: epidemiological study British Medical Journal , 328, 195 Chu, C.M., Cheng, V.C., Hung, I.F et al (2004a) Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings Thorax , 59, 252–56 Chu, C.M., Poon, L.L., Cheng, V.C et al (2004b) Initial viral load and the outcomes of SARS Canadian Medical Association Journal , 171, 1349–52 Cornelissen, L.A., Wierda, C.M., van derMeer, F.J et al (1997) Hemagglutinin-esterase, a novel structural protein of torovirus Journal of Virology, 71, 5277–86 Cornelissen, L.A., van Woensel, P.A., de Groot, R.J et al (1998) Cell culture-grown putative bovine respiratory torovirus identified as a coronavirus The Veterinary Record , 142, 683–86 Dare, R.K., Fry, A.M., Chittaganpitch, M et al (2007) Human coronavirus infections in rural Thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays The Journal of Infectious Diseases, 196, 1321–28 Drosten, C., Gunther, S., Preiser, W et al (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome The New England Journal of Medicine, 348, 1967–76 Duckmanton, L., Luan, B., Devenish, J et al (1997) Characterization of torovirus from human fecal specimens Virology, 239, 158–68 van Elden, L.J., van Loon, A.M., van Alphen, F et al (2004) Frequent detection of human coronaviruses in clinical specimens from patients with respiratory tract infection by use of a novel real-time reverse-transcriptase polymerase chain reaction The Journal of Infectious Diseases, 189, 652–57 Enjuanes, L., Brian, D., Cavanagh, D et al (2000) Coronaviridae, in Virus Taxonomy (eds M.H.V Rengenmortel, C.M Fauquet, D.H.L Bishop et al.), Academic Press New York, pp 835–49 Esper, F., Weibel, C., Ferguson, D et al (2005) Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children The Journal of Infectious Diseases, 191, 492–98 528 Principles and Practice of Clinical Virology, Sixth Edition Falsey, A.R., Walsh, E.E and Hayden, F.G (2002) Rhinovirus and coronavirus infection-associated hospitalizations among older adults The Journal of Infectious Diseases, 185, 1338–41 Farcas, G.A., Poutanen, S.M., Mazzulli, T et al (2005) Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus The Journal of Infectious Diseases, 191, 193–97 Fouchier, R.A., Kuiken, T., Schutten, M et al (2003) Aetiology: Koch’s postulates fulfilled for SARS virus Nature, 423, 240 Franks, T.J., Chong, P.Y., Chui, P et al (2003) Lung pathology of severe acute respiratory syndrome (SARS): A study of autopsy cases from Singapore Human Pathology, 34, 729 Freymuth, F., Vabret, A., Brouard, J et al (1999) Detection of viral, Chlamydia pneumoniae and Mycoplasma pneumoniae infections in exacerbations of asthma in children Journal of Clinical Virology, 13, 131–39 van Gageldonk-Lafeber, A.B., Heijnen, M.L., Bartelds, A.I et al (2005) A case-control study of acute respiratory tract infection in general practice patients in The Netherlands Clinical Infectious Diseases, 41, 490–97 Gallagher, T.M and Buchmeier, M.J (2001) Coronavirus spike proteins in viral entry and pathogenesis Virology, 279, 371–4 Garbino, J., Crespo, S., Aubert, J.D et al (2006) A prospective hospital-based study of the clinical impact of non-severe acute respiratory syndrome (non-SARS)-related human coronavirus infection Clinical Infectious Diseases, 43, 1009–15 Gillim-Ross, L and Subbarao, K (2006) Emerging respiratory viruses: challenges and vaccine strategies Clinical Microbiology Reviews, 19, 614–36 Gonzalez, J.M., Gomez-Puertas, P., Cavanagh, D et al (2003) A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Archives of Virology, 148, 2207–35 Gorbalenya, A.E., Enjuanes, L., Ziebuhr, J and Snijder, E.J (2006) Nidovirales: evolving the largest RNA virus genome Virus Research, 117, 17–37 Graat, J.M., Schouten, E.G., Heijnen, M.L et al (2003) A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection Journal of Clinical Epidemiology, 56, 1218–23 de Groot, R.J and Horzinek, M.C (1995) Feline infectious peritonitis, in The Coronaviridae (ed S.J Siddell), Plenum Press, New York, pp 293–315 Guan, Y., Zheng, B.J., He, Y.Q et al (2003) Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China Science, 302, 276–78 Haagmans, B.L and Osterhaus, A.D (2006) Coronaviruses and their therapy Antiviral Research, 71, 397–403 Haagmans, B.L., Kuiken, T., Martina, B.E et al (2004) Pegylated interferon-alpha protects type pneumocytes against SARS coronavirus infection in macaques Nature Medicine, 10, 290–93 Hamre, D and Beem, M (1972) Virologic studies of acute respiratory disease in young adults V Coronavirus 229E infections during six years of surveillance American Journal of Epidemiology, 96, 94–106 Hamre, D and Procknow, J.J (1966) A new virus isolated from the human respiratory tract Proceedings of the Society for Experimental Biology and Medicine, 121, 190–93 de Haan, C.A., Volders, H., Koetzner, C.A et al (2002) Coronaviruses maintain viability despite dramatic rearrangements of the strictly conserved genome organization Journal of Virology, 76, 12491–502 van der Hoek, L (2007) Human coronaviruses: what they cause? Antiviral Therapy, 12, 651–58 van der Hoek, L., Pyrc, K., Jebbink, M.F et al (2004) Identification of a new human coronavirus Nature Medicine, 10, 368–73 van der Hoek, L., Sure, K., Ihorst, G et al (2005) Croup is associated with the novel coronavirus NL63 PLoS Medicine, 2, e240 Hofmann, H., Pyrc, K., van der Hoek, L et al (2005) Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry Proceedings of the National Academy of Sciences of the United States of America, 102, 7988–93 Ip, W.K., Chan, K.H., Law, H.K et al (2005) Mannose-binding lectin in severe acute respiratory syndrome coronavirus infection The Journal of Infectious Diseases, 191, 1697–704 Jamieson, F.B., Wang, E.E., Bain, C et al (1998) Human torovirus: a new nosocomial gastrointestinal pathogen The Journal of Infectious Diseases, 178, 1263–69 Kam, Y.W., Kien, F., Roberts, A et al (2007) Antibodies against trimeric S glycoprotein protect hamsters against SARS-CoV challenge despite their capacity to mediate FcgammaRII-dependent entry into B cells in vitro Vaccine, 25, 729–40 Kistler, A., Avila, P.C., Rouskin, S et al (2007) Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity The Journal of Infectious Diseases, 196, 817–25 Koopmans, M.P., Goosen, E.S., Lima, A.A et al (1997) Association of torovirus with acute and persistent diarrhea in children The Pediatric Infectious Disease Journal , 16, 504–7 Coronaviruses and Toroviruses Ksiazek, T.G., Erdman, D., Goldsmith, C.S et al (2003) A novel coronavirus associated with severe acute respiratory syndrome The New England Journal of Medicine, 348, 1953–66 Lai, M.M and Cavanagh, D (1997) The molecular biology of coronaviruses Advances in Virus Research, 48, 1–100 Lau, S.K., Woo, P.C., Li, K.S et al (2005) Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Proceedings of the National Academy of Sciences of the United States of America, 102, 14040–45 Lau, S.K., Woo, P.C., Yip, C.C et al (2006) Coronavirus HKU1 and other coronavirus infections in Hong Kong Journal of Clinical Microbiology, 44, 2063–71 Lee, N., Allen Chan, K.C., Hui, D.S et al (2004) Effects of early corticosteroid treatment on plasma SARS-associated Coronavirus RNA concentrations in adult patients Journal of Clinical Virology, 31, 304–309 Leung, W.K., To, K.F., Chan, P.K et al (2003) Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection Gastroenterology, 125, 1011–17 Leung, C.W., Kwan, Y.W., Ko, P.W et al (2004a) Severe acute respiratory syndrome among children Pediatrics, 113, e535–e543 Leung, G.M., Chung, P.H., Tsang, T et al (2004b) SARS-CoV antibody prevalence in all Hong Kong patient contacts Emerging Infectious Diseases, 10, 1653–56 Li, W., Shi, Z., Yu, M et al (2005a) Bats are natural reservoirs of SARS-like coronaviruses Science, 310, 676–79 Li, W., Zhang, C., Sui, J et al (2005b) Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 The EMBO Journal , 24, 1634–43 Liang, G., Chen, Q., Xu, J et al (2004) Laboratory diagnosis of four recent sporadic cases of community-acquired SARS, Guangdong Province, China Emerging Infectious Diseases, 10, 1774–81 Lipsitch, M., Cohen, T., Cooper, B et al (2003) Transmission dynamics and control of severe acute respiratory syndrome Science, 300, 1966–70 Loutfy, M.R., Blatt, L.M., Siminovitch, K.A et al (2003) Interferon alfacon-1 plus corticosteroids in severe acute respiratory syndrome: a preliminary study JAMA: The Journal of the American Medical Association, 290, 3222–28 McIntosh, K., Kapikian, A.Z., Turner, H.C et al (1970) Seroepidemiologic studies of coronavirus infection in adults and children American Journal of Epidemiology, 91, 585–92 529 McIntosh, K., Ellis, E.F., Hoffman, L.S et al (1973) The association of viral and bacterial respiratory infections with exacerbations of wheezing in young asthmatic children The Journal of Pediatrics, 82, 578–90 McKean, M.C., Leech, M., Lambert, P.C et al (2001) A model of viral wheeze in nonasthmatic adults: symptoms and physiology The European Respiratory Journal , 18, 23–32 Makela, M.J., Puhakka, T., Ruuskanen, O et al (1998) Viruses and bacteria in the etiology of the common cold Journal of Clinical Microbiology, 36, 539–42 Masters, P.S (2006) The molecular biology of coronaviruses Advances in Virus Research, 66, 193–292 ter Meulen, J., Bakker, A.B., van den Brink, E.N et al (2004) Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets Lancet , 363, 2139–41 Morgenstern, B., Michaelis, M., Baer, P.C et al (2005) Ribavirin and interferon-beta synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines Biochemical and Biophysical Research Communications, 326, 905–8 Mossel, E.C., Wang, J., Jeffers, S et al (2007) SARS-CoV replicates in primary human alveolar type II cell cultures but not in type I-like cells Virology, 369, 288–98 Myint, S (1995) Human coronavirus infections, in The Coronaviridae (ed S.G Siddell), Plenum Press, New York, pp 389–401 Ng, E.K., Hui, D.S., Chan, K.C et al (2003) Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome Clinical Chemistry, 49, 1976–80 Nicholls, J.M., Poon, L.L., Lee, K.C et al (2003) Lung pathology of fatal severe acute respiratory syndrome Lancet , 361, 1773–78 Nicholls, J.M., Butany, J., Poon, L.L et al (2006) Time course and cellular localization of SARS-CoV nucleoprotein and RNA in lungs from fatal cases of SARS PLoS Medicine, 3, e27 Olsen, C.W (1993) A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination Veterinary Microbiology, 36, 1–37 Peiris, J.S., Chu, C.M., Cheng, V.C et al (2003a) Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Lancet , 361, 1767–72 Peiris, J.S., Lai, S.T., Poon, L.L et al (2003b) Coronavirus as a possible cause of severe acute respiratory syndrome Lancet , 361, 1319–25 530 Principles and Practice of Clinical Virology, Sixth Edition Peiris, J.S., Yuen, K.Y., Osterhaus, A.D and Stohr, K (2003c) The severe acute respiratory syndrome The New England Journal of Medicine, 349, 2431–41 Peiris, J.S.M., Guan, Y and Poon, L.L.M (2007) Severe acute respiratory syndrome (SARS), in Emerging Infections (eds W.M Scheld, D.C Hooper and J.M Huges), ASM Press, Washington, DC, pp 23–50 Pitkaranta, A., Virolainen, A., Jero, J et al (1998) Detection of rhinovirus, respiratory syncytial virus, and coronavirus infections in acute otitis media by reverse transcriptase polymerase chain reaction Pediatrics, 102, 291–95 Poon, L.L., Chu, D.K., Chan, K.H et al (2005a) Identification of a novel coronavirus in bats Journal of Virology, 79, 2001–9 Poon, L.L., Leung, C.S., Chan, K.H et al (2005b) Recurrent mutations associated with isolation and passage of SARS coronavirus in cells from non-human primates Journal of Medical Virology, 76, 435–40 Popova, R and Zhang, X (2002) The spike but not the hemagglutinin/esterase protein of bovine coronavirus is necessary and sufficient for viral infection Virology, 294, 222–36 Quan, P.L., Palacios, G., Jabado, O.J et al (2007) Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray Journal of Clinical Microbiology, 45, 2359–64 Raamsman, M.J., Locker, J.K., de Hooge, A et al (2000) Characterization of the coronavirus mouse hepatitis virus strain A59 small membrane protein E Journal of Virology, 74, 2333–42 Rabenau, H.F., Cinatl, J., Morgenstern, B et al (2005) Stability and inactivation of SARS coronavirus Medical Microbiology and Immunology, 194, 1–6 Rao, P.V., Kumari, S and Gallagher, T.M (1997) Identification of a contiguous 6-residue determinant in the MHV receptor that controls the level of virion binding to cells Virology, 229, 336–48 Riley, S., Fraser, C., Donnelly, C.A et al (2003) Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions Science, 300, 1961–66 Rockx, B., Sheahan, T., Donaldson, E et al (2007) Synthetic reconstruction of zoonotic and early human severe acute respiratory syndrome coronavirus isolates that produce fatal disease in aged mice Journal of Virology, 81, 7410–23 Rockx, B., Corti, D., Donaldson, E et al (2008) Structural basis for potent cross-neutralizing human monoclonal antibody protection against lethal human and zoonotic SARS-CoV challenge Journal of Virology, 82, 3220–35 Saif, L (2005) Comparative biology of animal coronaviruses: lessons for SARS, in Severe Acute Respiratory Syndrome (eds M Peiris, L.J Anderson, A.D.M.E Osterhaus et al), Blackwell Publishing, Oxford, pp 84–99 Saif, L (2006) Animal coronaviruses, in SARS: How a Global Epidemic was Stopped, World Health Organization, Geneva, pp 199–209 Salanueva, I.J., Carrascosa, J.L and Risco, C (1999) Structural maturation of the transmissible gastroenteritis coronavirus Journal of Virology, 73, 7952–64 Schickli, J.H., Zelus, B.D., Wentworth, D.E et al (1997) The murine coronavirus mouse hepatitis virus strain A59 from persistently infected murine cells exhibits an extended host range Journal of Virology, 71, 9499–07 Schultze, B and Herrler, G (1992) Bovine coronavirus uses N-acetyl-9-O-acetylneuraminic acid as a receptor determinant to initiate the infection of cultured cells The Journal of General Virology, 73 (Pt 4), 901–6 Seto, W.H., Tsang, D., Yung, R.W et al (2003) Effectiveness of precautions against droplets and contact in prevention of nosocomial transmission of severe acute respiratory syndrome (SARS) Lancet , 361, 1519–20 Shao, X., Guo, X., Esper, F et al (2007) Seroepidemiology of group I human coronaviruses in children Journal of Clinical Virology, 40, 207–13 Siddell, S.G (1995) The Coronaviridae: and introduction, in The Coronaviridae (ed S.G Siddell), Plenum Press, New York, pp 1–10 Sims, A.C., Baric, R.S., Yount, B et al (2005) Severe acute respiratory syndrome coronavirus infection of human ciliated airway epithelia: role of ciliated cells in viral spread in the conducting airways of the lungs Journal of Virology, 79, 15511–24 Sizun, J., Soupre, D., Giroux, J.D and Legrand, M.C (1995) Nosocomial respiratory infection due to coronavirus in neonatal intensive care units: prospective evaluation Archives de Pediatrie, 2, 1020–21 Sloots, T.P., McErlean, P., Speicher, D.J et al (2006) Evidence of human coronavirus HKU1 and human bocavirus in Australian children Journal of Clinical Virology, 35, 99–102 Sola, I., Moreno, J.L., Zuniga, S et al (2005) Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis Journal of Virology, 79, 2506–16 Stephensen, C.B., Casebolt, D.B and Gangopadhyay, N.N (1999) Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay Virus Research, 60, 181–89 Coronaviruses and Toroviruses Stohlman, S.A and Hinton, D.R (2001) Viral induced demyelination Brain Pathology, 11, 92–106 Subbarao, K., McAuliffe, J., Vogel, L et al (2004) Prior infection and passive transfer of neutralizing antibody prevent replication of severe acute respiratory syndrome coronavirus in the respiratory tract of mice Journal of Virology, 78, 3572–77 Tan, E.L., Ooi, E.E., Lin, C.Y et al (2004) Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs Emerging Infectious Diseases, 10, 581–86 Tan, K., Zelus, B.D., Meijers, R et al (2002) Crystal structure of murine sCEACAM1a[1,4]: a coronavirus receptor in the CEA family The EMBO Journal , 21, 2076–86 Thiel, V., Ivanov, K.A., Putics, A et al (2003) Mechanisms and enzymes involved in SARS coronavirus genome expression The Journal of General Virology, 84, 2305–15 Tyrrell, D.A.J and Bynoe, M.L (1965) Cultivation of a novel type of common-cold virus in organ cultures British Medical Journal , 1, 1467–70 Vabret, A., Mouthon, F., Mourez, T et al (2001) Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction Journal of Virological Methods, 97, 59–66 Vabret, A., Dina, J., Gouarin, S et al (2006) Detection of the new human coronavirus HKU1: a report of cases Clinical Infectious Diseases, 42, 634–39 van Vliet, A.L., Smits, S.L., Rottier, P.J and de Groot, R.J (2002) Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus The EMBO Journal , 21, 6571–80 Vijaykrishna, D., Smith, G.J., Zhang, J.X et al (2007) Evolutionary insights into the ecology of coronaviruses Journal of Virology, 81, 4012–20 Walsh, E.E., Falsey, A.R and Hennessey, P.A (1999) Respiratory syncytial and other virus infections in persons with chronic cardiopulmonary disease American Journal of Respiratory and Critical Care Medicine, 160, 791–95 Wang, D., Coscoy, L., Zylberberg, M et al (2002) Microarray-based detection and genotyping of viral pathogens Proceedings of the National Academy of Sciences of the United States of America, 99, 15687–92 Wang, D., Urisman, A., Liu, Y.T et al (2003) Viral discovery and sequence recovery using DNA microarrays PLoS Biology, 1, E2 531 Weiss, M and Horzinek, M.C (1987) The proposed family Toroviridae: agents of enteric infections Brief review Archives of Virology, 92, 1–15 Wentworth, D.E and Holmes, K.V (2007) Coronavirus binding and entry, in Coronaviruses: Molecular and Cellular Biology (ed V Thiel), Caister Academic Press, Norfolk, VA, pp 3–33 Wong, C.K., Lam, C.W., Wu, A.K et al (2004) Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome Clinical and Experimental Immunology, 136, 95–103 Woo, P.C., Lau, S.K., Wong, B.H et al (2004) False-positive results in a recombinant severe acute respiratory syndrome-associated coronavirus (SARS-CoV) nucleocapsid enzyme-linked immunosorbent assay due to HCoV-OC43 and HCoV-229E rectified by Western blotting with recombinant SARS-CoV spike polypeptide Journal of Clinical Microbiology, 42, 5885–88 Woo, P.C., Lau, S.K., Chu, C.M et al (2005a) Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Journal of Virology, 79, 884–95 Woo, P.C., Lau, S.K., Tsoi, H.W et al (2005b) Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia The Journal of Infectious Diseases, 192, 1898–907 Xu, R.H., He, J.F., Evans, M.R et al (2004) Epidemiologic clues to SARS origin in China Emerging Infectious Diseases, 10, 1030–37 Yi, C.E., Ba, L., Zhang, L et al (2005) Single amino acid substitutions in the severe acute respiratory syndrome coronavirus spike glycoprotein determine viral entry and immunogenicity of a major neutralizing domain Journal of Virology, 79, 11638–46 Yu, I.T., Li, Y., Wong, T.W et al (2004) Evidence of airborne transmission of the severe acute respiratory syndrome virus The New England Journal of Medicine, 350, 1731–39 Zhang, H., Zhou, G., Zhi, L et al (2005) Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection The Journal of Infectious Diseases, 192, 1355–61 Zhu, Z., Chakraborti, S., He, Y et al (2007) Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies Proceedings of the National Academy of Sciences of the United States of America, 104, 12123–28 ... clinical specimen (Figure 1. 5a) Real-time 10 Principles and Practice of Clinical Virology, Sixth Edition L +ve 10 11 12 13 14 15 16 17 18 19 20 -ve * M RB RA RA RB M RA RB Figure 1. 4 A 2% agarose gel... Remarks 12 8 Varicella Zoster Judith Breuer 11 2 13 3 Introduction 13 3 The Virus 13 3 Epidemiology 14 2 Clinical Features 14 3 Diagnosis of VZV Infection 14 8 Treatment 15 1 Prevention 15 3 Cytomegalovirus... Griffiths 12 Hepatitis Viruses 273 Tim J Harrison, Geoffrey M Dusheiko and Arie J Zuckerman 16 1 Introduction 16 1 The Virus 16 1 Epidemiology 16 6 Routes of Infection 16 7 Pathogenesis 16 8 Clinical