Avian Influenza and Newcastle Disease (eBook)

Ilaria Capua is "Revolutionary Mind" for 2008. This acknowledgement was granted by "Seed Magazine". The American magazine of science and technology each year selects 5 leaders in the international scientific community who have most influenced our opinions on the world, the mind and the universe. In 2006 virologist Ilaria Capua was studying samples of avian influenza from Africa. The World Health Organization asked Capua to deposit the genetic sequence of one of her samples into a database to which only a select few laboratories had access. She balked. "I said, 'Wait a minute, we're talking about a serious potential threat to human health. We know very little about how this virus is moving. Not enough scientists have had the opportunity to look at this virus.'" So Capua opted to put the sequence in GenBank, an open-access database, where it was downloaded 1,000 times in a single week. Capua's small act of rebellion was just the spark for a much larger challenge to the system. She started speaking out at meetings, urging her colleagues to stop putting their bird flu data in private databases. She joined forces with Peter Bogner, a strategic consultant, and a number of other virologists to establish the Global Initiative on Sharing Avian Influenza Data (GISAID), a consortium that facilitates collaboration among researchers and requires members to make their work on the virus publicly accessible. Capua hopes the work she's done to open up bird flu research can serve as an example to scientists studying other infectious diseases. Jean-Claude Bradley, a chemist at Drexel University who coined the phrase "open-notebook science," agrees. "That's where open science can really have an effect," Bradley says, "in research on disease processes. We could really use more people who are doing what Capua's doing. I think it makes for better science."

Foreword 11
Introductory Remarks 12
Preface 14
Acknowledgements 15
Contents 17
Contributors 19
1 Ecology, Epidemiology and Human Health Implications of Avian Influenza Virus Infections 21
1.1 Introduction 21
1.2 Aetiology, Including the Emergence of HPAI 21
1.3 Host Range 25
1.4 Transmission 27
1.5 Distribution and Spread 28
1.6 HPAI Outbreaks 30
1.7 Human Health Implications 31
1.8 Conclusion 33
References 34
2 Ecology and Epidemiology of Newcastle Disease 39
2.1 Introduction 39
2.2 Aetiology 39
2.3 Host Range 40
2.4 Molecular Basis of Viral Virulence 41
2.5 Transmission 42
2.6 Spread 43
2.7 Distribution 43
2.8 Human Health 44
2.9 Conclusion 44
References 44
3 Notification of Avian Influenza and Newcastle Disease to the World Organisation for Animal Health (OIE) 47
3.1 The World Organisation for Animal Health (OIE) and Its Mission 47
3.2 OIE Single Disease List 47
3.3 Notification and Epidemiological Information 48
3.4 Avian Influenza 48
3.5 Newcastle Disease 49
References 50
4 Emergency Response on Suspicion of an Avian Influenza or Newcastle Disease Outbreak 51
4.1 Introduction 51
4.2 Preparedness for AI Outbreak Management 51
4.3 Action at the Time of Suspicion 52
5 Necropsy Techniques and Collection of Samples 55
5.1 Necropsy 55
5.2 Collection of Specimens from Live Animals and Carcases 59
6 Clinical Traits and Pathology of Avian Influenza Infections, Guidelines for Farm Visit and Differential Diagnosis 64
6.1 Introduction 64
6.2 Low Pathogenicity Avian Influenza in Poultry 64
6.3 Highly Pathogenic Avian Influenza in Poultry 71
6.4 Guidelines for Farm Visits 86
6.5 Differential Diagnosis 87
7 Conventional Diagnosis of Avian Influenza 91
7.1 Isolation of Avian Influenza Virus 91
7.2 Virus Isolation 91
7.3 Serology 98
8 Molecular Diagnosis of Avian Influenza 104
8.1 Introduction and Basic Terminology for Molecular Diagnostic Tests 104
8.2 Two-Step and One-Step RT-PCR 104
8.3 Extraction of RNA from Clinical and Laboratory Samples 105
8.4 The Polymerase Chain Reaction 106
8.5 Real-Time PCR 110
8.6 Organisation of the Laboratory for Molecular Diagnostics 111
8.7 Samples to be Submitted for Molecular Detection of AI and Sample Preparation for PCR 111
8.8 Preparation of the PCR Mix 112
8.9 Detection and Analysis of the Reaction Product in Conventional PCR (End-Point PCR) 113
8.10 Detection of Type A Influenza Virus by End-Point RT-PCR 118
8.11 Protocol for the Subtype-Specific Detection of H5 Avian Influenza Virus Using End-Point RT-PCR 120
8.12 Protocol for the Subtype-Specific Detection of H7 Avian Influenza Virus Using End-Point RT-PCR 122
8.13 Detection of Type A Influenza Virus by Qualitative Real-Time PCR (M Gene) 124
8.14 Detection of Influenza Virus of H5 Haemagglutinin Subtype by Qualitative One-Step Real Time RT-PCR 125
8.15 Alternative Protocol for the Detection of H5 Avian Influenza Virus by Real-Time RT-PCR 126
8.16 Detection of Influenza Virus of H7 Haemagglutinin Subtype by Qualitative Real Time PCR (IZSVe Protocol) 127
References 128
9 Clinical Traits and Pathology of Newcastle Disease Infection and Guidelines for Farm Visit and Differential Diagnosis 129
9.1 Introduction 129
9.2 Chickens and Turkeys 129
9.3 Ostriches 131
9.4 Game Birds 132
9.5 Ducks, Geese and Swans 132
9.6 Pigeons (Columba livia) 132
9.7 Pet Birds 133
9.8 Gross Lesions 133
9.9 Guidelines for Farm Visits 135
9.10 Differential Diagnosis 137
References 137
10 Conventional Diagnosis of Newcastle Disease Virus Infection 139
10.1 Virus Isolation in Embryonated Eggs 139
10.2 Cell Cultures 139
10.3 Characterisation of Newcastle Disease Virus by Serological Methods 139
10.4 Serological Tests To Be Used for the Detection OF Specific Antibodies Against Newcastle Disease Virus 140
References 141
11 Molecular Diagnosis of Newcastle Disease Virus 142
11.1 Introduction 142
11.2 Detection and Typing of APMV-1 by End-Point RT-PCR and Restriction Endonuclease Analysis 142
11.3 Detection and Typing of APMV-1 by End-Point RT-PCR 144
11.4. Detection of APMV-1 by Qualitative One-step Real-time RT-PCR 146
References 147
12 General Rules for Decontamination Following an Outbreak of Avian Influenza or Newcastle Disease 148
12.1 Introduction 148
12.2 Choice of Disinfectant 148
12.3 Decontamination Procedures 151
12.4 Personal Decontamination 152
12.5 Vehicle and Car Decontamination 153
12.6 Disposal of Carcases 154
Appendix A: Practicalities of Decontamination with Formaldehyde Gas 161
Appendix B: Techniques of Humane Destruction of Animals 161
Appendix C: Design Parameters for an Effective Poultry Composting Facility 162
Websites 166
1 Annex Check List for Visit to Suspect Premise 168
2 Annex Epidemiological Investigation Form for Avian Influenza and Newcastle Disease Outbreaks 169
3 Annex Biosafety Procedures 183
4 Annex Laboratory Solutions 188
5 Annex Guidelines for Shipping Avian Influenza and Newcastle Disease Virus Samples to OIE Reference Laboratories 190
Subject Index 195