9 1 1 1 0- 1 5 18 N S S I FAO ANIMAL PRODUCTION AND HEALTH manual WWIILLDD BBIIRRDDSS AANNDD AAVVIIAANN IINNFFLLUUEENNZZAA An introduction to applied field research and disease sampling techniques Cover photographs: Left image: USGS Western Ecological Research Center Centre and right images: Rob Robinson manual5.indb Sec1:ii 19/03/2008 10:15:44 5 FAO ANIMAL PRODUCTION AND HEALTH manual WWIILLDD BBIIRRDDSS AANNDD AAVVIIAANN IINNFFLLUUEENNZZAA An introduction to applied field research and disease sampling techniques Darrell Whitworth, Scott Newman, Taej Mundkur, Phil Harris FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS Rome, 2007 manual5.indb Sec2:i 19/03/2008 10:16:56 Authors’ details Darrell Whitworth Wildlife Consultant Via delle Vignacce 12 - Staggiano 52100, Arezzo, Italy [email protected] Scott Newman Animal Health Service, Food and Agriculture Organization of the United Nations, Rome, Italy [email protected] Taej Mundkur Animal Health Service, Food and Agriculture Organization of the United Nations, Rome, Italy [email protected] Phil Harris Animal Health Service, Food and Agriculture Organization of the United Nations, Rome, Italy [email protected] Recommended citation FAO. 2007. Wild Birds and Avian Influenza: an introduction to applied field research and disease sampling techniques. Edited by D. Whitworth, S.H. Newman, T. Mundkur and P. Harris. FAO Animal Production and Health Manual, No. 5. Rome. (also available at www.fao.org/avianflu) The designations employed and the presentation of material in this information product do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations (FAO) concerning the legal or development status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed or recommended by FAO in preference to others of a similar nature that are not mentioned. The views expressed in this information product are those of the author(s) and do not necessarily reflect the views of FAO. ISBN 978-92-5-105908-1 All rights reserved. Reproduction and dissemination of material in this information product for educational or other non-commercial purposes are authorized without any prior written permission from the copyright holders provided the source is fully acknowledged. Reproduction of material in this information product for resale or other commercial purposes is prohibited without written permission of the copyright holders. Applications for such permission should be addressed to the Chief, Electronic Publishing Policy and Support Branch, Communication Division, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy or by e-mail to [email protected] © FAO 2007 manual5.indb Sec2:ii 19/03/2008 10:16:56 iii Contents Foreword v CHAPTER 1 Avian influenza and the H5N1 virus 1 Ecology and biochemical properties of avian influenza viruses 1 History of the H5N1 avian influenza virus 4 Surveillance strategies for avian influenza 10 References and information sources 11 CHAPTER 2 Wild birds and avian influenza 13 Avian influenza in wetland bird species 13 “Bridge” species 27 Migratory birds and spread of the H5N1 virus 29 References and information sources 32 CHAPTER 3 Wild bird capture techniques 33 Corral traps (round-ups) 34 Baited traps 37 Cannon nets 42 Mist netting 44 Miscellaneous capture methods 48 References and information sources 50 CHAPTER 4 Bird handling and ringing techniques 51 Bird handling and restraint 52 Physical and chemical restraining aides 58 Bird welfare 59 Ringing (banding) 60 Biometric measurements 64 References and information sources 71 manual5.indb Sec2:iii 19/03/2008 10:16:56 iv CHAPTER 5 Disease sampling procedures 73 Tracheal and cloacal swabs 74 Blood sampling 80 Faecal sampling 83 References and information sources 84 CHAPTER 6 Avian surveys and monitoring 85 Complete censuses 85 Sample plots 87 Trip transects 89 Point counts 91 Distance sampling 92 Capture-mark-recapture 93 References and information sources 94 CHAPTER 7 Radio telemetry and bird movements 95 Radio telemetry 95 Capture and radio-marking 99 VHF telemetry tracking 103 Data analysis 106 Mark-recapture (resight) studies 107 Stable isotope analysis 111 References and information sources 111 Annex 1: Guidance on taking photographs of birds for identification purposes 113 manual5.indb Sec2:iv 19/03/2008 10:16:56 v Foreword Although H5N1 highly pathogenic avian influenza (HPAI) virus has been known for over a decade, the enormous impact of outbreaks in poultry across Asia, Africa and Europe since 2003, as well as deaths in over 200 humans, over 230 million poultry and thousands of wild birds, has made H5N1 HPAI and “bird flu” a part of common daily parlance. However, the expression ‘highly pathogenic avian influenza’ is a chicken term, and should really not be used to describe the infection in other species (wild ducks, tigers, ferrets, or humans), even though the infection can be highly virulent in many species of animals. We prefer to call these infections AI virus infections or influenza viral infections of avian origin. In response to the geographic spread of H5N1 and the deaths it has caused in wild bird populations to various degrees, as well as the concern that certain species of wild birds may play a role in the introduction and dissemination of the H5N1 virus along their flyways, FAO has been particularly interested to understand the interactions between wild and domestic birds. Within the Emergency Centre for Transboundary Animal Diseases (ECTAD), FAO has established a Wildlife Disease Programme to promote regional cooperation and action and increase in-country national and regional capacity building through the training and edu- cation of biologists, veterinarians, ornithologists and others to better integrate a common understanding of pathogen transmission in affected environments. To support this work, it produced a Manual entitled Wild Bird Highly Pathogenic Avian Influenza Surveillance – sample collection from healthy, sick and dead birds in 2006. There is a wide variety of manuals available to understand the intricacies of the ecol- ogy and life cycles of wild bird species, including the wide spectrum of food and foraging habits, social interactions, migration strategies, nesting choices, habitat use. However, it was immediately apparent to FAO and other partners that there is a need for an introductory manual to support field efforts with regard to the study of bird populations and ecological aspects of avian influenza viruses. The topics covered in this Manual address monitoring technologies and sampling techniques, wild bird surveillance, some features of habitat use and migration ecology that are all important aspects of wildlife and disease ecology that need to be better researched. This Manual is a collaborative effort of FAO, the Agricultural Research Centre for International Development of France (CIRAD), BirdLife International, Percy FitzPatrick Institute of African Ornithology, United States Geological Survey (USGS), Wetlands International, Wildfowl and Wetlands Trust, UK (WWT) and Wildlife Conservation Society (WCS). The Manual has been brought to life by photographs kindly provided by a number of excel- lent photographers from around the world. FAO would like to thank Nyambayar Batbayar, Alexandre Caron, CIRAD, Ruth Cromie, Graeme Cumming, Karen M. Cunningham, Robert J. Dusek, Pieter van Eijk, Sasan Fereidouni, Clement Francis, J. Christian Franson, Friedrich- Loeffler Institut, Martin Gilbert, Mark Grantham, Nigel Jarrett, Rebecca Lee, Khanh Lam U Minh, Taej Mundkur, Rishad Naoroji, Kim Nelson, Scott Newman, PDSR/FAO Indonesia, Diann Prosser, Rob Robinson, Giuseppe Rossi, Paul Slota, Kristine Smith, David Stroud, John Takekawa, USGS Western Ecological Research Center, Alyn Walsh, Darrell Whitworth and manual5.indb Sec2:v 19/03/2008 10:16:56 vi Yuan Xiao for offering their photographs for our use. The illustrations were created by Darrell Whitworth and Claudia Ciarlantini. The contents of the Manual have greatly benefited from discussions, reviews and many suggestions made by Robyn Alders, Leon Bennun, Axel Braunlich, Alexandre Caron, Jackie Clark, Graeme Cumming, Ruth Cromie, Simon Delany, Leslie Dierauf, Paul Flint, Milton Friend, Nicolas Gaidet, Noburu Nakamura, Ward Hagemeijer, Richard Hearn, Jerry Hupp, Akiko Kamata, William Karesh, Rebecca Lee, Michael R. Miller, John Pearce and David Stroud. Special thanks to Darrell Whitworth, Scott Newman, Taej Mundkur and Phil Harris for their efforts in drafting and editing the text and assembling the Manual. DeSimone Lorenzo created the maps and Claudia Ciarlantini, Monica Umena and Cecilia Murguia kindly assist- ed in producing the Manual. Lastly we thank the governments of Canada, Sweden, Switzerland and United Kingdom which have supported the work of the Wildlife Disease Programme recognising the impor- tance of disease-livestock-wildlife-environment interactions. Their funding support to FAO has made the publication of this Manual possible. FAO encourages feedback and comments on this Manual. Juan Lubroth Head Emergency Prevention System for Transboundary Plant and Animal Diseases and Pests (EMPRES) Animal Health Service FAO, Rome manual5.indb Sec2:vi 19/03/2008 10:16:57 1 Chapter 1 Avian influenza and the H5N1 virus ECOLOGY AND BIOCHEMICAL PROPERTIES OF AVIAN INFLUENZA VIRUSES Avian influenza (AI) is an infectious disease of birds caused by type A influenza viruses of the Orthomyxoviridae family (Figure 1.1). These viruses most commonly infect poultry (e.g. domestic chickens, turkeys, ducks, quails and geese) as well as many types of wild birds. Some AI viruses are also known to infect a variety of mammals, including humans. FIGURE 1.1 Electron micrographs and diagram of an avian influenza virus T U T TI S N R I E L F F E O L H- C RI D E RI HA- haemagglutinin glycoprotein, M- Capsid, NA-neuraminidase glycoprotein, T: F RNP- ribonucleoprotein DI E R C manual5.indb 1 19/03/2008 10:16:57 2 Wild Birds and Avian Influenza: an introduction to applied field research and disease sampling techniques The different AI virus subtypes are distinguished by the haemagglutinin and neurami- nidase antigens (glycoproteins) that cover the virus surface (Figure 1.1). Sixteen different haemagglutinin (H1-H16) and nine different neuraminidase (N1-N9) antigens have been characterised and each viral subtype is identified by the particular antigen combination it possesses (e.g. H5N1 or H3N2). All 16 haemagglutinin and nine neuraminidase antigens have been identified in wild bird populations. Genetically, AI viruses are composed of eight distinct ribonucleic acid (RNA) segments. A particular AI virus subtype may include a variety of similar but distinct strains (the term “clades” is often used to describe these sub-populations), based on genetic sequences and the clustering – or not – of the isolates. The different strains originate either through genet- ic mutation as the virus replicates or via recombination (exchange of parts of a segment) or reassortment (exchange of a full segment) of genetic material between different viruses infecting a common host. Specific viral strains (e.g. A/bar-headed goose/Qinghai/5/2005 H5N1) are identified by: 1) influenza type; 2) host species from which the strain was iso- lated; 3) geographic location; 4) laboratory strain designation; 5) year of isolation1; and 6) viral subtype. AI viruses are classified as low pathogenic (LPAI) or highly pathogenic (HPAI) depending on their virulence in domestic chickens (Figure 1.2). Most AI poultry infec- tions are caused by LPAI strains that may produce a mild disease manifested by a variety of respiratory, enteric or reproductive signs (depending on the strain). Clinical signs may include decreases in activity, food consumption or egg production, coughing and sneezing, ruffled feathers, diarrhoea and/or tremors. Often, few visible clinical signs are noted and some LPAI outbreaks may go entirely undetected unless there is specific laboratory test- ing for the presence of the virus. Quality assured vaccines, when well applied and used in conjunction with other disease control measures (such as improved hygiene and care, and movement management), are effective in preventing the introduction of AI viruses and their spread within and among domestic flocks. AI viruses are transmitted via direct contact with an infected bird or indirectly via close exposure to materials contaminated with infected faeces or possibly respiratory secretions. However, AI viruses have limited ability to survive outside the host where persistence in the environment is highly dependent on moisture, temperature and salinity. AI viruses can, however, persist for years in ice in high latitude lakes and have been shown to persist for over one month in other cool, moist habitats. In fact, the viruses are most often encoun- tered in wetland habitats frequented by waterbird species, including Anatidae (ducks, geese and swans) and Charadriidae (shorebirds), which are the most common wild avian hosts of AI viruses. In wild birds, LPAI infection can affect foraging and migratory performance (van Gils et al. 2007), but most infected birds show no obvious clinical signs of disease. Common AI strains and their wild host populations have developed an evolutionary equilibrium over time whereby the virus does not cause serious disease or mortality. Periodically, wild birds, particularly ducks and geese, have been identified as the source of virus introductions to poultry. Reassortment or recombination between LPAI viruses in a common host can, but 1 Year of isolation does not necessarily correspond to its first appearance. manual5.indb 2 19/03/2008 10:16:58