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Zhang JL, Chen ZY, Lin SL, King CC, Chen CC, Chen PS. Airborne Avian Influenza Virus in Ambient Air in the Winter Habitats of Migratory Birds. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15365-15376. [PMID: 36288568 DOI: 10.1021/acs.est.2c04528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Outbreaks of avian influenza virus (AIV) have raised public concerns recently. Airborne AIV has been evaluated in live poultry markets and case farms; however, no study has discussed airborne AIV in ambient air in the winter habitats of migratory birds. Therefore, this study aimed to evaluate airborne AIV, specifically H5, H7, and H9, in a critical winter habitat of migratory birds and assess the factors influencing airborne AIV transmission in ambient air to provide novel insights into the epidemiology of avian influenza. A total of 357 ambient air samples were collected in the Aogu Wetland, Taiwan, Republic of China, between October 2017 and December 2019 and analyzed using quantitative real-time polymerase chain reaction. The effects of environmental factors including air pollutants, meteorological factors, and the species of the observed migratory birds on the concentration of airborne AIV were also analyzed. To our knowledge, this is the first study to investigate the relationship between airborne AIV in ambient air and the influence factors in the winter habitats of migratory birds, demonstrating the benefits of environmental sampling for infectious disease epidemiology. The positive rate of airborne H7 (12%) was higher than that of H5 (8%) and H9 (10%). The daily mean temperature and daily maximum temperature had a significant negative correlation with influenza A, H7, and H9. Cold air masses and bird migration were significantly associated with airborne H9 and H7, respectively. In addition, we observed a significant correlation between AIV and the number of pintails, common teals, Indian spot-billed ducks, northern shovelers, Eurasian wigeons, tufted ducks, pied avocets, black-faced spoonbills, and great cormorants. In conclusion, we demonstrated the potential for alternative surveillance approaches (monitoring bird species) as an indicator for influenza-related risks and identified cold air masses and the presence of specific bird species as potential drivers of the presence and/or the airborne concentration of AIV.
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Affiliation(s)
- Jia Lin Zhang
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City807, Taiwan, Republic of China
| | - Zi-Yu Chen
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City807, Taiwan, Republic of China
| | - Si-Ling Lin
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City807, Taiwan, Republic of China
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei City106, Taiwan, Republic of China
| | - Chen-Chih Chen
- Animal Biologics Pilot Production Center, National Pingtung University of Science and Technology, Pingtung City912, Taiwan, Republic of China
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung City912, Taiwan, Republic of China
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung City912, Taiwan, Republic of China
| | - Pei-Shih Chen
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City807, Taiwan, Republic of China
- Institute of Environmental Engineering, College of Engineering, National Sun Yat-Sen University, Kaohsiung City807, Taiwan, Republic of China
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung City807, Taiwan, Republic of China
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung City807, Taiwan, Republic of China
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2
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de Vries EM, Cogan NOI, Gubala AJ, Mee PT, O'Riley KJ, Rodoni BC, Lynch SE. Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology. Sci Rep 2022; 12:11886. [PMID: 35831457 PMCID: PMC9279447 DOI: 10.1038/s41598-022-16048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
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Affiliation(s)
- Ellen M de Vries
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aneta J Gubala
- Land Division, Defence Science & Technology Group, Fishermans Bend, VIC, 3207, Australia
| | - Peter T Mee
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Kim J O'Riley
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Stacey E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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3
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An overview of avian influenza in the context of the Australian commercial poultry industry. One Health 2020; 10:100139. [PMID: 32490131 PMCID: PMC7256052 DOI: 10.1016/j.onehlt.2020.100139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
From 1976 Australia has experienced seven highly pathogenic avian influenza (HPAI) outbreaks in poultry farms and there have been a total of 16 confirmed low pathogenic avian influenza (LPAI) cases in poultry in Australia at the time of writing. This paper describes all past LPAI and HPAI detections in Australian poultry and reviews avian influenza risk in the Australian commercial chicken industry. The factors that influence this risk are also discussed; notably the nomadic nature of Australian waterfowl, the increasing demand of free range poultry egg and meat production in Australia, and biosecurity practices implemented across farms including farm separations. Australia has experienced seven highly pathogenic avian influenza (HPAI) outbreaks in poultry farms There have been 16 confirmed low pathogenic avian influenza (LPAI) cases in poultry in Australia at the time of writing Australian waterfowl are nomadic in nature There is increasing demand of free range poultry production in Australia Mathematical models for avian influenza risk in Australia have been reviewed
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Knowledge and remaining gaps on the role of animal and human movements in the poultry production and trade networks in the global spread of avian influenza viruses - A scoping review. PLoS One 2020; 15:e0230567. [PMID: 32196515 PMCID: PMC7083317 DOI: 10.1371/journal.pone.0230567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022] Open
Abstract
Poultry production has significantly increased worldwide, along with the number of avian influenza (AI) outbreaks and the potential threat for human pandemic emergence. The role of wild bird movements in this global spread has been extensively studied while the role of animal, human and fomite movement within commercial poultry production and trade networks remains poorly understood. The aim of this work is to better understand these roles in relation to the different routes of AI spread. A scoping literature review was conducted according to the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) using a search algorithm combining twelve domains linked to AI spread and animal/human movements within poultry production and trade networks. Only 28 out of 3,978 articles retrieved dealt especially with the role of animal, human and fomite movements in AI spread within the international trade network (4 articles), the national trade network (8 articles) and the production network (16 articles). While the role of animal movements in AI spread within national trade networks has been largely identified, human and fomite movements have been considered more at risk for AI spread within national production networks. However, the role of these movements has never been demonstrated with field data, and production networks have only been partially studied and never at international level. The complexity of poultry production networks and the limited access to production and trade data are important barriers to this knowledge. There is a need to study the role of animal and human movements within poultry production and trade networks in the global spread of AI in partnership with both public and private actors to fill this gap.
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Wang S, Huang B, Ma X, Liu P, Wang Y, Zhang X, Zhu L, Fan Q, Sun Y, Wang K. Reverse-transcription recombinase-aided amplification assay for H7 subtype avian influenza virus. Transbound Emerg Dis 2019; 67:877-883. [PMID: 31714018 DOI: 10.1111/tbed.13411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/15/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
H7 subtype avian influenza virus infection is an emerging zoonosis in some Asian countries and an important avian disease worldwide. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H7 subtype avian influenza virus. Assays were performed at a single temperature (39°C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus, which are the other main respiratory viruses affecting birds. The analytical sensitivity was 102 RNA copies per reaction at a 95% probability level according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the κ value of the reverse-transcription recombinase-aided amplification assay in 342 avian clinical samples was 0.988 (p < .001). The sensitivity for avian clinical sample detection was 100% (95%CI, 90.40%-100%), and the specificity was 99.96% (95%CI, 97.83%-99.98%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting avian influenza H7 subtype virus.
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Affiliation(s)
- Suchun Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Baoxu Huang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xuejun Ma
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Ping Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yang Wang
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiaoguang Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Lin Zhu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Qingying Fan
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yawei Sun
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Kaicheng Wang
- China Animal Health and Epidemiology Center, Qingdao, China
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Barnes B, Scott A, Hernandez-Jover M, Toribio JA, Moloney B, Glass K. Modelling high pathogenic avian influenza outbreaks in the commercial poultry industry. Theor Popul Biol 2019; 126:59-71. [DOI: 10.1016/j.tpb.2019.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/23/2018] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
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Glass K, Barnes B, Scott A, Toribio JA, Moloney B, Singh M, Hernandez-Jover M. Modelling the impact of biosecurity practices on the risk of high pathogenic avian influenza outbreaks in Australian commercial chicken farms. Prev Vet Med 2019; 165:8-14. [PMID: 30851932 DOI: 10.1016/j.prevetmed.2019.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/29/2023]
Abstract
As of 2018, Australia has experienced seven outbreaks of highly pathogenic avian influenza (HPAI) in poultry since 1976, all of which involved chickens. There is concern that increases in free-range farming could heighten HPAI outbreak risk due to the potential for greater contact between chickens and wild birds that are known to carry low pathogenic avian influenza (LPAI). We use mathematical models to assess the effect of a shift to free-range farming on the risk of HPAI outbreaks of H5 or H7 in the Australian commercial chicken industry, and the potential for intervention strategies to reduce this risk. We find that a shift of 25% of conventional indoor farms to free-range farming practices would result in a 6-7% increase in the risk of a HPAI outbreak. Current practices to treat water are highly effective, reducing the risk of outbreaks by 25-28% compared to no water treatment. Halving wild bird presence in feed storage areas could reduce risk by 16-19% while halving wild bird access of potential bridge-species to sheds could reduce outbreak risk by 23-25%, and relatively small improvements in biosecurity measures could entirely compensate for increased risks due to the increasing proportion of free-range farms in the industry. The short production cycle and cleaning practices for chicken meat sheds considerably reduce the risk that an introduced low pathogenic avian influenza virus is maintained in the flock until it is detected as HPAI through increased mortality of chickens. These findings help explain HPAI outbreak history in Australia and suggest practical changes in biosecurity practices that could reduce the risk of future outbreaks.
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Affiliation(s)
- K Glass
- Research School of Population Health, Australian National University, Australia.
| | - B Barnes
- Research School of Population Health, Australian National University, Australia
| | - A Scott
- Sydney School of Veterinary Science, University of Sydney, Australia
| | - J-A Toribio
- Sydney School of Veterinary Science, University of Sydney, Australia
| | - B Moloney
- New South Wales Department of Primary Industries, Australia
| | - M Singh
- Sydney School of Veterinary Science, University of Sydney, Australia
| | - M Hernandez-Jover
- School of Animal and Veterinary Sciences and Graham Centre for Agricultural Innovation, Charles Sturt University, Australia
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Scott AB, Toribio JA, Singh M, Groves P, Barnes B, Glass K, Moloney B, Black A, Hernandez-Jover M. Low Pathogenic Avian Influenza Exposure Risk Assessment in Australian Commercial Chicken Farms. Front Vet Sci 2018; 5:68. [PMID: 29755987 PMCID: PMC5932326 DOI: 10.3389/fvets.2018.00068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
This study investigated the pathways of exposure to low pathogenic avian influenza (LPAI) virus among Australian commercial chicken farms and estimated the likelihood of this exposure occurring using scenario trees and a stochastic modeling approach following the World Organization for Animal Health methodology for risk assessment. Input values for the models were sourced from scientific literature and an on-farm survey conducted during 2015 and 2016 among Australian commercial chicken farms located in New South Wales and Queensland. Outputs from the models revealed that the probability of a first LPAI virus exposure to a chicken in an Australian commercial chicken farms from one wild bird at any point in time is extremely low. A comparative assessment revealed that across the five farm types (non-free-range meat chicken, free-range meat chicken, cage layer, barn layer, and free range layer farms), free-range layer farms had the highest probability of exposure (7.5 × 10-4; 5% and 95%, 5.7 × 10-4-0.001). The results indicate that the presence of a large number of wild birds on farm is required for exposure to occur across all farm types. The median probability of direct exposure was highest in free-range farm types (5.6 × 10-4 and 1.6 × 10-4 for free-range layer and free-range meat chicken farms, respectively) and indirect exposure was highest in non-free-range farm types (2.7 × 10-4, 2.0 × 10-4, and 1.9 × 10-4 for non-free-range meat chicken, cage layer, and barn layer farms, respectively). The probability of exposure was found to be lowest in summer for all farm types. Sensitivity analysis revealed that the proportion of waterfowl among wild birds on the farm, the presence of waterfowl in the range and feed storage areas, and the prevalence of LPAI in wild birds are the most influential parameters for the probability of Australian commercial chicken farms being exposed to avian influenza (AI) virus. These results highlight the importance of ensuring good biosecurity on farms to minimize the risk of exposure to AI virus and the importance of continuous surveillance of LPAI prevalence including subtypes in wild bird populations.
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Affiliation(s)
- Angela Bullanday Scott
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Jenny-Ann Toribio
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Mini Singh
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Peter Groves
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Belinda Barnes
- Quantitative Sciences, Department of Agriculture and Water Resources, Canberra, ACT, Australia
| | - Kathryn Glass
- College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia
| | - Barbara Moloney
- New South Wales Department of Primary Industries, Orange, NSW, Australia
| | - Amanda Black
- New South Wales Department of Primary Industries, Orange, NSW, Australia
| | - Marta Hernandez-Jover
- Graham Centre for Agricultural Innovation, School of Animal and Veterinary Sciences, Charles Sturt University and New South Wales Department of Primary Industries, Wagga Wagga, NSW, Australia.,School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
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Scott AB, Phalen D, Hernandez-Jover M, Singh M, Groves P, Toribio JALML. Wildlife Presence and Interactions with Chickens on Australian Commercial Chicken Farms Assessed by Camera Traps. Avian Dis 2018; 62:65-72. [DOI: 10.1637/11761-101917-reg.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Angela Bullanday Scott
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - David Phalen
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Marta Hernandez-Jover
- Graham Centre for Agricultural Innovation, Charles Sturt University, School of Animal and Veterinary Sciences, Locked Bag 588, Wagga Wagga, New South Wales, 2678, Australia
| | - Mini Singh
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Peter Groves
- School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
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