1
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Dao DT, Coleman KK, Bui VN, Bui AN, Tran LH, Nguyen QD, Than S, Pulscher LA, Marushchak LV, Robie ER, Nguyen-Viet H, Pham PD, Christy NC, Brooks JS, Nguyen HC, Rubrum AM, Webby RJ, Gray GC. High Prevalence of Highly Pathogenic Avian Influenza: A Virus in Vietnam's Live Bird Markets. Open Forum Infect Dis 2024; 11:ofae355. [PMID: 39015351 PMCID: PMC11250224 DOI: 10.1093/ofid/ofae355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
Background In recent years, Vietnam has suffered multiple epizootics of influenza in poultry. Methods From 10 January 2019 to 26 April 2021, we employed a One Health influenza surveillance approach at live bird markets (LBMs) and swine farms in Northern Vietnam. When the COVID-19 pandemic permitted, each month, field teams collected oral secretion samples from poultry and pigs, animal facility bioaerosol and fecal samples, and animal worker nasal washes at 4 LBMs and 5 swine farms across 5 sites. Initially samples were screened with molecular assays followed by culture in embryonated eggs (poultry swabs) or Madin-Darby canine kidney cells (human or swine swabs). Results Many of the 3493 samples collected had either molecular or culture evidence for influenza A virus, including 314 (37.5%) of the 837 poultry oropharyngeal swabs, 144 (25.1%) of the 574 bioaerosol samples, 438 (34.9%) of the 1257 poultry fecal swab samples, and 16 (1.9%) of the 828 human nasal washes. Culturing poultry samples yielded 454 influenza A isolates, 83 of which were H5, and 70 (84.3%) of these were highly pathogenic. Additionally, a positive human sample had a H9N2 avian-like PB1 gene. In contrast, the prevalence of influenza A in the swine farms was much lower with only 6 (0.4%) of the 1700 total swine farm samples studied, having molecular evidence for influenza A virus. Conclusions This study suggests that Vietnam's LBMs continue to harbor high prevalences of avian influenza A viruses, including many highly pathogenic H5N6 strains, which will continue to threaten poultry and humans.
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Affiliation(s)
- Duy Tung Dao
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Kristen K Coleman
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Department of Global, Environmental, and Occupational Health, University of Maryland School of Public Health, College Park, Maryland, USA
- Department of Veterinary Medicine, College of Agriculture and Natural Resources, University of Maryland, College Park, Maryland, USA
| | - Vuong N Bui
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Anh N Bui
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Long H Tran
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Quy D Nguyen
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Son Than
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Laura A Pulscher
- Division of Infectious Diseases, Department of Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lyudmyla V Marushchak
- Division of Infectious Diseases, Department of Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily R Robie
- Global Health Institute, Duke University, Durham, North Carolina, USA
| | | | - Phuc Duc Pham
- Center for Public Health and Ecosystem Research, Hanoi University of Public Health, Hanoi, Vietnam
| | | | - John S Brooks
- U.S. Naval Medical Research Unit INDO PACIFIC, Singapore, Singapore
| | - Huy C Nguyen
- U.S. Naval Medical Research Unit INDO PACIFIC, Singapore, Singapore
| | - Adam M Rubrum
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gregory C Gray
- Division of Infectious Diseases, Department of Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Global Health, School of Public and Population Health, University of Texas Medical Branch, Galveston, Texas, USA
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2
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Hennessey M, Barnett T. Method in limbo? Theoretical and empirical considerations in using thematic analysis by veterinary and One Health researchers. Prev Vet Med 2023; 221:106061. [PMID: 37944192 DOI: 10.1016/j.prevetmed.2023.106061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
This article spans a number of theoretical, empirical and practice junctures at the intersection of human and animal medicine and the social sciences. We discuss the way thematic analysis, a qualitative method borrowed from the social sciences, is being increasingly used by veterinary and One Health researchers to investigate a range of complex issues. By considering theoretical aspects of thematic analysis, we expand our discussion to question whether this tool, as well as other social science methods, is currently being used appropriately by veterinary and human health researchers. We suggest that additional engagement with social science theory would enrich research practices and improve findings. We argue that considerations of 'big theory' - ontological and epistemological positionings of the researcher - and 'small(er)' theory, the specific social theory in which research is situated, are both necessary. Our point of departure is that scientific discourse is not merely construction or ideology but a unique and continuing arena of debate, in part at least because of the elevation of self-criticism to a central tenet of its practice. We argue for further engagement with the core ideas and concepts outlined above and discuss them in what follows. In particular, and by way of focusing the point, we suggest that for veterinary, One Health, and human medical researchers to use thematic analysis to its maximum potential they should be encouraged to engage with both broader socio-economic theories and with questions of ontology and epistemology.
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Affiliation(s)
- Mathew Hennessey
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, UK.
| | - Tony Barnett
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, UK; Firoz Lalji Institute for Africa, London School of Economics, UK
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3
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Islam A, Rahman MZ, Hassan MM, Epstein JH, Klaassen M. Determinants for the presence of avian influenza virus in live bird markets in Bangladesh: Towards an easy fix of a looming one health issue. One Health 2023; 17:100643. [PMID: 38024264 PMCID: PMC10665153 DOI: 10.1016/j.onehlt.2023.100643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Highly pathogenic avian influenza virus subtype H5N1 endangers poultry, wildlife, and human health and is enzootic in large parts of Asia, with live bird markets (LBMs) as putative hotspots for their maintenance, amplification, and spread. To mitigate the extent of these and other avian influenza viruses (AIV) of concern, we aimed to increase our quantitative understanding of the factors determining the presence of avian influenza virus in LBM stalls. Between 2016 and 2017, we collected fecal or offal samples from 1008 stalls in 113 LBMs across the Dhaka and Rajshahi districts in Bangladesh. For each stall, samples were pooled and tested for the AIV matrix gene, followed by H5 and H9 subtyping using rRT-PCR. We detected Influenza A viral RNA in 49% of the stalls. Of the AIV positive samples, 52% and 24% were determined to be H5 and H9 viruses, respectively, which are both subtypes of considerable health concern. We used generalized linear mixed effect modelling to study AIV presence in individual stalls within LBMs as a function of 13 out of the 20 risk factors identified by FAO. We found that small and feasible improvements in cleaning and disinfection frequency, installing running water in stalls, and not mixing different breeds of chicken in the same cages had large impacts on the presence of AIV in stalls (Odds ratios 0.03-0.05). Next, cleaning vehicles used in poultry transport, not selling waterfowl with chickens in the same stall, buying stock directly from commercial farms, separating sick birds from healthy ones, and avoiding access by wild birds like house crows, also had major effects on lowering the risk of stalls having AIV (Odds ratios 0.16-0.33). These findings can be directly used in developing practical and affordable measures to reduce the prevalence of AIV in LBMs. Also, in settings with limited resources like Bangladesh, such mitigation may significantly contribute to reducing AIV circulation amongst poultry and spillover to wildlife and humans.
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Affiliation(s)
- Ariful Islam
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- EcoHealth Alliance, New York, NY 10018, USA
| | - Mohammed Ziaur Rahman
- One Health Laboratory, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Bangladesh
| | - Mohammad Mahmudul Hassan
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, Brisbane, QLD, Australia
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh
| | | | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
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4
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Le KT, Stevenson MA, Isoda N, Nguyen LT, Chu DH, Nguyen TN, Nguyen LV, Tien TN, Le TT, Matsuno K, Okamatsu M, Sakoda Y. A systematic approach to illuminate a new hot spot of avian influenza virus circulation in South Vietnam, 2016-2017. Transbound Emerg Dis 2021; 69:e831-e844. [PMID: 34734678 DOI: 10.1111/tbed.14380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/30/2021] [Accepted: 10/16/2021] [Indexed: 11/27/2022]
Abstract
In South Vietnam, live bird markets (LBMs) are key in the value chain of poultry products and spread of avian influenza virus (AIV) although they may not be the sole determinant of AIV prevalence. For this reason, a risk analysis of AIV prevalence was conducted accounting for all value chain factors. A cross-sectional study of poultry flock managers and poultry on backyard farms, commercial (high biosecurity) farms, LBMs and poultry delivery stations (PDSs) in four districts of Vinh Long province was conducted between December 2016 and August 2017. A total of 3597 swab samples were collected from birds from 101 backyard farms, 50 commercial farms, 58 sellers in LBMs and 19 traders in PDSs. Swab samples were submitted for AIV isolation. At the same time a questionnaire was administered to flock managers asking them to provide details of their knowledge, attitude and practices related to avian influenza. Multiple correspondence analysis and a mixed-effects multivariable logistic regression model were developed to identify enterprise and flock manager characteristics that increased the risk of AIV positivity. A total of 274 birds were positive for AIV isolation, returning an estimated true prevalence of 7.6% [95% confidence interval (CI): 6.8%-8.5%]. The odds of a bird being AIV positive if it was from an LBM or PDS were 45 (95% CI: 3.4-590) and 25 (95% CI: 1.4-460), respectively, times higher to the odds of a bird from a commercial poultry farm being AIV positive. The odds of birds being AIV positive for respondents with a mixed (uncertain or inconsistent) level and a low level of knowledge about AI were 5.0 (95% CI: 0.20-130) and 3.5 (95% CI: 0.2-62), respectively, times higher to the odd of birds being positive for respondents with a good knowledge of AI. LBMs and PDSs should receive specific emphasis in AI control programs in Vietnam. Our findings provide evidence to support the hypothesis that incomplete respondent knowledge of AI and AIV spread mechanism were associated with an increased risk of AIV positivity. Delivery of education programs specifically designed for those in each enterprise will assist in this regard. The timing and frequency of delivery of education programs are likely to be important if the turnover of those working in LBMs and PDSs is high.
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Affiliation(s)
- Kien Trung Le
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mark A Stevenson
- Faculty of Veterinary and Agricultural Sciences, Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Norikazu Isoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Lam Thanh Nguyen
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Department of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | - Duc-Huy Chu
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Vietnam
| | - Tien Ngoc Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Vietnam
| | - Long Van Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Vietnam
| | - Tien Ngoc Tien
- Regional Animal Health Office VII, Department of Animal Health, Ministry of Agriculture and Rural Development, Can Tho, Vietnam
| | - Tung Thanh Le
- Sub-Departments of Animal Health, Ministry of Agriculture and Rural Development, Vinh Long, Vietnam
| | - Keita Matsuno
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
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5
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Miguel MA, Kim SH, Lee SS, Cho YI. Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses. Animals (Basel) 2021; 11:2937. [PMID: 34679958 PMCID: PMC8532636 DOI: 10.3390/ani11102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.
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Affiliation(s)
| | | | | | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.A.M.); (S.-H.K.); (S.-S.L.)
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6
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Uwishema O, Adriano LF, Chalhoub E, Onyeaka H, Mhanna M, David SC, Nasrallah Y, Ribeiro LLPA, Berjaoui C. Bird flu outbreak amidst COVID-19 pandemic in South Africa: Efforts and challenges at hand. J Med Virol 2021; 93:5676-5679. [PMID: 34081338 PMCID: PMC8242854 DOI: 10.1002/jmv.27124] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/29/2023]
Abstract
Over the months of April and May 2021, South Africa has witnessed several outbreaks of highly infective avian influenza (H5N1) in different poultry farms. This came as a shock to a country that was already battling with the deadly COVID‐19 pandemic. The emergence of the virus has spurred import bans and massive culls in the poultry business. Local experts have also called for a restriction on the movement of people and cars in and out of their chicken farms. Employees have also been encouraged to shower in the mornings when they arrive at the farms and wear fresh clothes, as the flu spreads very quickly. In a country that is already facing the economic implications of the COVID‐19, this has the potential to cause a significant dent in the economy, as well as severely impact people's day‐to‐day life. Bird flu—also called avian influenza—is a viral infection that can infect not only birds but also humans and other animals. The threat of a new influenza pandemic has prompted countries to draft national strategic preparedness plans to prevent, contain and mitigate the next human influenza pandemic. This paper describes the South African burden, current efforts, and preparedness against the avian influenza virus.
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Affiliation(s)
- Olivier Uwishema
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Clinton Global Initiative University, New York, New York, USA.,Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Lubanga F Adriano
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,University of Malawi College of Medicine, Blantyre, Malawi
| | - Elie Chalhoub
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, University of Saint Joseph of Beirut, Beirut, Lebanon
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Melissa Mhanna
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, University of Saint Joseph of Beirut, Beirut, Lebanon
| | - Success C David
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of pharmaceutical Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Yves Nasrallah
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,School of Medicine and Medical Sciences, Holy Spirit University of Kaslik, Beirut, Lebanon
| | - Lucas L P A Ribeiro
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,School of Medicine, University of Fortaleza, Fortaleza, Ceará, Brazil
| | - Christin Berjaoui
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
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7
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Park YR, Lee YN, Lee DH, Si YJ, Baek YG, Bunnary S, Theary R, Tum S, Kye SJ, Lee MH, Park CK, Lee YJ. Phylogeographic analysis of H5N1 highly pathogenic avian influenza virus isolated in Cambodia from 2018 to 2019. INFECTION GENETICS AND EVOLUTION 2020; 86:104599. [PMID: 33096302 DOI: 10.1016/j.meegid.2020.104599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/09/2022]
Abstract
Since 2004, several outbreaks of highly pathogenic avian influenza (HPAI) have been reported in Cambodia. Until 2013, all H5N1 viruses identified in Cambodia belonged to clade 1 and its subclades. H5N1 HPAI viruses belonging to clade 2.3.2.1c have been dominant since the beginning of 2014, with various genotypes (KH1-KH5) reported. Here, we isolated nine H5N1 HPAI viruses from domestic poultry farms and slaughterhouses in Cambodia during 2018-2019 and performed phylogenetic analysis of whole genome sequences. All isolates were classified as H5 clade 2.3.2.1c viruses and all harbored multi-basic amino acid sequences (PQRERRRKR/GLF) at the haemagglutinin (HA) cleavage site. Phylogenetic analysis revealed that the H5N1 isolates in this study belonged to the KH2 genotype, the dominant genotype in Cambodia in 2015. Phylogenetic analysis of the HA gene showed that the isolates were divided into two groups (A and B). The results of Bayesian discrete phylogeography analysis revealed that the viral migration pathways from Vietnam to Cambodia (Bayes factor value: 734,039.01; posterior probability: 1.00) and from Cambodia to Vietnam (Bayes factor value: 26,199.95; posterior probability: 1.00) were supported by high statistical values. These well-supported viral migrations between Vietnam and Cambodia demonstrate that viral transmission continued in both directions. Several factors may have contributed to this, including the free-grazing duck system and movement of poultry-related products. Thus, the results emphasize the need for an enhanced international surveillance program to better understand transboundary infection and evolution of H5N1 HPAI viruses, along with implementation of more stringent international trade controls on poultry and poultry products.
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Affiliation(s)
- Yu-Ri Park
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea; College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, Republic of Korea
| | - Yu-Na Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - Young-Jae Si
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Yoon-Gi Baek
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Seng Bunnary
- Department of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Ren Theary
- Department of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Sothyra Tum
- Department of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Soo-Jeong Kye
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Myoung-Heon Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, Republic of Korea.
| | - Youn-Jeong Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea.
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8
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Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinformatics 2020; 36:2098-2104. [PMID: 31790143 DOI: 10.1093/bioinformatics/btz882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/01/2019] [Accepted: 11/22/2019] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative. RESULTS We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities. AVAILABILITY AND IMPLEMENTATION Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Jean Artois
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Tommy T Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Alice Fusaro
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Isabella Monne
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy.,Animal Production and Health Laboratory, Joint FAO/IAEA Division, 2444 Seibersdorf, Austria
| | | | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Wantanee Kalpravidh
- Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok 10200, Thailand
| | | | - Filip Claes
- Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok 10200, Thailand
| | - Scott H Newman
- Food and Agriculture Organization of the United Nations, Regional Office for Africa, Accra, Ghana
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, Los Angeles, CA, USA.,Department of Biostatistics, Fielding School of Public Health, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
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9
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Barnett T, Pfeiffer DU, Ahasanul Hoque M, Giasuddin M, Flora MS, Biswas PK, Debnath N, Fournié G. Practising co-production and interdisciplinarity: Challenges and implications for one health research. Prev Vet Med 2020; 177:104949. [PMID: 32203814 PMCID: PMC7218707 DOI: 10.1016/j.prevetmed.2020.104949] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 01/21/2023]
Abstract
We review the nature of interdisciplinary research in relation to One Health, a perspective on human-animal health which would appear to merit close interdisciplinary cooperation to inform public health policy. We discuss the relationship between biological sciences, epidemiology and the social sciences and note that interdisciplinary work demands attention be given to a range of often neglected epistemological and methodological issues. Epidemiologists may sometimes adopt social science techniques as "bolt-ons"1 to their research without having a complete understanding of how the social sciences work. The paper introduces a range of social science concepts and applies them to the challenges of understanding and practicing participatory and local epidemiology. We consider the problem of co-production of knowledge about One Health and zoonotic diseases in relation to funding structures, working in large international teams and explore some of the often-neglected realities of working across disciplines and cultures. We do this in part by applying the concept of value-chain to the research process.
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Affiliation(s)
- Tony Barnett
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, 15-17 Keppel Street, Bloomsbury, London WC1E 7HT, United Kingdom; Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, United Kingdom; Humanitarian and Conflict Response Institute, University of Manchester, Ellen Wilkinson Building, Manchester M15 6JA, United Kingdom.
| | - Dirk Udo Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, United Kingdom; Centre for Applied One Health Research and Policy Advice, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Md Ahasanul Hoque
- Department of Medicine & Surgery, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Zakir Hossain Road, Khulshi, Bangladesh
| | | | | | - Paritosh Kumar Biswas
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Zakir Hossain Road, Khulshi, Bangladesh
| | - Nitish Debnath
- Teaching and Training Pet Hospital and Research Center, Chattogram Veterinary and Animal Sciences University, Sector #18, Road #114, Plot: 5B, Purbachol, Dhaka, Bangladesh; Centre on Global Health Security, Chatham House, 10 St James's Square, St. James's, London SW1Y 4LE, United Kingdom
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, United Kingdom
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10
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Park YR, Lee YN, Lee DH, Baek YG, Si YJ, Meeduangchanh P, Theppangna W, Douangngeun B, Kye SJ, Lee MH, Park CK, Lee YJ. Genetic and pathogenic characteristics of clade 2.3.2.1c H5N1 highly pathogenic avian influenza viruses isolated from poultry outbreaks in Laos during 2015-2018. Transbound Emerg Dis 2019; 67:947-955. [PMID: 31769586 DOI: 10.1111/tbed.13430] [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: 08/26/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Since 2004, there have been multiple outbreaks of H5 highly pathogenic avian influenza (HPAI) viruses in Laos. Here, we isolated H5N1 HPAI viruses from poultry outbreaks in Laos during 2015-2018 and investigated their genetic characteristics and pathogenicity in chickens. Phylogenetic analysis revealed that the isolates belonged to clade 2.3.2.1c and that they differed from previous Laos viruses with respect to genetic composition. In particular, the isolates were divided into two genotypes, each of which had a different NS segments. The results of possible migration analysis suggested a high likelihood that the Laos isolates were introduced from neighbouring countries, particularly Vietnam. The recent Laos isolate, A/Duck/Laos/NL-1504599/2018, had an intravenous pathogenicity index score of 3.0 and showed a 50% chicken lethal dose of 102.5 EID50 /0.1 ml, indicating high pathogenicity. The isolated viruses exhibited no critical substitution in the markers associated with mammalian adaptation, but possess markers related to neuraminidase inhibitor resistance. These results emphasize the need for ongoing surveillance of circulating influenza virus in South-East Asia, including Laos, to better prepare for and mitigate global spread of H5 HPAI.
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Affiliation(s)
- Yu-Ri Park
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea.,College of Veterinary Medicine, Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Yu-Na Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - Yoon-Gi Baek
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Young-Jae Si
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | | | | | | | - Soo-Jeong Kye
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Myoung-Heon Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine, Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Youn-Jeong Lee
- Avian Influenza Research Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
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11
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Karo-Karo D, Pribadi ES, Sudirman FX, Kurniasih SW, Indasari I, Muljono DH, Koch G, Stegeman JA. Highly Pathogenic Avian Influenza A(H5N1) Outbreaks in West Java Indonesia 2015-2016: Clinical Manifestation and Associated Risk Factors. Microorganisms 2019; 7:E327. [PMID: 31500141 PMCID: PMC6788193 DOI: 10.3390/microorganisms7090327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/20/2019] [Accepted: 09/05/2019] [Indexed: 01/13/2023] Open
Abstract
Knowledge of outbreaks and associated risk factors is helpful to improve control of the Highly Pathogenic Avian Influenza A(H5N1) virus (HPAI) in Indonesia. This study was conducted to detect outbreaks of HPAI H5N1 in endemically infected regions by enhanced passive surveillance, to describe the clinical manifestation of these outbreaks and identify associated risk factors. From November 2015 to November 2016, HPAI outbreak investigations were conducted in seven districts of West Java. In total 64 outbreaks were confirmed out of 75 reported suspicions and outbreak characteristics were recorded. The highest mortality was reported in backyard chickens (average 59%, CI95%: 49-69%). Dermal apoptosis and lesions (64%, CI95%: 52-76%) and respiratory signs (39%, CI95%: 27-51%) were the clinical signs observed overall most frequently, while neurological signs were most frequently observed in ducks (68%, CI95%: 47-90%). In comparison with 60 non-infected control farms, the rate of visitor contacts onto a farm was associated with the odds of HPAI infection. Moreover, duck farms had higher odds of being infected than backyard farms, and larger farms had lower odds than small farms. Results indicate that better external biosecurity is needed to reduce transmission of HPAI A(H5N1) in Indonesia.
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Affiliation(s)
- Desniwaty Karo-Karo
- Department of Farm Animal Health, Faculty of Veterinary Medicine Utrecht University, 3584 CL Utrecht, The Netherlands
- Centre for Diagnostic Standard of Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Jakarta 13220, Indonesia
| | - Eko Sugeng Pribadi
- Center for Tropical Animal Studies, Institute of Research and Community Empowerment, Bogor Agricultural University, Bogor 16129, Indonesia
| | | | | | - Iin Indasari
- West Java Province Animal Health Agency, Bandung 40135, Indonesia
| | | | - Guus Koch
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands
| | - Jan Arend Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine Utrecht University, 3584 CL Utrecht, The Netherlands.
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12
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Suttie A, Karlsson EA, Deng YM, Hurt AC, Greenhill AR, Barr IG, Dussart P, Horwood PF. Avian influenza in the Greater Mekong Subregion, 2003-2018. INFECTION GENETICS AND EVOLUTION 2019; 74:103920. [PMID: 31201870 DOI: 10.1016/j.meegid.2019.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
The persistent circulation of avian influenza viruses (AIVs) is an ongoing problem for many countries in South East Asia, causing large economic losses to both the agricultural and health sectors. This review analyses AIV diversity, evolution and the risk of AIV emergence in humans in countries of the Greater Mekong Subregion (GMS): Cambodia, Laos, Myanmar, Thailand and Vietnam (excluding China). The analysis was based on AIV sequencing data, serological studies, published journal articles and AIV outbreak reports available from January 2003 to December 2018. All countries of the GMS have suffered losses due repeated outbreaks of highly pathogenic (HP) H5N1 that has also caused human cases in all GMS countries. In Laos, Myanmar and Vietnam AIV outbreaks in domestic poultry have also been caused by clade 2.3.4.4 H5N6. A diverse range of low pathogenic AIVs (H1-H12) have been detected in poultry and wild bird species, though surveillance for and characterization of these subtypes is limited. Subtype H3, H4, H6 and H11 viruses have been detected over prolonged periods; whilst H1, H2, H7, H8, H10 and H12 viruses have only been detected transiently. H9 AIVs circulate endemically in Cambodia and Vietnam with seroprevalence data indicating human exposure to H9 AIVs in Cambodia, Thailand and Vietnam. As surveillance studies focus heavily on the detection of H5 AIVs in domestic poultry further research is needed to understand the true level of AIV diversity and the risk AIVs pose to humans in the GMS.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia; School of Applied and Biomedical Sciences, Federation University, Churchill, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Erik A Karlsson
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andrew R Greenhill
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Philippe Dussart
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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13
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A systematic study towards evolutionary and epidemiological dynamics of currently predominant H5 highly pathogenic avian influenza viruses in Vietnam. Sci Rep 2019; 9:7723. [PMID: 31118431 PMCID: PMC6531488 DOI: 10.1038/s41598-019-42638-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
This study aimed to elucidate virus, host and environmental dynamics of Vietnamese H5 highly pathogenic avian influenza viruses (HPAIVs) during 2014–2017. Epidemiologically, H5 HPAIVs were frequently detected in apparently healthy domestic and Muscovy ducks and therefore these are preferred species for H5 HPAIV detection in active surveillance. Virologically, clade 2.3.2.1c and 2.3.4.4 H5 HPAIVs were predominant and exhibited distinct phylogeographic evolution. Clade 2.3.2.1c viruses clustered phylogenetically in North, Central and South regions, whilst clade 2.3.4.4 viruses only detected in North and Central regions formed small groups. These viruses underwent diverse reassortment with existence of at least 12 genotypes and retained typical avian-specific motifs. These H5 HPAIVs exhibited large antigenic distance from progenitor viruses and commercial vaccines currently used in poultry. Bayesian phylodynamic analysis inferred that clade 2.3.2.1c viruses detected during 2014–2017 were likely descended from homologous clade viruses imported to Vietnam previously and/or preexisting Chinese viruses during 2012–2013. Vietnamese clade 2.3.4.4 viruses closely shared genetic traits with contemporary foreign spillovers, suggesting that there existed multiple transboundary virus dispersals to Vietnam. This study provides insights into the evolution of Vietnamese H5 HPAIVs and highlights the necessity of strengthening control measures such as, preventive surveillance and poultry vaccination.
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14
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Nguyen LT, Stevenson MA, Firestone SM, Sims LD, Chu DH, Nguyen LV, Nguyen TN, Le KT, Isoda N, Matsuno K, Okamatsu M, Kida H, Sakoda Y. Spatiotemporal and risk analysis of H5 highly pathogenic avian influenza in Vietnam, 2014-2017. Prev Vet Med 2019; 178:104678. [PMID: 31113666 DOI: 10.1016/j.prevetmed.2019.04.007] [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: 09/24/2018] [Revised: 03/10/2019] [Accepted: 04/13/2019] [Indexed: 10/27/2022]
Abstract
The aim of this study was to describe the spatiotemporal distribution of H5 HPAI outbreak reports for the period 2014-2017 and to identify factors associated with H5 HPAI outbreak reports. Throughout the study period, a total of 139 outbreaks of H5 HPAI in poultry were reported, due to either H5N1 (96 outbreaks) or H5N6 (43 outbreaks) subtype viruses. H5N1 HPAI outbreaks occurred in all areas of Vietnam while H5N6 HPAI outbreaks were only reported in the northern and central provinces. We counted the number of H5N1 and H5N6 outbreak report-positive districts per province over the four-year study period and calculated the provincial-level standardized morbidity ratio for H5N1 and H5N6 outbreak reports as the observed number of positive districts divided by the expected number. A mixed-effects, zero-inflated Poisson regression model was developed to identify risk factors for outbreak reports of each H5N1 and H5N6 subtype virus. Spatially correlated and uncorrelated random effects terms were included in this model to identify areas of the country where outbreak reports occurred after known risk factors had been accounted-for. The presence of an outbreak report in a province in the previous 6-12 months increased the provincial level H5N1 outbreak report risk by a factor of 2.42 (95% Bayesian credible interval [CrI] 1.27-4.60) while 1000 bird increases in the density of chickens decreased provincial level H5N6 outbreak report risk by a factor of 0.65 (95% CrI 0.38 to 0.97). We document distinctly different patterns in the spatial and temporal distribution of H5N1 and H5N6 outbreak reports. Most of the variation in H5N1 report risk was accounted-for by the fixed effects included in the zero-inflated Poisson model. In contrast, the amount of unaccounted-for risk in the H5N6 model was substantially greater than the H5N1 model. For H5N6 we recommend that targeted investigations should be carried out in provinces with relatively large spatially correlated random effect terms to identify likely determinants of disease. Similarly, investigations should be carried out in provinces with relatively low spatially correlated random effect terms to identify protective factors for disease and/or reasons for failure to report.
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Affiliation(s)
- Lam Thanh Nguyen
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan; Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Mark A Stevenson
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Simon M Firestone
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Leslie D Sims
- Asia Pacific Veterinary Information Services, Montmorency, Victoria, 3094, Australia
| | - Duc Huy Chu
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Viet Nam
| | - Long Van Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Viet Nam
| | - Tien Ngoc Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi, Viet Nam
| | - Kien Trung Le
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Norikazu Isoda
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; Global Institution for Collaborative Research and Education, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Keita Matsuno
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan; Global Institution for Collaborative Research and Education, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Hiroshi Kida
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; Global Institution for Collaborative Research and Education, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan; Global Institution for Collaborative Research and Education, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan.
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15
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Optimising the detectability of H5N1 and H5N6 highly pathogenic avian influenza viruses in Vietnamese live-bird markets. Sci Rep 2019; 9:1031. [PMID: 30705346 PMCID: PMC6355762 DOI: 10.1038/s41598-018-37616-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/07/2018] [Indexed: 12/25/2022] Open
Abstract
Live bird markets (LBMs) are major targets for avian influenza virus (AIV) surveillance programmes. While sampling the LBM environment has become a widely used alternative to the labour-intensive sampling of live poultry, the design of surveillance programmes and the interpretation of their results are compromised by the lack of knowledge about the effectiveness of these sampling strategies. We used latent class models and a unique empirical dataset collated in Vietnamese LBMs to estimate the sensitivity and specificity of five different sample types for detecting AIVs subtypes H5N1 and H5N6: oropharyngeal duck samples, solid and liquid wastes, poultry drinking water and faeces. Results suggest that the sensitivity of environmental samples for detecting H5N1 viruses is equivalent to that of oropharyngeal duck samples; however, taking oropharyngeal duck samples was estimated to be more effective in detecting H5N6 viruses than taking any of the four environmental samples. This study also stressed that the specificity of the current surveillance strategy in LBMs was not optimal leading to some false positive LBMs. Using simulations, we identified 42 sampling strategies more parsimonious than the current strategy and expected to be highly sensitive for both viruses at the LBM level. All of these strategies involved the collection of both environmental and oropharyngeal duck samples.
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16
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Mostafa A, Abdelwhab EM, Mettenleiter TC, Pleschka S. Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview. Viruses 2018; 10:v10090497. [PMID: 30217093 PMCID: PMC6165440 DOI: 10.3390/v10090497] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/24/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
Influenza A viruses (IAVs) possess a great zoonotic potential as they are able to infect different avian and mammalian animal hosts, from which they can be transmitted to humans. This is based on the ability of IAV to gradually change their genome by mutation or even reassemble their genome segments during co-infection of the host cell with different IAV strains, resulting in a high genetic diversity. Variants of circulating or newly emerging IAVs continue to trigger global health threats annually for both humans and animals. Here, we provide an introduction on IAVs, highlighting the mechanisms of viral evolution, the host spectrum, and the animal/human interface. Pathogenicity determinants of IAVs in mammals, with special emphasis on newly emerging IAVs with pandemic potential, are discussed. Finally, an overview is provided on various approaches for the prevention of human IAV infections.
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Affiliation(s)
- Ahmed Mostafa
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany.
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza 12622, Egypt.
| | - Elsayed M Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany.
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17
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Livestock and livelihoods of smallholder cattle-owning households in Cambodia: the contribution of on-farm and off-farm activities to income and food security. Trop Anim Health Prod 2018; 50:1747-1761. [PMID: 29796792 DOI: 10.1007/s11250-018-1615-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/03/2018] [Indexed: 10/16/2022]
Abstract
The majority of smallholder farming households in Cambodia are rurally based and rely on agriculture to support their livelihoods. However, in recent years, growth in the agriculture sector has stagnated with farmers facing several challenges including declining prices for traditional crops and irregular rainfall patterns. This has led to a need for farmers to diversify income sources with livestock promoted as a more viable livelihood activity, particularly the raising of cattle and poultry. However, uncertain profitability of livestock activities is a common perception by smallholders, especially where animals have not been traditionally viewed as a primary income source. To address this, information is required which compares the income and expenses associated with livestock raising to other on-farm activities and off-farm sources. This study reports on a survey of livelihood survey of 17 male and 21 female representatives of 20 households owning cattle in Cambodia, comparing the associated income and expenses of the various livelihood activities in the 12-month period from January to December 2016. Combined total household income from both on-farm and off-farm sources ranged from USD875 to 17730 with an average of USD6779, representing 51% and 49% from on-farm and off-farm activities, respectively. Cattle raising was the most common source of on-farm income (85%), contributing USD1064 and representing 22% of total household income. General household expenses, such as food and transportation (including expenses associated with off-farm employment), represented the majority of total household expenses (79%). Gross profit calculations indicated higher values for pig raising (USD1841.79), cattle (USD950.80) and non-rice crops (USD884) whilst the highest gross margin value was recorded for cattle (89.33%) followed by vegetables (85.27%) and non-rice crops (83.08%). Whilst wet season and dry season rice returned a negative gross profit value of USD197.27 and USD90.60 on average per household, respectively, both were ranked as most important for household consumption, followed by poultry, providing the main source of energy (rice) and protein (chicken meat) and sustaining household food requirements. The study concludes that although smallholder cattle-owning households in Cambodia undertake a diverse range of on-farm activities, as cattle raising provides a superior income source due to higher returns and lower variable costs, it could be promoted as a preferred livelihood activity by agencies conducting rural extension activities. Although consideration of available labour and monetary funds to invest in cattle raising is required, it was observed that income from off-farm sources may prove beneficial in providing the additional monetary funds to support cattle-raising activities and assist in providing generally poor smallholder households with enhanced economic resilience.
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18
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Lickfett TM, Clark E, Gehring TM, Alm EW. Detection of Influenza A viruses at migratory bird stopover sites in Michigan, USA. Infect Ecol Epidemiol 2018; 8:1474709. [PMID: 29805786 PMCID: PMC5965024 DOI: 10.1080/20008686.2018.1474709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/25/2018] [Indexed: 11/04/2022] Open
Abstract
Introduction: Influenza A viruses have the potential to cause devastating illness in humans and domestic poultry. Wild birds are the natural reservoirs of Influenza A viruses and migratory birds are implicated in their global dissemination. High concentrations of this virus are excreted in the faeces of infected birds and faecal contamination of shared aquatic habitats can lead to indirect transmission among birds via the faecal-oral route. The role of migratory birds in the spread of avian influenza has led to large-scale surveillance efforts of circulating avian influenza viruses through direct sampling of live and dead wild birds. Environmental monitoring of bird habitats using molecular detection methods may provide additional information on the persistence of influenza virus at migratory stopover sites distributed across large spatial scales. Materials and methods: In the current study, faecal and water samples were collected at migratory stopover sites and evaluated for Influenza A by real-time quantitative reverse transcriptase PCR. Results and Discussion: This study found that Influenza A was detected at 53% of the evaluated stopover sites, and 7% and 4.8% of the faecal and water samples, respectively, tested positive for Influenza A virus. Conclusion: Environmental monitoring detected Influenza A at stopover sites used by migratory birds.
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Affiliation(s)
- Todd M Lickfett
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.,Region 6 Ecological Services, U.S. Fish and Wildlife Service, Lakewood, CO, USA
| | - Erica Clark
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.,Silver Spring, MD, USA
| | - Thomas M Gehring
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
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19
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Mellor KC, Meyer A, Elkholly DA, Fournié G, Long PT, Inui K, Padungtod P, Gilbert M, Newman SH, Vergne T, Pfeiffer DU, Stevens KB. Comparative Epidemiology of Highly Pathogenic Avian Influenza Virus H5N1 and H5N6 in Vietnamese Live Bird Markets: Spatiotemporal Patterns of Distribution and Risk Factors. Front Vet Sci 2018; 5:51. [PMID: 29675418 PMCID: PMC5896172 DOI: 10.3389/fvets.2018.00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/27/2018] [Indexed: 01/08/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Vietnam since 2003, whilst outbreaks of HPAI H5N6 virus are more recent, having only been reported since 2014. Although the spatial distribution of H5N1 outbreaks and risk factors for virus occurrence has been extensively studied, there have been no comparative studies for H5N6. Data collected through active surveillance of Vietnamese live bird markets (LBMs) between 2011 and 2015 were used to explore and compare the spatiotemporal distributions of H5N1- and H5N6-positive LBMs. Conditional autoregressive models were developed to quantify spatiotemporal associations between agroecological factors and the two HPAI strains using the same set of predictor variables. Unlike H5N1, which exhibited a strong north–south divide, with repeated occurrence in the extreme south of a cluster of high-risk provinces, H5N6 was homogeneously distributed throughout Vietnam. Similarly, different agroecological factors were associated with each strain. Sample collection in the months of January and February and higher average maximum temperature were associated with higher likelihood of H5N1-positive market-day status. The likelihood of market days being positive for H5N6 increased with decreased river density, and with successive Rounds of data collection. This study highlights marked differences in spatial patterns and risk factors for H5N1 and H5N6 in Vietnam, suggesting the need for tailored surveillance and control approaches.
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Affiliation(s)
- Kate C Mellor
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Anne Meyer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Doaa A Elkholly
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Pham T Long
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Ken Inui
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Pawin Padungtod
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
| | - Scott H Newman
- Country Office for Vietnam, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam.,Country Office for Ethiopia, Food and Agriculture Organization of the United Nations, Addis Ababa, Ethiopia
| | - Timothée Vergne
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.,Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD), Montpellier, France.,UMR 1225 INRA, ENVT Interactions Hôtes - Agents Pathogènes (IHAP), University of Toulouse, Toulouse, France
| | - Dirk U Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.,College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kim B Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
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20
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Yoo SJ, Kwon T, Lyoo YS. Challenges of influenza A viruses in humans and animals and current animal vaccines as an effective control measure. Clin Exp Vaccine Res 2018; 7:1-15. [PMID: 29399575 PMCID: PMC5795040 DOI: 10.7774/cevr.2018.7.1.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/07/2017] [Accepted: 12/12/2017] [Indexed: 11/28/2022] Open
Abstract
Influenza A viruses (IAVs) are genetically diverse and variable pathogens that share various hosts including human, swine, and domestic poultry. Interspecies and intercontinental viral spreads make the ecology of IAV more complex. Beside endemic IAV infections, human has been exposed to pandemic and zoonotic threats from avian and swine influenza viruses. Animal health also has been threatened by high pathogenic avian influenza viruses (in domestic poultry) and reverse zoonosis (in swine). Considering its dynamic interplay between species, prevention and control against IAV should be conducted effectively in both humans and animal sectors. Vaccination is one of the most efficient tools against IAV. Numerous vaccines against animal IAVs have been developed by a variety of vaccine technologies and some of them are currently commercially available. We summarize several challenges in control of IAVs faced by human and animals and discuss IAV vaccines for animal use with those application in susceptible populations.
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Affiliation(s)
- Sung J. Yoo
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Taeyong Kwon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Young S. Lyoo
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
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21
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Zhou Y, Kang X, Xiong D, Zhu S, Zheng H, Xu Y, Guo Y, Pan Z, Jiao X. Molecular and functional characterization of pigeon (Columba livia) tumor necrosis factor receptor-associated factor 3. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 69:51-59. [PMID: 28024872 DOI: 10.1016/j.dci.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
Tumor necrosis factor receptor-associated factor 3 (TRAF3) plays a key antiviral role by promoting type I interferon production. We cloned the pigeon TRAF3 gene (PiTRAF3) according to its predicted mRNA sequence to investigate its function. The 1704-bp full-length open reading frame encodes a 567-amino acid protein. One Ring finger, two TRAF-type Zinc fingers, one Coiled coil, and one MATH domain were inferred. RT-PCR showed that PiTRAF3 was expressed in all tissues, with relatively weak expression in the heart and liver. In HEK293T cells, over-expression of wild-type, △Ring, △Zinc finger, and △Coiled coil PiTRAF3, but not a △MATH form, significantly increased IFN-β promoter activity. Zinc finger and Coiled coil domains were essential for NF-κB activation. In chicken HD11 cells, PiTRAF3 increased IFN-β promoter activity and four domains were all contributing. R848 stimulation of pigeon peripheral blood mononuclear cells and splenocytes significantly increased expression of PiTRAF3 and the inflammatory cytokine genes CCL5, IL-8, and IL-10. These data demonstrate TRAF3's innate immune function and improve understanding of its involvement in poultry antiviral defense.
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Affiliation(s)
- Yingying Zhou
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Xilong Kang
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Dan Xiong
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Shanshan Zhu
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Huijuan Zheng
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Ying Xu
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Yaxin Guo
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China
| | - Zhiming Pan
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.
| | - Xinan Jiao
- Key Laboratory of Zoonoses in Jiangsu Province, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.
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22
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Abstract
The complexity and connectedness of eco-social processes have major influence on the emergence and spread of infectious diseases amongst humans and animals. The disciplinary nature of most research activity has made it difficult to improve our understanding of interactions and feedback loops within the relevant systems. Influenced by the One Health approach, increasing efforts have recently been made to address this knowledge gap. Disease emergence and spread is strongly influenced by host density and contact structures, pathogen characteristics and pathogen population and molecular evolutionary dynamics in different host species, and host response to infection. All these mechanisms are strongly influenced by eco-social processes, such as globalization and urbanization, which lead to changes in global ecosystem dynamics, including patterns of mobility, human population density and contact structures, and food production and consumption. An improved understanding of epidemiological and eco-social processes, including their interdependence, will be essential to be able to manage diseases in these circumstances. The interfaces between wild animals, domestic animals and humans need to be examined to identify the main risk pathways and put in place appropriate mitigation. Some recent examples of emerging infectious disease are described to illustrate eco-social processes that are influencing disease emergence and spread.
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23
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Osbjer K, Berg M, Sokerya S, Chheng K, San S, Davun H, Magnusson U, Olsen B, Zohari S. Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia. Transbound Emerg Dis 2016; 64:1557-1568. [PMID: 27484711 DOI: 10.1111/tbed.12547] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/27/2022]
Abstract
Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.
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Affiliation(s)
- K Osbjer
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - M Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - S Sokerya
- Centre for Livestock and Agriculture Development, Phnom Penh, Cambodia
| | - K Chheng
- National Institute of Public Health, Phnom Penh, Cambodia
| | - S San
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - H Davun
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - U Magnusson
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - B Olsen
- Infectious Diseases, Zoonosis Science Center, Department of Medical Sciences and IMBIM, Uppsala University (UU), Uppsala, Sweden
| | - S Zohari
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
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24
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Dual immunosensor based on methylene blue-electroadsorbed graphene oxide for rapid detection of the influenza A virus antigen. Talanta 2016; 155:250-7. [DOI: 10.1016/j.talanta.2016.04.047] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/13/2016] [Accepted: 04/23/2016] [Indexed: 01/26/2023]
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25
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Fournié G, Tripodi A, Nguyen TTT, Nguyen VT, Tran TT, Bisson A, Pfeiffer DU, Newman SH. Investigating poultry trade patterns to guide avian influenza surveillance and control: a case study in Vietnam. Sci Rep 2016; 6:29463. [PMID: 27405887 PMCID: PMC4942603 DOI: 10.1038/srep29463] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/20/2016] [Indexed: 02/05/2023] Open
Abstract
Live bird markets are often the focus of surveillance activities monitoring avian influenza viruses (AIV) circulating in poultry. However, in order to ensure a high sensitivity of virus detection and effectiveness of management actions, poultry management practices features influencing AIV dynamics need to be accounted for in the design of surveillance programmes. In order to address this knowledge gap, a cross-sectional survey was conducted through interviews with 791 traders in 18 Vietnamese live bird markets. Markets greatly differed according to the sources from which poultry was obtained, and their connections to other markets through the movements of their traders. These features, which could be informed based on indicators that are easy to measure, suggest that markets could be used as sentinels for monitoring virus strains circulating in specific segments of the poultry production sector. AIV spread within markets was modelled. Due to the high turn-over of poultry, viral amplification was likely to be minimal in most of the largest markets. However, due to the large number of birds being introduced each day, and challenges related to cleaning and disinfection, environmental accumulation of viruses at markets may take place, posing a threat to the poultry production sector and to public health.
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Affiliation(s)
- Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, University of London, United Kingdom
| | - Astrid Tripodi
- Emergency Center for the Control of Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam
| | - Thi Thanh Thuy Nguyen
- Emergency Center for the Control of Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam
| | | | | | - Andrew Bisson
- Emergency Center for the Control of Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam
| | - Dirk U Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, University of London, United Kingdom
| | - Scott H Newman
- Emergency Center for the Control of Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam
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26
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Cuong NV, Truc VNT, Nhung NT, Thanh TT, Chieu TTB, Hieu TQ, Men NT, Mai HH, Chi HT, Boni MF, van Doorn HR, Thwaites GE, Carrique-Mas JJ, Hoa NT. Highly Pathogenic Avian Influenza Virus A/H5N1 Infection in Vaccinated Meat Duck Flocks in the Mekong Delta of Vietnam. Transbound Emerg Dis 2016; 63:127-35. [PMID: 26748550 PMCID: PMC4819680 DOI: 10.1111/tbed.12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 11/26/2022]
Abstract
We investigated episodes of suspected highly pathogenic avian influenza (HPAI)-like illness among 12 meat duck flocks in two districts in Tien Giang province (Mekong Delta, Vietnam) in November 2013. In total, duck samples from 8 of 12 farms tested positive for HPAI virus subtype A/haemagglutinin 5 and neuraminidase 1 (H5N1) by real-time RT-PCR. Sequencing results confirmed clade of 2.3.2.1.c as the cause of the outbreaks. Most (7/8) laboratory-confirmed positive flocks had been vaccinated with inactivated HPAI H5N1 clade 2.3.4 vaccines <6 days prior to onset of clinical signs. A review of vaccination data in relation to estimated production in the area suggested that vaccination efforts were biased towards larger flocks and that vaccination coverage was low [21.2% ducks vaccinated with two shots (range by district 7.4-34.9%)]. The low-coverage data, the experimental evidence of lack of cross-protection conferred by the currently used vaccines based on clade 2.3.4 together with the short lifespan of meat duck flocks (60-70 days), suggest that vaccination is not likely to be effective as a tool for control of H5N1 infection in meat duck flocks in the area.
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Affiliation(s)
- N V Cuong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - V N T Truc
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- University of Science, Ho Chi Minh City, Vietnam
| | - N T Nhung
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - T T Thanh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - T T B Chieu
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - T Q Hieu
- Sub-Department of Animal Health, Tien Giang Province, Vietnam
| | - N T Men
- Sub-Department of Animal Health, Tien Giang Province, Vietnam
| | - H H Mai
- Sub-Department of Animal Health, Tien Giang Province, Vietnam
| | - H T Chi
- Sub-Department of Animal Health, Tien Giang Province, Vietnam
| | - M F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK
| | - H R van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK
| | - G E Thwaites
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK
| | - J J Carrique-Mas
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK
| | - N T Hoa
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK
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27
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Millman AJ, Havers F, Iuliano AD, Davis CT, Sar B, Sovann L, Chin S, Corwin AL, Vongphrachanh P, Douangngeun B, Lindblade KA, Chittaganpitch M, Kaewthong V, Kile JC, Nguyen HT, Pham DV, Donis RO, Widdowson MA. Detecting Spread of Avian Influenza A(H7N9) Virus Beyond China. Emerg Infect Dis 2016; 21:741-9. [PMID: 25897654 PMCID: PMC4412232 DOI: 10.3201/eid2105.141756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This virus is unlikely to have spread substantially among humans in Vietnam, Thailand, Cambodia, and Laos. During February 2013–March 2015, a total of 602 human cases of low pathogenic avian influenza A(H7N9) were reported; no autochthonous cases were reported outside mainland China. In contrast, since highly pathogenic avian influenza A(H5N1) reemerged during 2003 in China, 784 human cases in 16 countries and poultry outbreaks in 53 countries have been reported. Whether the absence of reported A(H7N9) outside mainland China represents lack of spread or lack of detection remains unclear. We compared epidemiologic and virologic features of A(H5N1) and A(H7N9) and used human and animal influenza surveillance data collected during April 2013–May 2014 from 4 Southeast Asia countries to assess the likelihood that A(H7N9) would have gone undetected during 2014. Surveillance in Vietnam and Cambodia detected human A(H5N1) cases; no A(H7N9) cases were detected in humans or poultry in Southeast Asia. Although we cannot rule out the possible spread of A(H7N9), substantial spread causing severe disease in humans is unlikely.
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28
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Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P. Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. Mol Biol Evol 2015; 32:3264-75. [PMID: 26341298 DOI: 10.1093/molbev/msv185] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Since its first isolation in 1996 in Guangdong, China, the highly pathogenic avian influenza virus (HPAIV) H5N1 has circulated in avian hosts for almost two decades and spread to more than 60 countries worldwide. The role of different avian hosts and the domestic-wild bird interface has been critical in shaping the complex HPAIV H5N1 disease ecology, but remains difficult to ascertain. To shed light on the large-scale H5N1 transmission patterns and disentangle the contributions of different avian hosts on the tempo and mode of HPAIV H5N1 dispersal, we apply Bayesian evolutionary inference techniques to comprehensive sets of hemagglutinin and neuraminidase gene sequences sampled between 1996 and 2011 throughout Asia and Russia. Our analyses demonstrate that the large-scale H5N1 transmission dynamics are structured according to different avian flyways, and that the incursion of the Central Asian flyway specifically was driven by Anatidae hosts coinciding with rapid rate of spread and an epidemic wavefront acceleration. This also resulted in long-distance dispersal that is likely to be explained by wild bird migration. We identify a significant degree of asymmetry in the large-scale transmission dynamics between Anatidae and Phasianidae, with the latter largely representing poultry as an evolutionary sink. A joint analysis of host dynamics and continuous spatial diffusion demonstrates that the rate of viral dispersal and host diffusivity is significantly higher for Anatidae compared with Phasianidae. These findings complement risk modeling studies and satellite tracking of wild birds in demonstrating a continental-scale structuring into areas of H5N1 persistence that are connected through migratory waterfowl.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
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29
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Abstract
The role and significance of wildlife-livestock interfaces in disease ecology has largely been neglected, despite recent interest in animals as origins of emerging diseases in humans. Scoping review methods were applied to objectively assess the relative interest by the scientific community in infectious diseases at interfaces between wildlife and livestock, to characterize animal species and regions involved, as well as to identify trends over time. An extensive literature search combining wildlife, livestock, disease, and geographical search terms yielded 78,861 publications, of which 15,998 were included in the analysis. Publications dated from 1912 to 2013 and showed a continuous increasing trend, including a shift from parasitic to viral diseases over time. In particular there was a significant increase in publications on the artiodactyls-cattle and bird-poultry interface after 2002 and 2003, respectively. These trends could be traced to key disease events that stimulated public interest and research funding. Among the top 10 diseases identified by this review, the majority were zoonoses. Prominent wildlife-livestock interfaces resulted largely from interaction between phylogenetically closely related and/or sympatric species. The bird-poultry interface was the most frequently cited wildlife-livestock interface worldwide with other interfaces reflecting regional circumstances. This review provides the most comprehensive overview of research on infectious diseases at the wildlife-livestock interface to date.
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30
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Paul MC, Figuié M, Kovitvadhi A, Valeix S, Wongnarkpet S, Poolkhet C, Kasemsuwan S, Ducrot C, Roger F, Binot A. Collective resistance to HPAI H5N1 surveillance in the Thai cockfighting community: Insights from a social anthropology study. Prev Vet Med 2015; 120:106-14. [PMID: 25800453 DOI: 10.1016/j.prevetmed.2015.02.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 02/16/2015] [Accepted: 02/20/2015] [Indexed: 11/17/2022]
Abstract
Farmers may organize themselves to collectively manage risks such as animal diseases. Our study shows some evidence of such organization among fighting cock owners in Thailand. Fighting cocks were specifically targeted by HPAI (Highly Pathogenic Avian Influenza) H5N1 surveillance and control measures in Thailand because they were thought to pose a high risk of spreading diseases. In this work, we used a social-anthropological approach to gain an inside view of the issues associated with HPAI H5N1 surveillance in the cockfighting community in Thailand. Based on a qualitative analysis of data collected through in-depth interviews and observation of cockfighters' practices, we found that fighting cock owners share a sense of belonging to the same community based on a common culture, values, interests, practices, and internal rules, including rules to manage poultry diseases. During the HPAI H5N1 outbreaks, these rules may have contributed to mitigating the potential risk associated with the intense movements of fighting cocks inside the country. Nevertheless, this community, despite the high awareness and know-how of its members regarding poultry diseases, has shown a strong reluctance to comply with HPAI surveillance programs. We suggest that this reluctance is due to important gaps between the logic and rationales underlying surveillance and those associated with cockfighting activities. Our study highlights the need for multi and trans-disciplinary research involving the social sciences to analyze interactions between stakeholders and the collective actions implemented by communities to face risks.
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Affiliation(s)
- Mathilde C Paul
- Université de Toulouse, INP, Ecole Nationale Vétérinaire de Toulouse, ENVT, INRA, UMR 1225 IHAP Interactions Hôtes - Agents Pathogènes, Toulouse F-31076, France; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UR AGIRs, UPR22, TA C-22/E, Campus International de Baillarguet, Montpellier F-34398, France; Institut National de Recherche Agronomique (INRA), UR 346 Epidémiologie Animale, F-63122 Saint-Genès-Champanelle, France.
| | - Muriel Figuié
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR MOISA, Campus de Lavalette, Montpellier F-34398, France
| | - Attawit Kovitvadhi
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand; Department of Agricultural, Forest and Food Sciences, University of Torino, via Largo P. Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Sophie Valeix
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UR AGIRs, UPR22, TA C-22/E, Campus International de Baillarguet, Montpellier F-34398, France; Institute of Development Studies, University of Sussex, Library Road, Brighton BN1 9RE, United Kingdom
| | - Sirichai Wongnarkpet
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Chaithep Poolkhet
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Suwicha Kasemsuwan
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Christian Ducrot
- Institut National de Recherche Agronomique (INRA), UR 346 Epidémiologie Animale, F-63122 Saint-Genès-Champanelle, France
| | - François Roger
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UR AGIRs, UPR22, TA C-22/E, Campus International de Baillarguet, Montpellier F-34398, France
| | - Aurélie Binot
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UR AGIRs, UPR22, TA C-22/E, Campus International de Baillarguet, Montpellier F-34398, France
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31
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Emerging and Reemerging Infectious Disease Threats. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7151803 DOI: 10.1016/b978-1-4557-4801-3.00014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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32
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Conrad PA, Meek LA, Dumit J. Operationalizing a One Health approach to global health challenges. Comp Immunol Microbiol Infect Dis 2013; 36:211-6. [PMID: 23711930 DOI: 10.1016/j.cimid.2013.03.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 11/30/2022]
Abstract
The One Health approach, which recognizes the interconnectedness of human, animal and ecosystem health, encourages collaboration between diverse disciplines to address complex health problems. The advantages and challenges posed by these interdisciplinary collaborations are described in this review. Learning networks where diverse participants can openly share processes, best practices, and case studies are discussed as a strategy for conducting transdisciplinary One Health research and tackling complex global health problems. The 11 papers in this special issue are also introduced as they illustrate how a One Health approach can be applied to better understand and control zoonotic pathogens, engage community stakeholders in One Health research and utilize wildlife species, most notably sea otters and birds, as sentinels of ecosystem health. Collaboration is rarely without complications; however, drawing on these insights may benefit the process of operationalizing the One Health approach to address today's global health challenges.
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Affiliation(s)
- Patricia A Conrad
- One Health Institute and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA.
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