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Boonyapisitsopa S, Chaiyawong S, Charoenkul K, Udom K, Chamsai E, Jairak W, Tunterak W, Bunpapong N, Amonsin A. Genetic characterization of low-pathogenic avian influenza subtypes H10N6 and H10N7 from free-grazing ducks in Thailand. Vet World 2024; 17:2166-2176. [PMID: 39507787 PMCID: PMC11536749 DOI: 10.14202/vetworld.2024.2166-2176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 08/30/2024] [Indexed: 11/08/2024] Open
Abstract
Background and Aim Free-grazing duck (FGD) raising is a unique domestic duck production system that is widely practiced in several Asian countries, including Thailand. FGD is a significant reservoir for influenza A viruses (IAVs). In this study, we genetically characterized IAV-H10N6 and IAV-H10N7 isolated from avian influenza surveillance in FGDs in Thailand. Materials and Methods We collected 640 swab samples from 29 FGD flocks located in 6 provinces of Thailand. IAVs were isolated from swab samples using egg inoculation. Hemagglutination test-positive samples were then subjected to IAV detection. Viral RNA was subjected to IAV detection using real-time reverse-transcription polymerase chain reaction (rRT-PCR) specific to matrix (M) gene. IAV subtypes were identified using the RT-PCR assay specific to all hemagglutinin and neuraminidase subtypes. Whole-genome sequencing of IAVs was performed to genetically characterize IAV-H10N6 and IAV-H10N7. Results Our results showed that 41 (6.41%) samples tested positive for IAV using rRT-PCR specific to the M gene. Among these, only two IAVs were subtypes as IAV-H10N6 and IAV-H10N7 and were subjected to whole-genome sequencing. IAV-H10N6 and IAV-H10N7 belonged to the Eurasian lineage and did not show any evidence of reassortment from the North American lineage. The viruses exhibited low-pathogenic characteristics and preferred binding to avian-type receptors. Genetic analysis revealed no mutations in PB2 and M genes, unlike human IAV-H10N3 and IAV-H10N8, which exhibited increased virulence in mammals. Conclusion IAV-H10N6 and IAV-H10N7 viruses have less potential as zoonotic viruses. However, IAV in FGDs should be monitored for novel reassortant or zoonotic viruses. This study provides information on the genetic characteristics and diversity of IAV-H10N6 and IAV-H10N7 that are circulated in FGDs in Thailand.
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Affiliation(s)
- Supanat Boonyapisitsopa
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Supassama Chaiyawong
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kamonpan Charoenkul
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kitikhun Udom
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ekkapat Chamsai
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Waleemas Jairak
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wikanda Tunterak
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Napawan Bunpapong
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alongkorn Amonsin
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Emerging and Re-emerging Infectious Diseases in Animals, Center of Excellence, and One Health Research Cluster, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Paungpin W, Thongdee M, Ketchim N, Chaiwattanarungruengpaisan S, Saechin A, Sariya L, Kaewchot S, Puthavathana P, Wiriyarat W. Evidence of Influenza A Virus Infection in Cynomolgus Macaques, Thailand. Vet Sci 2022; 9:vetsci9030132. [PMID: 35324860 PMCID: PMC8950150 DOI: 10.3390/vetsci9030132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Little is known about the ecology of influenza A virus (IAV) in nonhuman primates (NHPs). We conducted active surveillance of IAV among 672 cynomolgus macaques (Macaca fascicularis) living in 27 free-ranging colonies in Thailand between March and November 2019. A hemagglutination inhibition (HI) assay was employed as the screening test against 16 subtypes of avian influenza virus (AIV) and two strains of the H1 subtype of human influenza virus. The serum samples with HI titers ≥20 were further confirmed by microneutralization (MN) assay. Real-time RT-PCR assay was performed to detect the conserved region of the influenza matrix (M) gene. The seropositive rate for subtypes of IAV, including AIV H1 (1.6%, 11/672), AIV H2 (15.2%, 102/672), AIV H3 (0.3%, 2/672), AIV H9 (3.4%, 23/672), and human H1 (NP-045) (0.9%, 6/672), was demonstrated. We also found antibody against more than one subtype of IAV in 15 out of 128 positive tested sera (11.7%). Moreover, influenza genome could be detected in 1 out of 245 pool swab samples (0.41%). Evidence of IAV infection presented here emphasizes the role of NHPs in the ecology of the virus. Our findings highlight the need to further conduct a continuous active surveillance program in NHP populations.
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Affiliation(s)
- Weena Paungpin
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Metawee Thongdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Natthaphat Ketchim
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Somjit Chaiwattanarungruengpaisan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Aeknarin Saechin
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Ladawan Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
| | - Supakarn Kaewchot
- Department of National Parks, Wildlife and Plant Conservation, Bangkok 10900, Thailand;
| | - Pilaipan Puthavathana
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Witthawat Wiriyarat
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (W.P.); (M.T.); (N.K.); (S.C.); (A.S.); (L.S.)
- Correspondence:
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3
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Jing J, Wang L, Wang G, Dai Z, Ren W, Yi C, Wei J, Xu C. A human infection case with avian-origin H10N3 influenza virus. Quant Imaging Med Surg 2021; 11:4508-4510. [PMID: 34604005 DOI: 10.21037/qims-21-592] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/18/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Jisheng Jing
- Department of Infectious Diseases, Jurong People's Hospital, Jiangsu University, Zhenjiang, China
| | - Longyu Wang
- Public Health and Therapy Center of Nanjing, Nanjing, China.,Nanjing Infectious Diseases Clinical Medical Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guocheng Wang
- Department of Infectious Diseases, Jurong People's Hospital, Jiangsu University, Zhenjiang, China
| | - Zaodong Dai
- Department of Infectious Diseases, Jurong People's Hospital, Jiangsu University, Zhenjiang, China
| | - Weigang Ren
- Public Health and Therapy Center of Nanjing, Nanjing, China.,Nanjing Infectious Diseases Clinical Medical Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Changhua Yi
- Public Health and Therapy Center of Nanjing, Nanjing, China.,Nanjing Infectious Diseases Clinical Medical Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jie Wei
- Public Health and Therapy Center of Nanjing, Nanjing, China.,Nanjing Infectious Diseases Clinical Medical Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chuanjun Xu
- Department of Radiology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
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4
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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: 1.7] [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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5
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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: 0.7] [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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6
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Retkute R, Jewell CP, Van Boeckel TP, Zhang G, Xiao X, Thanapongtharm W, Keeling M, Gilbert M, Tildesley MJ. Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control. Prev Vet Med 2018; 159:171-181. [PMID: 30314780 PMCID: PMC6193140 DOI: 10.1016/j.prevetmed.2018.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/15/2018] [Accepted: 09/15/2018] [Indexed: 11/29/2022]
Abstract
The Highly Pathogenic Avian Influenza (HPAI) subtype H5N1 virus persists in many countries and has been circulating in poultry, wild birds. In addition, the virus has emerged in other species and frequent zoonotic spillover events indicate that there remains a significant risk to human health. It is crucial to understand the dynamics of the disease in the poultry industry to develop a more comprehensive knowledge of the risks of transmission and to establish a better distribution of resources when implementing control. In this paper, we develop a set of mathematical models that simulate the spread of HPAI H5N1 in the poultry industry in Thailand, utilising data from the 2004 epidemic. The model that incorporates the intensity of duck farming when assessing transmision risk provides the best fit to the spatiotemporal characteristics of the observed outbreak, implying that intensive duck farming drives transmission of HPAI in Thailand. We also extend our models using a sequential model fitting approach to explore the ability of the models to be used in “real time” during novel disease outbreaks. We conclude that, whilst predictions of epidemic size are estimated poorly in the early stages of disease outbreaks, the model can infer the preferred control policy that should be deployed to minimise the impact of the disease.
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Affiliation(s)
- Renata Retkute
- School of Life Sciences and Institute of Mathematics, University of Warwick, UK.
| | - Chris P Jewell
- Faculty of Health and Medicine, Furness College, Lancaster University, UK
| | | | - Geli Zhang
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiangming Xiao
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | | | - Matt Keeling
- School of Life Sciences and Institute of Mathematics, University of Warwick, UK
| | - Marius Gilbert
- Biological Control and Spatial Ecology Universite Libre de Bruxelles, Belgium
| | - Michael J Tildesley
- School of Life Sciences and Institute of Mathematics, University of Warwick, UK
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7
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Zhang M, Zhang X, Xu K, Teng Q, Liu Q, Li X, Yang J, Xu J, Chen H, Zhang X, Li Z. Characterization of the Pathogenesis of H10N3, H10N7, and H10N8 Subtype Avian Influenza Viruses Circulating in Ducks. Sci Rep 2016; 6:34489. [PMID: 27678170 PMCID: PMC5039634 DOI: 10.1038/srep34489] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
Three H10 subtype avian influenza viruses were isolated from domestic ducks in China, designated as SH602/H10N8, FJ1761/H10N3 and SX3180/H10N7, with an intravenous pathogenicity index (IVPI) of 0.39, 1.60, and 1.27, respectively. These H10 viruses showed a complex pathology pattern in different species, although full genome characterizations of the viruses could not identify any molecular determinant underlying the observed phenotypes. Our findings describe the pathobiology of the three H10 subtype AIVs in chickens, ducks, and mice. FJ1761/H10N3 evolved E627K and Q591K substitutions in the gene encoding the PB2 protein in infected mice with severe lung damage, suggesting that H10 subtype avian influenza viruses are a potential threat to mammals.
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Affiliation(s)
- Miaomiao Zhang
- Shanghai Public Health Clinical Center, Fudan University Shanghai 201508 P. R. China.,Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China
| | - Xingxing Zhang
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China
| | - Kaidi Xu
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
| | - Qinfang Liu
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
| | - Xuesong Li
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
| | - Jianmei Yang
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University Shanghai 201508 P. R. China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University Shanghai 201508 P. R. China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences, Shanghai 200241 P. R. China.,Animal Influenza Virus Evolution and Pathogenesis Innovation Team of The Agricultural Science and Technology Innovation Team, Shanghai 200241 P. R. China
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Predicting Avian Influenza Co-Infection with H5N1 and H9N2 in Northern Egypt. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13090886. [PMID: 27608035 PMCID: PMC5036719 DOI: 10.3390/ijerph13090886] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/22/2016] [Accepted: 09/01/2016] [Indexed: 11/26/2022]
Abstract
Human outbreaks with avian influenza have been, so far, constrained by poor viral adaptation to non-avian hosts. This could be overcome via co-infection, whereby two strains share genetic material, allowing new hybrid strains to emerge. Identifying areas where co-infection is most likely can help target spaces for increased surveillance. Ecological niche modeling using remotely-sensed data can be used for this purpose. H5N1 and H9N2 influenza subtypes are endemic in Egyptian poultry. From 2006 to 2015, over 20,000 poultry and wild birds were tested at farms and live bird markets. Using ecological niche modeling we identified environmental, behavioral, and population characteristics of H5N1 and H9N2 niches within Egypt. Niches differed markedly by subtype. The subtype niches were combined to model co-infection potential with known occurrences used for validation. The distance to live bird markets was a strong predictor of co-infection. Using only single-subtype influenza outbreaks and publicly available ecological data, we identified areas of co-infection potential with high accuracy (area under the receiver operating characteristic (ROC) curve (AUC) 0.991).
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Genetic characterization of influenza A (H7N6) virus isolated from a live-bird market in Thailand. Arch Virol 2016; 161:1315-22. [PMID: 26795160 DOI: 10.1007/s00705-016-2759-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
A one-year influenza A virus (IAV) monitoring program was conducted in a live-bird market (LBM) in Thailand. Using one-step real-time RT-PCR (rRT-PCR), 2.39 % of live birds were found to be IAV positive. Twenty viruses could be identified as IAV subtype H7N6. Eight IAV-H7N6 viruses were subjected to whole-genome sequencing and genetic characterization. Phylogenetic analysis showed that the HA gene of Thai H7N6 is grouped with those of the H7 Eurasian viruses. The NA gene is closely related to those of the N6 Eurasian viruses. This is the first report of IAV subtype H7N6 in Thailand.
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Sequence and phylogenetic analysis of H2N7 avian influenza viruses isolated from domestic ducks in Zhejiang Province, Eastern China, 2013. Virus Genes 2014; 48:391-6. [PMID: 24442671 DOI: 10.1007/s11262-014-1033-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/06/2014] [Indexed: 10/25/2022]
Abstract
Two H2N7 avian influenza viruses (AIVs) were isolated from domestic ducks in live poultry markets in Zhejiang Province, Eastern China, 2013. All viruses were characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that the viruses clustered in the Eurasian lineage of AIVs and originated from genes reassortment among different viruses co-circulating in domestic ducks in Eastern China. The hemagglutinin cleavage site of all viruses indicated that the two strains were low-pathogenic avian influenza viruses. Considering the important role of the domestic ducks in the dissemination and reassortment of AIVs, continued surveillance of circulating H2 subtype AIVs in domestic ducks in live poultry markets is needed.
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