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Chadha A, Dara R, Pearl DL, Sharif S, Poljak Z. Predictive analysis for pathogenicity classification of H5Nx avian influenza strains using machine learning techniques. Prev Vet Med 2023; 216:105924. [PMID: 37224663 DOI: 10.1016/j.prevetmed.2023.105924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 03/17/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
Over the past decades, avian influenza (AI) outbreaks have been reported across different parts of the globe, resulting in large-scale economic and livestock loss and, in some cases raising concerns about their zoonotic potential. The virulence and pathogenicity of H5Nx (e.g., H5N1, H5N2) AI strains for poultry could be inferred through various approaches, and it has been frequently performed by detecting certain pathogenicity markers in their haemagglutinin (HA) gene. The utilization of predictive modeling methods represents a possible approach to exploring this genotypic-phenotypic relationship for assisting experts in determining the pathogenicity of circulating AI viruses. Therefore, the main objective of this study was to evaluate the predictive performance of different machine learning (ML) techniques for in-silico prediction of pathogenicity of H5Nx viruses in poultry, using complete genetic sequences of the HA gene. We annotated 2137 H5Nx HA gene sequences based on the presence of the polybasic HA cleavage site (HACS) with 46.33% and 53.67% of sequences previously identified as highly pathogenic (HP) and low pathogenic (LP), respectively. We compared the performance of different ML classifiers (e.g., logistic regression (LR) with the lasso and ridge regularization, random forest (RF), K-nearest neighbor (KNN), Naïve Bayes (NB), support vector machine (SVM), and convolutional neural network (CNN)) for pathogenicity classification of raw H5Nx nucleotide and protein sequences using a 10-fold cross-validation technique. We found that different ML techniques can be successfully used for the pathogenicity classification of H5 sequences with ∼99% classification accuracy. Our results indicate that for pathogenicity classification of (1) aligned deoxyribonucleic acid (DNA) and protein sequences, with NB classifier had the lowest accuracies of 98.41% (+/-0.89) and 98.31% (+/-1.06), respectively; (2) aligned DNA and protein sequences, with LR (L1/L2), KNN, SVM (radial basis function (RBF)) and CNN classifiers had the highest accuracies of 99.20% (+/-0.54) and 99.20% (+/-0.38), respectively; (3) unaligned DNA and protein sequences, with CNN's achieved accuracies of 98.54% (+/-0.68) and 99.20% (+/-0.50), respectively. ML methods show potential for regular classification of H5Nx virus pathogenicity for poultry species, particularly when sequences containing regular markers were frequently present in the training dataset.
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Affiliation(s)
- Akshay Chadha
- School of Computer Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Rozita Dara
- School of Computer Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - David L Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Shayan Sharif
- Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Using geospatial methods to measure the risk of environmental persistence of avian influenza virus in South Carolina. Spat Spatiotemporal Epidemiol 2020; 34:100342. [PMID: 32807394 DOI: 10.1016/j.sste.2020.100342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/07/2020] [Accepted: 03/20/2020] [Indexed: 11/24/2022]
Abstract
Avian influenza (AIV) is a highly contagious virus that can infect both wild birds and domestic poultry. This study aimed to define areas within the state of South Carolina (SC) at heightened risk for environmental persistence of AIV using geospatial methods. Environmental factors known to influence AIV survival were identified through the published literature and using a multi-criteria decision analysis with GIS was performed. Risk was defined using five categories following the World Organization for Animal Health Risk Assessment Guidelines. Less than 1% of 1km grid cells in SC showed a high risk of AIV persistence. Approximately 2% - 17% of counties with high or very high environmental risk also had medium to very high numbers of commercial poultry operations. Results can be used to improve surveillance activities and to inform biosecurity practices and emergency preparedness efforts.
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Nimmanapalli R, Gupta V. Vaccines the tugboat for prevention-based animal production. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149732 DOI: 10.1016/b978-0-12-816352-8.00020-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The world population is growing at a faster rate day-by-day and the demands for animal products are also increasing to meet the food security worldwide. For sustained production of animals products, healthy livestock and poultry farming are the major concerns as animals are susceptible to various infectious agents viz. bacteria, virus, and parasites leading to huge economical losses in the form of livestock’s morbidity and mortality. Besides, zoonotic nature of some infectious pathogens of animals is also raising concern for human safety. Vaccination of animals against various diseases present in different geographical regions is a best known strategy for prevention of different disease outbreaks both in organized and unorganized livestock and poultry sectors. Vaccines had played a major role in eradication of different dreaded diseases of livestock sectors globally. In this article we have discussed different vaccine types, various vaccine strategies used for the development of more efficacious and safe vaccines and commercially available vaccines for livestock and poultry.
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RETRACTED ARTICLE: Insights into the role of turkeys as potential intermediate host for influenza viruses. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933916000520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Genetic Evidence Supports Sporadic and Independent Introductions of Subtype H5 Low-Pathogenic Avian Influenza A Viruses from Wild Birds to Domestic Poultry in North America. J Virol 2018; 92:JVI.00913-18. [PMID: 30045988 DOI: 10.1128/jvi.00913-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/04/2018] [Indexed: 11/20/2022] Open
Abstract
Wild-bird origin influenza A viruses (IAVs or avian influenza) have led to sporadic outbreaks among domestic poultry in the United States and Canada, resulting in economic losses through the implementation of costly containment practices and destruction of birds. We used evolutionary analyses of virus sequence data to determine that 78 H5 low-pathogenic avian influenza viruses (LPAIVs) isolated from domestic poultry in the United States and Canada during 2001 to 2017 resulted from 18 independent virus introductions from wild birds. Within the wild-bird reservoir, the hemagglutinin gene segments of H5 LPAIVs exist primarily as two cocirculating genetic sublineages, and our findings suggest that the H5 gene segments flow within each migratory bird flyway and among adjacent flyways, with limited exchange between the nonadjacent Atlantic and Pacific Flyways. Phylogeographic analyses provided evidence that IAVs from dabbling ducks and swans/geese contributed to the emergence of viruses among domestic poultry. H5 LPAIVs isolated from commercial farm poultry (i.e., turkey) that were descended from a single introduction typically remained a single genotype, whereas those from live-bird markets sometimes led to multiple genotypes, reflecting the potential for reassortment with other IAVs circulating within live-bird markets. H5 LPAIVs introduced from wild birds to domestic poultry represent economic threats to the U.S. poultry industry, and our data suggest that such introductions have been sporadic, controlled effectively through production monitoring and a stamping-out policy, and are, therefore, unlikely to result in sustained detections in commercial poultry operations.IMPORTANCE Integration of viral genome sequencing into influenza surveillance for wild birds and domestic poultry can elucidate evolutionary pathways of economically costly poultry pathogens. Evolutionary analyses of H5 LPAIVs detected in domestic poultry in the United States and Canada during 2001 to 2017 suggest that these viruses originated from repeated introductions of IAVs from wild birds, followed by various degrees of reassortment. Reassortment was observed where biosecurity was low and where opportunities for more than one virus to circulate existed (e.g., congregations of birds from different premises, such as live-bird markets). None of the H5 lineages identified were maintained for the long term in domestic poultry, suggesting that management strategies have been effective in minimizing the impacts of virus introductions on U.S. poultry production.
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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: 27] [Impact Index Per Article: 4.5] [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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Rauff D, Strydom C, Abolnik C. Evolutionary consequences of a decade of vaccination against subtype H6N2 influenza. Virology 2016; 498:226-239. [DOI: 10.1016/j.virol.2016.08.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 01/12/2023]
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In ovo and in vitro susceptibility of American alligators (Alligator mississippiensis) to avian influenza virus infection. J Wildl Dis 2015; 51:187-98. [PMID: 25380354 DOI: 10.7589/2013-12-321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Avian influenza has emerged as one of the most ubiquitous viruses within our biosphere. Wild aquatic birds are believed to be the primary reservoir of all influenza viruses; however, the spillover of H5N1 highly pathogenic avian influenza (HPAI) and the recent swine-origin pandemic H1N1 viruses have sparked increased interest in identifying and understanding which and how many species can be infected. Moreover, novel influenza virus sequences were recently isolated from New World bats. Crocodilians have a slow rate of molecular evolution and are the sister group to birds; thus they are a logical reptilian group to explore susceptibility to influenza virus infection and they provide a link between birds and mammals. A primary American alligator (Alligator mississippiensis) cell line, and embryos, were infected with four, low pathogenic avian influenza (LPAI) strains to assess susceptibility to infection. Embryonated alligator eggs supported virus replication, as evidenced by the influenza virus M gene and infectious virus detected in allantoic fluid and by virus antigen staining in embryo tissues. Primary alligator cells were also inoculated with the LPAI viruses and showed susceptibility based upon antigen staining; however, the requirement for trypsin to support replication in cell culture limited replication. To assess influenza virus replication in culture, primary alligator cells were inoculated with H1N1 human influenza or H5N1 HPAI viruses that replicate independent of trypsin. Both viruses replicated efficiently in culture, even at the 30 C temperature preferred by the alligator cells. This research demonstrates the ability of wild-type influenza viruses to infect and replicate within two crocodilian substrates and suggests the need for further research to assess crocodilians as a species potentially susceptible to influenza virus infection.
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Abdelwhab ESM, Veits J, Mettenleiter TC. Genetic changes that accompanied shifts of low pathogenic avian influenza viruses toward higher pathogenicity in poultry. Virulence 2013; 4:441-52. [PMID: 23863606 PMCID: PMC5359749 DOI: 10.4161/viru.25710] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 11/19/2022] Open
Abstract
Avian influenza viruses (AIV) of H5 and H7 subtypes exhibit two different pathotypes in poultry: infection with low pathogenic (LP) strains results in minimal, if any, health disturbances, whereas highly pathogenic (HP) strains cause severe morbidity and mortality. LPAIV of H5 and H7 subtypes can spontaneously mutate into HPAIV. Ten outbreaks caused by HPAIV are known to have been preceded by circulation of a predecessor LPAIV in poultry. Three of them were caused by H5N2 subtype and seven involved H7 subtype in combination with N1, N3, or N7. Here, we review those outbreaks and summarize the genetic changes which resulted in the transformation of LPAIV to HPAIV under natural conditions. Mutations that were found directly in those outbreaks are more likely to be linked to virulence, pathogenesis, and early adaptation of AIV.
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Affiliation(s)
- El-Sayed M Abdelwhab
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
| | - Jutta Veits
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
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Vaccination and acute phase mediator production in chickens challenged with low pathogenic avian influenza virus; novel markers for vaccine efficacy? Vaccine 2012; 30:3097-105. [DOI: 10.1016/j.vaccine.2012.02.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/07/2012] [Accepted: 02/20/2012] [Indexed: 12/11/2022]
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González-Reiche AS, Morales-Betoulle ME, Alvarez D, Betoulle JL, Müller ML, Sosa SM, Perez DR. Influenza a viruses from wild birds in Guatemala belong to the North American lineage. PLoS One 2012; 7:e32873. [PMID: 22427902 PMCID: PMC3302778 DOI: 10.1371/journal.pone.0032873] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 02/01/2012] [Indexed: 12/18/2022] Open
Abstract
The role wild bird species play in the transmission and ecology of avian influenza virus (AIV) is well established; however, there are significant gaps in our understanding of the worldwide distribution of these viruses, specifically about the prevalence and/or significance of AIV in Central and South America. As part of an assessment of the ecology of AIV in Guatemala, we conducted active surveillance in wild birds on the Pacific and Atlantic coasts. Cloacal and tracheal swab samples taken from resident and migratory wild birds were collected from February 2007 to January 2010.1913 samples were collected and virus was detected by real time RT-PCR (rRT-PCR) in 28 swab samples from ducks (Anas discors). Virus isolation was attempted for these positive samples, and 15 isolates were obtained from the migratory duck species Blue-winged teal. The subtypes identified included H7N9, H11N2, H3N8, H5N3, H8N4, and H5N4. Phylogenetic analysis of the viral sequences revealed that AIV isolates are highly similar to viruses from the North American lineage suggesting that bird migration dictates the ecology of these viruses in the Guatemalan bird population.
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Affiliation(s)
- Ana S. González-Reiche
- Department of Veterinary Medicine, University of Maryland College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, United States of America
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
- * E-mail: (ASG); (DRP)
| | - María E. Morales-Betoulle
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
| | - Danilo Alvarez
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
| | - Jean-Luc Betoulle
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
- Fundación Para el Ecodesarrollo y la Conservación (FUNDAECO), Guatemala City, Guatemala
| | - Maria L. Müller
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
| | - Silvia M. Sosa
- Laboratorio de Ecología de Arbovirus y Virus Zoonóticos, Centro de Estudios en Salud, Universidad del Valle de Guatemala (CES-UVG), Guatemala City, Guatemala
| | - Daniel R. Perez
- Department of Veterinary Medicine, University of Maryland College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, United States of America
- * E-mail: (ASG); (DRP)
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Yee KS, Novick CA, Halvorson DA, Dao N, Carpenter TE, Cardona CJ. Prevalence of low pathogenicity avian influenza virus during 2005 in two U.S. live bird market systems. Avian Dis 2011; 55:236-42. [PMID: 21793439 DOI: 10.1637/9427-061610-reg.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Oropharyngeal and cloacal swabs were collected from poultry sold in two live bird market (LBM) systems to estimate the prevalence of low pathogenicity avian influenza virus (LPAIV) shedding during the summer and fall of 2005. Random sampling was conducted in three LBMs in Minnesota where 50 birds were sampled twice weekly for 4 wk, and in three LBMs in a California marketing system. A stratified systematic sampling method was used to collect samples from Southern California LBMs, where LPAIV was detected during routine surveillance. No LPAIV was detected in the LBM system in Minnesota where realtime reverse transcription-PCR (RT-PCR) was conducted on oropharyngeal samples. RT-PCR was performed on swabs taken from 290 of 14,000, 65 of 252, and 60 of 211 birds at the three Southern California LBMs. The number of samples collected was based on the number of birds, age of the birds, and number of species present in the LBM. Virus isolation, subtyping, and sequencing of the hemagglutinin, neuraminidase, and other internal protein genes was performed on AIV-positive samples. The estimated prevalence of LPAIV in California was 0.345% in an LBM/supply farm with multiple ages of Japanese quail, 3% in an LBM with multiple ages and strains of chickens present, and 49.8% in an LBM with multiple species, multiple strains, and multiple ages. The positive virus samples were all LPAIV H6N2 and closely related to viruses isolated from Southern California in 2001 and 2004. Little or no comingling of poultry may contribute to little or no LPAIV detection in the LBMs.
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Affiliation(s)
- Karen S Yee
- Center for Animal Disease Modeling and Surveillance, Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Li J, zu Dohna H, Cardona CJ, Miller J, Carpenter TE. Emergence and genetic variation of neuraminidase stalk deletions in avian influenza viruses. PLoS One 2011; 6:e14722. [PMID: 21373190 PMCID: PMC3044137 DOI: 10.1371/journal.pone.0014722] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 01/24/2011] [Indexed: 11/18/2022] Open
Abstract
When avian influenza viruses (AIVs) are transmitted from their reservoir hosts (wild waterfowl and shorebirds) to domestic bird species, they undergo genetic changes that have been linked to higher virulence and broader host range. Common genetic AIV modifications in viral proteins of poultry isolates are deletions in the stalk region of the neuraminidase (NA) and additions of glycosylation sites on the hemagglutinin (HA). Even though these NA deletion mutations occur in several AIV subtypes, they have not been analyzed comprehensively. In this study, 4,920 NA nucleotide sequences, 5,596 HA nucleotide and 4,702 HA amino acid sequences were analyzed to elucidate the widespread emergence of NA stalk deletions in gallinaceous hosts, the genetic polymorphism of the deletion patterns and association between the stalk deletions in NA and amino acid variants in HA. Forty-seven different NA stalk deletion patterns were identified in six NA subtypes, N1–N3 and N5–N7. An analysis that controlled for phylogenetic dependence due to shared ancestry showed that NA stalk deletions are statistically correlated with gallinaceous hosts and certain amino acid features on the HA protein. Those HA features included five glycosylation sites, one insertion and one deletion. The correlations between NA stalk deletions and HA features are HA-NA-subtype-specific. Our results demonstrate that stalk deletions in the NA proteins of AIV are relatively common. Understanding the NA stalk deletion and related HA features may be important for vaccine and drug development and could be useful in establishing effective early detection and warning systems for the poultry industry.
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Affiliation(s)
- Jinling Li
- Center for Animal Disease Modeling and Surveillance, University of California Davis, Davis, California, United States of America
| | - Heinrich zu Dohna
- Center for Animal Disease Modeling and Surveillance, University of California Davis, Davis, California, United States of America
| | - Carol J. Cardona
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Joy Miller
- National Center for Medical Intelligence, Fort Detrick, Maryland, United States of America
| | - Tim E. Carpenter
- Center for Animal Disease Modeling and Surveillance, University of California Davis, Davis, California, United States of America
- * E-mail:
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Passage of low-pathogenic avian influenza (LPAI) viruses mediates rapid genetic adaptation of a wild-bird isolate in poultry. Arch Virol 2011; 156:565-76. [DOI: 10.1007/s00705-010-0891-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 12/10/2010] [Indexed: 10/18/2022]
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Ferro PJ, Budke CM, Peterson MJ, Cox D, Roltsch E, Merendino T, Nelson M, Lupiani B. Multiyear surveillance for avian influenza virus in waterfowl from wintering grounds, Texas coast, USA. Emerg Infect Dis 2010; 16:1224-30. [PMID: 20678315 PMCID: PMC3298295 DOI: 10.3201/eid1608.091864] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
This surveillance can help in assessments of the prevalence of wild animal-to-human transmission. We studied the prevalence of influenza A virus in wintering waterfowl from the Central Flyway on the Gulf Coast of Texas. Of 5,363 hunter-harvested migratory and resident waterfowl and wetland-associated game birds sampled during 3 consecutive hunting seasons (September–January 2006–07, 2007–08, and 2008–09), real-time reverse transcription–PCR detected influenza A matrix sequences in 8.5% of samples, H5 in 0.7%, and H7 in 0.6%. Virus isolation yielded 134 influenza A viruses, including N1–N9, H1–H7, H10, and H11 subtypes. Low-pathogenicity H7 subtype was isolated during January, September, and November 2007 and January 2008; low-pathogenicity H5 subtype was isolated during November and December 2007.
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Pillai SPS, Pantin-Jackwood M, Yassine HM, Saif YM, Lee CW. The high susceptibility of turkeys to influenza viruses of different origins implies their importance as potential intermediate hosts. Avian Dis 2010; 54:522-6. [PMID: 20521688 DOI: 10.1637/8770-033109-review.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Several previous reports and our studies show that waterfowl-origin influenza viruses can be more easily transmitted to domestic turkeys than chickens. Similarly, studies indicate turkeys to be better hosts for low pathogenic avian influenza viruses isolated from commercial poultry operations and live bird markets in comparison to chickens. Low 50% infectious-dose titers of wild bird as well as poultry-adapted viruses for turkeys further suggest that turkeys can be easily infected following a low-dose exposure. Also, interspecies transmission of swine influenza viruses to turkeys occurs frequently. These findings suggest the role of turkeys as suitable intermediate hosts that can be easily infected with influenza viruses of different origins and that turkeys can act as source of infection for other land-based poultry or even mammals.
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Affiliation(s)
- S P S Pillai
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Wooster 44691, USA
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Dlugolenski D, Hauck R, Hogan RJ, Michel F, Mundt E. Production of H5-specific monoclonal antibodies and the development of a competitive enzyme-linked immunosorbent assay for detection of H5 antibodies in multiple species. Avian Dis 2010; 54:644-9. [PMID: 20521708 DOI: 10.1637/8683-030909-resnote.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The hemagglutinin gene of an avian influenza virus (AIV) A/duck/NC/674964/07 (H5N2) was cloned and expressed in a baculovirus system (H5-Bac). In parallel, a recombinant hemagglutinin of A/Vietnam/1203/04 (H5N1) was expressed in mammalian cells, purified, and used for generation of H5-specific monoclonal antibodies (MAb). The purified H5-Bac was used to develop a competitive enzyme-linked immunosorbent assay (cELISA) to detect H5 antibodies in a species-independent approach using one of the established H5-specific MAbs as the competitor antibody. The cELISA performed with influenza antibody-free sera or with sera of animals infected with other than H5-encoding AIV showed no significant inhibition of H5-MAb binding, indicating high test specificity. In contrast, sera of poultry (chickens, turkeys, ducks) experimentally infected with H5-encoding AIV were able to significantly inhibit the binding of the MAb in a species-independent approach. Comparison of the results of the cELISA with results obtained by a hemagglutination inhibition assay showed a gradient of the sensitivity (turkeys > ducks > chicken). The described results show that H5-specific antibodies in sera can be detected in a species-independent approach by using a recombinant protein.
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Affiliation(s)
- Daniel Dlugolenski
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA
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Pillai SPS, Pantin-Jackwood M, Suarez DL, Saif YM, Lee CW. Pathobiological characterization of low-pathogenicity H5 avian influenza viruses of diverse origins in chickens, ducks and turkeys. Arch Virol 2010; 155:1439-51. [PMID: 20577770 DOI: 10.1007/s00705-010-0727-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 06/12/2010] [Indexed: 11/25/2022]
Abstract
We undertook one of the most comprehensive studies on the replication and intraspecies transmission characteristics of low-pathogenicity avian influenza viruses in ducks, chickens and turkeys. Our results indicated that most of these isolates could replicate and be transmitted in poultry without inducing clinical disease. However, differences in transmission to contact control birds were noted, emphasizing the importance of having contact control cage mates in biological characterization experiments. Ducks supported the replication of viruses of wild aquatic bird origin in their respiratory and digestive tracts equally well. The viruses from wild aquatic birds were not effectively transmitted among chickens. In contrast, the wild-bird isolates and viruses of domestic bird origin from live-bird markets and commercial poultry operations replicated and were transmitted more efficiently in turkeys than in chickens or ducks. We also found a lower minimal infectious dose requirement for infection of turkeys compared to chickens and ducks. Our data support an important role of turkeys as being more susceptible hosts for avian influenza viruses than domestic ducks and chickens. These results highlight the role of turkeys as intermediate or bridging hosts in the transmission of influenza viruses from wild birds to land-based domestic poultry or among different land-based bird species.
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Affiliation(s)
- S P S Pillai
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA
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Pfeiffer J, Suarez DL, Sarmento L, To TL, Nguyen T, Pantin-Jackwood MJ. Efficacy of Commercial Vaccines in Protecting Chickens and Ducks Against H5N1 Highly Pathogenic Avian Influenza Viruses from Vietnam. Avian Dis 2010; 54:262-71. [DOI: 10.1637/8715-031909-reg.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhou H, Yu Z, Hu Y, Tu J, Zou W, Peng Y, Zhu J, Li Y, Zhang A, Yu Z, Ye Z, Chen H, Jin M. The special neuraminidase stalk-motif responsible for increased virulence and pathogenesis of H5N1 influenza A virus. PLoS One 2009; 4:e6277. [PMID: 19609439 PMCID: PMC2707603 DOI: 10.1371/journal.pone.0006277] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 06/10/2009] [Indexed: 12/03/2022] Open
Abstract
The variation of highly pathogenic avian influenza H5N1 virus results in gradually increased virulence in poultry, and human cases continue to accumulate. The neuraminidase (NA) stalk region of influenza virus varies considerably and may associate with its virulence. The NA stalk region of all N1 subtype influenza A viruses can be divided into six different stalk-motifs, H5N1/2004-like (NA-wt), WSN-like, H5N1/97-like, PR/8-like, H7N1/99-like and H5N1/96-like. The NA-wt is a special NA stalk-motif which was first observed in H5N1 influenza virus in 2000, with a 20-amino acid deletion in the 49th to 68th positions of the stalk region. Here we show that there is a gradual increase of the special NA stalk-motif in H5N1 isolates from 2000 to 2007, and notably, the special stalk-motif is observed in all 173 H5N1 human isolates from 2004 to 2007. The recombinant H5N1 virus with the special stalk-motif possesses the highest virulence and pathogenicity in chicken and mice, while the recombinant viruses with the other stalk-motifs display attenuated phenotype. This indicates that the special stalk-motif has contributed to the high virulence and pathogenicity of H5N1 isolates since 2000. The gradually increasing emergence of the special NA stalk-motif in H5N1 isolates, especially in human isolates, deserves attention by all.
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Affiliation(s)
- Hongbo Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Zhengjun Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Yong Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Jiagang Tu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Wei Zou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Yaping Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Jiping Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Yongtao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccine Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
- * E-mail: (HC); (MJ)
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, the People's Republic of China
- * E-mail: (HC); (MJ)
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Mundt E, Gay L, Jones L, Saavedra G, Tompkins SM, Tripp RA. Replication and pathogenesis associated with H5N1, H5N2, and H5N3 low-pathogenic avian influenza virus infection in chickens and ducks. Arch Virol 2009; 154:1241-8. [PMID: 19575275 DOI: 10.1007/s00705-009-0437-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 06/18/2009] [Indexed: 11/30/2022]
Abstract
A comparative study examining replication and disease pathogenesis associated with low-pathogenic H5N1, H5N2, or H5N3 avian influenza virus (AIV) infection of chickens and ducks was performed. The replication and pathogenesis of highly pathogenic AIV (HPAIV) has received substantial attention; however, the behavior of low-pathogenic AIVs, which serve as precursors to HPAIVs, has received less attention. Thus, chickens or ducks were inoculated with an isolate from a wild bird [A/Mute Swan/MI/451072/06 (H5N1)] or isolates from chickens [A/Ck/PA/13609/93 (H5N2), A/Ck/TX/167280-4/02 (H5N3)], and virus replication, induction of a serological response, and disease pathogenesis were investigated, and the hemagglutinin and neuraminidase (NA) gene sequences of the isolates were determined. Virus isolated from tracheal and cloacal swabs showed that H5N1 replicated better in ducks, whereas H5N2 and H5N3 replicated better in chickens. Comparison of the NA gene sequences showed that chicken-adapted H5N2 and H5N3 isolates both have a deletion of 20 amino acids in the NA stalk region, which was absent in the H5N1 isolate. Histopathological examination of numerous organs showed that H5N2 and H5N3 isolates caused lesions in chickens in a variety of organs, but to a greater extent in the respiratory and intestinal tracts, whereas H5N1 lesions in ducks were observed mainly in the respiratory tract. This study suggests that the H5N1, H5N2, and H5N3 infections occurred at distinct sites in chicken and ducks, and that comparative studies in different model species are needed to better understand the factors influencing the evolution of these viruses.
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Affiliation(s)
- Egbert Mundt
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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Brahmakshatriya V, Lupiani B, Brinlee JL, Cepeda M, Pillai SD, Reddy SM. Preliminary study for evaluation of avian influenza virus inactivation in contaminated poultry products using electron beam irradiation. Avian Pathol 2009; 38:245-50. [DOI: 10.1080/03079450902912150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Molecular characterization of low pathogenic avian influenza viruses, isolated from food products imported into Singapore. Vet Microbiol 2009; 138:304-17. [PMID: 19464126 PMCID: PMC7125998 DOI: 10.1016/j.vetmic.2009.04.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 04/04/2009] [Accepted: 04/14/2009] [Indexed: 12/09/2022]
Abstract
We have completed the genetic characterization of all eight gene segments for four low pathogenic avian influenza (LPAI) viruses. The objective of this study was to detect the presence of novel signatures that may serve as early warning indicators of the conversion of LPAI viruses to high pathogenic avian influenza (HPAI) viruses. This study included three H5N2 and one H5N3 viruses that were isolated from live poultry imported into Singapore as part of the national avian influenza virus (AIV) surveillance program. Based on the molecular criterion of the World Organisation for Animal Health (OIE), sequence analysis with the translated amino acid (aa) sequence of the hemagglutinin (HA) gene revealed the absence of multibasic aa at the HA cleavage site, identifying all four virus isolates as LPAI. Detailed phylogenetic tree analyses using the HA and neuraminidase (NA) genes clustered these isolates in the Eurasian H5 lineage, but away from the HPAI H5 subtypes. This analysis further revealed that the internal genes clustered to different avian and swine subtypes, suggesting that the four isolates may possibly share their ancestry with these different influenza subtypes. Our results suggest that the four LPAI isolates in this study contained mainly avian signatures, and the phylogenetic tree for the internal genes further suggests the potential for reassortment with other different circulating avian subtypes. This is the first comprehensive report on the genetic characterization of LPAI H5N2/3 viruses isolated in South-East Asia.
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Efficient capture of infectious H5 avian influenza virus utilizing magnetic beads coated with anionic polymer. Biochem Biophys Res Commun 2008; 377:85-8. [DOI: 10.1016/j.bbrc.2008.09.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 09/17/2008] [Indexed: 11/16/2022]
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Mohammed SL, Lehmann HP, Kim GR. A proposed taxonomy for characterization and assessment of avian influenza outbreaks. Int J Med Inform 2008; 78:182-92. [PMID: 18805050 DOI: 10.1016/j.ijmedinf.2008.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2007] [Revised: 06/28/2008] [Accepted: 06/30/2008] [Indexed: 11/19/2022]
Abstract
PURPOSE The speed and high potential impact of avian influenza's (AI) on local bird populations, poultry economies and human health make timely and coordinated characterization, assessment and response to possible threats essential. To collaborate effectively, stakeholders (public health, medical, veterinary, and agricultural professionals) must be able to communicate and record findings, assessments, and actions in a standard fashion. We seek to discern a taxonomy of concepts and relationships that are important to the stakeholder community when sharing information about the characterization and assessment of an AI outbreak, according to a consistent and common perspective, interpretation, and level of detail. METHODS To derive concepts relevant to AI characterization and assessment, we reviewed selected journal articles, reporting and laboratory forms, and public health websites associated with AI case reporting. We mapped concepts to existing medical terminologies within the Unified Medical Language System when possible, using the National Library of Medicine's MetaMap program. RESULTS From 54 distinct information sources, we extracted 1113 concepts, of which 533 mapped to 15 medical terminologies; 580 did not map to specific terminologies. Using a combination of semantic type-relationship matching and expert consensus, we constructed the proposed taxonomy, with linkages to existing terminologies where pragmatic. CONCLUSION The proposed taxonomy describes core knowledge, data and communication needs for the characterization and assessment of AI outbreaks in the context of existing medical terminologies across different domains. We also describe areas for further work.
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Affiliation(s)
- Sule L Mohammed
- Division of Health Sciences Informatics, School of Medicine, Johns Hopkins University, 2024 East Monument Street, Suite 1-201, Baltimore, MD 21205, USA.
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Tewari D, Zellers C, Acland H, Pedersen JC. Automated extraction of avian influenza virus for rapid detection using real-time RT-PCR. J Clin Virol 2007; 40:142-5. [PMID: 17875401 DOI: 10.1016/j.jcv.2007.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 07/16/2007] [Accepted: 07/19/2007] [Indexed: 11/15/2022]
Abstract
BACKGROUND Highly pathogenic H5N1 avian influenza (AI) poses a grave risk to human health. An important aspect of influenza control is rapid diagnosis. OBJECTIVES This study describes the efficiency of AI-RNA extraction utilizing silica-based magnetic beads with robotics and its detection with an influenza A matrix gene real-time RT-PCR from tracheal swabs, and compares it to virus isolation and manual spin column extractions. STUDY DESIGN Analytical sensitivity was assessed by performing dilution analysis and detection of H2N2 AI viral RNA. Diagnostic sensitivity and specificity was assessed by analyzing tracheal swabs collected from H7N2 infected and uninfected chickens. RESULTS Both manual and robotic extractions detected AI virus at 1log(10)EID(50)/ml. Diagnostic sensitivity and specificity of matrix gene detection with the automated extraction method for chicken tracheal swab specimens was similar to that of virus isolation and the manual extraction method. There were only three discordant results among 212 tested specimens. CONCLUSION The main advantages of automated robotic viral nucleic acid extraction are high throughput processing; hands-free operation; and reduction in human and technical error. This study demonstrates successful detection of influenza A virus with magnetic beads utilizing the Qiagen MagAttract cell kit on a BioRobot M48 platform.
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Affiliation(s)
- Deepanker Tewari
- Microbiology Services, Pennsylvania Veterinary Laboratory, Harrisburg, PA 17110, USA.
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Spackman E, Swayne DE, Suarez DL, Senne DA, Pedersen JC, Killian ML, Pasick J, Handel K, Pillai SPS, Lee CW, Stallknecht D, Slemons R, Ip HS, Deliberto T. Characterization of low-pathogenicity H5N1 avian influenza viruses from North America. J Virol 2007; 81:11612-9. [PMID: 17728231 PMCID: PMC2168782 DOI: 10.1128/jvi.01368-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wild-bird surveillance in North America for avian influenza (AI) viruses with a goal of early identification of the Asian H5N1 highly pathogenic AI virus has identified at least six low-pathogenicity H5N1 AI viruses between 2004 and 2006. The hemagglutinin (HA) and neuraminidase (NA) genes from all 6 H5N1 viruses and an additional 38 North American wild-bird-origin H5 subtype and 28 N1 subtype viruses were sequenced and compared with sequences available in GenBank by phylogenetic analysis. Both HA and NA were phylogenetically distinct from those for viruses from outside of North America and from those for viruses recovered from mammals. Four of the H5N1 AI viruses were characterized as low pathogenicity by standard in vivo pathotyping tests. One of the H5N1 viruses, A/MuteSwan/MI/451072-2/06, was shown to replicate to low titers in chickens, turkeys, and ducks. However, transmission of A/MuteSwan/MI/451072-2/06 was more efficient among ducks than among chickens or turkeys based on virus shed. The 50% chicken infectious dose for A/MuteSwan/MI/451072-2/06 and three other wild-waterfowl-origin H5 viruses were also determined and were between 10(5.3) and 10(7.5) 50% egg infective doses. Finally, seven H5 viruses representing different phylogenetic clades were evaluated for their antigenic relatedness by hemagglutination inhibition assay, showing that the antigenic relatedness was largely associated with geographic origin. Overall, the data support the conclusion that North American H5 wild-bird-origin AI viruses are low-pathogenicity wild-bird-adapted viruses and are antigenically and genetically distinct from the highly pathogenic Asian H5N1 virus lineage.
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Affiliation(s)
- Erica Spackman
- Southeast Poultry Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, 934 College Station Road, Athens, GA 30605, USA.
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Pasick J, Handel K, Robinson J, Bowes V, Li Y, Leighton T, Kehler H, Ridd D, Cottam-Birt C. Relationship between H5N2 avian influenza viruses isolated from wild and domestic ducks in British Columbia, Canada. Avian Dis 2007; 51:429-31. [PMID: 17494600 DOI: 10.1637/7570-033106r.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the summer of 2005 a Canadian national surveillance program for influenza A viruses in wild aquatic birds was initiated. The program involved collaboration between federal and provincial levels of government and was coordinated by the Canadian Cooperative Wildlife Health Centre. The surveillance plan targeted young-of-the-year Mallards along with other duck species at six sampling locations along the major migratory flyways across Canada. Beginning in early August, cloacal swabs were taken from 704 ducks on two lakes adjacent to one another near Kamloops, British Columbia. The swabs were screened for the presence of influenza A RNA using a real-time reverse transcription-polymerase chain reaction (RRT-PCR) assay that targets the M1 gene. Swab samples that gave positive results underwent further testing using H5- and H7-specific RRT-PCR assays. One hundred and seventy-four cloacal swab specimens gave positive or suspicious results for the presence of an H5 virus. A portion of these (28/35) were confirmed using an H5-specific conventional reverse transcription-polymerase chain reaction assay and an H5 virus was eventually isolated from 24/127 swab specimens. Neuraminidase typing revealed the presence of H5N2 and H5N9 viruses. In mid-November of 2005 an H5N2 virus was detected in a commercial duck operation in the lower mainland of British Columbia, approximately 120 km from where the H5N2-positive wild ducks were sampled. Molecular genetic analysis of the H5N2 viruses isolated from wild and domestic ducks was carried out to determine their kinship.
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Affiliation(s)
- John Pasick
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada R3E 3M4
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Abstract
Pandemic influenza virus has its origins in avian influenza viruses. The highly pathogenic avian influenza virus subtype H5N1 is already panzootic in poultry, with attendant economic consequences. It continues to cross species barriers to infect humans and other mammals, often with fatal outcomes. Therefore, H5N1 virus has rightly received attention as a potential pandemic threat. However, it is noted that the pandemics of 1957 and 1968 did not arise from highly pathogenic influenza viruses, and the next pandemic may well arise from a low-pathogenicity virus. The rationale for particular concern about an H5N1 pandemic is not its inevitability but its potential severity. An H5N1 pandemic is an event of low probability but one of high human health impact and poses a predicament for public health. Here, we review the ecology and evolution of highly pathogenic avian influenza H5N1 viruses, assess the pandemic risk, and address aspects of human H5N1 disease in relation to its epidemiology, clinical presentation, pathogenesis, diagnosis, and management.
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Affiliation(s)
- J S Malik Peiris
- Department of Microbiology, University Pathology Building, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong, SAR, People's Republic of China.
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Ma HC, Chen JM, Chen JW, Sun YX, Li JM, Wang ZL. The panorama of the diversity of H5 subtype influenza viruses. Virus Genes 2006; 34:283-7. [PMID: 16924425 DOI: 10.1007/s11262-006-0018-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
To elucidate the global diversity of H5 influenza viruses from a dynamic view, haemagglutinin (HA) sequences of 170 isolates were selected and analyzed in this study. Our results showed that H5 influenza isolates could be divided into two distinct lineages that circulated in the Eastern Hemisphere and the Western Hemisphere, respectively. This may be due to the separate migration routes and habitats of birds in the two hemispheres. The two distinct lineages, having existed at least for decades, possibly began divergence in 1850s. Each of the two distinct HA lineages could be further divided into some sublineages, but there was little correlation between the minor lineages and their isolation places, isolation time, neuraminidase subtypes, host species or virulence. The panorama of the diversity of H5 influenza viruses presented here integrated all known H5 epidemics including the current severe H5N1 avian epidemics in the Eastern Hemisphere and suggested that H5 virulent viruses could originate from multiple sublineages and associate with multiple NA subtypes. Our study provided a framework for the studies on the evolution and epidemiology of H5 influenza viruses.
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Affiliation(s)
- Hong-Chao Ma
- Chinese Center for Animal Health and Epidemiology, Nanjing Road 369#, Qingdao 266032, China
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Payungporn S, Chutinimitkul S, Chaisingh A, Damrongwantanapokin S, Nuansrichay B, Pinyochon W, Amonsin A, Donis RO, Theamboonlers A, Poovorawan Y. Discrimination between highly pathogenic and low pathogenic H5 avian influenza A viruses. Emerg Infect Dis 2006; 12:700-1. [PMID: 16715581 PMCID: PMC3294708 DOI: 10.3201/eid1204.051427] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - Ruben O. Donis
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Abstract
The number of avian species in which coronaviruses have been detected has doubled in the past couple of years. While the coronaviruses in these species have all been in coronavirus Group 3, as for the better known coronaviruses of the domestic fowl (infectious bronchitis virus [IBV], in Gallus gallus), turkey (Meleagris gallopavo) and pheasant (Phasianus colchicus), there is experimental evidence to suggest that birds are not limited to infection with Group 3 coronaviruses. In China coronaviruses have been isolated from peafowl (Pavo), guinea fowl (Numida meleagris; also isolated in Brazil), partridge (Alectoris) and also from a non-gallinaceous bird, the teal (Anas), all of which were being reared in the vicinity of domestic fowl. These viruses were closely related in genome organization and in gene sequences to IBV. Indeed, gene sequencing and experimental infection of chickens indicated that the peafowl isolate was the H120 IB vaccine strain, while the teal isolate was possibly a field strain of a nephropathogenic IBV. Thus the host range of IBV does extend beyond the chicken. Most recently, Group 3 coronaviruses have been detected in greylag goose (Anser anser), mallard duck (Anas platyrhynchos) and pigeon (Columbia livia). It is clear from the partial genome sequencing of these viruses that they are not IBV, as they have two additional small genes near the 3' end of the genome. Twenty years ago a coronavirus was isolated after inoculation of mice with tissue from the coastal shearwater (Puffinus puffinus). While it is not certain whether the virus was actually from the shearwater or from the mice, recent experiments have shown that bovine coronavirus (a Group 2 coronavirus) can infect and also cause enteric disease in turkeys. Experiments with some Group 1 coronaviruses (all from mammals, to date) have shown that they are not limited to replicating or causing disease in a single host. SARS-coronavirus has a wide host range. Clearly there is the potential for the emergence of new coronavirus diseases in domestic birds, from both avian and mammalian sources. Modest sequence conservation within gene 1 has enabled the design of oligonucleotide primers for use in diagnostic reverse transcriptase-polymerase chain reactions, which will be useful for the detection of new coronaviruses.
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Affiliation(s)
- Dave Cavanagh
- Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, RG20 7NN, UK.
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Gambaryan A, Tuzikov A, Pazynina G, Bovin N, Balish A, Klimov A. Evolution of the receptor binding phenotype of influenza A (H5) viruses. Virology 2005; 344:432-8. [PMID: 16226289 DOI: 10.1016/j.virol.2005.08.035] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Revised: 06/28/2005] [Accepted: 08/26/2005] [Indexed: 11/25/2022]
Abstract
Receptor specificity of influenza A/H5 viruses including human 2003-04 isolates was studied. All but two isolates preserved high affinity to Sia2-3Gal (avian-like) receptors. However, two isolates (February, 2003, Hong Kong) demonstrated decreased affinity to Sia2-3Gal and moderate affinity to a Sia2-6Gal (human-like) receptors. These two viruses had a unique Ser227-Asn change in the hemagglutinin molecule. Thus, a single amino acid substitution can significantly alter receptor specificity of avian H5N1 viruses, providing them with an ability to bind to receptors optimal for human influenza viruses. Asian 2003-04 H5 isolates from chickens and humans demonstrated highest affinity to the sulfated trisaccharide Neu5Acalpha2-3Galbeta1-4(6-HSO3)GlcNAcbeta (Su-3'SLN) receptor but, in contrast to 1997 isolates, had increased affinity to fucosylated Su-3'SLN. American poultry H5 viruses also had increased affinity to Su-3'SLN. These data demonstrate that the genetic evolution of avian influenza A(H5N1) viruses is accompanied during adaptation to poultry by the evolution of their receptor specificity.
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Affiliation(s)
- Alexandra Gambaryan
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, 142782 Moscow, Russia.
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Tang Y, Lee CW, Zhang Y, Senne DA, Dearth R, Byrum B, Perez DR, Suarez DL, Saif YM. Isolation and characterization of H3N2 influenza A virus from turkeys. Avian Dis 2005; 49:207-13. [PMID: 16094824 DOI: 10.1637/7288-101304r] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Five 34-wk-old turkey breeder layer flocks in separate houses of 2550 birds each in a single farm in Ohio experienced a drop in egg production from late January to early February 2004. Tracheal swabs (n = 60), cloacal swabs (n = 50), and convalescent sera (n = 110) from the flocks were submitted to the laboratory for diagnostics. Virus isolation was attempted in specific-pathogen free embryonating chicken eggs and Vero and MDCK cells. Virus characterization was performed using agar gel immunodiffusion, the hemagglutination test, the hemagglutination inhibition test, the virus neutralization test, reverse transcription-polymerase chain reaction, sequencing, and phylogenetic analysis. A presumptive influenza virus was successfully propagated and isolated on the first passage in MDCK cells, but initially not in Vero cells or specific-pathogen free chicken embryos. After two passages in MDCK cells, it was possible to propagate the isolate in specific-pathogen free chicken embryos. Preliminary sequence analysis of the isolated virus confirmed that it was influenza A virus with almost 100% (235/236) identity with the matrix gene of a swine influenza A virus, A/Swine/Illinois/100084/01 (H1N2). However, it was not possible to subtype the virus using conventional serotyping methods. The results of genetic characterization of the isolated virus showed that it was the H3N2 subtype and was designated as A/Turkey/OH/313053/04 (H3N2). Phylogenetic analysis of the eight gene segments of the virus showed that A/Turkey/OH/313053/04 (H3N2) isolate was most closely related to the triple-reassortant H3N2 swine viruses [A/Swine/WI/14094/99 (H3N2)] that have been circulating among pigs in the United States since 1998, which contains gene segments from avian, swine, and human viruses. The A/Turkey/OH/313053/04 (H3N2) isolated from turkeys in this study was classified as a low pathogenic avian influenza A virus because it only caused a drop in egg production with minor other clinical signs and no mortality.
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Affiliation(s)
- Y Tang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
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Lee CW, Swayne DE, Linares JA, Senne DA, Suarez DL. H5N2 avian influenza outbreak in Texas in 2004: the first highly pathogenic strain in the United States in 20 years? J Virol 2005; 79:11412-21. [PMID: 16103192 PMCID: PMC1193578 DOI: 10.1128/jvi.79.17.11412-11421.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In early 2004, an H5N2 avian influenza virus (AIV) that met the molecular criteria for classification as a highly pathogenic AIV was isolated from chickens in the state of Texas in the United States. However, clinical manifestations in the affected flock were consistent with avian influenza caused by a low-pathogenicity AIV and the representative virus (A/chicken/Texas/298313/04 [TX/04]) was not virulent for experimentally inoculated chickens. The hemagglutinin (HA) gene of the TX/04 isolate was similar in sequence to A/chicken/Texas/167280-4/02 (TX/02), a low-pathogenicity AIV isolate recovered from chickens in Texas in 2002. However, the TX/04 isolate had one additional basic amino acid at the HA cleavage site, which could be attributed to a single point mutation. The TX/04 isolate was similar in sequence to TX/02 isolate in several internal genes (NP, M, and NS), but some genes (PA, PB1, and PB2) had sequence of a clearly different origin. The TX/04 isolate also had a stalk deletion in the NA gene, characteristic of a chicken-adapted AIV. By analyzing viruses constructed by in vitro mutagenesis followed by reverse genetics, we found that the pathogenicity of the TX/04 virus could be increased in vitro and in vivo by the insertion of an additional basic amino acid at the HA cleavage site and not by the loss of a glycosylation site near the cleavage site. Our study provides the genetic and biologic characteristics of the TX/04 isolate, which highlight the complexity of the polygenic nature of the virulence of influenza viruses.
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Affiliation(s)
- Chang-Won Lee
- Southeast Poultry Research Laboratory, USDA-ARS, Athens, GA 30605, USA
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Lee CW, Suarez DL. Application of real-time RT-PCR for the quantitation and competitive replication study of H5 and H7 subtype avian influenza virus. J Virol Methods 2004; 119:151-8. [PMID: 15158597 DOI: 10.1016/j.jviromet.2004.03.014] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2004] [Revised: 03/24/2004] [Accepted: 03/25/2004] [Indexed: 11/23/2022]
Abstract
Avian influenza (AI) viruses are endemic in wild birds and if transmitted to poultry can cause serious economic losses. In the study of AI, the quantitation of virus shed from infected birds is valuable in pathogenesis studies and to determine the effectiveness of vaccines, and is performed routinely by cultivation of virus containing samples using embryonating chicken eggs (ECE) and expressed by 50% egg infectious dose (EID(50)). Although, this assay is accurate and is the standard test for infectious virus titration, the method is laborious, requires a large number of ECE, and takes at least 7 days to determine results. In this study, a one-tube hydrolysis fluorescent probe based real-time RT-PCR (RRT-PCR) was applied for the quantitation of AI virus and compared with conventional virus titration method. A strong positive correlation was observed between the amount of RNA determined by quantitative RRT-PCR and the EID(50)s determined by conventional methods. This RRT-PCR test was further applied in the study of competitive replication of co-infected H5 and H7 subtype viruses in chickens. Using hemagglutinin subtype specific probes, we were able to determine the amount of individual subtype virus, which could not have easily been done with conventional methods. This RRT-PCR based quantitation of AI virus, which is specific, sensitive, easy to perform, and rapid, will be useful for virological, pathogenesis, and protection studies.
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Affiliation(s)
- Chang-Won Lee
- Southeast Poultry Research Laboratory, USDA-ARS, 934 College Station Road, Athens, GA 30605, USA
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