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Burrough ER, Magstadt DR, Petersen B, Timmermans SJ, Gauger PC, Zhang J, Siepker C, Mainenti M, Li G, Thompson AC, Gorden PJ, Plummer PJ, Main R. Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024. Emerg Infect Dis 2024; 30:1335-1343. [PMID: 38683888 PMCID: PMC11210653 DOI: 10.3201/eid3007.240508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
We report highly pathogenic avian influenza A(H5N1) virus in dairy cattle and cats in Kansas and Texas, United States, which reflects the continued spread of clade 2.3.4.4b viruses that entered the country in late 2021. Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows. Cow-to-cow transmission appears to have occurred because infections were observed in cattle on Michigan, Idaho, and Ohio farms where avian influenza virus-infected cows were transported. Although the US Food and Drug Administration has indicated the commercial milk supply remains safe, the detection of influenza virus in unpasteurized bovine milk is a concern because of potential cross-species transmission. Continued surveillance of highly pathogenic avian influenza viruses in domestic production animals is needed to prevent cross-species and mammal-to-mammal transmission.
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Prosser DJ, Kent CM, Sullivan JD, Patyk KA, McCool MJ, Torchetti MK, Lantz K, Mullinax JM. Using an adaptive modeling framework to identify avian influenza spillover risk at the wild-domestic interface. Sci Rep 2024; 14:14199. [PMID: 38902400 PMCID: PMC11189914 DOI: 10.1038/s41598-024-64912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024] Open
Abstract
The wild to domestic bird interface is an important nexus for emergence and transmission of highly pathogenic avian influenza (HPAI) viruses. Although the recent incursion of HPAI H5N1 Clade 2.3.4.4b into North America calls for emergency response and planning given the unprecedented scale, readily available data-driven models are lacking. Here, we provide high resolution spatial and temporal transmission risk models for the contiguous United States. Considering virus host ecology, we included weekly species-level wild waterfowl (Anatidae) abundance and endemic low pathogenic avian influenza virus prevalence metrics in combination with number of poultry farms per commodity type and relative biosecurity risks at two spatial scales: 3 km and county-level. Spillover risk varied across the annual cycle of waterfowl migration and some locations exhibited persistent risk throughout the year given higher poultry production. Validation using wild bird introduction events identified by phylogenetic analysis from 2022 to 2023 HPAI poultry outbreaks indicate strong model performance. The modular nature of our approach lends itself to building upon updated datasets under evolving conditions, testing hypothetical scenarios, or customizing results with proprietary data. This research demonstrates an adaptive approach for developing models to inform preparedness and response as novel outbreaks occur, viruses evolve, and additional data become available.
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Affiliation(s)
- Diann J Prosser
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA.
| | - Cody M Kent
- Volunteer to the U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
- Department of Environmental Science and Technology, University of Maryland, College Park, MD, 20742, USA
- Department of Biology, Frostburg State University, Frostburg, MD, 21532, USA
| | - Jeffery D Sullivan
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
| | - Kelly A Patyk
- U.S. Department of Agriculture, Animal Plant and Health Inspection Service, Veterinary Services, Strategy and Policy, Center for Epidemiology and Animal Health, Fort Collins, CO, 80521, USA
| | - Mary-Jane McCool
- U.S. Department of Agriculture, Animal Plant and Health Inspection Service, Veterinary Services, Strategy and Policy, Center for Epidemiology and Animal Health, Fort Collins, CO, 80521, USA
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, 50010, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, 50010, USA
| | - Jennifer M Mullinax
- Department of Environmental Science and Technology, University of Maryland, College Park, MD, 20742, USA
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Franzo G, Legnardi M, Faustini G, Baston R, Poletto F, Cecchinato M, Tucciarone CM. Tracing the Flight: Investigating the Introduction of Avian Metapneumovirus (aMPV) A and B. Animals (Basel) 2024; 14:1786. [PMID: 38929405 PMCID: PMC11200574 DOI: 10.3390/ani14121786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Avian metapneumovirus (aMPV) has been identified as an important cause of respiratory and reproductive disease, leading to significant productive losses worldwide. Different subtypes have been found to circulate in different regions, with aMPV-A and B posing a significant burden especially in the Old World, and aMPV-C in North America, albeit with limited exceptions of marginal economic relevance. Recently, both aMPV-A and aMPV-B have been reported in the U.S.; however, the route of introduction has not been investigated. In the present study, the potential importation pathways have been studied through phylogenetic and phylodynamic analyses based on a broad collection of partial attachment (G) protein sequences collected worldwide. aMPV-B circulating in the U.S. seems the descendant of Eastern Asian strains, which, in turn, are related to European ones. A likely introduction pathway mediated by wild bird migration through the Beringian crucible, where the East Asian and Pacific American flight paths intersect, appears likely and was previously reported for avian influenza. aMPV-A, on the other hand, showed a Mexican origin, involving strains related to Asian ones. Given the low likelihood of trade or illegal importation, the role of wild birds appears probable also in this case, since the region is covered by different flight paths directed in a North-South direction through America. Since the information on the role of wild birds in aMPV epidemiology is still scarce and scattered, considering the significant practical implications for the poultry industry demonstrated by recent U.S. outbreaks, further surveys on wild birds are encouraged.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy; (M.L.); (G.F.); (R.B.); (F.P.); (M.C.); (C.M.T.)
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Larbi I, Arbi M, Souiai O, Tougorti H, Butcher GD, Nsiri J, Badr C, Behi IE, Lachhab J, Ghram A. Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia. Virus Res 2024; 344:199348. [PMID: 38467378 PMCID: PMC10995884 DOI: 10.1016/j.virusres.2024.199348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections. The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.
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Affiliation(s)
- Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia.
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Halima Tougorti
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Gary David Butcher
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Chaima Badr
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Jihene Lachhab
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
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Chauhan RP, Fogel R, Limson J. Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa. Microorganisms 2023; 11:2802. [PMID: 38004813 PMCID: PMC10672864 DOI: 10.3390/microorganisms11112802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
White spot syndrome virus is a highly contagious pathogen affecting shrimp farming worldwide. The host range of this virus is primarily limited to crustaceans, such as shrimps, crabs, prawns, crayfish, and lobsters; however, several species of non-crustaceans, including aquatic insects, piscivorous birds, and molluscs may serve as the vectors for ecological dissemination. The present study was aimed at studying the faecal virome of domestic chickens (Gallus gallus domesticus) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (n = 35) were collected from domestic chickens in December 2022. The cloacal swab specimens were pooled-each pool containing five cloacal swabs-for metagenomic analysis using a sequence-independent single-primer amplification protocol, followed by Nanopore MinION sequencing. While the metagenomic sequencing generated several contigs aligning with reference genomes of animal viruses, one striking observation was the presence of a White spot syndrome virus genome in one pool of cloacal swab specimens. The generated White spot syndrome virus genome was 273,795 bp in size with 88.5% genome coverage and shared 99.94% nucleotide sequence identity with a reference genome reported in China during 2018 (GenBank accession: NC_003225.3). The Neighbour-Joining tree grouped South African White spot syndrome virus genome with other White spot syndrome virus genomes reported from South East Asia. To our knowledge, this is the first report of a White spot syndrome virus genome generated from domestic chickens. The significance of White spot syndrome virus infection in domestic chickens is yet to be determined.
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Affiliation(s)
| | | | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa; (R.P.C.); (R.F.)
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Youk S, Torchetti MK, Lantz K, Lenoch JB, Killian ML, Leyson C, Bevins SN, Dilione K, Ip HS, Stallknecht DE, Poulson RL, Suarez DL, Swayne DE, Pantin-Jackwood MJ. H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021-April 2022. Virology 2023; 587:109860. [PMID: 37572517 DOI: 10.1016/j.virol.2023.109860] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American wild bird avian influenza viruses. Reassortments of up to five internal genes generated a total of 21 distinct clusters; of these, six genotypes represented 92% of the HPAIVs examined. By phylodynamic analyses, most detections in domestic birds were shown to be point-source transmissions from wild birds, with limited farm-to-farm spread.
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Affiliation(s)
- Sungsu Youk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA; Microbiology Laboratory, Department of Medicine, College of Medicine, Chungbuk National University, Chungbuk, South Korea
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Julianna B Lenoch
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Christina Leyson
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Sarah N Bevins
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Krista Dilione
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Hon S Ip
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch, Madison, WI, USA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - David L Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - David E Swayne
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Mary J Pantin-Jackwood
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA.
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7
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Saavedra I, Rabadán-González J, Aragonés D, Figuerola J. Can Citizen Science Contribute to Avian Influenza Surveillance? Pathogens 2023; 12:1183. [PMID: 37764991 PMCID: PMC10535995 DOI: 10.3390/pathogens12091183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/01/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Global change is an important driver of the increase in emerging infectious diseases in recent decades. In parallel, interest in nature has increased, and different citizen science platforms have been developed to record wildlife observations from the general public. Some of these platforms also allow registering the observations of dead or sick birds. Here, we test the utility of live, sick and dead observations of birds recorded on the platform Observation.org for the early detection of highly pathogenic avian influenza virus (HPAIV) outbreaks in the wild in Belgium and The Netherlands. There were no significant differences in the morbidity/mortality rate through Observation.org one to four weeks in advance. However, the results show that the HPAIV outbreaks officially reported by the World Organisation for Animal Health (WOAH) overlapped in time with sudden increases in the records of sick and dead birds in the wild. In addition, in two of the five main HPAIV outbreaks recorded between 2016 and 2021, wild Anseriformes mortality increased one to two months before outbreak declaration. Although we cannot exclude that this increase was related to other causes such as other infectious diseases, we propose that Observation.org is a useful nature platform to complement animal health surveillance in wild birds. We propose possible approaches to improve the utility of the platform for pathogen surveillance in wildlife and discuss the potential for HPAIV outbreak detection systems based on citizen science to complement current surveillance programs of health authorities.
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Affiliation(s)
- Irene Saavedra
- Consejo Superior de Investigaciones Científicas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
| | | | - David Aragonés
- Remote Sensing and GIS Laboratory (LAST-EBD), Consejo Superior de Investigaciones Cientificas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
| | - Jordi Figuerola
- Consejo Superior de Investigaciones Científicas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
- CIBER Epidemiology and Public Health (CIBERESP), E-28028 Madrid, Spain
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Han Y, Hellgren O, Wu Q, Liu J, Jin T, Bensch S, Ding P. Seasonal variations of intensity of avian malaria infection in the Thousand Island Lake System, China. Parasit Vectors 2023; 16:218. [PMID: 37403099 DOI: 10.1186/s13071-023-05848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Migratory birds play an important part in the spread of parasites, with more or less impact on resident birds. Previous studies focus on the prevalence of parasites, but changes in infection intensity over time have rarely been studied. As infection intensity can be quantified by qPCR, we measured infection intensity during different seasons, which is important for our understanding of parasite transmission mechanisms. METHODS Wild birds were captured at the Thousand Island Lake with mist nets and tested for avian hemosporidiosis infections using nested PCR. Parasites were identified using the MalAvi database. Then, we used qPCR to quantify the infection intensity. We analyzed the monthly trends of intensity for all species and for different migratory status, parasite genera and sexes. RESULTS Of 1101 individuals, 407 were infected (37.0%) of which 95 were newly identified and mainly from the genus Leucocytozoon. The total intensity trend shows peaks at the start of summer, during the breeding season of hosts and during the over-winter season. Different parasite genera show different monthly trends. Plasmodium causes high prevalence and infection intensity of winter visitors. Female hosts show significant seasonal trends of infection intensity. CONCLUSIONS The seasonal changes of infection intensity is consistent with the prevalence. Peaks occur early and during the breeding season and then there is a downward trend. Spring relapses and avian immunity are possible reasons that could explain this phenomenon. In our study, winter visitors have a higher prevalence and infection intensity, but they rarely share parasites with resident birds. This shows that they were infected with Plasmodium during their departure or migration and rarely transmit the disease to resident birds. The different infection patterns of different parasite species may be due to vectors or other ecological properties.
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Affiliation(s)
- Yuxiao Han
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Zhejiang, China
| | - Olof Hellgren
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Qiang Wu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Zhejiang, China
| | - Juan Liu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Zhejiang, China
| | - Tinghao Jin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Zhejiang, China
| | - Staffan Bensch
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Zhejiang, China.
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Gass JD, Hill NJ, Damodaran L, Naumova EN, Nutter FB, Runstadler JA. Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016-Early 2022. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6030. [PMID: 37297634 PMCID: PMC10252585 DOI: 10.3390/ijerph20116030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterized ecological and environmental predictors of virus spread between geographic regions by constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). The findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the United States (US), H5Nx viruses spread at a greater rate between US-based regions as compared to prior spread in Europe. We established that geographic proximity is a predictor of virus spread between regions, implying that intercontinental transport across the Atlantic Ocean is relatively rare. An increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and the US during an actively evolving intercontinental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125, USA
| | | | - Elena N. Naumova
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02155, USA
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
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Hort HM, Ibaraki M, Schwartz FW. Temporal and Spatial Synchronicity in West Nile Virus Cases Along the Central Flyway, USA. GEOHEALTH 2023; 7:e2022GH000708. [PMID: 37181010 PMCID: PMC10171186 DOI: 10.1029/2022gh000708] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/18/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023]
Abstract
This study of West Nile virus (WNV) examined the possibility of avian transmission to explain synchronicity in the year-to-year variability of WNV case numbers from Texas northward to the Dakotas, and reasons for the large case numbers on the northern Great Plains. We determined correlation coefficients between annual disease incidence per 100,000 people among states within the Great Plains Region, as well as the Central Flyway. There was spatial and temporal synchronicity, as evidenced by Pearson "r," with values along the core of the Central Flyway (Oklahoma, Kansas, Nebraska, and South Dakota) varying between 0.69 and 0.79. Correlations for North Dakota (r = 0.6), however, were affected by local conditions. The concept of relative amplification is helpful in explaining why northerly states along the Central Flyway have larger annual case numbers per 100,000 than Texas but preserve the temporal signal. States differed in their capacity for amplifying the temporal signal in case numbers. For example, Nebraska, South Dakota, and North Dakota case numbers were commonly amplified relative to Texas, with Oklahoma and Kansas deamplified. Relative amplification factors for all states increased as a function of increasing case numbers in Texas. Thus, increased numbers of initially infected birds in Texas likely led to the rapid intensification of the zoonotic cycle as compared to more typical years. The study also confirmed the importance of winter weather in locally modulating disease cases. North Dakota appeared most impacted by these factors to the extent of reducing WNV case numbers in colder years and years with deep snow.
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Affiliation(s)
| | - M. Ibaraki
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
| | - F. W. Schwartz
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
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Perlas A, Bertran K, Abad FX, Borrego CM, Nofrarías M, Valle R, Pailler-García L, Ramis A, Cortey M, Acuña V, Majó N. Persistence of low pathogenic avian influenza virus in artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160902. [PMID: 36526195 DOI: 10.1016/j.scitotenv.2022.160902] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Avian influenza viruses (AIVs) can affect wildlife, poultry, and humans, so a One Health perspective is needed to optimize mitigation strategies. Migratory waterfowl globally spread AIVs over long distances. Therefore, the study of AIV persistence in waterfowl staging and breeding areas is key to understanding their transmission dynamics and optimizing management strategies. Here, we used artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate (day/night cycles of photosynthetic active radiation and temperature, low water velocity, and similar microbiome to lowland rivers and stagnant water bodies) and then manipulated temperature and sediment presence (i.e., 10-13 °C vs. 16-18 °C, and presence vs. absence of sediments). An H1N1 low pathogenic AIV (LPAIV) strain was spiked in the streams, and water and sediment samples were collected at different time points until 14 days post-spike to quantify viral RNA and detect infectious particles. Viral RNA was detected until the end of the experiment in both water and sediment samples. In water samples, we observed a significant combined effect of temperature and sediments in viral decay, with higher viral genome loads in colder streams without sediments. In sediment samples, we didn't observe any significant effect of temperature. In contrast to prior laboratory-controlled studies that detect longer persistence times, infectious H1N1 LPAIV was isolated in water samples till 2 days post-spike, and none beyond. Infectious H1N1 LPAIV wasn't isolated from any sediment sample. Our results suggest that slow flowing freshwater surface waters may provide conditions facilitating bird-to-bird transmission for a short period when water temperature are between 10 and 18 °C, though persistence for extended periods (e.g., weeks or months) may be less likely. We hypothesize that experiments simulating real environments, like the one described here, provide a more realistic approach for assessing environmental persistence of AIVs.
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Affiliation(s)
- Albert Perlas
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Kateri Bertran
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Francesc Xavier Abad
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona (UdG), Plaça Sant Domènec 3, 17004 Girona, Spain.
| | - Miquel Nofrarías
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Rosa Valle
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Lola Pailler-García
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Antonio Ramis
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Martí Cortey
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona (UdG), Plaça Sant Domènec 3, 17004 Girona, Spain.
| | - Natàlia Majó
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
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12
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Zhang G, Li B, Raghwani J, Vrancken B, Jia R, Hill SC, Fournié G, Cheng Y, Yang Q, Wang Y, Wang Z, Dong L, Pybus OG, Tian H. Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020. Mol Biol Evol 2023; 40:msad019. [PMID: 36703230 PMCID: PMC9922686 DOI: 10.1093/molbev/msad019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Migratory birds play a critical role in the rapid spread of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. Elucidating the timing and pattern of virus transmission is essential therefore for understanding the spatial dissemination of these viruses. In this study, we surveyed >27,000 wild birds in China, tracked the year-round migration patterns of 20 bird species across China since 2006, and generated new HPAI H5N8 virus genomic data. Using this new data set, we investigated the seasonal transmission dynamics of HPAI H5N8 viruses across Eurasia. We found that introductions of HPAI H5N8 viruses to different Eurasian regions were associated with the seasonal migration of wild birds. Moreover, we report a backflow of HPAI H5N8 virus lineages from Europe to Asia, suggesting that Europe acts as both a source and a sink in the global HPAI virus transmission network.
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Affiliation(s)
- Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Jayna Raghwani
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Ru Jia
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guillaume Fournié
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Yanchao Cheng
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuxin Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
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13
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Alkie TN, Lopes S, Hisanaga T, Xu W, Suderman M, Koziuk J, Fisher M, Redford T, Lung O, Joseph T, Himsworth CG, Brown IH, Bowes V, Lewis NS, Berhane Y. A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways. Virus Evol 2022; 8:veac077. [PMID: 36105667 PMCID: PMC9463990 DOI: 10.1093/ve/veac077] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 08/14/2023] Open
Abstract
From 2016 to 2020, high pathogenicity avian influenza (HPAI) H5 viruses circulated in Asia, Europe, and Africa, causing waves of infections and the deaths of millions of wild and domestic birds and presenting a zoonotic risk. In late 2021, H5N1 HPAI viruses were isolated from poultry in Canada and also retrospectively from a great black-backed gull (Larus marinus), raising concerns that the spread of these viruses to North America was mediated by migratory wild bird populations. In February and April 2022, H5N1 HPAI viruses were isolated from a bald eagle (Haliaeetus leucocephalus) and broiler chickens in British Columbia, Canada. Phylogenetic analysis showed that the virus from bald eagle was genetically related to H5N1 HPAI virus isolated in Hokkaido, Japan, in January 2022. The virus identified from broiler chickens was a reassortant H5N1 HPAI virus with unique constellation genome segments containing PB2 and NP from North American lineage LPAI viruses, and the remaining gene segments were genetically related to the original Newfoundland-like H5N1 HPAI viruses detected in November and December 2021 in Canada. This is the first report of H5 HPAI viruses' introduction to North America from the Pacific and the North Atlantic-linked flyways and highlights the expanding risk of genetically distinct virus introductions from different geographical locations and the potential for local reassortment with both the American lineage LPAI viruses in wild birds and with both Asian-like and European-like H5 HPAI viruses. We also report the presence of some amino acid substitutions across each segment that might contribute to the replicative efficiency of these viruses in mammalian host, evade adaptive immunity, and pose a potential zoonotic risk.
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Affiliation(s)
- Tamiru N Alkie
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Sara Lopes
- Department of Pathobiology and Population Sciences, Hawkshead Campus, The Royal Veterinary College Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - Tamiko Hisanaga
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Wanhong Xu
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Matthew Suderman
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Janice Koziuk
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Mathew Fisher
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Tony Redford
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
- Department of Biological Sciences, University of Manitoba, 50 Sifton Rd., Winnipeg, Manitoba R3T 2M5, Canada
| | - Tomy Joseph
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Chelsea G Himsworth
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
- Canadian Wildlife Health Cooperative British Columbia, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
- School of Population and Public Health, University of British Columbia, 2206 E Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ian H Brown
- International Reference Laboratory for AI, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Victoria Bowes
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Nicola S Lewis
- Department of Pathobiology and Population Sciences, Hawkshead Campus, The Royal Veterinary College Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
- International Reference Laboratory for AI, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
- Department of Animal Science, University of Manitoba, Chancellors Cir, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Dr., Saskatoon, Saskatchewan S7N 5B4, Canada
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14
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Prosser DJ, Chen J, Ahlstrom CA, Reeves AB, Poulson RL, Sullivan JD, McAuley D, Callahan CR, McGowan PC, Bahl J, Stallknecht DE, Ramey AM. Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America. PLoS Pathog 2022; 18:e1010605. [PMID: 35666770 PMCID: PMC9203021 DOI: 10.1371/journal.ppat.1010605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/16/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
Wild waterbirds, the natural reservoirs for avian influenza viruses, undergo migratory movements each year, connecting breeding and wintering grounds within broad corridors known as flyways. In a continental or global view, the study of virus movements within and across flyways is important to understanding virus diversity, evolution, and movement. From 2015 to 2017, we sampled waterfowl from breeding (Maine) and wintering (Maryland) areas within the Atlantic Flyway (AF) along the east coast of North America to investigate the spatio-temporal trends in persistence and spread of influenza A viruses (IAV). We isolated 109 IAVs from 1,821 cloacal / oropharyngeal samples targeting mallards (Anas platyrhynchos) and American black ducks (Anas rubripes), two species having ecological and conservation importance in the flyway that are also host reservoirs of IAV. Isolates with >99% nucleotide similarity at all gene segments were found between eight pairs of birds in the northern site across years, indicating some degree of stability among genome constellations and the possibility of environmental persistence. No movement of whole genome constellations were identified between the two parts of the flyway, however, virus gene flow between the northern and southern study locations was evident. Examination of banding records indicate direct migratory waterfowl movements between the two locations within an annual season, providing a mechanism for the inferred viral gene flow. Bayesian phylogenetic analyses provided evidence for virus dissemination from other North American wild birds to AF dabbling ducks (Anatinae), shorebirds (Charidriformes), and poultry (Galliformes). Evidence was found for virus dissemination from shorebirds to gulls (Laridae), and dabbling ducks to shorebirds and poultry. The findings from this study contribute to the understanding of IAV ecology in waterfowl within the AF.
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Affiliation(s)
- Diann J. Prosser
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Jiani Chen
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Christina A. Ahlstrom
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Andrew B. Reeves
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jeffery D. Sullivan
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Daniel McAuley
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Carl R. Callahan
- U.S. Fish and Wildlife Service, Chesapeake Bay Field Office, Annapolis, Maryland, United States of America
| | - Peter C. McGowan
- U.S. Fish and Wildlife Service, Chesapeake Bay Field Office, Annapolis, Maryland, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrew M. Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
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15
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Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NYH, Lynch SE, Martin S, McArthur M, O’Riley K, Read AJ, Warner S, Hoye BJ, Lisovski S, Leen T, Hurt AC, Butler J, Broz I, Davies KR, Mileto P, Neave MJ, Stevens V, Breed AC, Lam TTY, Holmes EC, Klaassen M, Wong FYK. Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathog 2022; 18:e1010150. [PMID: 35536868 PMCID: PMC9089890 DOI: 10.1371/journal.ppat.1010150] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/13/2022] [Indexed: 12/03/2022] Open
Abstract
Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | | | | | - Graham W. Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | | | | | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Md. Ahasanul Hoque
- Chattogram (previously Chittagong) Veterinary and Animal Sciences University, Khulshi, Bangladesh
| | - Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Peter D. Kirkland
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Nina Yu-Hsin Kung
- Animal Biosecurity & Welfare, Biosecurity Queensland, Department of Agriculture and Fisheries, Health Food Science Precinct, Coopers Plains, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Sue Martin
- Department of Primary Industries, Parks, Water and Environment, Hobart, Australia
| | - Michaela McArthur
- Department of Primary Industries and Regional Development, Kensington, Australia
| | - Kim O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Andrew J. Read
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Trent Leen
- Geelong Field & Game, Geelong, Australia
- Wetlands Environmental Taskforce, Field & Game Australia, Seymour, Australia
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jeff Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Ivano Broz
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Kelly R. Davies
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Patrick Mileto
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Matthew J. Neave
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Andrew C. Breed
- Department of Agriculture, Water and the Environment, Canberra, Australia
- University of Queensland, St. Lucia, Australia
| | - Tommy T. Y. Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, PR China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
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16
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Hicks JT, Edwards K, Qiu X, Kim DK, Hixson JE, Krauss S, Webby RJ, Webster RG, Bahl J. Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian influenza A subtypes among North American wild reservoir species. PLoS Pathog 2022; 18:e1009973. [PMID: 35417497 PMCID: PMC9037922 DOI: 10.1371/journal.ppat.1009973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/25/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Wild birds can carry avian influenza viruses (AIV), including those with pandemic or panzootic potential, long distances. Even though AIV has a broad host range, few studies account for host diversity when estimating AIV spread. We analyzed AIV genomic sequences from North American wild birds, including 303 newly sequenced isolates, to estimate interspecies and geographic viral transition patterns among multiple co-circulating subtypes. Our results show high transition rates within Anseriformes and Charadriiformes, but limited transitions between these orders. Patterns of transition between species were positively associated with breeding habitat range overlap, and negatively associated with host genetic distance. Distance between regions (negative correlation) and summer temperature at origin (positive correlation) were strong predictors of transition between locations. Taken together, this study demonstrates that host diversity and ecology can determine evolutionary processes that underlie AIV natural history and spread. Understanding these processes can provide important insights for effective control of AIV.
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Affiliation(s)
- Joseph T. Hicks
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Kimberly Edwards
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Do-Kyun Kim
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - James E. Hixson
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - Scott Krauss
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
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17
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Badruzzaman ATM, Rahman MM, Hasan M, Hossain MK, Husna A, Hossain FMA, Giasuddin M, Uddin MJ, Islam MR, Alam J, Eo SK, Fasina FO, Ashour HM. Semi-Scavenging Poultry as Carriers of Avian Influenza Genes. Life (Basel) 2022; 12:life12020320. [PMID: 35207607 PMCID: PMC8879534 DOI: 10.3390/life12020320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023] Open
Abstract
Ducks are the natural reservoir of influenza A virus and the central host for the avian influenza virus (AIV) subtype H5N1, which is highly pathogenic. Semi-scavenging domestic ducks allow for the reemergence of new influenza subtypes which could be transmitted to humans. We collected 844 cloacal swabs from semi-scavenging ducks inhabiting seven migratory bird sanctuaries of Bangladesh for the molecular detection of avian influenza genes. We detected the matrix gene (M gene) using real-time RT-PCR (RT-qPCR). Subtyping of the AIV-positive samples was performed by RT-qPCR specific for H5, H7, and H9 genes. Out of 844 samples, 21 (2.488%) were positive for AIV. Subtyping of AIV positive samples (n = 21) revealed that nine samples (42.85%) were positive for the H9 subtype, five (23.80%) were positive for H5, and seven (33.33%) were negative for the three genes (H5, H7, and H9). We detected the same genes after propagating the virus in embryonated chicken eggs from positive samples. Semi-scavenging ducks could act as carriers of pathogenic AIV, including the less pathogenic H9 subtype. This can enhance the pathogenicity of the virus in ducks by reassortment. The large dataset presented in our study from seven areas should trigger further studies on AIV prevalence and ecology.
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Affiliation(s)
- A T M Badruzzaman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (A.T.M.B.); (M.M.R.); (M.K.H.); (A.H.); (F.M.A.H.)
| | - Md. Masudur Rahman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (A.T.M.B.); (M.M.R.); (M.K.H.); (A.H.); (F.M.A.H.)
| | - Mahmudul Hasan
- National Reference Laboratory for Avian Influenza, Bangladesh Livestock Research Institute, Savar, Dhaka 1340, Bangladesh; (M.H.); (M.G.)
| | - Mohammed Kawser Hossain
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (A.T.M.B.); (M.M.R.); (M.K.H.); (A.H.); (F.M.A.H.)
| | - Asmaul Husna
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (A.T.M.B.); (M.M.R.); (M.K.H.); (A.H.); (F.M.A.H.)
| | - Ferdaus Mohd Altaf Hossain
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (A.T.M.B.); (M.M.R.); (M.K.H.); (A.H.); (F.M.A.H.)
| | - Mohammed Giasuddin
- National Reference Laboratory for Avian Influenza, Bangladesh Livestock Research Institute, Savar, Dhaka 1340, Bangladesh; (M.H.); (M.G.)
| | - Md Jamal Uddin
- ABEx Bio-Research Center, East Azampur, Dhaka 1230, Bangladesh;
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Mohammad Rafiqul Islam
- Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka 1215, Bangladesh;
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka 1349, Bangladesh;
| | - Seong-Kug Eo
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan 54596, Korea;
| | - Folorunso Oludayo Fasina
- Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations (ECTAD-FAO), United Nations Office in Nairobi (UNON), UN Avenue, Gigiri, Nairobi 00100, Kenya;
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort 0110, South Africa
| | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL 33701, USA
- Correspondence:
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Bianchini EA, Bogiatto RJ, Donatello RA, Casazza ML, Ackerman JT, De La Cruz SEW, Cline TD. Host Correlates of Avian Influenza Virus Infection in Wild Waterfowl of the Sacramento Valley, California. Avian Dis 2021; 66:20-28. [DOI: 10.1637/aviandiseases-d-21-00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/15/2021] [Indexed: 11/05/2022]
Affiliation(s)
| | - Raymond J. Bogiatto
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
| | - Robin A. Donatello
- Department of Mathematics and Statistics, California State University, Chico, Chico, CA 95929
| | - Michael L. Casazza
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Joshua T. Ackerman
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Susan E. W. De La Cruz
- United States Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592
| | - Troy D. Cline
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
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Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology. Pathogens 2021; 10:pathogens10050630. [PMID: 34065291 PMCID: PMC8161317 DOI: 10.3390/pathogens10050630] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/21/2022] Open
Abstract
Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Migratory birds, especially waterfowl, are a natural reservoir of the avian influenza virus; they carry and exchange different virus strains along their migration routes, leading to antigenic drift and antigenic shift, which results in the emergence of novel HPAI viruses. This requires monitoring over time and in different locations to allow for the upkeep of relevant knowledge on avian influenza virus evolution and the prevention of novel epizootic and epidemic outbreaks. In this review, we assess the role of migratory birds in the spread and introduction of influenza strains on a global level, based on recent data. Our analysis sheds light on the details of viral dissemination linked to avian migration, the viral exchange between migratory waterfowl and domestic poultry, virus ecology in general, and viral evolution as a process tightly linked to bird migration. We also provide insight into methods used to detect and quantify avian influenza in the wild. This review may be beneficial for the influenza research community and may pave the way to novel strategies of avian influenza and HPAI zoonosis outbreak monitoring and prevention.
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20
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Characterization of the Plasmodium and Haemoproteus parasite community in temperate-tropical birds during spring migration. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2021; 15:12-21. [PMID: 33936944 PMCID: PMC8079335 DOI: 10.1016/j.ijppaw.2021.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 11/21/2022]
Abstract
Animal movements, especially avian migration, can be a mechanism for the large-scale dispersal and geographic range expansion of parasites. The host-parasite relationships among birds during migration have yet to be fully explored. We characterized the haemosporidian parasite lineages in passerines during spring migration on the Texas coast of the Gulf of Mexico, and identified associations among wintering origin (US, Central America, South America) and foraging height (canopy, understory, ground) and infection status. We examined 743 samples representing 52 species of 10 families over six years, 2014-2019. We used PCR and DNA sequencing of the haemosporidian cytB gene from avian blood samples to determine infection status with the genera Plasmodium and Haemoproteus and characterize the lineages of blood parasites. We found an overall haemosporidian infection prevalence of 48.4% among neotropical migrant and Texas wintering birds. Among families, Icterids had the highest prevalence (75%, 24 individuals, 4 species sampled) whereas Parulids had the lowest prevalence (38.4%, 177 individuals, 18 species sampled). Among infected birds, Plasmodium spp. infections were more common than Haemoproteus spp. infections in species that winter in Central America compared to those that winter in the US or South America. Similarly, among infected birds, Plasmodium spp. infections were more common than Haemoproteus spp. infections in species that forage on the ground or in the understory compared to those that forage in the canopy. Infected birds harbored 65 different haemosporidian lineages (71% Plasmodium; 29% Haemoproteus) of which 17 lineages have never previously been reported and six lineages were documented for the first time in North America, having been previously detected only in Central or South America. These data are consistent with the premise that intercontinental parasite dispersal may be facilitated by passerine birds. Future studies focused on surveillance, the probability of establishment of parasite lineages, and the use of individual bird tracking methods to understand infection dispersion over time will allow a more comprehensive understanding of changing avian host-haemosporidian relationships.
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21
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Gorsich EE, Webb CT, Merton AA, Hoeting JA, Miller RS, Farnsworth ML, Swafford SR, DeLiberto TJ, Pedersen K, Franklin AB, McLean RG, Wilson KR, Doherty PF. Continental-scale dynamics of avian influenza in U.S. waterfowl are driven by demography, migration, and temperature. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e2245. [PMID: 33098602 PMCID: PMC7988533 DOI: 10.1002/eap.2245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/20/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based application of bird banding/recovery data to investigate the migration-based drivers of AIV and their relative importance compared to well-characterized local drivers (e.g., demography, environmental persistence). We compared among regression models reflecting hypothesized ecological processes and evaluated their ability to predict AIV in space and time using within and out-of-sample validation. We found that predictors of AIV were associated with multiple mechanisms at local and continental scales. Hypotheses characterizing local epidemic dynamics were strongly supported, with age, the age-specific aggregation of migratory birds in an area and temperature being the best predictors of infection. Hypotheses defining larger, network-based features of the migration processes, such as clustering or between-cluster mixing explained less variation but were also supported. Therefore, our results support a role for local processes in driving the continental distribution of AIV.
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Affiliation(s)
- Erin E. Gorsich
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUnited Kingdom
- The Zeeman Institute: Systems Biology and Infectious Disease Epidemiology Research (SBIDER)University of WarwickCoventryCV4 7ALUnited Kingdom
- Department of BiologyColorado State UniversityFort CollinsColorado80521USA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColorado80521USA
| | - Colleen T. Webb
- Department of BiologyColorado State UniversityFort CollinsColorado80521USA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColorado80521USA
| | - Andrew A. Merton
- Department of StatisticsColorado State UniversityFort CollinsColorado80521USA
| | - Jennifer A. Hoeting
- Department of StatisticsColorado State UniversityFort CollinsColorado80521USA
| | - Ryan S. Miller
- Centers for Epidemiology and Animal HealthUSDA APHIS Veterinary ServicesFort CollinsColorado80526USA
| | - Matthew L. Farnsworth
- Centers for Epidemiology and Animal HealthUSDA APHIS Veterinary ServicesFort CollinsColorado80526USA
| | - Seth R. Swafford
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
- National Wildlife Refuge SystemUS Fish and Wildlife ServiceYazoo CityMississippi39194USA
| | - Thomas J. DeLiberto
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Kerri Pedersen
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
- USDA APHIS Wildlife ServicesRaleighNorth Carolina27606USA
| | - Alan B. Franklin
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Robert G. McLean
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Kenneth R. Wilson
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado80521USA
| | - Paul F. Doherty
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado80521USA
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22
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Trovão NS, Nolting JM, Slemons RD, Nelson MI, Bowman AS. The Evolutionary Dynamics of Influenza A Viruses Circulating in Mallards in Duck Hunting Preserves in Maryland, USA. Microorganisms 2020; 9:microorganisms9010040. [PMID: 33375548 PMCID: PMC7823399 DOI: 10.3390/microorganisms9010040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022] Open
Abstract
Duck hunting preserves (DHP) have resident populations of farm-raised mallard ducks, which create potential foci for the evolution of novel influenza A viruses (IAVs). Through an eleven-year (2003–2013) IAV surveillance project in seven DHPs in Maryland, USA, we frequently identified IAVs in the resident, free-flying mallard ducks (5.8% of cloacal samples were IAV-positive). The IAV population had high genetic diversity, including 12 HA subtypes and 9 NA subtypes. By sequencing the complete genomes of 290 viruses, we determined that genetically diverse IAVs were introduced annually into DHP ducks, predominantly from wild birds in the Anatidae family that inhabit the Atlantic and Mississippi flyways. The relatively low viral gene flow observed out of DHPs suggests that raised mallards do not sustain long-term viral persistence nor do they serve as important sources of new viruses in wild birds. Overall, our findings indicate that DHPs offer reliable samples of the diversity of IAV subtypes, and could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations, which would provide a cost-efficient strategy for long-term IAV monitoring. Such monitoring could allow for early identification and characterization of viruses that threaten bird species of high economic and environmental interest.
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Affiliation(s)
- Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20814, USA; (N.S.T.); (M.I.N.)
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacqueline M. Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
| | - Richard D. Slemons
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20814, USA; (N.S.T.); (M.I.N.)
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
- Correspondence:
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23
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Mateus-Anzola J, Gaytan-Cruz L, Montoya-Carrillo C, Ivan Sánchez-Betancourt J, Zarza H, Segura-Velázquez R, Ojeda-Flores R. Molecular identification and phylogenetic characterization of influenza A virus at a wildlife-livestock interface in Mexico. Transbound Emerg Dis 2020; 68:3563-3573. [PMID: 33350099 DOI: 10.1111/tbed.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
Influenza A virus (IAV) outbreaks constitute a constant threat to public health and pose a remarkable impact on socio-economic systems worldwide. Interactions between wild and domestic birds, humans and swine can lead to spillover events. Backyard livestock systems in proximity to wetlands represent high-risk areas for viral spread. However, some gaps remain in our knowledge of IAV transmission at the wildlife-livestock interface in Mexico. Hence, the study aimed at molecular identification and phylogenetic characterization of IAV in the wild duck-backyard livestock interface at a wetland of Mexico. A total of 875 animals were tested by real-time RT-PCR (qRT-PCR). We detected IAV in 3.68% of the wild ducks sampled during the winter season 2016-2017. Nonetheless, the samples obtained from backyard poultry and swine tested negative. The highest IAV frequency (11.10%) was found in the Mexican duck (Anas diazi). Subtypes H1N1, H3N2 and H5N2 were detected. Phylogenetic analyses revealed that IAV detected in wild birds from the Lerma wetlands was mostly related to swine and poultry IAV strains previously isolated in the United States and Mexico. Except, the UIFMVZ377/H5N2 related to North American waterbirds. In conclusion, the co-circulation of three IAV subtypes in wild ducks close to backyard farms in Mexico, as well as the local identification of influenza viruses genetically related to Mexican and North American IAV strains, highlights the importance of the Lerma marshes for influenza surveillance given the close interaction among wild birds, poultry, pigs and humans.
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Affiliation(s)
- Jessica Mateus-Anzola
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Liliana Gaytan-Cruz
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cecilia Montoya-Carrillo
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Ivan Sánchez-Betancourt
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Heliot Zarza
- Departamento de Ciencias Ambientales, CBS, Universidad Autónoma Metropolitana Unidad Lerma, México, México
| | - René Segura-Velázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Unidad de Investigación, Ciudad de México, México
| | - Rafael Ojeda-Flores
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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Chen YM, Holmes EC, Chen X, Tian JH, Lin XD, Qin XC, Gao WH, Liu J, Wu ZD, Zhang YZ. Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis. Sci Rep 2020; 10:18870. [PMID: 33139761 PMCID: PMC7608656 DOI: 10.1038/s41598-020-75904-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.
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Affiliation(s)
- Yan-Mei Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China
| | - Xin-Cheng Qin
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Wen-Hua Gao
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Jing Liu
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Zhong-Dao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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Lee K, Yu D, Martínez-López B, Yoon H, Kang SI, Hong SK, Lee I, Kang Y, Jeong W, Lee E. Fine-scale tracking of wild waterfowl and their impact on highly pathogenic avian influenza outbreaks in the Republic of Korea, 2014-2015. Sci Rep 2020; 10:18631. [PMID: 33122803 PMCID: PMC7596240 DOI: 10.1038/s41598-020-75698-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
Wild migratory waterfowl are considered one of the most important reservoirs and long-distance carriers of highly pathogenic avian influenza (HPAI). Our study aimed to explore the spatial and temporal characteristics of wild migratory waterfowl’s wintering habitat in the Republic of Korea (ROK) and to evaluate the impact of these habitats on the risk of HPAI outbreaks in commercial poultry farms. The habitat use of 344 wild migratory waterfowl over four migration cycles was estimated based on tracking records. The association of habitat use with HPAI H5N8 outbreaks in poultry farms was evaluated using a multilevel logistic regression model. We found that a poultry farm within a wild waterfowl habitat had a 3–8 times higher risk of HPAI outbreak than poultry farms located outside of the habitat. The range of wild waterfowl habitats increased during autumn migration, and was associated with the epidemic peak of HPAI outbreaks on domestic poultry farms in the ROK. Our findings provide a better understanding of the dynamics of HPAI infection in the wildlife–domestic poultry interface and may help to establish early detection, and cost-effective preventive measures.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Daesung Yu
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea.
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Hachung Yoon
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Sung-Il Kang
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Seong-Keun Hong
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Ilseob Lee
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Yongmyung Kang
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Wooseg Jeong
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
| | - Eunesub Lee
- Veterinary Epidemiology Division, Animal and Plant Quarantine Agency (QIA), Gimcheon, Republic of Korea
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26
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Youk S, Lee DH, Killian ML, Pantin-Jackwood MJ, Swayne DE, Torchetti MK. Highly Pathogenic Avian Influenza A(H7N3) Virus in Poultry, United States, 2020. Emerg Infect Dis 2020; 26:2966-2969. [PMID: 33030423 PMCID: PMC7706930 DOI: 10.3201/eid2612.202790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An outbreak of low-pathogenicity avian influenza A(H7N3) virus of North American wild bird lineage occurred on commercial turkey farms in North Carolina and South Carolina, USA, during March-April 2020. The virus mutated to the highly pathogenic form in 1 house on 1 farm via recombination with host 28S rRNA.
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27
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Luczo JM, Prosser DJ, Pantin-Jackwood MJ, Berlin AM, Spackman E. The pathogenesis of a North American H5N2 clade 2.3.4.4 group A highly pathogenic avian influenza virus in surf scoters (Melanitta perspicillata). BMC Vet Res 2020; 16:351. [PMID: 32967673 PMCID: PMC7513502 DOI: 10.1186/s12917-020-02579-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Background Aquatic waterfowl, particularly those in the order Anseriformes and Charadriiformes, are the ecological reservoir of avian influenza viruses (AIVs). Dabbling ducks play a recognized role in the maintenance and transmission of AIVs. Furthermore, the pathogenesis of highly pathogenic AIV (HPAIV) in dabbling ducks is well characterized. In contrast, the role of diving ducks in HPAIV maintenance and transmission remains unclear. In this study, the pathogenesis of a North American A/Goose/1/Guangdong/96-lineage clade 2.3.4.4 group A H5N2 HPAIV, A/Northern pintail/Washington/40964/2014, in diving sea ducks (surf scoters, Melanitta perspicillata) was characterized. Results Intrachoanal inoculation of surf scoters with A/Northern pintail/Washington/40964/2014 (H5N2) HPAIV induced mild transient clinical disease whilst concomitantly shedding high virus titers for up to 10 days post-inoculation (dpi), particularly from the oropharyngeal route. Virus shedding, albeit at low levels, continued to be detected up to 14 dpi. Two aged ducks that succumbed to HPAIV infection had pathological evidence for co-infection with duck enteritis virus, which was confirmed by molecular approaches. Abundant HPAIV antigen was observed in visceral and central nervous system organs and was associated with histopathological lesions. Conclusions Collectively, surf scoters, are susceptible to HPAIV infection and excrete high titers of HPAIV from the respiratory and cloacal tracts whilst being asymptomatic. The susceptibility of diving sea ducks to H5 HPAIV highlights the need for additional research and surveillance to further understand the contribution of diving ducks to HPAIV ecology.
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Affiliation(s)
- Jasmina M Luczo
- Department of Agriculture-Agricultural Research Service, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, U.S., 934 College Station Road, Athens, GA, 30605, USA
| | - Diann J Prosser
- US Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, MD, 20708, USA
| | - Mary J Pantin-Jackwood
- Department of Agriculture-Agricultural Research Service, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, U.S., 934 College Station Road, Athens, GA, 30605, USA
| | - Alicia M Berlin
- US Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, MD, 20708, USA
| | - Erica Spackman
- Department of Agriculture-Agricultural Research Service, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, U.S., 934 College Station Road, Athens, GA, 30605, USA.
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Wille M, Holmes EC. The Ecology and Evolution of Influenza Viruses. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038489. [PMID: 31871237 DOI: 10.1101/cshperspect.a038489] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The patterns and processes of influenza virus evolution are of fundamental importance, underpinning such traits as the propensity to emerge in new host species and the ability to rapidly generate antigenic variation. Herein, we review key aspects of the ecology and evolution of influenza viruses. We begin with an exploration of the origins of influenza viruses within the orthomyxoviruses, showing how our perception of the evolutionary history of these viruses has been transformed with metagenomic sequencing. We then outline the diversity of virus subtypes in different species and the processes by which these viruses have emerged in new hosts, with a particular focus on the role played by segment reassortment. We then turn our attention to documenting the spread and phylodynamics of seasonal influenza A and B viruses in human populations, including the drivers of antigenic evolution, and finish with a discussion of virus diversity and evolution at the scale of individual hosts.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney 2006, Australia
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Knowledge and remaining gaps on the role of animal and human movements in the poultry production and trade networks in the global spread of avian influenza viruses - A scoping review. PLoS One 2020; 15:e0230567. [PMID: 32196515 PMCID: PMC7083317 DOI: 10.1371/journal.pone.0230567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022] Open
Abstract
Poultry production has significantly increased worldwide, along with the number of avian influenza (AI) outbreaks and the potential threat for human pandemic emergence. The role of wild bird movements in this global spread has been extensively studied while the role of animal, human and fomite movement within commercial poultry production and trade networks remains poorly understood. The aim of this work is to better understand these roles in relation to the different routes of AI spread. A scoping literature review was conducted according to the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) using a search algorithm combining twelve domains linked to AI spread and animal/human movements within poultry production and trade networks. Only 28 out of 3,978 articles retrieved dealt especially with the role of animal, human and fomite movements in AI spread within the international trade network (4 articles), the national trade network (8 articles) and the production network (16 articles). While the role of animal movements in AI spread within national trade networks has been largely identified, human and fomite movements have been considered more at risk for AI spread within national production networks. However, the role of these movements has never been demonstrated with field data, and production networks have only been partially studied and never at international level. The complexity of poultry production networks and the limited access to production and trade data are important barriers to this knowledge. There is a need to study the role of animal and human movements within poultry production and trade networks in the global spread of AI in partnership with both public and private actors to fill this gap.
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Assessing the role of live poultry trade in community-structured transmission of avian influenza in China. Proc Natl Acad Sci U S A 2020; 117:5949-5954. [PMID: 32123088 PMCID: PMC7084072 DOI: 10.1073/pnas.1906954117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The live poultry trade is thought to play an important role in the spread and maintenance of highly pathogenic avian influenza A viruses (HP AIVs) in Asia. Despite an abundance of small-scale observational studies, the role of the poultry trade in disseminating AIV over large geographic areas is still unclear, especially for developing countries with complex poultry production systems. Here we combine virus genomes and reconstructed poultry transportation data to measure and compare the spatial spread in China of three key subtypes of AIV: H5N1, H7N9, and H5N6. Although it is difficult to disentangle the contribution of confounding factors, such as bird migration and spatial distance, we find evidence that the dissemination of these subtypes among domestic poultry is geographically continuous and likely associated with the intensity of the live poultry trade in China. Using two independent data sources and network analysis methods, we report a regional-scale community structure in China that might explain the spread of AIV subtypes in the country. The identification of this structure has the potential to inform more targeted strategies for the prevention and control of AIV in China.
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31
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Twabela AT, Okamatsu M, Tshilenge GM, Mpiana S, Masumu J, Nguyen LT, Matsuno K, Monne I, Zecchin B, Sakoda Y. Molecular, antigenic, and pathogenic characterization of H5N8 highly pathogenic avian influenza viruses isolated in the Democratic Republic of Congo in 2017. Arch Virol 2019; 165:87-96. [PMID: 31707455 DOI: 10.1007/s00705-019-04456-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022]
Abstract
In May 2017, high mortality of chickens and Muscovy ducks due to the H5N8 highly pathogenic avian influenza virus (HPAIV) was reported in the Democratic Republic of Congo (DR Congo). In this study, we assessed the molecular, antigenic, and pathogenic features in poultry of the H5N8 HPAIV from the 2017 Congolese outbreaks. Phylogenetic analysis of the eight viral gene segments revealed that all 12 DR Congo isolates clustered in clade 2.3.4.4B together with other H5N8 HPAIVs isolated in Africa and Eurasia, suggesting a possible common origin of these viruses. Antigenically, a slight difference was observed between the Congolese isolates and a representative virus from group C in the same clade. After intranasal inoculation with a representative DR Congo virus, high pathogenicity was observed in chickens and Muscovy ducks but not in Pekin ducks. Viral replication was higher in chickens than in Muscovy duck and Pekin duck organs; however, neurotropism was pronounced in Muscovy ducks. Our data confirmed the high pathogenicity of the DR Congo virus in chickens and Muscovy ducks, as observed in the field. National awareness and strengthening surveillance in the region are needed to better control HPAIVs.
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Affiliation(s)
- Augustin T Twabela
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.,Central Veterinary Laboratory of Kinshasa, Kinshasa I, Gombe, Democratic Republic of Congo
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | | | - Serge Mpiana
- Central Veterinary Laboratory of Kinshasa, Kinshasa I, Gombe, Democratic Republic of Congo
| | - Justin Masumu
- Central Veterinary Laboratory of Kinshasa, Kinshasa I, Gombe, Democratic Republic of Congo
| | - Lam Thanh Nguyen
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Keita Matsuno
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy
| | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan. .,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan.
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Theys K, Lemey P, Vandamme AM, Baele G. Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. Front Public Health 2019; 7:208. [PMID: 31428595 PMCID: PMC6688121 DOI: 10.3389/fpubh.2019.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 07/12/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.
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Affiliation(s)
- Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
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Marcelino VR, Wille M, Hurt AC, González-Acuña D, Klaassen M, Schlub TE, Eden JS, Shi M, Iredell JR, Sorrell TC, Holmes EC. Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biol 2019; 17:31. [PMID: 30961590 PMCID: PMC6454771 DOI: 10.1186/s12915-019-0649-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations. RESULTS We found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters. CONCLUSIONS These transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.
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Affiliation(s)
- Vanessa R Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia. .,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia. .,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Daniel González-Acuña
- Laboratorio de Parásitos y Enfermedades de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, 3349001, Concepción, Chile
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3216, Australia
| | - Timothy E Schlub
- Faculty of Medicine and Health, Sydney School of Public Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
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A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus. PLoS Comput Biol 2019; 15:e1006875. [PMID: 30865618 PMCID: PMC6433293 DOI: 10.1371/journal.pcbi.1006875] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 03/25/2019] [Accepted: 02/17/2019] [Indexed: 11/30/2022] Open
Abstract
West Nile virus (WNV)—a mosquito-borne arbovirus—entered the USA through New York City in 1999 and spread to the contiguous USA within three years while transitioning from epidemic outbreaks to endemic transmission. The virus is transmitted by vector competent mosquitoes and maintained in the avian populations. WNV spatial distribution is mainly determined by the movement of residential and migratory avian populations. We developed an individual-level heterogeneous network framework across the USA with the goal of understanding the long-range spatial distribution of WNV. To this end, we proposed three distance dispersal kernels model: 1) exponential—short-range dispersal, 2) power-law—long-range dispersal in all directions, and 3) power-law biased by flyway direction —long-range dispersal only along established migratory routes. To select the appropriate dispersal kernel we used the human case data and adopted a model selection framework based on approximate Bayesian computation with sequential Monte Carlo sampling (ABC-SMC). From estimated parameters, we find that the power-law biased by flyway direction kernel is the best kernel to fit WNV human case data, supporting the hypothesis of long-range WNV transmission is mainly along the migratory bird flyways. Through extensive simulation from 2014 to 2016, we proposed and tested hypothetical mitigation strategies and found that mosquito population reduction in the infected states and neighboring states is potentially cost-effective. The underlying pattern of West Nile virus (WNV) geographic spread across the United States is not completely clear, which is a necessary step for continental or state level mitigation strategies to reduce WNV transmission. We report a network model that explains the geographic spread of WNV in the United States. West Nile virus is a mosquito-borne pathogen that infects many avian species with different movement ranges. From our research, we found that migration patterns and routes play an essential role in the WNV spatial distribution. The virus spreads in all directions at short distances because of local birds and short-distance migratory birds. However, the virus also disperses long distances along the avian migratory routes. Our model is designed to be flexible and therefore can be used to explore spreading patterns of other infectious diseases in other geographic locations.
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Ratanakorn P, Suwanpakdee S, Wiriyarat W, Eiamampai K, Chaichoune K, Wiratsudakul A, Sariya L, Puthavathana P. Satellite telemetry tracks flyways of Asian Openbill storks in relation to H5N1 avian influenza spread and ecological change. BMC Vet Res 2018; 14:349. [PMID: 30445946 PMCID: PMC6240270 DOI: 10.1186/s12917-018-1683-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/01/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asian Openbills, Anastomus oscitans, have long been known to migrate from South to Southeast Asia for breeding and nesting. In Thailand, the first outbreak of H5N1 highly pathogenic avian influenza (HPAI) infection in the Openbills coincided with the outbreak in the poultry. Therefore, the flyways of Asian Openbills was determined to study their role in the spread of H5N1 HPAI virus to poultry and wild birds, and also within their flocks. RESULTS Flyways of 5 Openbills from 3 colonies were monitored using Argos satellite transmitters with positioning by Google Earth Programme between 2007 and 2013. None of the Openbills tagged with satellite telemeters moved outside of Thailand. Their home ranges or movement areas varied from 1.6 to 23,608 km2 per month (95% utility distribution). There was no positive result of the viral infection from oral and cloacal swabs of the Openbills and wild birds living in the vicinity by viral isolation and genome detection during 2007 to 2010 whereas the specific antibody was not detected on both Openbills and wild birds by using microneutralization assay after 2008. The movement of these Openbills did not correlate with H5N1 HPAI outbreaks in domestic poultry but correlated with rice crop rotation and populations of the apple snails which are their preferred food. Viral spread within the flocks of Openbills was not detected. CONCLUSIONS This study showed that Openbills played no role in the spread of H5N1 HPAI virus, which was probably due to the very low prevalence of the virus during the monitoring period. This study revealed the ecological factors that control the life cycle of Asian Openbills.
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Affiliation(s)
- Parntep Ratanakorn
- Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Sarin Suwanpakdee
- Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, 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
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Krairat Eiamampai
- Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, 10900, Thailand
| | - Kridsada Chaichoune
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Anuwat Wiratsudakul
- Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - 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
| | - Pilaipan Puthavathana
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand.
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Lisovski S, van Dijk JG, Klinkenberg D, Nolet BA, Fouchier RA, Klaassen M. The roles of migratory and resident birds in local avian influenza infection dynamics. J Appl Ecol 2018; 55:2963-2975. [PMID: 30337766 PMCID: PMC6188652 DOI: 10.1111/1365-2664.13154] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/14/2018] [Indexed: 12/29/2022]
Abstract
Migratory birds are an increasing focus of interest when it comes to infection dynamics and the spread of avian influenza viruses (AIV). However, we lack detailed understanding migratory birds' contribution to local AIV prevalence levels and their downstream socio-economic costs and threats.To explain the potential differential roles of migratory and resident birds in local AIV infection dynamics, we used a susceptible-infectious-recovered (SIR) model. We investigated five (mutually non- exclusive) mechanisms potentially driving observed prevalence patterns: 1) a pronounced birth pulse (e.g. the synchronised annual influx of immunologically naïve individuals), 2) short-term immunity, 3) increase of susceptible migrants, 4) differential susceptibility to infection (i.e. transmission rate) for migrants and residents, and 5) replacement of migrants during peak migration.SIR models describing all possible combinations of the five mechanisms were fitted to individual AIV infection data from a detailed longitudinal surveillance study in the partially migratory mallard duck (Anas platyrhynchos). During autumn and winter, the local resident mallard community also held migratory mallards that exhibited distinct AIV infection dynamics.Replacement of migratory birds during peak migration in autumn was found to be the most important mechanism driving the variation in local AIV infection patterns. This suggests that a constant influx of migratory birds, likely immunological naïve to locally circulating AIV strains, is required to predict the observed temporal prevalence patterns and the distinct differences in prevalence between residents and migrants.Synthesis and applications. Our analysis reveals a key mechanism that could explain the amplifying role of migratory birds in local avian influenza virus infection dynamics; the constant flow and replacement of migratory birds during peak migration. Aside from monitoring efforts, in order to achieve adequate disease management and control in wildlife - with knock-on effects for livestock and humans, - we conclude that it is crucial, in future surveillance studies, to record host demographical parameters such as population density, timing of birth and turnover of migrants.
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Affiliation(s)
- Simeon Lisovski
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, Australia
- Swiss Ornithological Institute, Seerose 1, CH-6204 Sempach, Switzerland
| | - Jacintha G.B. van Dijk
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), The Netherlands
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Don Klinkenberg
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Bart A. Nolet
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), The Netherlands
- Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | | | - Marcel Klaassen
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, Australia
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Belser JA, Brock N, Sun X, Jones J, Zanders N, Hodges E, Pulit-Penaloza JA, Wentworth D, Tumpey TM, Davis T, Maines TR. Mammalian Pathogenesis and Transmission of Avian Influenza A(H7N9) Viruses, Tennessee, USA, 2017. Emerg Infect Dis 2018; 24:149-152. [PMID: 29260672 PMCID: PMC5749443 DOI: 10.3201/eid2401.171574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Infections with low pathogenicity and highly pathogenic avian influenza A(H7N9) viruses affected poultry in 4 states in the southeastern United States in 2017. We evaluated pathogenicity and transmission of representative viruses in mouse and ferret models and examined replication kinetics in human respiratory tract cells. These viruses can cause respiratory infections in mammalian models.
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Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem. J Virol 2018; 92:JVI.00433-18. [PMID: 29769347 PMCID: PMC6052287 DOI: 10.1128/jvi.00433-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/12/2018] [Indexed: 01/17/2023] Open
Abstract
Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian flyway, the East Africa/West Asia flyway, and the Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found a substantial subtype diversity of viruses that varied in prevalence from year to year. Low-pathogenic AIV (LPAIV) subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, and two highly pathogenic AIVs (HPAIVs) belonging to clade 2.3.4.4, H5N5 and H5N8, were found. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide sequence diversity for LPAIVs among different host species. Hemagglutinin clade 2.3.4.4 H5N8 viruses, which circulated in Eurasia during 2014 and 2015, did not reassort, but analysis after their subsequent dissemination during 2016 and 2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions, with maintenance of local AIVs in Georgia, whereas other lineages showed considerable genetic interrelationships with viruses circulating in other parts of Eurasia and Africa, despite relative undersampling in the area. IMPORTANCE Waterbirds (e.g., gulls and ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate the dispersal of AIVs at intercontinental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or reassort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates AIV evolutionary dynamics within a multihost ecosystem at a stopover site where three major migratory flyways intersect. Our analysis of this ecosystem over a 6-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to mitigating both the risk of incursion into domestic poultry and the potential risk to mammalian hosts, including humans.
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