1
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Lee K, Yeom M, Vu TTH, Do HQ, Na W, Lee M, Jeong DG, Cheon DS, Song D. Characterization of highly pathogenic avian influenza A (H5N1) viruses isolated from cats in South Korea, 2023. Emerg Microbes Infect 2024; 13:2290835. [PMID: 38044871 PMCID: PMC10810616 DOI: 10.1080/22221751.2023.2290835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Affiliation(s)
- Kyungmoon Lee
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Minjoo Yeom
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | | | - Hai-Quynh Do
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Woonsung Na
- College of Veterinary Medicine, Chonnam University, Gwangju, South Korea
| | | | - Dae Gwin Jeong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | | | - Daesub Song
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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2
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Yin S, Xu C, Zhang Y, de Boer WF, Mundkur T, Artois J, Velkers FC, Takekawa JY, Si Y, Tian H, Han GZ, Chen Y, Chai H, Cui L, Huang ZYX. Strong and consistent effects of waterbird composition on HPAI H5 occurrences across Europe. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024:e3010. [PMID: 38978282 DOI: 10.1002/eap.3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 07/10/2024]
Abstract
Since 2014, highly pathogenic avian influenza (HPAI) H5 viruses of clade 2.3.4.4 have been dominating the outbreaks across Europe, causing massive deaths among poultry and wild birds. However, the factors shaping these broad-scale outbreak patterns, especially those related to waterbird community composition, remain unclear. In particular, we do not know whether these risk factors differ from those of other H5 clades. Addressing this knowledge gap is important for predicting and preventing future HPAI outbreaks. Using extensive waterbird survey datasets from about 6883 sites, we here explored the effect of waterbird community composition on HPAI H5Nx (clade 2.3.4.4) spatial patterns in the 2016/2017 and 2020/2021 epidemics in Europe, and compared it with the 2005/2006 HPAI H5N1 (clade 2.2) epidemic. We showed that HPAI H5 occurrences in wild birds in the three epidemics were strongly associated with very similar waterbird community attributes, which suggested that, in nature, similar interspecific transmission processes operate between the HPAI H5 subtypes or clades. Importantly, community phylogenetic diversity consistently showed a negative association with H5 occurrence in all three epidemics, suggesting a dilution effect of phylogenetic diversity. In contrast, waterbird community variables showed much weaker associations with HPAI H5Nx occurrence in poultry. Our results demonstrate that models based on previous epidemics can predict future HPAI H5 patterns in wild birds, implying that it is important to include waterbird community factors in future HPAI studies to predict outbreaks and improve surveillance activities.
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Affiliation(s)
- Shenglai Yin
- Department of Zoology, School of Life Sciences, Nanjing Forestry University, Nanjing, China
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chi Xu
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yong Zhang
- Department of Zoology, School of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands
| | | | - Jean Artois
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
| | - Francisca C Velkers
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Yali Si
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Beijing Normal University, Beijing, China
| | - Guan-Zhu Han
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Beijing Normal University, Beijing, China
| | - Hongliang Chai
- Department of Wildlife Conservation and Management, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Lijuan Cui
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zheng Y X Huang
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
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3
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Barnes AP, Sparks N, Helgesen IS, Soliman T. Financial impacts of a housing order on commercial free range egg layers in response to highly pathogenic avian influenza. Prev Vet Med 2024; 228:106209. [PMID: 38714017 DOI: 10.1016/j.prevetmed.2024.106209] [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: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024]
Abstract
Recent annual outbreaks of Highly Pathogenic Avian Influenza (HPAI) have led to mandatory housing orders on commercial free-range flocks. Indefinite periods of housing, after poultry have had access to range, could have production and financial consequences for free range egg producers. The impact of these housing orders on the performance of commercial flocks is seldom explored at a business level, predominantly due to the paucity of commercially sensitive data. The aim of this paper is to assess the financial and production impacts of a housing order on commercial free-range egg layers. We use a unique data set showing week by week performance of layers gathered from 9 UK based farms over the period 2020-2022. These data cover an average of 100,000 laying hens and include two imposed housing orders, in 2020/2021 and in 2021/22. We applied a random intercept linear regression to assess impacts on physical outputs and inputs, bird mortality and the impacts on revenue, feed costs and margin over feed cost. Feed use and feed costs per bird increased during the housing order which is a consequence of increased control over diet intake in housed compared to ranged birds. An increase in revenue was also found, ostensibly due to a higher proportion of large eggs produced, leading to a higher margin over feed cost. Overall, these large commercial poultry sheds were able to mitigate some of the potential adverse economic effects of housing orders. Potential negative impacts may occur dependant on the duration of the housing order and those farms with less control over their input costs.
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Affiliation(s)
- Andrew P Barnes
- Department of Rural Economy, Environment and Society, SRUC, West Mains Road, Edinburgh, Scotland EH9 3JG, UK.
| | - Nick Sparks
- Department of Rural Economy, Environment and Society, SRUC, West Mains Road, Edinburgh, Scotland EH9 3JG, UK
| | - Irmelin S Helgesen
- Department of Economics, NTNU, Postboks 8900, Trondheim, Torgarden 7491, Norway
| | - Tarek Soliman
- Department of Rural Economy, Environment and Society, SRUC, West Mains Road, Edinburgh, Scotland EH9 3JG, UK
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4
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Sah R, Srivastava S, Kumar S, Mehta R, Donovan S, Sierra-Carrero L, Luna C, Woc-Colburn L, Cardona-Ospina JA, Hinestroza-Jordan M, Wessolossky M, Rodriguez-Morales AJ. Concerns on H5N1 avian influenza given the outbreak in U.S. dairy cattle. LANCET REGIONAL HEALTH. AMERICAS 2024; 35:100785. [PMID: 38818112 PMCID: PMC11137502 DOI: 10.1016/j.lana.2024.100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]
Affiliation(s)
- Ranjit Sah
- Green City Hospital, Tokha, Kathmandu, Nepal
- Department of Microbiology, Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, India
- Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Shriyansh Srivastava
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Rachana Mehta
- Dr Lal PathLabs Nepal, Chandol, Kathmandu 44600, Nepal
- Medical Laboratories Techniques Department, AL-Mustaqbal University, 51001, Hillah, Babil, Iraq
| | - Suzanne Donovan
- David Geffen School of Medicine at UCLA Medical Center, Los Angeles, CA, USA
| | | | - Camila Luna
- Faculty of Health Sciences, Universidad Cientifica del Sur, Lima, Peru
| | | | - Jaime A. Cardona-Ospina
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de las Américas-Institución Universitaria Visión de las Américas, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group, Instituto para la Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
| | - Monica Hinestroza-Jordan
- Division of Infectious Diseases, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Mireya Wessolossky
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Cientifica del Sur, Lima, Peru
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de las Américas-Institución Universitaria Visión de las Américas, Pereira, Colombia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
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5
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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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6
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Wang H, Lei D, Xu B, Li X, Fang R, Tang Y. Continuous surveillance of pathogens detects excretion of avian orthoreovirus and parvovirus by several wild waterfowl: possible wild bird reservoirs. Poult Sci 2024; 103:103940. [PMID: 38909506 DOI: 10.1016/j.psj.2024.103940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/25/2024] Open
Abstract
Migratory wild birds can carry various pathogens, such as influenza A virus, which can spread to globally and cause disease outbreaks and epidemics. Continuous epidemiological surveillance of migratory wild birds is of great significance for the early warning, prevention, and control of epidemics. To investigate the pathogen infection status of migratory wild birds in eastern China, fecal samples were collected from wetlands to conduct pathogen surveillance. The results showed that duck orthoreovirus (DRV) and goose parvovirus (GPV) nucleic acid were detected positive in the fecal samples collected from wild ducks, egrets, and swan. Phylogenetic analysis of the amplified viral genes reveals that the isolates were closely related to the prevalent strains in the regions involved in East Asian-Australasian (EAA) migratory flyway. Phylogenetic analysis of the amplified viral genes confirmed that they were closely related to circulating strains in the regions involved in the EAA migration pathway. The findings of this study have expanded the host range of the orthoreovirus and parvovirus, and revealed possible virus transmission between wild migratory birds and poultry.
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Affiliation(s)
- Hongzhi Wang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Di Lei
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Boyi Xu
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Xuyong Li
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Rendong Fang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.
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7
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Bordes L, Gerhards NM, Peters S, van Oort S, Roose M, Dresken R, Venema S, Vrieling M, Engelsma M, van der Poel WHM, de Swart RL. H5N1 clade 2.3.4.4b avian influenza viruses replicate in differentiated bovine airway epithelial cells cultured at air-liquid interface. J Gen Virol 2024; 105. [PMID: 38922678 DOI: 10.1099/jgv.0.002007] [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: 06/27/2024] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses are responsible for disease outbreaks in wild birds and poultry, resulting in devastating losses to the poultry sector. Since 2020, an increasing number of outbreaks of HPAI H5N1 was seen in wild birds. Infections in mammals have become more common, in most cases in carnivores after direct contact with infected birds. Although ruminants were previously not considered a host species for HPAI viruses, in March 2024 multiple outbreaks of HPAI H5N1 were detected in goats and cattle in the United States. Here, we have used primary bronchus-derived well-differentiated bovine airway epithelial cells (WD-AECs) cultured at air-liquid interface to assess the susceptibility and permissiveness of bovine epithelial cells to infection with European H5N1 virus isolates. We inoculated bovine WD-AECs with three low-passage HPAI clade 2.3.4.4b H5N1 virus isolates and detected rapid increases in viral genome loads and infectious virus during the first 24 h post-inoculation, without substantial cytopathogenic effects. Three days post-inoculation infected cells were still detectable by immunofluorescent staining. These data indicate that multiple lineages of HPAI H5N1 may have the propensity to infect the respiratory tract of cattle and support extension of avian influenza surveillance efforts to ruminants. Furthermore, this study underscores the benefit of WD-AEC cultures for pandemic preparedness by providing a rapid and animal-free assessment of the host range of an emerging pathogen.
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Affiliation(s)
- Luca Bordes
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Stan Peters
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Marit Roose
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Romy Dresken
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Sandra Venema
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Marc Engelsma
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Rik L de Swart
- Wageningen Bioveterinary Research, Lelystad, Netherlands
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8
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Tammes P. Spread of avian influenza among poultry specialists in England during winter 2022/23: National poultry housing order and environmental drivers. DIALOGUES IN HEALTH 2024; 4:100165. [PMID: 38516217 PMCID: PMC10954017 DOI: 10.1016/j.dialog.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 03/23/2024]
Abstract
Purpose To examine the impact of the national poultry housing order the UK government introduced on 7 November 2022 on the spreading of the avian influenza virus among poultry premises. Methods A longitudinal design with 15 weeks of infected poultry specialist incidence rates per 100 poultry specialists during the 2022/23 winter for 8 English regions. A multilevel regression model was used to analyse repeated measurements. Time was level-1 unit and regions level-2 unit resulting in 120 observations. Random intercept models included interactions between housing order and weekly infected wild birds, poultry density, or weekly average temperatures divided into terciles. In models where these variables were not included as an interaction term they were introduced as confounders. Results After the introduction of the housing order, it took 3 weeks for a considerable reduction in poultry specialist incidence rates. Reduction in incidence rates was strongest in regions with highest poultry density, from 1.27 (95%CI 0.99 to 1.56) to 0.30 (95%CI 0.09 to 0.52). Considerable reductions were also seen in regions with most detected infected wild birds. Conclusion The housing order was successful in reducing infected poultry specialist incidence rates three weeks after its introduction. Strongest impact in regions with highest poultry density.
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Affiliation(s)
- Peter Tammes
- University of Bristol, Bristol Medical School: Population Health Sciences, Bristol, United Kingdom
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9
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Lin S, Chen J, Li K, Liu Y, Fu S, Xie S, Zha A, Xin A, Han X, Shi Y, Xu L, Liao M, Jia W. Evolutionary dynamics and comparative pathogenicity of clade 2.3.4.4b H5 subtype avian influenza viruses, China, 2021-2022. Virol Sin 2024; 39:358-368. [PMID: 38679333 DOI: 10.1016/j.virs.2024.04.004] [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: 09/26/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
The recent concurrent emergence of H5N1, H5N6, and H5N8 avian influenza viruses (AIVs) has led to significant avian mortality globally. Since 2020, frequent human-animal interactions have been documented. To gain insight into the novel H5 subtype AIVs (i.e., H5N1, H5N6 and H5N8), we collected 6102 samples from various regions of China between January 2021 and September 2022, and identified 41 H5Nx strains. Comparative analyses on the evolution and biological properties of these isolates were conducted. Phylogenetic analysis revealed that the 41 H5Nx strains belonged to clade 2.3.4.4b, with 13 related to H5N1, 19 to H5N6, and 9 to H5N8. Analysis based on global 2.3.4.4b viruses showed that all the viruses described in this study were likely originated from H5N8, exhibiting a heterogeneous evolutionary history between H5N1 and H5N6 during 2015-2022 worldwide. H5N1 showed a higher rate of evolution in 2021-2022 and more sites under positive selection pressure in 2015-2022. The antigenic profiles of the novel H5N1 and H5N6 exhibited notable variations. Further hemagglutination inhibition assay suggested that some A(H5N1) viruses may be antigenically distinct from the circulating H5N6 and H5N8 strains. Mammalian challenge assays demonstrated that the H5N8 virus (21GD001_H5N8) displayed the highest pathogenicity in mice, followed by the H5N1 virus (B1557_H5N1) and then the H5N6 virus (220086_H5N6), suggesting a heterogeneous virulence profile of H5 AIVs in the mammalian hosts. Based on the above results, we speculate that A(H5N1) viruses have a higher risk of emergence in the future. Collectively, these findings unveil a new landscape of different evolutionary history and biological characteristics of novel H5 AIVs in clade 2.3.4.4b, contributing to a better understanding of designing more effective strategies for the prevention and control of novel H5 AIVs.
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MESH Headings
- Animals
- China/epidemiology
- Phylogeny
- Influenza in Birds/virology
- Influenza in Birds/epidemiology
- Evolution, Molecular
- Mice
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A Virus, H5N1 Subtype/classification
- Influenza A Virus, H5N1 Subtype/isolation & purification
- Influenza A Virus, H5N8 Subtype/genetics
- Influenza A Virus, H5N8 Subtype/pathogenicity
- Influenza A Virus, H5N8 Subtype/classification
- Influenza A Virus, H5N8 Subtype/isolation & purification
- Virulence
- Influenza A virus/genetics
- Influenza A virus/pathogenicity
- Influenza A virus/classification
- Chickens/virology
- Mice, Inbred BALB C
- Female
- Birds/virology
- Humans
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Affiliation(s)
- Siru Lin
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Junhong Chen
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ke Li
- Institute of Poultry Management and Diseases, Yunnan Animal Science and Veterinary Institute, Kunming, 650000, China
| | - Yang Liu
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Siyuan Fu
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Shumin Xie
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Aimin Zha
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Aiguo Xin
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Xinyu Han
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Shi
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Lingyu Xu
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, 510642, China.
| | - Weixin Jia
- National Avian Influenza Para-Reference Laboratory, Guangdong Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, 510642, China.
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10
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Shemmings-Payne W, De Silva D, Warren CJ, Thomas S, Slomka MJ, Reid SM, James J, Banyard AC, Brown IH, Ward AI. Repeatability and reproducibility of hunter-harvest sampling for avian influenza virus surveillance in Great Britain. Res Vet Sci 2024; 173:105279. [PMID: 38704977 DOI: 10.1016/j.rvsc.2024.105279] [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: 10/11/2023] [Revised: 02/20/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Emerging pathogens can threaten human and animal health, necessitating reliable surveillance schemes to enable preparedness. We evaluated the repeatability and reproducibility of a method developed previously during a single year at one study site. Hunter-harvested ducks and geese were sampled for avian influenza virus at three discrete locations in the UK. H5N1 highly pathogenic avian influenza (HPAIV) was detected in four species (mallard [Anas platyrhynchos], Eurasian teal [Anas crecca], Eurasian wigeon [Mareca penelope] and pink-footed goose [Anser brachyrhynchus]) across all three locations and two non-HPAIV H5N1, influenza A positive detections were made from a mallard and Eurasian wigeon at two locations. Virus was detected within 1-to-4 days of sampling at every location. Application of rapid diagnostic methods to samples collected from hunter-harvested waterfowl offers potential as an early warning system for the surveillance and monitoring of emerging and existing strains of avian influenza A viruses in key avian species.
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Affiliation(s)
| | - Dilhani De Silva
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK
| | - Caroline J Warren
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK
| | - Saumya Thomas
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK
| | - Marek J Slomka
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK
| | - Scott M Reid
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK
| | - Joe James
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK; WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone KT15 3NB, UK
| | - Ashley C Banyard
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK; WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone KT15 3NB, UK
| | - Ian H Brown
- Animal and Plant Health Agency, Weybridge, New Haw, Surrey KT15 3NB, UK; WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone KT15 3NB, UK
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11
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Furey C, Scher G, Ye N, Kercher L, DeBeauchamp J, Crumpton JC, Jeevan T, Patton C, Franks J, Rubrum A, Alameh MG, Fan SHY, Phan AT, Hunter CA, Webby RJ, Weissman D, Hensley SE. Development of a nucleoside-modified mRNA vaccine against clade 2.3.4.4b H5 highly pathogenic avian influenza virus. Nat Commun 2024; 15:4350. [PMID: 38782954 PMCID: PMC11116520 DOI: 10.1038/s41467-024-48555-z] [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: 05/04/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
mRNA lipid nanoparticle (LNP) vaccines would be useful during an influenza virus pandemic since they can be produced rapidly and do not require the generation of egg-adapted vaccine seed stocks. Highly pathogenic avian influenza viruses from H5 clade 2.3.4.4b are circulating at unprecedently high levels in wild and domestic birds and have the potential to adapt to humans. Here, we generate an mRNA lipid nanoparticle (LNP) vaccine encoding the hemagglutinin (HA) glycoprotein from a clade 2.3.4.4b H5 isolate. The H5 mRNA-LNP vaccine elicits strong T cell and antibody responses in female mice, including neutralizing antibodies and broadly-reactive anti-HA stalk antibodies. The H5 mRNA-LNP vaccine elicits antibodies at similar levels compared to whole inactivated vaccines in female mice with and without prior H1N1 exposures. Finally, we find that the H5 mRNA-LNP vaccine is immunogenic in male ferrets and prevents morbidity and mortality of animals following 2.3.4.4b H5N1 challenge. Together, our data demonstrate that a monovalent mRNA-LNP vaccine expressing 2.3.4.4b H5 is immunogenic and protective in pre-clinical animal models.
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MESH Headings
- Animals
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Female
- Mice
- Ferrets
- Nanoparticles/chemistry
- Male
- Influenza A Virus, H5N1 Subtype/immunology
- Influenza A Virus, H5N1 Subtype/genetics
- Antibodies, Viral/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/virology
- mRNA Vaccines/immunology
- Antibodies, Neutralizing/immunology
- Mice, Inbred BALB C
- Influenza in Birds/prevention & control
- Influenza in Birds/immunology
- Influenza in Birds/virology
- Humans
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Messenger/metabolism
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Birds/virology
- Lipids/chemistry
- Liposomes
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Affiliation(s)
- Colleen Furey
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabrielle Scher
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Naiqing Ye
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lisa Kercher
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeri Carol Crumpton
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Trushar Jeevan
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher Patton
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - John Franks
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam Rubrum
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mohamad-Gabriel Alameh
- Infectious Disease Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Anthony T Phan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Drew Weissman
- Infectious Disease Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Graziosi G, Lupini C, Favera FD, Martini G, Dosa G, Trevisani G, Garavini G, Mannelli A, Catelli E. Characterizing the domestic-wild bird interface through camera traps in an area at risk for avian influenza introduction in Northern Italy. Poult Sci 2024; 103:103892. [PMID: 38865769 PMCID: PMC11223120 DOI: 10.1016/j.psj.2024.103892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
Direct or indirect interactions between sympatric wildlife and poultry can lead to interspecies disease transmission. Particularly, avian influenza (AI) is a viral epidemic disease for which the poultry-wild bird interface shapes the risks of new viral introductions into poultry holdings. Given this background, the study hereby presented aimed to identify wild bird species in poultry house surroundings and characterize the spatiotemporal patterns of these visits. Eight camera traps were deployed for a year (January to December 2021) in 3 commercial chicken layer farms, including free-range and barn-type setups, located in a densely populated poultry area in Northern Italy at high risk for AI introduction via wild birds. Camera traps' positions were chosen based on wildlife signs identified during preliminary visits to the establishments studied. Various methods, including time series analysis, correspondence analysis, and generalized linear models, were employed to analyze the daily wild bird visits. A total of 1,958 camera trap days yielded 5,978 videos of wild birds from 27 different species and 16 taxonomic families. The animals were predominantly engaged in foraging activities nearby poultry houses. Eurasian magpies (Pica pica), ring-necked pheasants (Phasianus colchicus), and Eurasian collared doves (Streptopelia decaocto) were the most frequent visitors. Mallards (Anas platyrhynchos), an AI reservoir species, were observed only in a farm located next to a fishing sport lake. Time series analysis indicated that wild bird visits increased during spring and winter. Farm and camera trap location also influenced visit frequencies. Overall, the results highlighted specific species that could be prioritized for future AI epidemiological surveys. However, further research is required to assess their susceptibility and infectivity to currently circulating AI viruses, essential for identifying novel bridge hosts.
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Affiliation(s)
- Giulia Graziosi
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy.
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
| | - Francesco Dalla Favera
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
| | - Gabriella Martini
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), Imola, Bologna 40026, Italy
| | - Geremia Dosa
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), Imola, Bologna 40026, Italy
| | | | - Gloria Garavini
- Veterinary Services of Eurovo Group, Imola, Bologna 40026, Italy
| | - Alessandro Mannelli
- Department of Veterinary Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
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13
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Acharya KP, Phuyal S. To vaccinate or not against highly pathogenic avian influenza? THE LANCET. MICROBE 2024:S2666-5247(24)00107-1. [PMID: 38761814 DOI: 10.1016/s2666-5247(24)00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/20/2024]
Affiliation(s)
- Krishna Prasad Acharya
- Animal Disease Investigation and Control Division (ADICD), Department of Livestock Services (DLS), Hariharbhawan, Lalitpur 44600, Nepal.
| | - Sarita Phuyal
- Central Referral Veterinary Hospital, Department of Livestock Services (DLS), Tripureshwar, Kathmandu, Nepal
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14
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Krueger A, Myles DJF, Rice CP, Taylor TK, Hurwitz C, Morris J, Robinson S. Responding to avian influenza A H5N1 detection on a hospital property in Maine-An interdisciplinary approach. Zoonoses Public Health 2024; 71:331-335. [PMID: 38009284 DOI: 10.1111/zph.13097] [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: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/10/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND The risk of infection with avian influenza A viruses currently circulating in wild and domestic birds in the Americas is considered low for the general public; however, detections in humans have been reported and warning signs of increased zoonotic potential have been identified. In December 2022, two Canada geese residing on the grounds of an urban hospital in Maine tested positive for influenza A H5N1 clade 2.3.4.4b. AIMS Given the opportunity for exposure to staff and hospital visitors through potentially infected faeces on the property, public health authorities determined mitigation efforts were needed to prevent the spread of disease. The ensuing response relied on collaboration between the public health and animal health agencies to guide the hospital through efforts in preventing possible zoonotic transmission to humans. MATERIALS AND METHODS Mitigation efforts included staff communication and education, environmental cleaning and disinfection, enhanced illness surveillance among staff and patients, and exposure and source reduction. RESULTS No human H5N1 cases were identified, and no additional detections in birds on the property occurred. Hospital staff identified barriers to preparedness resulting from a lack of understanding of avian influenza A viruses and transmission prevention methods, including avian influenza risk in resident wild bird populations and proper wildlife management methods. CONCLUSION As this virus continues to circulate at the animal-human interface, this event and resulting response highlights the need for influenza A H5N1 risk awareness and guidance for facilities and groups not traditionally involved in avian influenza responses.
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Affiliation(s)
- Anna Krueger
- Maine Center for Disease Control and Prevention, Augusta, Maine, United States
| | - Devin J F Myles
- Maine Center for Disease Control and Prevention, Augusta, Maine, United States
- MCD Global Health, Hallowell, Maine, United States
| | - Carrie P Rice
- Maine Center for Disease Control and Prevention, Augusta, Maine, United States
- MCD Global Health, Hallowell, Maine, United States
| | - Tegwin K Taylor
- Maine Department of Inland Fisheries & Wildlife, Augusta, Maine, United States
| | - Carolyn Hurwitz
- Maine Department of Agriculture, Conservation & Forestry, Augusta, Maine, United States
| | - Jesse Morris
- United States Department of Agriculture Animal and Plant Health Inspection Service, Riverdale, Maryland, United States
| | - Sara Robinson
- Maine Center for Disease Control and Prevention, Augusta, Maine, United States
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15
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Focosi D, Franchini M, Senefeld JW, Joyner MJ, Sullivan DJ, Pekosz A, Maggi F, Casadevall A. Passive immunotherapies for the next influenza pandemic. Rev Med Virol 2024; 34:e2533. [PMID: 38635404 DOI: 10.1002/rmv.2533] [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: 10/17/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Influenzavirus is among the most relevant candidates for a next pandemic. We review here the phylogeny of former influenza pandemics, and discuss candidate lineages. After briefly reviewing the other existing antiviral options, we discuss in detail the evidences supporting the efficacy of passive immunotherapies against influenzavirus, with a focus on convalescent plasma.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Massimo Franchini
- Division of Hematology and Transfusion Medicine, Mantua Hospital, Mantua, Italy
| | - Jonathon W Senefeld
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Kinesiology and Community Health, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Michael J Joyner
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - David J Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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16
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Ahrens AK, Jónsson SR, Svansson V, Brugger B, Beer M, Harder TC, Pohlmann A. Iceland: an underestimated hub for the spread of high-pathogenicity avian influenza viruses in the North Atlantic. J Gen Virol 2024; 105:001985. [PMID: 38695722 PMCID: PMC11170123 DOI: 10.1099/jgv.0.001985] [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: 02/02/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
High-pathogenicity avian influenza viruses (HPAIVs) of the goose/Guangdong lineage are enzootically circulating in wild bird populations worldwide. This increases the risk of entry into poultry production and spill-over to mammalian species, including humans. Better understanding of the ecological and epizootiological networks of these viruses is essential to optimize mitigation measures. Based on full genome sequences of 26 HPAIV samples from Iceland, which were collected between spring and autumn 2022, as well as 1 sample from the 2023 summer period, we show that 3 different genotypes of HPAIV H5N1 clade 2.3.4.4b were circulating within the wild bird population in Iceland in 2022. Furthermore, in 2023 we observed a novel introduction of HPAIV H5N5 of the same clade to Iceland. The data support the role of Iceland as an utmost northwestern distribution area in Europe that might act also as a potential bridging point for intercontinental spread of HPAIV across the North Atlantic.
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Affiliation(s)
- Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald –Isle of Riems, Germany
| | - Stefán Ragnar Jónsson
- The Institute for Experimental Pathology at Keldur, University of Iceland, Reykjavík, Iceland
| | - Vilhjálmur Svansson
- The Institute for Experimental Pathology at Keldur, University of Iceland, Reykjavík, Iceland
| | - Brigitte Brugger
- The Icelandic Food and Veterinary Authority (MAST), Austurvegi 64, Selfossi, Iceland
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald –Isle of Riems, Germany
| | - Timm C. Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald –Isle of Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald –Isle of Riems, Germany
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17
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Mao Q, Li Z, Li Y, Zhang Y, Liu S, Yin X, Peng C, Ma R, Li J, Hou G, Jiang W, Liu H. H5N1 high pathogenicity avian influenza virus in migratory birds exhibiting low pathogenicity in mallards increases its risk of transmission and spread in poultry. Vet Microbiol 2024; 292:110038. [PMID: 38458047 DOI: 10.1016/j.vetmic.2024.110038] [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: 01/24/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
In 2020, an H5N1 avian influenza virus of clade 2.3.4.4b was detected in Europe for the first time and was spread throughout the world by wild migratory birds, resulting in the culling of an unprecedented number of wild birds and poultry due to the epidemic. In February 2023, we isolated and identified a strain of H5N1 high pathogenicity avian influenza virus from a swab sample from a grey crane in Ningxia, China. Phylogenetic analysis of the Hemagglutinin (HA) gene showed that the virus belonged to clade 2.3.4.4b, and several gene segments were closely related to H5N1 viruses infecting humans in China. Analysis of key amino acid sites revealed that the virus contained multiple amino acid substitutions that facilitate enhanced viral replication and mammalian pathogenicity. The results of animal challenge experiments showed that the virus is highly pathogenic to chickens, moderately pathogenic to BALB/c mice, and highly infectious but not lethal to mallards. Moreover, the virus exhibited minor antigenic drift compared with the H5-Re14 vaccine strain. To this end, we need to pay more attention to the monitoring of wild birds to prevent further spread of viruses to poultry and mammals, including humans.
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Affiliation(s)
- Qiuyan Mao
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China; College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou 311300, PR China
| | - Zhixin Li
- Ningxia Hui Autonomous Region Animal Disease Prevention and Control Center, Yinchuan 750001, PR China
| | - Yuecheng Li
- Monitoring Center for Terrestrial Wildlife Epidemic Diseases, Yinchuan 750001, PR China
| | - Yaxin Zhang
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China; College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Shuo Liu
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China
| | - Xin Yin
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China
| | - Cheng Peng
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China
| | - Rui Ma
- Monitoring Center for Terrestrial Wildlife Epidemic Diseases, Yinchuan 750001, PR China
| | - Jinping Li
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China
| | - Guangyu Hou
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China
| | - Wenming Jiang
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China.
| | - Hualei Liu
- Avian Diseases Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, PR China.
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18
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Fusaro A, Zecchin B, Giussani E, Palumbo E, Agüero-García M, Bachofen C, Bálint Á, Banihashem F, Banyard AC, Beerens N, Bourg M, Briand FX, Bröjer C, Brown IH, Brugger B, Byrne AMP, Cana A, Christodoulou V, Dirbakova Z, Fagulha T, Fouchier RAM, Garza-Cuartero L, Georgiades G, Gjerset B, Grasland B, Groza O, Harder T, Henriques AM, Hjulsager CK, Ivanova E, Janeliunas Z, Krivko L, Lemon K, Liang Y, Lika A, Malik P, McMenamy MJ, Nagy A, Nurmoja I, Onita I, Pohlmann A, Revilla-Fernández S, Sánchez-Sánchez A, Savic V, Slavec B, Smietanka K, Snoeck CJ, Steensels M, Svansson V, Swieton E, Tammiranta N, Tinak M, Van Borm S, Zohari S, Adlhoch C, Baldinelli F, Terregino C, Monne I. High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe-Why trends of virus evolution are more difficult to predict. Virus Evol 2024; 10:veae027. [PMID: 38699215 PMCID: PMC11065109 DOI: 10.1093/ve/veae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.
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Affiliation(s)
- Alice Fusaro
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Bianca Zecchin
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Edoardo Giussani
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Elisa Palumbo
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Montserrat Agüero-García
- Ministry of Agriculture, Fisheries and Food, Laboratorio Central de Veterinaria (LCV), Ctra. M-106, Km 1,4 Algete, Madrid 28110, Spain
| | - Claudia Bachofen
- Federal Department of Home Affairs FDHA Institute of Virology and Immunology IVI, Sensemattstrasse 293, Mittelhäusern 3147, Switzerland
| | - Ádám Bálint
- Veterinary Diagnostic Directorate (NEBIH), Laboratory of Virology, National Food Chain Safety Office, Tábornok utca 2, Budapest 1143, Hungary
| | - Fereshteh Banihashem
- Department of Microbiology, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Ashley C Banyard
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Nancy Beerens
- Department of Virology Wageningen Bioveterinary Research, Houtribweg 39, Lelystad 8221 RA, The Netherlands
| | - Manon Bourg
- Luxembourgish Veterinary and Food Administration (ALVA), State Veterinary Laboratory, 1 Rue Louis Rech, Dudelange 3555, Luxembourg
| | - Francois-Xavier Briand
- Agence Nationale de Sécurité Sanitaire, de l’Alimentation, de l’Environnement et du Travail, Laboratoire de Ploufragan-Plouzané-Niort, Unité de Virologie, Immunologie, Parasitologie Avaires et Cunicoles, 41 Rue de Beaucemaine – BP 53, Ploufragan 22440, France
| | - Caroline Bröjer
- Department of Pathology and Wildlife Disease, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Ian H Brown
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Brigitte Brugger
- Icelandic Food and Veterinary Authority, Austurvegur 64, Selfoss 800, Iceland
| | - Alexander M P Byrne
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Armend Cana
- Kosovo Food and Veterinary Agency, Sector of Serology and Molecular Diagnostics, Kosovo Food and Veterinary Laboratory, Str Lidhja e Pejes, Prishtina 10000, Kosovo
| | - Vasiliki Christodoulou
- Laboratory for Animal Health Virology Section Veterinary Services (1417), 79, Athalassa Avenue Aglantzia, Nicosia 2109, Cyprus
| | - Zuzana Dirbakova
- Department of Animal Health, State Veterinary Institute, Pod Dráhami 918, Zvolen 96086, Slovakia
| | - Teresa Fagulha
- I.P. (INIAV, I.P.), Avenida da República, Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras 2780 – 157, Portugal
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Dr. Molewaterplein 40, Rotterdam 3015 GD, The Netherlands
| | - Laura Garza-Cuartero
- Department of Agriculture, Food and the Marine, Central Veterinary Research Laboratory (CVRL), Backweston Campus, Stacumny Lane, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - George Georgiades
- Thessaloniki Veterinary Centre (TVC), Department of Avian Diseases, 26th October Street 80, Thessaloniki 54627, Greece
| | - Britt Gjerset
- Immunology & Virology department, Norwegian Veterinary Institute, Arboretveien 57, Oslo Pb 64, N-1431 Ås, Norway
| | - Beatrice Grasland
- Agence Nationale de Sécurité Sanitaire, de l’Alimentation, de l’Environnement et du Travail, Laboratoire de Ploufragan-Plouzané-Niort, Unité de Virologie, Immunologie, Parasitologie Avaires et Cunicoles, 41 Rue de Beaucemaine – BP 53, Ploufragan 22440, France
| | - Oxana Groza
- Republican Center for Veterinary Diagnostics (NRL), 3 street Murelor, Chisinau 2051, Republic of Moldova
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Ana Margarida Henriques
- I.P. (INIAV, I.P.), Avenida da República, Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras 2780 – 157, Portugal
| | - Charlotte Kristiane Hjulsager
- Department for Virus and Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, Copenhagen DK-2300, Denmark
| | - Emiliya Ivanova
- National Reference Laboratory for Avian Influenza and Newcastle Disease, National Diagnostic and Research Veterinary Medical Institute (NDRVMI), 190 Lomsko Shose Blvd., Sofia 1231, Bulgaria
| | - Zygimantas Janeliunas
- National Food and Veterinary Risk Assessment Institute (NFVRAI), Kairiukscio str. 10, Vilnius 08409, Lithuania
| | - Laura Krivko
- Institute of Food Safety, Animal Health and Environment (BIOR), Laboratory of Microbilogy and Pathology, 3 Lejupes Street, Riga 1076, Latvia
| | - Ken Lemon
- Virological Molecular Diagnostic Laboratory, Veterinary Sciences Division, Department of Virology, Agri-Food and Bioscience Institute (AFBI), Stoney Road, Belfast BT4 3SD, Northern Ireland
| | - Yuan Liang
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, Frederiksberg 1870, Denmark
| | - Aldin Lika
- Animal Health Department, Food Safety and Veterinary Institute, Rruga Aleksandër Moisiu 10, Tirana 1001, Albania
| | - Péter Malik
- Veterinary Diagnostic Directorate (NEBIH), Laboratory of Virology, National Food Chain Safety Office, Tábornok utca 2, Budapest 1143, Hungary
| | - Michael J McMenamy
- Virological Molecular Diagnostic Laboratory, Veterinary Sciences Division, Department of Virology, Agri-Food and Bioscience Institute (AFBI), Stoney Road, Belfast BT4 3SD, Northern Ireland
| | - Alexander Nagy
- Department of Molecular Biology, State Veterinary Institute Prague, Sídlištní 136/24, Praha 6-Lysolaje 16503, Czech Republic
| | - Imbi Nurmoja
- National Centre for Laboratory Research and Risk Assessment (LABRIS), Kreutzwaldi 30, Tartu 51006, Estonia
| | - Iuliana Onita
- Institute for Diagnosis and Animal Health (IDAH), Str. Dr. Staicovici 63, Bucharest 050557, Romania
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Sandra Revilla-Fernández
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Robert Koch Gasse 17, Mödling 2340, Austria
| | - Azucena Sánchez-Sánchez
- Ministry of Agriculture, Fisheries and Food, Laboratorio Central de Veterinaria (LCV), Ctra. M-106, Km 1,4 Algete, Madrid 28110, Spain
| | - Vladimir Savic
- Croatian Veterinary Institute, Poultry Centre, Heinzelova 55, Zagreb 10000, Croatia
| | - Brigita Slavec
- University of Ljubljana – Veterinary Faculty/National Veterinary Institute, Gerbičeva 60, Ljubljana 1000, Slovenia
| | - Krzysztof Smietanka
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantow 57, Puławy 24-100, Poland
| | - Chantal J Snoeck
- Luxembourg Institute of Health (LIH), Department of Infection and Immunity, 29 Rue Henri Koch, Esch-sur-Alzette 4354, Luxembourg
| | - Mieke Steensels
- Avian Virology and Immunology, Sciensano, Rue Groeselenberg 99, Ukkel 1180, Ukkel, Belgium
| | - Vilhjálmur Svansson
- Biomedical Center, Institute for Experimental Pathology, University of Iceland, Keldnavegi 3 112 Reykjavík Ssn. 650269 4549, Keldur 851, Iceland
| | - Edyta Swieton
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantow 57, Puławy 24-100, Poland
| | - Niina Tammiranta
- Finnish Food Authority, Animal Health Diagnostic Unit, Veterinary Virology, Mustialankatu 3, Helsinki FI-00790, Finland
| | - Martin Tinak
- Department of Animal Health, State Veterinary Institute, Pod Dráhami 918, Zvolen 96086, Slovakia
| | - Steven Van Borm
- Avian Virology and Immunology, Sciensano, Rue Groeselenberg 99, Ukkel 1180, Ukkel, Belgium
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Cornelia Adlhoch
- European Centre for Disease Prevention and Control, Gustav III:s boulevard 40, Solna 169 73, Sweden
| | | | - Calogero Terregino
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Isabella Monne
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
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Reperant L, Russell CA, Osterhaus A. Scientific highlights of the 9th ESWI Influenza Conference. ONE HEALTH OUTLOOK 2024; 6:5. [PMID: 38561784 PMCID: PMC10986029 DOI: 10.1186/s42522-024-00099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The European Scientific Working Group on Influenza (ESWI) held the 9th ESWI Influenza Conference in Valencia from 17-20 September 2023. Here we provide a summary of twelve key presentations, covering major topics on influenza virus, respiratory syncytial virus (RSV) and SARS coronavirus 2 (SARS-CoV-2) including: infection processes beyond acute respiratory disease, long COVID, vaccines against influenza and RSV, the implications of the potential extinction of influenza B virus Yamagata lineage, and the threats posed by zoonotic highly pathogenic avian influenza viruses.
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Affiliation(s)
| | - Colin A Russell
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Albert Osterhaus
- Center of Infection Medicine and Zoonosis Research and the University of Veterinary Medicine Hannover, Hannover, Germany.
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20
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Graziosi G, Lupini C, Gobbo F, Zecchin B, Quaglia G, Pedrazzoli S, Lizzi G, Dosa G, Martini G, Terregino C, Catelli E. Genetic Diversity of Avian Influenza Viruses Detected in Waterbirds in Northeast Italy Using Two Different Sampling Strategies. Animals (Basel) 2024; 14:1018. [PMID: 38612257 PMCID: PMC11010841 DOI: 10.3390/ani14071018] [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: 02/28/2024] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Avian influenza viruses (AIVs), which circulate endemically in wild aquatic birds, pose a significant threat to poultry and raise concerns for their zoonotic potential. From August 2021 to April 2022, a multi-site cross-sectional study involving active AIV epidemiological monitoring was conducted in wetlands of the Emilia-Romagna region, northern Italy, adjacent to densely populated poultry areas. A total of 129 cloacal swab samples (CSs) and 407 avian faecal droppings samples (FDs) were collected, with 7 CSs (5.4%) and 4 FDs (1%) testing positive for the AIV matrix gene through rRT-PCR. A COI-barcoding protocol was applied to recognize the species of origin of AIV-positive FDs. Multiple low-pathogenic AIV subtypes were identified, and five of these were isolated, including an H5N3, an H1N1, and three H9N2 in wild ducks. Following whole-genome sequencing, phylogenetic analyses of the hereby obtained strains showed close genetic relationships with AIVs detected in countries along the Black Sea/Mediterranean migratory flyway. Notably, none of the analyzed gene segments were genetically related to HPAI H5N1 viruses of clade 2.3.4.4b isolated from Italian poultry during the concurrent 2021-2022 epidemic. Overall, the detected AIV genetic diversity emphasizes the necessity for ongoing monitoring in wild hosts using diverse sampling strategies and whole-genome sequencing.
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Affiliation(s)
- Giulia Graziosi
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
| | - Federica Gobbo
- Comparative Biomedical Sciences Division, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, PD, Italy; (F.G.); (B.Z.); (C.T.)
| | - Bianca Zecchin
- Comparative Biomedical Sciences Division, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, PD, Italy; (F.G.); (B.Z.); (C.T.)
| | - Giulia Quaglia
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
| | - Sara Pedrazzoli
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
| | - Gabriele Lizzi
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
| | - Geremia Dosa
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), 40026 Imola, BO, Italy; (G.D.); (G.M.)
| | - Gabriella Martini
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), 40026 Imola, BO, Italy; (G.D.); (G.M.)
| | - Calogero Terregino
- Comparative Biomedical Sciences Division, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, PD, Italy; (F.G.); (B.Z.); (C.T.)
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, BO, Italy; (C.L.); (G.Q.); (S.P.); (G.L.); (E.C.)
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21
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Zeng J, Du F, Xiao L, Sun H, Lu L, Lei W, Zheng J, Wang L, Shu S, Li Y, Zhang Q, Tang K, Sun Q, Zhang C, Long H, Qiu Z, Zhai K, Li Z, Zhang G, Sun Y, Wang D, Zhang Z, Lycett SJ, Gao GF, Shu Y, Liu J, Du X, Pu J. Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic. J Virol 2024; 98:e0140123. [PMID: 38358287 PMCID: PMC10949427 DOI: 10.1128/jvi.01401-23] [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: 09/12/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.
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Affiliation(s)
- Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Fanshu Du
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Linna Xiao
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Honglei Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Lu
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jialu Zheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Lu Wang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Sicheng Shu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yudong Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiang Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Kang Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qianru Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zekai Qiu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ke Zhai
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zhichao Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Geli Zhang
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Yipeng Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhengwang Zhang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Samantha J. Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology of Chinese Academy of Medical Science (CAMS)/Peking Union Medical College (PUMC), Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Juan Pu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Valentin J, Ingrao F, Rauw F, Lambrecht B. Protection conferred by an H5 DNA vaccine against highly pathogenic avian influenza in chickens: The effect of vaccination schedules. Vaccine 2024; 42:1487-1497. [PMID: 38350766 DOI: 10.1016/j.vaccine.2023.11.058] [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: 07/14/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 02/15/2024]
Abstract
H5 highly pathogenic avian influenza (HPAI) viruses of the Asian lineage (A/goose/Guangdong/1/96) belonging to clade 2.3.4.4 have spread worldwide through wild bird migration in two major waves: in 2014/2015 (clade 2.3.4.4c), and since 2016 up to now (clade 2.3.4.4b). Due to the increasing risk of these H5 HPAI viruses to establish and persist in the wild bird population, implementing vaccination in certain sensitive areas could be a complementary measure to the disease control strategies already applied. In this study, the efficacy of a novel DNA vaccine, encoding a H5 gene (A/gyrfalcon/Washington/41088-6/2014 strain) of clade 2.3.4.4c was evaluated in specific pathogen-free (SPF) white leghorn chickens against a homologous and heterologous H5 HPAI viruses. A single vaccination at 2 weeks of age (1 dose), and a vaccination at 2 weeks of age, boosted at 4 weeks (2 doses), with or without adjuvant were characterized. The groups that received 1 dose with or without adjuvant as well as 2 doses with adjuvant demonstrated full clinical protection and a significant or complete reduction of viral shedding against homologous challenge at 6 and 25 weeks of age. The heterologous clade 2.3.4.4b challenge of 6-week-old chickens vaccinated with 2 doses with or without adjuvant showed similar results, indicating good cross-protection induced by the DNA vaccine. Long lasting humoral immunity was observed in vaccinated chickens up to 18 or 25 weeks of age, depending on the vaccination schedule. The analysis of viral transmission after homologous challenge showed that sentinels vaccinated with 2 doses with adjuvant were fully protected against mortality with no excretion detected. This study of H5 DNA vaccine efficacy confirmed the important role that this type of so-called third-generation vaccine could play in the fight against H5 HPAI viruses.
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Affiliation(s)
- Julie Valentin
- Sciensano, Service of Avian Virology and Immunology, 1180 Brussels, Belgium.
| | - Fiona Ingrao
- Sciensano, Service of Avian Virology and Immunology, 1180 Brussels, Belgium.
| | - Fabienne Rauw
- Sciensano, Service of Avian Virology and Immunology, 1180 Brussels, Belgium.
| | - Bénédicte Lambrecht
- Sciensano, Service of Avian Virology and Immunology, 1180 Brussels, Belgium.
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23
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Lamb JS, Tornos J, Lejeune M, Boulinier T. Rapid loss of maternal immunity and increase in environmentally mediated antibody generation in urban gulls. Sci Rep 2024; 14:4357. [PMID: 38388645 PMCID: PMC10884025 DOI: 10.1038/s41598-024-54796-1] [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: 12/04/2023] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Monitoring pathogen circulation in wildlife sentinel populations can help to understand and predict the spread of disease at the wildlife-livestock-human interface. Immobile young provide a useful target population for disease surveillance, since they can be easily captured for sampling and their levels of antibodies against infectious agents can provide an index of localized circulation. However, early-life immune responses include both maternally-derived antibodies and antibodies resulting from exposure to pathogens, and disentangling these two processes requires understanding their individual dynamics. We conducted an egg-swapping experiment in an urban-nesting sentinel seabird, the yellow-legged gull, and measured antibody levels against three pathogens of interest (avian influenza virus AIV, Toxoplasma gondii TOX, and infectious bronchitis virus IBV) across various life stages, throughout chick growth, and between nestlings raised by biological or non-biological parents. We found that levels of background circulation differed among pathogens, with AIV antibodies widely present across all life stages, TOX antibodies rarer, and IBV antibodies absent. Antibody titers declined steadily from adult through egg, nestling, and chick stages. For the two circulating pathogens, maternal antibodies declined exponentially after hatching at similar rates, but the rate of linear increase due to environmental exposure was significantly higher in the more prevalent pathogen (AIV). Differences in nestling antibody levels due to parental effects also persisted longer for AIV (25 days, vs. 14 days for TOX). Our results suggest that yellow-legged gulls can be a useful sentinel population of locally transmitted infectious agents, provided that chicks are sampled at ages when environmental exposure outweighs maternal effects.
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Affiliation(s)
- Juliet S Lamb
- Centre d'Écologie Fonctionnelle et Évolutive (CEFE), UMR CNRS 5175, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France.
- The Nature Conservancy, Cold Spring Harbor, NY, USA.
| | - Jérémy Tornos
- Centre d'Écologie Fonctionnelle et Évolutive (CEFE), UMR CNRS 5175, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Mathilde Lejeune
- Centre d'Écologie Fonctionnelle et Évolutive (CEFE), UMR CNRS 5175, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Thierry Boulinier
- Centre d'Écologie Fonctionnelle et Évolutive (CEFE), UMR CNRS 5175, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
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24
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Kuchinski KS, Coombe M, Mansour SC, Cortez GAP, Kalhor M, Himsworth CG, Prystajecky NA. Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats. Appl Environ Microbiol 2024; 90:e0084223. [PMID: 38259077 PMCID: PMC10880596 DOI: 10.1128/aem.00842-23] [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: 05/23/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Diverse influenza A viruses (IAVs) circulate in wild birds, including highly pathogenic strains that infect poultry and humans. Consequently, surveillance of IAVs in wild birds is a cornerstone of agricultural biosecurity and pandemic preparedness. Surveillance is traditionally done by testing wild birds directly, but obtaining these specimens is labor intensive, detection rates can be low, and sampling is often biased toward certain avian species. As a result, local incursions of dangerous IAVs are rarely detected before outbreaks begin. Testing environmental specimens from wild bird habitats has been proposed as an alternative surveillance strategy. These specimens are thought to contain diverse IAVs deposited by a broad range of avian hosts, including species that are not typically sampled by surveillance programs. To enable this surveillance strategy, we developed a targeted genomic sequencing method for characterizing IAVs in these challenging environmental specimens. It combines custom hybridization probes, unique molecular index-based library construction, and purpose-built bioinformatic tools, allowing IAV genomic material to be enriched and analyzed with single-fragment resolution. We demonstrated our method on 90 sediment specimens from wetlands around Vancouver, Canada. We recovered 2,312 IAV genome fragments originating from all eight IAV genome segments. Eleven hemagglutinin subtypes and nine neuraminidase subtypes were detected, including H5, the current global surveillance priority. Our results demonstrate that targeted genomic sequencing of environmental specimens from wild bird habitats could become a valuable complement to avian influenza surveillance programs.IMPORTANCEIn this study, we developed genome sequencing tools for characterizing avian influenza viruses in sediment from wild bird habitats. These tools enable an environment-based approach to avian influenza surveillance. This could improve early detection of dangerous strains in local wild birds, allowing poultry producers to better protect their flocks and prevent human exposures to potential pandemic threats. Furthermore, we purposefully developed these methods to contend with viral genomic material that is diluted, fragmented, incomplete, and derived from multiple strains and hosts. These challenges are common to many environmental specimens, making these methods broadly applicable for genomic pathogen surveillance in diverse contexts.
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Affiliation(s)
- Kevin S. Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Coombe
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Sarah C. Mansour
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabrielle Angelo P. Cortez
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marzieh Kalhor
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea G. Himsworth
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Natalie A. Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Provincial Health Services Authority, Vancouver, British Columbia, Canada
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25
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Fair JM, Al-Hmoud N, Alrwashdeh M, Bartlow AW, Balkhamishvili S, Daraselia I, Elshoff A, Fakhouri L, Javakhishvili Z, Khoury F, Muzyka D, Ninua L, Tsao J, Urushadze L, Owen J. Transboundary determinants of avian zoonotic infectious diseases: challenges for strengthening research capacity and connecting surveillance networks. Front Microbiol 2024; 15:1341842. [PMID: 38435695 PMCID: PMC10907996 DOI: 10.3389/fmicb.2024.1341842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
As the climate changes, global systems have become increasingly unstable and unpredictable. This is particularly true for many disease systems, including subtypes of highly pathogenic avian influenzas (HPAIs) that are circulating the world. Ecological patterns once thought stable are changing, bringing new populations and organisms into contact with one another. Wild birds continue to be hosts and reservoirs for numerous zoonotic pathogens, and strains of HPAI and other pathogens have been introduced into new regions via migrating birds and transboundary trade of wild birds. With these expanding environmental changes, it is even more crucial that regions or counties that previously did not have surveillance programs develop the appropriate skills to sample wild birds and add to the understanding of pathogens in migratory and breeding birds through research. For example, little is known about wild bird infectious diseases and migration along the Mediterranean and Black Sea Flyway (MBSF), which connects Europe, Asia, and Africa. Focusing on avian influenza and the microbiome in migratory wild birds along the MBSF, this project seeks to understand the determinants of transboundary disease propagation and coinfection in regions that are connected by this flyway. Through the creation of a threat reduction network for avian diseases (Avian Zoonotic Disease Network, AZDN) in three countries along the MBSF (Georgia, Ukraine, and Jordan), this project is strengthening capacities for disease diagnostics; microbiomes; ecoimmunology; field biosafety; proper wildlife capture and handling; experimental design; statistical analysis; and vector sampling and biology. Here, we cover what is required to build a wild bird infectious disease research and surveillance program, which includes learning skills in proper bird capture and handling; biosafety and biosecurity; permits; next generation sequencing; leading-edge bioinformatics and statistical analyses; and vector and environmental sampling. Creating connected networks for avian influenzas and other pathogen surveillance will increase coordination and strengthen biosurveillance globally in wild birds.
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Affiliation(s)
- Jeanne M. Fair
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Nisreen Al-Hmoud
- Bio-Safety and Bio-Security Center, Royal Scientific Society, Amman, Jordan
| | - Mu’men Alrwashdeh
- Bio-Safety and Bio-Security Center, Royal Scientific Society, Amman, Jordan
| | - Andrew W. Bartlow
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Ivane Daraselia
- Center of Wildlife Disease Ecology, Ilia State University, Tbilisi, Georgia
| | | | | | - Zura Javakhishvili
- Center of Wildlife Disease Ecology, Ilia State University, Tbilisi, Georgia
| | - Fares Khoury
- Department of Biology and Biotechnology, American University of Madaba, Madaba, Jordan
| | - Denys Muzyka
- National Scientific Center, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | | | - Jean Tsao
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States
| | - Lela Urushadze
- National Center for Disease Control and Public Health (NCDC) of Georgia, Tbilisi, Georgia
| | - Jennifer Owen
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States
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Glazunova A, Krasnova E, Bespalova T, Sevskikh T, Lunina D, Titov I, Sindryakova I, Blokhin A. A highly pathogenic avian influenza virus H5N1 clade 2.3.4.4 detected in Samara Oblast, Russian Federation. Front Vet Sci 2024; 11:1244430. [PMID: 38389580 PMCID: PMC10881870 DOI: 10.3389/fvets.2024.1244430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Avian influenza (AI) is a global problem impacting birds and mammals, causing economic losses in commercial poultry farms and backyard settings. In 2022, over 8,500 AI cases were reported worldwide, with the H5 subtype being responsible for many outbreaks in wild and domestic birds. In the territory of the Russian Federation, outbreaks of AI have been massively reported since 2020, both among domestic bird species and wild bird species. Wild migratory birds often serve as natural reservoirs for AI viruses, and interactions between bird species can lead to the emergence of new, highly pathogenic variants through genetic recombination between strains. In order to combat the widespread outbreaks of the disease and potential risks of further spread in 2021, monitoring studies were conducted in the Samara Oblast, the southeastern region of European Russian Federation. These studies aimed to diagnose and characterize circulating AI virus variants among wild migratory birds during waterfowl hunting in areas of mass nesting. Among the 98 shot birds, a highly pathogenic A/H5N1 AI virus was detected in a Eurasian Teal from the Bolshechernigovsky district. It was classified into clade 2.3.4.4 based on the cleavage site structure of HA. Phylogenetic analysis showed a high relatedness of the identified strain in the Samara Oblast with field isolates from Russia, Nigeria, Bangladesh, and Benin. The article emphasizes the importance of monitoring AI virus spread in both wild and poultry, highlighting the need for timely information exchange to assess risks. Further comprehensive studies are necessary to understand virus dissemination pathways.
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Affiliation(s)
- Anastasia Glazunova
- Federal Research Center for Virology and Microbiology, Branch in Samara, Samara, Russia
| | - Elena Krasnova
- Federal Research Center for Virology and Microbiology, Branch in Samara, Samara, Russia
| | - Tatiana Bespalova
- Federal Research Center for Virology and Microbiology, Branch in Samara, Samara, Russia
| | - Timofey Sevskikh
- Federal Research Center for Virology and Microbiology, Samara, Russia
| | - Daria Lunina
- Federal Research Center for Virology and Microbiology, Branch in Samara, Samara, Russia
| | - Ilya Titov
- Federal Research Center for Virology and Microbiology, Samara, Russia
| | - Irina Sindryakova
- Federal Research Center for Virology and Microbiology, Samara, Russia
| | - Andrey Blokhin
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, Nizhny Novgorod, Russia
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27
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Funk M, Spronken MI, Bestebroer TM, de Bruin AC, Gultyaev AP, Fouchier RA, te Velthuis AJ, Richard M. Transient RNA structures underlie highly pathogenic avian influenza virus genesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.574333. [PMID: 38370829 PMCID: PMC10871305 DOI: 10.1101/2024.01.11.574333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease and high fatality in poultry1. They emerge exclusively from H5 and H7 low pathogenic avian influenza viruses (LPAIVs)2. Although insertion of a furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene was identified decades ago as the genetic basis for LPAIV-to-HPAIV transition3,4, the exact mechanisms underlying said insertion have remained unknown. Here we used an innovative combination of bioinformatic models to predict RNA structures forming around the influenza virus RNA polymerase during replication, and circular sequencing5 to reliably detect nucleotide insertions. We show that transient H5 hemagglutinin RNA structures predicted to trap the polymerase on purine-rich sequences drive nucleotide insertions characteristic of MBCSs, providing the first strong empirical evidence of RNA structure involvement in MBCS acquisition. Insertion frequencies at the H5 cleavage site were strongly affected by substitutions in flanking genomic regions altering predicted transient RNA structures. Introduction of H5-like cleavage site sequences and structures into an H6 hemagglutinin resulted in MBCS-yielding insertions never observed before in H6 viruses. Our results demonstrate that nucleotide insertions that underlie H5 HPAIV emergence result from a previously unknown RNA-structure-driven diversity-generating mechanism, which could be shared with other RNA viruses.
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Affiliation(s)
- Mathis Funk
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Monique I. Spronken
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anja C.M. de Bruin
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Alexander P. Gultyaev
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS); Leiden University, 2300 RA Leiden, The Netherlands
| | - Ron A.M. Fouchier
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology; Princeton University, 08544 New Jersey, United States
| | - Mathilde Richard
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
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28
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Hubbard LE, Givens CE, Stelzer EA, Killian ML, Kolpin DW, Szablewski CM, Poulson RL. Environmental Surveillance and Detection of Infectious Highly Pathogenic Avian Influenza Virus in Iowa Wetlands. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2023; 10:1181-1187. [PMID: 38106530 PMCID: PMC10720465 DOI: 10.1021/acs.estlett.3c00668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/19/2023]
Abstract
Avian influenza viruses (AIVs) infect both wild birds and domestic poultry, resulting in economically costly outbreaks that have the potential to impact public health. Currently, a knowledge gap exists regarding the detection of infectious AIVs in the aquatic environment. In response to the 2021-2022 Eurasian strain highly pathogenic avian influenza (HPAI) A/goose/Guangdong/1/1996 clade 2.3.4.4 lineage H5 outbreak, an AIV environmental outbreak response study was conducted using a One Health approach. An optimized method was used to temporally sample (April and May 2022) and analyze (culture and molecular methods) surface water from five water bodies (four wetlands and one lake used as a comparison location) in areas near confirmed HPAI detections in wild bird or poultry operations. Avian influenza viruses were isolated from water samples collected in April from all four wetlands (not from the comparison lake sample); HPAI H5N1 was isolated from one wetland. No virus was isolated from the May samples. Several factors, including increased water temperatures, precipitation, biotic and abiotic factors, and absence of AIV-contaminated fecal material due to fewer waterfowl present, may have contributed to the lack of virus isolation from May samples. Results demonstrate surface water as a plausible medium for transmission of AIVs, including the HPAI virus.
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Affiliation(s)
- Laura E. Hubbard
- U.S.
Geological Survey, Upper Midwest Water Science
Center, 1 Gifford Pinchot
Drive, Madison, Wisconsin 53726, United States
| | - Carrie E. Givens
- U.S.
Geological Survey, Upper Midwest Water Science
Center, 5840 Enterprise
Drive, Lansing, Michigan 48911 United States
| | - Erin A. Stelzer
- U.S.
Geological Survey, Ohio-Kentucky-Indiana
Water Science Center, 6460 Busch Blvd, Ste 100, Columbus, Ohio 43229 United States
| | - Mary L. Killian
- U.S.
Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, 1920 Dayton Avenue, Ames, Iowa 50010 United States
| | - Dana W. Kolpin
- U.S.
Geological Survey, Central Midwest Water
Science Center, 400 S.
Clinton Street, Rm 269, Iowa City, Iowa 52240, United States
| | - Christine M. Szablewski
- Influenza
Division, Centers for Disease Control and
Prevention, Atlanta, Georgia 30329 United States
| | - Rebecca L. Poulson
- Southeastern
Cooperative Wildlife Disease Study, Department of Population Health,
College of Veterinary Medicine, University
of Georgia, 589 D.W.
Brooks Drive, Athens, Georgia 30602, United States
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29
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Zhao W, Liu X, Zhang X, Qiu Z, Jiao J, Li Y, Gao R, Wang X, Hu J, Liu X, Hu S, Jiao X, Peng D, Gu M, Liu X. Virulence and transmission characteristics of clade 2.3.4.4b H5N6 subtype avian influenza viruses possessing different internal gene constellations. Virulence 2023; 14:2250065. [PMID: 37635408 PMCID: PMC10464537 DOI: 10.1080/21505594.2023.2250065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Clade 2.3.4.4 H5N6 avian influenza virus (AIV) has been predominant in poultry in China, and the circulating haemagglutinin (HA) gene has changed from clade 2.3.4.4h to clade 2.3.4.4b in recent years. In 2021, we isolated four H5N6 viruses from ducks during the routine surveillance of AIV in China. The whole-genome sequencing results demonstrated that the four isolates all belonged to the currently prevalent clade 2.3.4.4b but had different internal gene constellations, which could be divided into G1 and G2 genotypes. Specifically, G1 possessed H9-like PB2 and PB1 genes on the H5-like genetic backbone while G2 owned an H3-like PB1 gene and the H5-like remaining internal genes. By determining the characteristics of H5N6 viruses, including growth performance on different cells, plaque-formation ability, virus attachment ability, and pathogenicity and transmission in different animal models, we found that G1 strains were more conducive to replication in mammalian cells (MDCK and A549) and BALB/c mice than G2 strains. However, G2 strains were more advantageously replicated in avian cells (CEF and DF-1) and slightly more transmissible in waterfowls (mallards) than G1 strains. This study enriched the epidemiological data of H5 subtype AIV to further understand its dynamic evolution, and laid the foundation for further research on the mechanism of low pathogenic AIV internal genes in generating novel H5 subtype reassortants.
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Affiliation(s)
- Wanchen Zhao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xin Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinyu Zhang
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiwei Qiu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jun Jiao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yang Li
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruyi Gao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoquan Wang
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jiao Hu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaowen Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shunlin Hu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinan Jiao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Daxin Peng
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Min Gu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiufan Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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Aznar I, Kohnle L, Stoicescu A, van Houtum A, Zancanaro G. Annual report on surveillance for avian influenza in poultry and wild birds in Member States of the European Union in 2022. EFSA J 2023; 21:e8480. [PMID: 38099051 PMCID: PMC10719745 DOI: 10.2903/j.efsa.2023.8480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
All European Union (EU) Member States (MSs) are required to implement surveillance for avian influenza (AI) in poultry and wild birds and (i) to notify the outbreaks, when relevant and (ii) to report the results to the responsible authority. In addition, Iceland, Norway, Switzerland and the United Kingdom (Northern Ireland) also implement ongoing surveillance programmes to monitor occurrences of avian influenza viruses (AIVs) in poultry and wild birds. EFSA received a mandate from the European Commission to collate, validate, analyse and summarise the data resulting from these AI surveillance programmes in an annual report. The present report summarises the results of the surveillance activities carried out in MSs, Iceland, Norway, Switzerland and the United Kingdom (Northern Ireland) in 2022. Overall, the 31 reporting countries (RCs) sampled 22,171 poultry establishments (PEs) during the 2022 surveillance activity: 18,490 PEs were sampled for serological testing and 3775 were sampled for virological testing. Some PEs were therefore sampled for both type of analytical methods. Out of the 18,490 PEs sampled for serological testing, 15 (0.08%) were seropositive for influenza A(H5) viruses. Out of the 3775 PEs sampled for virological testing, 74 PEs (1.96%) were positive to the virological assay for influenza A(H5) viruses. Seropositive PEs were found in four RCs (Belgium, Poland, Spain and Sweden) and as in previous years, the highest percentages of seropositive PEs were found in PEs raising breeding geese and waterfowl game birds. Out of these 15 seropositive PEs, 3 also tested positive by polymerase chain reaction (PCR) for influenza A (H5) viruses - 2 for highly pathogenic avian influenza virus (HPAIV) and 1 low pathogenic avian influenza (LPAI) (H5N3). In relation to the virological surveys, 10 RCs (32%) out of the 31 reported the detection of A (H5) viruses in 74 PEs, covering 12 different poultry categories. More specifically, 54 reported HPAIV A(H5N1), 17 HPAIV (H5N8), 2 AIV (H5N1) with unknown virus pathogenicity and 1 low pathogenic avian influenza (LPAI) (H5N3). Additionally, six PEs tested positive for undefined AIVs in three RCs. A total of 32,143 wild birds were sampled, with 4163 (12.95%) wild birds testing positive for HPAIVs by PCR, from 25 RCs. In contrast to previous years, out of the 4163 wild birds testing positive for HPAIv, subtype A(H5N1) virus was the main influenza A virus subtype identified among the wild bird testing positive for HPAIVs (3942; 95%). In addition, RCs also reported 984 wild birds testing positive for low pathogenic avian influenza (LPAI). Out of those, for 660 (67%) it was ascertained that the subtype was non-A(H5/H7); 260 (26%) wild birds tested positive for LPAIv of A(H5 or H7) subtypes and the remaining 64 (7%) LPAI viruses were belonging to other H-subtypes.
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31
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Baechlein C, Kleinschmidt S, Hartmann D, Kammeyer P, Wöhlke A, Warmann T, Herms L, Kühl B, Beineke A, Wohlsein P, Harder T, Runge M. Neurotropic Highly Pathogenic Avian Influenza A(H5N1) Virus in Red Foxes, Northern Germany. Emerg Infect Dis 2023; 29:2509-2512. [PMID: 37987587 PMCID: PMC10683810 DOI: 10.3201/eid2912.230938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
In a 1-year survey of wild terrestrial predators in northern Germany, we found that 5 of 110 foxes were infected with contemporary avian influenza A(H5N1) viruses, forming a temporal cluster during January‒March 2023. Encephalitis and strong cerebral virus replication but only sporadic mammalian-adaptive viral polymerase basic 2 protein E627K mutations were seen.
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32
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Sakuma S, Tanikawa T, Tsunekuni R, Mine J, Kumagai A, Miyazawa K, Takadate Y, Uchida Y. Experimental Infection of Chickens with H5N8 High Pathogenicity Avian Influenza Viruses Isolated in Japan in the Winter of 2020-2021. Viruses 2023; 15:2293. [PMID: 38140534 PMCID: PMC10748181 DOI: 10.3390/v15122293] [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: 11/14/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
During the winter of 2020-2021, numerous outbreaks of high pathogenicity avian influenza (HPAI) were caused by viruses of the subtype H5N8 in poultry over a wide region in Japan. The virus can be divided into five genotypes-E1, E2, E3, E5, and E7. The major genotype responsible for the outbreaks was E3, followed by E2. To investigate the cause of these outbreaks, we experimentally infected chickens with five representative strains of each genotype. We found that the 50% chicken infectious dose differed by up to 75 times among the five strains, and the titer of the E3 strains (102.75 50% egg infectious dose (EID50)) was the lowest, followed by that of the E2 strains (103.50 EID50). In viral transmission experiments, in addition to the E3 and E2 strains, the E5 strain was transmitted to naïve chickens with high efficiency (>80%), whereas the other strains had low efficiencies (<20%). We observed a clear difference in the virological characteristics among the five strains isolated in the same season. The higher infectivity of the E3 and E2 viruses in chickens may have caused the large number of HPAI outbreaks in Japan during this season.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuko Uchida
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba 305-0856, Ibaraki, Japan; (S.S.); (T.T.); (R.T.); (J.M.); (A.K.); (K.M.); (Y.T.)
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33
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Pantin-Jackwood MJ, Spackman E, Leyson C, Youk S, Lee SA, Moon LM, Torchetti MK, Killian ML, Lenoch JB, Kapczynski DR, Swayne DE, Suarez DL. Pathogenicity in Chickens and Turkeys of a 2021 United States H5N1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared to Two Previous H5N8 Clade 2.3.4.4 Viruses. Viruses 2023; 15:2273. [PMID: 38005949 PMCID: PMC10674317 DOI: 10.3390/v15112273] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (U.S.) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early U.S. H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the U.S. (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and turkeys. The mean bird infective dose (BID50) of the 2021 H5N1 virus was approximately 2.6 log10 50% embryo infective dose (EID50) in chickens and 2.2 log10 EID50 in turkeys, and the virus transmitted to contact-exposed turkeys but not chickens. The BID50 for the 2016 H5N8 virus was also slightly different in chickens and turkeys (4.2 and 4.7 log10 EID50, respectively); however, the BID50 for the 2014 H5N8 virus was higher for chickens than turkeys (3.9 and ~0.9 log10 EID50, respectively). With all viruses, turkeys took longer to die (MDTs of 2.6-8.2 days for turkeys and 1-4 days for chickens), which increased the virus shedding period and facilitated transmission to contacts.
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Affiliation(s)
- Mary J. Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
- Department of Medicine, College of Medicine, Chungbuk National University, Cheongju-si 28644, Chungbuk, Republic of Korea
| | - Scott A. Lee
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Linda M. Moon
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Mia K. Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Mary L. Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Julianna B. Lenoch
- Wildlife Services, National Wildlife Disease Program, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, CO 80521, USA
| | - Darrell R. Kapczynski
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David E. Swayne
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
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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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35
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Liu S, Liu Y, Chen B, Lu X, Jiang D, Geng L, Wang X, Peng K, Du C, Ren T, Yang X. The complete mitochondrial genome of Morishitium polonicum (Trematoda, Cyclocoelidae) and its phylogenetic implications. Parasitol Res 2023; 122:2609-2620. [PMID: 37688591 DOI: 10.1007/s00436-023-07959-4] [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: 04/18/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023]
Abstract
Trematodes can adversely impact the health and survival of wild animals. The trematode family Cyclocoelidae, which includes large digenean bird parasites, lacks molecular analysis, and reclassifications have not been supported. This study produced the first fully assembled and annotated mitochondrial genome sequence for the trematode Morishitium polonicum. The whole length of the M. polonicum (GenBank accession number: OP930879) mitogenome is 14083 bp, containing 22 transfer ribonucleic acids (tRNAs), 2 ribosomal RNAs (rRNAs, rrnL and rrnS), and a noncoding control section (D-loop) 13777 to 13854 bp in length. The 12 PCG areas have 3269 codons and a total length of 10053 bp, which makes up 71.38% of the mitochondrial genome's overall sequence. Most (10/12) of the PCGs that code for proteins begin with ATG, while the nad4L and nad1 genes have a GTG start codon. Phylogenetic analysis using the concatenated nucleotide sequences of 12 PCGs, and the ML tree analysis results showed that M. polonicum is more closely related to with Echinostomatidae and Fasciolidae, which indicates that the family Cyclocoelidae is more closely associated with Echinochasmidae. This study provides mtDNA information, and analysis of mitogenomic structure and evolution. Moreover, we aimed to understand the phylogenetic relationships of this fluke.
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Affiliation(s)
- Shuang Liu
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China
| | - Yafang Liu
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China
| | - Bin Chen
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China
| | - Xinyan Lu
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China
| | - Dandan Jiang
- School of Public Health, Dali University, Dali, 671000, China
| | - Ling Geng
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China
| | - Xuan Wang
- Nanchang University Queen Mary School, Nanchang, 330031, China
| | - Kexin Peng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Chunhong Du
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, 671000, China
| | - Tianguang Ren
- Nursing College, Dali University, Dali, 671000, China.
| | - Xing Yang
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, 671000, People's Republic of China.
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36
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Pepin KM, Leach CB, Barrett NL, Ellis JW, VanDalen KK, Webb CT, Shriner SA. Environmental transmission of influenza A virus in mallards. mBio 2023; 14:e0086223. [PMID: 37768062 PMCID: PMC10653830 DOI: 10.1128/mbio.00862-23] [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: 04/05/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Wild birds are the natural reservoir hosts of influenza A viruses. Highly pathogenic strains of influenza A viruses pose risks to wild birds, poultry, and human health. Thus, understanding how these viruses are transmitted between birds is critical. We conducted an experiment where we experimentally infected mallards which are ducks that are commonly exposed to influenza viruses. We exposed several contact ducks to the experimentally infected duck to estimate the probability that a contact duck would become infected from either exposure to the virus shed directly from the infected duck or shared water contaminated with the virus from the infected duck. We found that environmental transmission from contaminated water best predicted the probability of transmission to naïve contact ducks, relatively low levels of virus in the water were sufficient to cause infection, and the probability of a naïve duck becoming infected varied over time.
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Affiliation(s)
- Kim M. Pepin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Clinton B. Leach
- Department of Fish Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Nicole L. Barrett
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Jeremy W. Ellis
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Kaci K. VanDalen
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Colleen T. Webb
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Susan A. Shriner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
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37
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Martelli L, Fornasiero D, Scarton F, Spada A, Scolamacchia F, Manca G, Mulatti P. Study of the Interface between Wild Bird Populations and Poultry and Their Potential Role in the Spread of Avian Influenza. Microorganisms 2023; 11:2601. [PMID: 37894259 PMCID: PMC10609042 DOI: 10.3390/microorganisms11102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Water birds play a crucial role in disseminating and amplifying avian influenza viruses (AIVs) in the environment. However, they may have limited interactions with domestic facilities, raising the hypothesis that other wild birds may play the bridging role in introducing AIVs into poultry. An ornithocoenosis study, based on census-transect and camera-trapping methods, was conducted in 2019 in ten poultry premises in northeast Italy to characterize the bird communities and envisage the species that might act as bridge hosts for AIVs. The data collected were explored through a series of multivariate analyses (correspondence analysis and non-metric multidimensional scaling), and biodiversity indices (observed and estimated richness, Shannon entropy and Pielou's evenness). The analyses revealed a high level of complexity in the ornithic population, with 147 censused species, and significant qualitative and quantitative differences in wild bird species composition, both in space and in time. Among these, only a few were observed in close proximity to the farm premises (i.e., Magpies, Blackbirds, Cattle Egrets, Pheasants, Eurasian Collared Doves, and Wood Pigeons), thus suggesting their potential role in spilling over AIVs to poultry; contrarily, waterfowls appeared to be scarcely inclined to close visits, especially during autumn and winter seasons. These findings stress the importance of ongoing research on the wild-domestic bird interface, advocating for a wider range of species to be considered in AIVs surveillance and prevention programs.
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Affiliation(s)
- Luca Martelli
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (L.M.); (F.S.); (G.M.)
| | - Diletta Fornasiero
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (L.M.); (F.S.); (G.M.)
| | | | - Arianna Spada
- SELC Soc. Coop., 30175 Venice, Italy; (F.S.); (A.S.)
| | - Francesca Scolamacchia
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (L.M.); (F.S.); (G.M.)
| | - Grazia Manca
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (L.M.); (F.S.); (G.M.)
| | - Paolo Mulatti
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (L.M.); (F.S.); (G.M.)
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38
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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39
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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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40
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Malmberg JL, Miller M, Jennings-Gaines J, Allen SE. Mortality in Wild Turkeys (Meleagris gallopavo) Associated with Natural Infection with H5N1 Highly Pathogenic Avian Influenza Virus (HPAIV) Subclade 2.3.4.4. J Wildl Dis 2023; 59:767-773. [PMID: 37486883 DOI: 10.7589/jwd-d-22-00161] [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: 10/25/2022] [Accepted: 03/27/2023] [Indexed: 07/26/2023]
Abstract
A Eurasian strain of H5N1 highly pathogenic avian influenza virus (HPAIV) was first detected in North America in December 2021 and has since been confirmed in numerous wild and domestic avian species. In April 2022, 41 Wild Turkeys (Meleagris gallopavo) were found dead in Johnson County, Wyoming, USA adjacent to a property with confirmed HPAIV in a backyard poultry flock. Oropharyngeal swabs were collected from 11 of the 41 turkeys and necropsy was performed on seven. Avian influenza virus RNA was detected in all 11 turkeys by real-time reverse-transcription PCR. Acute, multiorgan necrosis was observed grossly and identified in all seven turkeys evaluated by histopathology, most consistently in the lung, spleen, liver, gastrointestinal tract, and gonads. Lesions indicate high virulence of subclade 2.3.4.4b H5N1 HPAIV in Wild Turkeys, with infections presenting as clusters of acute mortality. Although documented cases of HPAIV in Wild Turkeys are rare, these findings signify a risk of spillback from domestic poultry, which may be heightened by the recent rise in backyard poultry ownership and the use of peridomestic habitat by wild birds. Additional research is needed to better understand the risk of disease transmission at the interface of Wild Turkeys and backyard poultry and the potential conservation and management implications of HPAIV in wild gallinaceous birds.
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Affiliation(s)
- Jennifer L Malmberg
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Wyoming State Veterinary Laboratory, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Current affiliation and address: National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, 4101 LaPorte Avenue, Fort Collins, Colorado 80521, USA
| | - Myrna Miller
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Wyoming State Veterinary Laboratory, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
| | - Jessica Jennings-Gaines
- Veterinary Services, Wildlife Health Laboratory, Wyoming Game and Fish Department, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
| | - Samantha E Allen
- Veterinary Services, Wyoming Game and Fish Department, 1212 South Adams Street, Laramie, Wyoming 82070, USA
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41
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Provencher JF, Wilcox AAE, Gibbs S, Howes LA, Mallory ML, Pybus M, Ramey AM, Reed ET, Sharp CM, Soos C, Stasiak I, Leafloor JO. BAITING AND BANDING: EXPERT OPINION ON HOW BAIT TRAPPING MAY INFLUENCE THE OCCURRENCE OF HIGHLY PATHOGENIC AVIAN INFLUENZA (HPAI) AMONG DABBLING DUCKS. J Wildl Dis 2023; 59:590-600. [PMID: 37578749 DOI: 10.7589/jwd-d-22-00163] [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: 11/03/2022] [Accepted: 05/09/2023] [Indexed: 08/15/2023]
Abstract
A Eurasian lineage highly pathogenic avian influenza virus (HPAIV) of the clade 2.3.4.4b (Goose/Guangdong lineage) was detected in migratory bird populations in North America in December 2021, and it, along with its reassortants, have since caused wild and domestic bird outbreaks across the continent. Relative to previous outbreaks, HPAIV cases among wild birds in 2022 exhibited wider geographic extent within North America and higher levels of mortality, suggesting the potential for population-level impacts. Given the possible conservation implications of HPAIV in wild birds, natural resource managers have sought guidance on actions that may mitigate negative effects of disease among North American bird populations, including modification of existing management practices. Banding of waterfowl is a critical tool for population management for several harvested species in North America, but some banding techniques, such as bait trapping, can lead to increased congregation of waterfowl, potentially altering HPAIV transmission. We used an expert opinion exercise to assess how bait trapping of dabbling ducks in Canada may influence HPAIV transmission and wild bird health. The expert group found that it is moderately likely that bait trapping of dabbling ducks in wetlands will significantly increase the transmission of HPAIV among individual ducks, but there is a low probability that this will result in significant population-level effects on North American dabbling ducks. Considering the lack of empirical work studying how capture and handling methods may change transmission of HPAIV among waterfowl, as well as the importance of bait trapping for waterfowl management in North America, future work should focus on filling knowledge gaps pertaining to the influence of baiting on HPAIV occurrence to better inform banding procedures and management decision making.
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Affiliation(s)
- Jennifer F Provencher
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, 1125 Colonel By Dr., Ottawa, Ontario K1S 5B6, Canada
| | - Alana A E Wilcox
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, 1125 Colonel By Dr., Ottawa, Ontario K1S 5B6, Canada
| | - Samantha Gibbs
- Wildlife Health Office, U.S. Fish and Wildlife Service, Lower Suwannee National Wildlife Refuge, 16450 NW 31st Place, Chiefland, Florida 32626, USA
| | - Lesley-Anne Howes
- Canadian Wildlife Service, Environment and Climate Change Canada, National Wildlife Research Centre, 1125 Colonel By Dr., Ottawa, Ontario K1S 5B6, Canada
| | - Mark L Mallory
- Acadia University, 33 Westwood Ave., Wolfville, Nova Scotia B4P 2R6, Canada
| | - Margo Pybus
- Alberta Fish and Wildlife, Government of Alberta, 6909-116 St., Edmonton, Alberta T6H 4P2, Canada
| | - Andrew M Ramey
- U.S. Geological Survey Alaska Science Center, 4210 University Dr., Anchorage, Alaska 99508, USA
| | - Eric T Reed
- Canadian Wildlife Service, Environment and Climate Change Canada, 5019 52nd St., PO Box 2310, Yellowknife, Northwest Territories X1A 2P7, Canada
| | - Chris M Sharp
- Canadian Wildlife Service, Environment and Climate Change Canada, Environmental Science and Technology Centre, 335 River Rd, Ottawa, Ontario K1V 1C7, Canada
| | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Prairie and Northern Wildlife Research Centre, 115 Perimeter Rd, Saskatoon, Saskatchewan S7N 0X4, Canada
| | - Iga Stasiak
- Ministry of Environment, Government of Saskatchewan, 112 Research Dr., Saskatoon, Saskatchewan S7N 3R3, Canada
| | - Jim O Leafloor
- Canadian Wildlife Service, Environment and Climate Change Canada, Unit 510, 234 Donald St., Winnipeg, Manitoba R3C 1M8, Canada
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42
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Yin S, Li N, Xu W, Becker DJ, de Boer WF, Xu C, Mundkur T, Fountain-Jones NM, Li C, Han GZ, Wu Q, Prosser DJ, Cui L, Huang ZYX. Functional traits explain waterbirds' host status, subtype richness, and community-level infection risk for avian influenza. Ecol Lett 2023; 26:1780-1791. [PMID: 37586885 DOI: 10.1111/ele.14294] [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: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Species functional traits can influence pathogen transmission processes, and consequently affect species' host status, pathogen diversity, and community-level infection risk. We here investigated, for 143 European waterbird species, effects of functional traits on host status and pathogen diversity (subtype richness) for avian influenza virus at species level. We then explored the association between functional diversity and HPAI H5Nx occurrence at the community level for 2016/17 and 2021/22 epidemics in Europe. We found that both host status and subtype richness were shaped by several traits, such as diet guild and dispersal ability, and that the community-weighted means of these traits were also correlated with community-level risk of H5Nx occurrence. Moreover, functional divergence was negatively associated with H5Nx occurrence, indicating that functional diversity can reduce infection risk. Our findings highlight the value of integrating trait-based ecology into the framework of diversity-disease relationship, and provide new insights for HPAI prediction and prevention.
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Affiliation(s)
- Shenglai Yin
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ning Li
- Institute of Applied Ecology, Nanjing Xiaozhuang University, Nanjing, China
| | - Wenjie Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands
| | - Chi Xu
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Taej Mundkur
- Wetlands International, Ede, The Netherlands
- Good Earth Environmental, Arnhem, The Netherlands
| | | | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiang Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Diann J Prosser
- Eastern Ecological Science Center, United States Geological Survey, Laurel, Maryland, USA
| | - Lijuan Cui
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zheng Y X Huang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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43
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Xu Y, Tang L, Gu X, Bo S, Ming L, Ma M, Zhao C, Sun K, Liu Y, He G. Characterization of avian influenza A (H4N2) viruses isolated from wild birds in Shanghai during 2019 to 2021. Poult Sci 2023; 102:102948. [PMID: 37604021 PMCID: PMC10465953 DOI: 10.1016/j.psj.2023.102948] [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: 04/28/2023] [Revised: 07/04/2023] [Accepted: 07/17/2023] [Indexed: 08/23/2023] Open
Abstract
The H4 subtype of avian influenza viruses has been widely distributed among wild birds. During the surveillance of the avian influenza virus in Shanghai from 2019 to 2021, a total of 4,451 samples were collected from wild birds, among which 46 H4 subtypes of avian influenza viruses were identified, accounting for 7.40% of the total positive samples. The H4 subtype viruses have a wide range of hosts, including the spot-billed duck, common teal, and other wild birds in Anseriformes. Among all H4 subtypes, the most abundant are the H4N2 viruses. To clarify the genetic characteristics of H4N2 viruses, the whole genome sequences of 20 H4N2 viruses were analyzed. Phylogenetical analysis showed that all 8 genes of these viruses belonged to the Eurasian lineage and closely clustered with low pathogenic avian influenza viruses from countries along the East Asia-Australia migratory route. However, the PB1 gene of 1 H4N2 virus (NH21920) might provide its internal gene for highly pathogenic avian influenza H5N8 viruses in Korea and Japan. At least 10 genotypes were identified in these viruses, indicating that they underwent multiple complex recombination events. Our study has provided a better epidemiological understanding of the H4N2 viruses in wild birds. Considering the mutational potential, comprehensive surveillance of the H4N2 virus in both poultry and wild birds is imperative.
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Affiliation(s)
- Yuting Xu
- School of Life Science, East China Normal University, Shanghai, China
| | - Ling Tang
- Shanghai Wildlife and Protected Natural Areas Research Center, Shanghai, China
| | - Xiaojun Gu
- Shanghai Landscaping & City Appearance Administrative Bureau, Shanghai, China
| | - Shunqi Bo
- Shanghai Landscaping & City Appearance Administrative Bureau, Shanghai, China
| | - Le Ming
- School of Life Science, East China Normal University, Shanghai, China
| | - Min Ma
- School of Life Science, East China Normal University, Shanghai, China
| | | | - Kaibo Sun
- Shanghai Forestry Station, Shanghai, China
| | - Yuyi Liu
- Shanghai Landscaping & City Appearance Administrative Bureau, Shanghai, China
| | - Guimei He
- School of Life Science, East China Normal University, Shanghai, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai, China.
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Teitelbaum CS, Masto NM, Sullivan JD, Keever AC, Poulson RL, Carter DL, Blake-Bradshaw AG, Highway CJ, Feddersen JC, Hagy HM, Gerhold RW, Cohen BS, Prosser DJ. North American wintering mallards infected with highly pathogenic avian influenza show few signs of altered local or migratory movements. Sci Rep 2023; 13:14473. [PMID: 37660131 PMCID: PMC10475108 DOI: 10.1038/s41598-023-40921-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
Avian influenza viruses pose a threat to wildlife and livestock health. The emergence of highly pathogenic avian influenza (HPAI) in wild birds and poultry in North America in late 2021 was the first such outbreak since 2015 and the largest outbreak in North America to date. Despite its prominence and economic impacts, we know relatively little about how HPAI spreads in wild bird populations. In January 2022, we captured 43 mallards (Anas platyrhynchos) in Tennessee, USA, 11 of which were actively infected with HPAI. These were the first confirmed detections of HPAI H5N1 clade 2.3.4.4b in the Mississippi Flyway. We compared movement patterns of infected and uninfected birds and found no clear differences; infected birds moved just as much during winter, migrated slightly earlier, and migrated similar distances as uninfected birds. Infected mallards also contacted and shared space with uninfected birds while on their wintering grounds, suggesting ongoing transmission of the virus. We found no differences in body condition or survival rates between infected and uninfected birds. Together, these results show that HPAI H5N1 clade 2.3.4.4b infection was unrelated to body condition or movement behavior in mallards infected at this location during winter; if these results are confirmed in other seasons and as HPAI H5N1 continues to evolve, they suggest that these birds could contribute to the maintenance and dispersal of HPAI in North America. Further research on more species across larger geographic areas and multiple seasons would help clarify potential impacts of HPAI on waterfowl and how this emerging disease spreads at continental scales, across species, and potentially between wildlife and domestic animals.
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Affiliation(s)
- Claire S Teitelbaum
- Akima Systems Engineering, Herndon, VA, USA.
- Contractor to U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA.
- Bay Area Environmental Research Institute and NASA Ames Research Center, Moffett Field, CA, USA.
| | - Nicholas M Masto
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Jeffery D Sullivan
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA
| | - Allison C Keever
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Deborah L Carter
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - Cory J Highway
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | | | - Heath M Hagy
- U.S. Fish and Wildlife Service, National Wildlife Refuge System, Stanton, TN, USA
| | - Richard W Gerhold
- University of Tennessee College of Veterinary Medicine, Knoxville, TN, USA
| | - Bradley S Cohen
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Diann J Prosser
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA
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Charostad J, Rezaei Zadeh Rukerd M, Mahmoudvand S, Bashash D, Hashemi SMA, Nakhaie M, Zandi K. A comprehensive review of highly pathogenic avian influenza (HPAI) H5N1: An imminent threat at doorstep. Travel Med Infect Dis 2023; 55:102638. [PMID: 37652253 DOI: 10.1016/j.tmaid.2023.102638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/13/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
Avian influenza viruses (AIVs) are globally challenging due to widespread circulation and high mortality rates. Highly pathogenic avian influenza (HPAI) strains like H5N1 have caused significant outbreaks in birds. Since 2003 to 14 July 2023, the World Health Organization (WHO) has documented 878 cases of HPAI H5N1 infection in humans and 458 (52.16%) fatalities in 23 countries. Recent outbreaks in wild birds, domestic birds, sea lions, minks, and etc., and the occurrence of genetic variations among HPAI H5N1 strains raise concerns about potential transmission and public health risks. This paper aims to provide a comprehensive overview of the current understanding and new insights into HPAI H5N1. It begins with an introduction to the significance of studying this virus and highlighting the need for updated knowledge. The origin and evaluation of HPAI H5N1 are examined, shedding light on its emergence, and spread across different geographic regions. The genome organization and structural biology of the H5N1 virus are explored, providing insights into its molecular composition and key structural features. This manuscript also delves into the phylogeny, evolution, mutational trends, reservoirs, and transmission routes of HPAI H5N1. The immune response against HPAI H5N1 and its implications for vaccine development are analyzed, along with an exploration of the pathogenesis and clinical manifestations of HPAI H5N1 in human cases. Furthermore, diagnostic tools and preventive and therapeutic strategies are discussed, highlighting the current approaches and potential future directions for better management of the potential pandemic.
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Affiliation(s)
- Javad Charostad
- Department of Microbiology, Faculty of Medicine, Shahid Sadoghi University of Medical Science, Yazd, Iran
| | - Mohammad Rezaei Zadeh Rukerd
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran; Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Shahab Mahmoudvand
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Department of Virology, School of Medicine, Hamadan University of Medical Science, Hamadan, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Nakhaie
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran.
| | - Keivan Zandi
- Arrowhead Pharmaceuticals, San Diego, CA, USA; Tropical Infectious Diseases Research and Education Center (TIDREC), University of Malaya, Kuala Lumpur, Malaysia.
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Alkie TN, Byrne AMP, Jones MEB, Mollett BC, Bourque L, Lung O, James J, Yason C, Banyard AC, Sullivan D, Signore AV, Lang AS, Baker M, Dawe B, Brown IH, Berhane Y. Recurring Trans-Atlantic Incursion of Clade 2.3.4.4b H5N1 Viruses by Long Distance Migratory Birds from Northern Europe to Canada in 2022/2023. Viruses 2023; 15:1836. [PMID: 37766243 PMCID: PMC10536465 DOI: 10.3390/v15091836] [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: 07/30/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
In December 2022 and January 2023, we isolated clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) viruses from six American crows (Corvus brachyrhynchos) from Prince Edward Island and a red fox (Vulpes vulpes) from Newfoundland, Canada. Using full-genome sequencing and phylogenetic analysis, these viruses were found to fall into two distinct phylogenetic clusters: one group containing H5N1 viruses that had been circulating in North and South America since late 2021, and the other one containing European H5N1 viruses reported in late 2022. The transatlantic re-introduction for the second time by pelagic/Icelandic bird migration via the same route used during the 2021 incursion of Eurasian origin H5N1 viruses into North America demonstrates that migratory birds continue to be the driving force for transcontinental dissemination of the virus. This new detection further demonstrates the continual long-term threat of H5N1 viruses for poultry and mammals and the subsequent impact on various wild bird populations wherever these viruses emerge. The continual emergence of clade 2.3.4.4b H5Nx viruses requires vigilant surveillance in wild birds, particularly in areas of the Americas, which lie within the migratory corridors for long-distance migratory birds originating from Europe and Asia. Although H5Nx viruses have been detected at higher rates in North America since 2021, a bidirectional flow of H5Nx genes of American origin viruses to Europe has never been reported. In the future, coordinated and systematic surveillance programs for HPAI viruses need to be launched between European and North American agencies.
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Affiliation(s)
- Tamiru N. Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Megan E. B. Jones
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Benjamin C. Mollett
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Joe James
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Carmencita Yason
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Ashley C. Banyard
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Daniel Sullivan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Anthony V. Signore
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Meghan Baker
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Beverly Dawe
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Dub T, Mäkelä H, Van Kleef E, Leblond A, Mercier A, Hénaux V, Bouyer F, Binot A, Thiongane O, Lancelot R, Delconte V, Zamuner L, Van Bortel W, Arsevska E. Epidemic intelligence activities among national public and animal health agencies: a European cross-sectional study. BMC Public Health 2023; 23:1488. [PMID: 37542208 PMCID: PMC10401758 DOI: 10.1186/s12889-023-16396-y] [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: 02/08/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Epidemic Intelligence (EI) encompasses all activities related to early identification, verification, analysis, assessment, and investigation of health threats. It integrates an indicator-based (IBS) component using systematically collected surveillance data, and an event-based component (EBS), using non-official, non-verified, non-structured data from multiple sources. We described current EI practices in Europe by conducting a survey of national Public Health (PH) and Animal Health (AH) agencies. We included generic questions on the structure, mandate and scope of the institute, on the existence and coordination of EI activities, followed by a section where respondents provided a description of EI activities for three diseases out of seven disease models. Out of 81 gatekeeper agencies from 41 countries contacted, 34 agencies (42%) from 26 (63%) different countries responded, out of which, 32 conducted EI activities. Less than half (15/32; 47%) had teams dedicated to EI activities and 56% (18/34) had Standard Operating Procedures (SOPs) in place. On a national level, a combination of IBS and EBS was the most common data source. Most respondents monitored the epidemiological situation in bordering countries, the rest of Europe and the world. EI systems were heterogeneous across countries and diseases. National IBS activities strongly relied on mandatory laboratory-based surveillance systems. The collection, analysis and interpretation of IBS information was performed manually for most disease models. Depending on the disease, some respondents did not have any EBS activity. Most respondents conducted signal assessment manually through expert review. Cross-sectoral collaboration was heterogeneous. More than half of the responding institutes collaborated on various levels (data sharing, communication, etc.) with neighbouring countries and/or international structures, across most disease models. Our findings emphasise a notable engagement in EI activities across PH and AH institutes of Europe, but opportunities exist for better integration, standardisation, and automatization of these efforts. A strong reliance on traditional IBS and laboratory-based surveillance systems, emphasises the key role of in-country laboratories networks. EI activities may benefit particularly from investments in cross-border collaboration, the development of methods that can automatise signal assessment in both IBS and EBS data, as well as further investments in the collection of EBS data beyond scientific literature and mainstream media.
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Affiliation(s)
- Timothee Dub
- Department of Health security, Finish Institute for Health and Welfare, Helsinki, Finland.
| | - Henna Mäkelä
- Department of Health security, Finish Institute for Health and Welfare, Helsinki, Finland
| | - Esther Van Kleef
- Department of Public Health, Institute of tropical medicine, Antwerp, Belgium
| | - Agnes Leblond
- UMR EPIA, INRAE, VetAgro Sup, University of Lyon, Marcy l'Etoile, F-69280, France
| | - Alizé Mercier
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Viviane Hénaux
- Unité Epidémiologie et appui à la surveillance, Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (Anses), Lyon, France
| | - Fanny Bouyer
- Groupe d'Expérimentation et de Recherche: Développement et Actions Locales (GERDAL), Angers, France
| | - Aurelie Binot
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Oumy Thiongane
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Renaud Lancelot
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Valentina Delconte
- OpenGeoHub foundation, Agro Business Park 10, Wageningen, The Netherlands
| | - Lea Zamuner
- OpenGeoHub foundation, Agro Business Park 10, Wageningen, The Netherlands
| | - Wim Van Bortel
- Outbreak Research Team, Department of Biomedical Sciences, Institute of tropical medicine, Antwerp, Belgium
- Unit of Entomology, Department of Biomedical Sciences, Institute of tropical medicine, Antwerp, Belgium
| | - Elena Arsevska
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
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Hepp B, Lorieux F, Degaugue A, Oberto J. VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes. Bioinformatics 2023; 39:btad528. [PMID: 37624923 PMCID: PMC10471898 DOI: 10.1093/bioinformatics/btad528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
MOTIVATION Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data. RESULTS We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated. AVAILABILITY AND IMPLEMENTATION VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.
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Affiliation(s)
- Benjamin Hepp
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Florence Lorieux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Augustin Degaugue
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Jacques Oberto
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
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Harder T, de Wit S, Gonzales JL, Ho JHP, Mulatti P, Prajitno TY, Stegeman A. Epidemiology-driven approaches to surveillance in HPAI-vaccinated poultry flocks aiming to demonstrate freedom from circulating HPAIV. Biologicals 2023; 83:101694. [PMID: 37494751 DOI: 10.1016/j.biologicals.2023.101694] [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: 04/13/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Incursion pressure of high pathogenicity avian influenza viruses (HPAIV) by secondary spread among poultry holdings and/or from infected migratory wild bird populations increases worldwide. Vaccination as an additional layer of protection of poultry holdings using appropriately matched vaccines aims at reducing clinical sequelae of HPAIV infection, disrupting HPAIV transmission, curtailing economic losses and animal welfare problems and cutting exposure risks of zoonotic HPAIV at the avian-human interface. Products derived from HPAIV-vaccinated poultry should not impose any risk of virus spread or exposure. Vaccination can be carried out with zero-tolerance for infection in vaccinated herds and must then be flanked by appropriate surveillance which requires tailoring at several levels: (i) Controlling appropriate vaccination coverage and adequate population immunity in individual flocks and across vaccinated populations; (ii) assessing HPAI-infection trends in unvaccinated and vaccinated parts of the poultry population to provide early detection of new/re-emerged HPAIV outbreaks; and (iii) proving absence of HPAIV circulation in vaccinated flocks ideally by real time-monitoring. Surveillance strategies, i.e. selecting targets, tools and random sample sizes, must be accommodated to the specific epidemiologic and socio-economic background. Methodological approaches and practical examples from three countries or territories applying AI vaccination under different circumstances are reviewed here.
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Affiliation(s)
- Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler Institute, Greifswald-Insel Riems, Germany.
| | - Sjaak de Wit
- Royal GD, Deventer, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jose L Gonzales
- Epidemiology, Bio-informatics & Animal Models, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jeremy H P Ho
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Paolo Mulatti
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Teguh Y Prajitno
- Japfa Comfeed Indonesia, Vaksindo Satwa Nusantara, Animal Health & Laboratory Services, Jakarta, Indonesia
| | - Arjan Stegeman
- Department Population Health Sciences, Farm Animal Health, Veterinary Epidemiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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50
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Rafique S, Rashid F, Mushtaq S, Ali A, Li M, Luo S, Xie L, Xie Z. Global review of the H5N8 avian influenza virus subtype. Front Microbiol 2023; 14:1200681. [PMID: 37333639 PMCID: PMC10272346 DOI: 10.3389/fmicb.2023.1200681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Orthomyxoviruses are negative-sense, RNA viruses with segmented genomes that are highly unstable due to reassortment. The highly pathogenic avian influenza (HPAI) subtype H5N8 emerged in wild birds in China. Since its emergence, it has posed a significant threat to poultry and human health. Poultry meat is considered an inexpensive source of protein, but due to outbreaks of HPAI H5N8 from migratory birds in commercial flocks, the poultry meat industry has been facing severe financial crises. This review focuses on occasional epidemics that have damaged food security and poultry production across Europe, Eurasia, the Middle East, Africa, and America. HPAI H5N8 viral sequences have been retrieved from GISAID and analyzed. Virulent HPAI H5N8 belongs to clade 2.3.4.4b, Gs/GD lineage, and has been a threat to the poultry industry and the public in several countries since its first introduction. Continent-wide outbreaks have revealed that this virus is spreading globally. Thus, continuous sero- and viro-surveillance both in commercial and wild birds, and strict biosecurity reduces the risk of the HPAI virus appearing. Furthermore, homologous vaccination practices in commercial poultry need to be introduced to overcome the introduction of emergent strains. This review clearly indicates that HPAI H5N8 is a continuous threat to poultry and people and that further regional epidemiological studies are needed.
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Affiliation(s)
- Saba Rafique
- SB Diagnostic Laboratory, Sadiq Poultry Pvt. Ltd, Rawalpindi, Pakistan
| | - Farooq Rashid
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Sajda Mushtaq
- SB Diagnostic Laboratory, Sadiq Poultry Pvt. Ltd, Rawalpindi, Pakistan
| | - Akbar Ali
- Poultry Research Institute, Rawalpindi, Pakistan
| | - Meng Li
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Liji Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
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