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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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2
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Leguia M, Garcia-Glaessner A, Muñoz-Saavedra B, Juarez D, Barrera P, Calvo-Mac C, Jara J, Silva W, Ploog K, Amaro L, Colchao-Claux P, Johnson CK, Uhart MM, Nelson MI, Lescano J. Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru. Nat Commun 2023; 14:5489. [PMID: 37679333 PMCID: PMC10484921 DOI: 10.1038/s41467-023-41182-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) A/H5N1 viruses (lineage 2.3.4.4b) are rapidly invading the Americas, threatening wildlife, poultry, and potentially evolving into the next global pandemic. In November 2022 HPAI arrived in Peru, triggering massive pelican and sea lion die-offs. We report genomic characterization of HPAI/H5N1 in five species of marine mammals and seabirds (dolphins, sea lions, sanderlings, pelicans and cormorants). Peruvian viruses belong to lineage 2.3.4.4b, but they are 4:4 reassortants where 4 genomic segments (PA, HA, NA and MP) position within the Eurasian lineage that initially entered North America from Eurasia, while the other 4 genomic segments (PB2, PB1, NP and NS) position within the American lineage (clade C) that circulated in North America. These viruses are rapidly accruing mutations, including mutations of concern, that warrant further examination and highlight an urgent need for active local surveillance to manage outbreaks and limit spillover into other species, including humans.
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Affiliation(s)
- Mariana Leguia
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru.
| | - Alejandra Garcia-Glaessner
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
| | - Breno Muñoz-Saavedra
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
| | - Diana Juarez
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
| | - Patricia Barrera
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
| | - Carlos Calvo-Mac
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
| | - Javier Jara
- Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru
| | - Walter Silva
- Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru
| | - Karl Ploog
- Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru
| | - Lady Amaro
- Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru
| | | | - Christine K Johnson
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Marcela M Uhart
- EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Martha I Nelson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jesus Lescano
- Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru
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Lin M, Yao QC, Liu J, Huo M, Zhou Y, Chen M, Li Y, Gao Y, Ge Y. Evolution and Reassortment of H6 Subtype Avian Influenza Viruses. Viruses 2023; 15:1547. [PMID: 37515233 PMCID: PMC10383184 DOI: 10.3390/v15071547] [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: 06/30/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The H6 subtype of avian influenza virus (H6 AIV) is the most detected AIV subtype in poultry and wild birds. It causes economic losses to the poultry industry, and the most important, H6 AIV may have the ability to infect mammals, which is a great threat to public health security. In addition, the H6 subtype can serve as a precursor to providing internal genes for other highly pathogenic AIVs, posing a potential threat. H6 AIV currently face to the high positive detection rate and harmless nature of H6 AIV and because not highly effective H6 subtype vaccine available on the market. In this study, we focused on the prevalence of H6 AIV in poultry and wild birds, phylogenetic analysis, genetic variation characteristics, selection analysis, and prevention and control to provide relevant references for the scientific prevention and control of H6 AIV in future.
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Affiliation(s)
- Mingqin Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qiu-Cheng Yao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jing Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Miaotong Huo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan Zhou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Minyi Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuanguo Li
- Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun 130000, China
| | - Yuwei Gao
- Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun 130000, China
| | - Ye Ge
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
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Ferreri LM, Carnaccini S, Olivera V, Pereda A, Rajao D, Perez DR. South American H4N2 influenza A virus improved replication in chicken trachea after low number of passages. Front Vet Sci 2023; 10:1182550. [PMID: 37323837 PMCID: PMC10264679 DOI: 10.3389/fvets.2023.1182550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction of influenza A viruses (FLUAV) into poultry from waterfowl is frequent, producing economic burden and increasing the probability of human infections. We have previously described the presence of FLUAV in wild birds in Argentina with unique evolutionary trajectories belonging to a South American lineage different from the North American and Eurasian lineages. Adaptability of this South American lineage FLUAV to poultry species is still poorly understood. In the present report, we evaluated the capacity of an H4N2 FLUAV from the South American lineage to adapt to chickens after low number of passages. We found that five mutations were acquired after five passages in 3-days-old chickens. These mutations produced a virus with better infectivity in ex vivo trachea explants but overall lower infection in lung explants. Infection of 3-week-old chickens persisted for a longer period and was detected in more tissues than the parental virus, suggesting adaptation of the H4N2 influenza A virus to chicken.
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Affiliation(s)
- Lucas M. Ferreri
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Instituto de Virologia CICVyA, Instituto Nacional de Technologia Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Silvia Carnaccini
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Valeria Olivera
- Instituto de Virologia CICVyA, Instituto Nacional de Technologia Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Ariel Pereda
- Programa Nacional de Sanidad Animal, Instituto Nacional de Technología Agropecuária (INTA), Castelar, Buenos Aires, Argentina
| | - Daniela Rajao
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Daniel R. Perez
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Ruiz S, Galdames P, Baumberger C, Gonzalez MA, Rojas C, Oyarzun C, Orozco K, Mattar C, Freiden P, Sharp B, Schultz-Cherry S, Hamilton-West C, Jimenez-Bluhm P. Remote Sensing and Ecological Variables Related to Influenza A Prevalence and Subtype Diversity in Wild Birds in the Lluta Wetland of Northern Chile. Viruses 2023; 15:1241. [PMID: 37376541 DOI: 10.3390/v15061241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The Lluta River is the northernmost coastal wetland in Chile, representing a unique ecosystem and an important source of water in the extremely arid Atacama Desert. During peak season, the wetland is home to more than 150 species of wild birds and is the first stopover point for many migratory species that arrive in the country along the Pacific migratory route, thereby representing a priority site for avian influenza virus (AIV) surveillance in Chile. The aim of this study was to determine the prevalence of influenza A virus (IAV) in the Lluta River wetland, identify subtype diversity, and evaluate ecological and environmental factors that drive the prevalence at the study site. The wetland was studied and sampled from September 2015 to October 2020. In each visit, fresh fecal samples of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index-NDVI), and water body size were determined. A generalized linear mixed model (GLMM) was built to assess the association between AIV prevalence and explanatory variables. Influenza positive samples were sequenced, and the host species was determined by barcoding. Of the 4349 samples screened during the study period, overall prevalence in the wetland was 2.07% (95% CI: 1.68 to 2.55) and monthly prevalence of AIV ranged widely from 0% to 8.6%. Several hemagglutinin (HA) and neuraminidase (NA) subtypes were identified, and 10 viruses were isolated and sequenced, including low pathogenic H5, H7, and H9 strains. In addition, several reservoir species were recognized (both migratory and resident birds), including the newly identified host Chilean flamingo (Phoenicopterus chilensis). Regarding environmental variables, prevalence of AIV was positively associated with NDVI (OR = 3.65, p < 0.05) and with the abundance of migratory birds (OR = 3.57, p < 0.05). These results emphasize the importance of the Lluta wetland as a gateway to Chile for viruses that come from the Northern Hemisphere and contribute to the understanding of AIV ecological drivers.
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Affiliation(s)
- Soledad Ruiz
- Escuela de Medicina Veterinaria, Facultad de Ciencias Biológicas, Facultad de Medicina, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Pablo Galdames
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Cecilia Baumberger
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Maria Antonieta Gonzalez
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Camila Rojas
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Cristobal Oyarzun
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Katherinne Orozco
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Cristian Mattar
- Laboratory for Analysis of the Biosphere (LAB), Universidad de Chile, Santiago 8330111, Chile
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bridgette Sharp
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher Hamilton-West
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8330111, Chile
| | - Pedro Jimenez-Bluhm
- Escuela de Medicina Veterinaria, Facultad de Ciencias Biológicas, Facultad de Medicina, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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Cui M, Huang Y, Wang X, Bian X, Du L, Yan Y, Gu J, Dong W, Zhou J, Liao M. Genetic characterization and evolution of H6N6 subtype avian influenza viruses. Front Microbiol 2022; 13:963218. [PMID: 35979484 PMCID: PMC9376297 DOI: 10.3389/fmicb.2022.963218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
H6-subtype avian influenza virus (AIV) was prevalent in the world and could sporadically infect humans. Here, a new chicken-derived H6N6-subtype AIV strain A/chicken/Zhejiang/49/2021 (ZJ49) was isolated in Zhejiang Province, China in 2021. Phylogenetic analysis by Maximum likelihood methods showed that H6-subtype AIVs were classed into 13 groups according to HA gene. The ZJ49 strain belonged to the G12 group, which mainly consisted of strains from Asian and dominated in recent years. Based on NA gene, H6-subtype AIVs were divided into N6.1 and N6.2 clades according to the NA gene. The ZJ49 isolate was located in the N6.2e clade, which mainly consisted of the H5N6-subtype AIVs. Phylogenetic analysis by Bayesian methods showed that the effective quantity size of H6-subtype AIVs increased around 1990, reached a peak around 2015, declined after 2015, then kept in a stable level after 2018. The reassortment analysis predicted that the PB2, PA, and NA genes of ZJ49 may recombine with H5-subtype AIVs. The amino acid at 222 position of HA gene of ZJ49 strain mutated from A to V, suggesting that ZJ49 has a potential ability to cross species barriers. The four glycosylation sites were highly conserved, implying less impact on the fold and conception of HA stem structure. Our results revealed the complicated evolution, reassortment, and mutations of receptor binding sites of H6-subtype AIVs, which emphasize the importance to continuously monitor the epidemiology and evolution of H6-subtype AIVs.
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Affiliation(s)
- Mingxian Cui
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yanming Huang
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Xingbo Wang
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Xiyi Bian
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Liuyang Du
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Weiren Dong
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Jiyong Zhou,
| | - Min Liao
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Min Liao,
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Rimondi A, Olivera VS, Soria I, Parisi GD, Rumbo M, Perez DR. Few Amino Acid Mutations in H6 Influenza A Virus From South American Lineage Increase Viral Replication Efficiency in Poultry. Front Microbiol 2022; 13:953738. [PMID: 35966706 PMCID: PMC9363787 DOI: 10.3389/fmicb.2022.953738] [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: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
In chickens, infections due to influenza A virus (IAV) can be mild to severe and lethal. The study of IAV infections in poultry has been mostly limited to strains from the North American and Eurasian lineages, whereas limited information exists on similar studies with strains from the South American lineage (SAm). To better evaluate the risk of introduction of a prototypical SAm IAV strain into poultry, chickens were infected with a wild-type SAm origin strain (WT557/H6N2). The resulting virus progeny was serially passaged in chickens 20 times, and the immunopathological effects of the last passage virus, 20Ch557/H6N2, in chickens were compared to those of the parental strain. A comparison of complete viral genome sequences indicated that the 20Ch557/H6N2 strain contained 13 amino acid differences compared to the wild-type strain. Five of these mutations are in functionally relevant regions of the viral surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). However, despite higher and more prolonged virus shedding in chickens inoculated with the 20Ch557/H6N2 strain compared to those that received the WT557/H6N2 strain, transmission to naïve chickens was not observed for either group. Analyses by flow cytometry of mononuclear cells and lymphocyte subpopulations from the lamina propria and intraepithelial lymphocytic cells (IELs) from the ileum revealed a significant increase in the percentages of CD3+TCRγδ+ IELs in chickens inoculated with the 20Ch557/H6N2 strain compared to those inoculated with the WT557/H6N2 strain.
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Affiliation(s)
- Agustina Rimondi
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA-CONICET, Castelar, Argentina
| | - Valeria S. Olivera
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA-CONICET, Castelar, Argentina
| | - Ivana Soria
- Instituto de Virología e Innovaciones Tecnológicas, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA-CONICET, Castelar, Argentina
| | - Gustavo D. Parisi
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Martin Rumbo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP-CONICET-UNLP), La Plata, Argentina
| | - Daniel R. Perez
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Cui J, Cui P, Shi J, Fan W, Xing X, Gu W, Zhang Y, Zhang Y, Zeng X, Jiang Y, Chen P, Yang H, Chen Y, Liu J, Liu L, Tian G, Lu Y, Chen H, Li C, Deng G. Continued evolution of H6 avian influenza viruses isolated from farms in China between 2014 and 2018. Transbound Emerg Dis 2022; 69:2156-2172. [PMID: 34192815 DOI: 10.1111/tbed.14212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/04/2021] [Accepted: 06/27/2021] [Indexed: 12/22/2022]
Abstract
H6 avian influenza virus (AIV) is one of the most prevalent AIV subtypes in the world. Our previous studies have demonstrated that H6 AIVs isolated from live poultry markets pose a potential threat to human health. In recent years, increasing number of H6 AIVs has been constantly isolated from poultry farms. In order to understand the biological characteristics of H6 AIVs in the context of farms, here, we analyzed the phylogenetic relationships, antigenicity, replication in mice and receptor binding properties of H6 AIVs isolated from farms in China between 2014 and 2018. Phylogenetic analysis showed that 19 different genotypes were formed among 20 representative H6 viruses. Notably, the internal genes of these H6 viruses exhibited complicated relationships with different subtypes of AIVs worldwide, indicating that these viruses are the products of complex and frequent reassortment events. Antigenic analysis revealed that 13 viruses tested were divided into three antigenic groups. 10 viruses examined could all replicate in the respiratory organs of infected mice without prior adaptation. Receptor binding analysis demonstrated that some of the H6 AIVs bound to both α-2, 3-linked glycans (avian-type receptor) and α-2, 6-linked glycans (human-type receptor), thereby posing a potential threat to human health. Together, these findings revealed the prevalence, complicated genetic evolution, diverse antigenicity, and dual receptor binding specificity of H6 AIVs in the settings of poultry farms, which emphasize the importance to continuously monitor the evolution and biological properties of H6 AIVs in nature.
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Affiliation(s)
- Jiaqi Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Pengfei Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Weifeng Fan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Xin Xing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Wenli Gu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yuancheng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Xianying Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yongping Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Pucheng Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Huanliang Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Jinxiong Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Guobin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yixin Lu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Guohua Deng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
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Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NYH, Lynch SE, Martin S, McArthur M, O’Riley K, Read AJ, Warner S, Hoye BJ, Lisovski S, Leen T, Hurt AC, Butler J, Broz I, Davies KR, Mileto P, Neave MJ, Stevens V, Breed AC, Lam TTY, Holmes EC, Klaassen M, Wong FYK. Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathog 2022; 18:e1010150. [PMID: 35536868 PMCID: PMC9089890 DOI: 10.1371/journal.ppat.1010150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/13/2022] [Indexed: 12/03/2022] Open
Abstract
Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | | | | | - Graham W. Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | | | | | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Md. Ahasanul Hoque
- Chattogram (previously Chittagong) Veterinary and Animal Sciences University, Khulshi, Bangladesh
| | - Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Peter D. Kirkland
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Nina Yu-Hsin Kung
- Animal Biosecurity & Welfare, Biosecurity Queensland, Department of Agriculture and Fisheries, Health Food Science Precinct, Coopers Plains, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Sue Martin
- Department of Primary Industries, Parks, Water and Environment, Hobart, Australia
| | - Michaela McArthur
- Department of Primary Industries and Regional Development, Kensington, Australia
| | - Kim O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Andrew J. Read
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Trent Leen
- Geelong Field & Game, Geelong, Australia
- Wetlands Environmental Taskforce, Field & Game Australia, Seymour, Australia
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jeff Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Ivano Broz
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Kelly R. Davies
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Patrick Mileto
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Matthew J. Neave
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Andrew C. Breed
- Department of Agriculture, Water and the Environment, Canberra, Australia
- University of Queensland, St. Lucia, Australia
| | - Tommy T. Y. Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, PR China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
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Novel Low Pathogenic Avian Influenza H6N1 in Backyard Chicken in Easter Island (Rapa Nui), Chilean Polynesia. Viruses 2022; 14:v14040718. [PMID: 35458448 PMCID: PMC9031230 DOI: 10.3390/v14040718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond.
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Abstract
Avian influenza viruses pose a continuous threat to both poultry and human health, with significant economic impact. The ability of viruses to reassort and jump the species barrier into mammalian hosts generates a constant pandemic threat. H10Nx avian viruses have been shown to replicate in mammalian species without prior adaptation and have caused significant human infection and fatalities. They are able to rapidly reassort with circulating poultry strains and go undetected due to their low pathogenicity in chickens. Novel detections of both human reassortant strains and increasing endemicity of H10Nx poultry infections highlight the increasing need for heightened surveillance and greater understanding of the distribution, tropism, and infection capabilities of these viruses. In this minireview, we highlight the gap in the current understanding of this subtype and its prevalence across a vast range of host species and geographical locations.
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Bravo-Vasquez N, Yao J, Jimenez-Bluhm P, Meliopoulos V, Freiden P, Sharp B, Estrada L, Davis A, Cherry S, Livingston B, Danner A, Schultz-Cherry S, Hamilton-West C. Equine-Like H3 Avian Influenza Viruses in Wild Birds, Chile. Emerg Infect Dis 2020; 26:2887-2898. [PMID: 33219648 PMCID: PMC7706983 DOI: 10.3201/eid2612.202063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since their discovery in the United States in 1963, outbreaks of infection with equine influenza virus (H3N8) have been associated with serious respiratory disease in horses worldwide. Genomic analysis suggests that equine H3 viruses are of an avian lineage, likely originating in wild birds. Equine-like internal genes have been identified in avian influenza viruses isolated from wild birds in the Southern Cone of South America. However, an equine-like H3 hemagglutinin has not been identified. We isolated 6 distinct H3 viruses from wild birds in Chile that have hemagglutinin, nucleoprotein, nonstructural protein 1, and polymerase acidic genes with high nucleotide homology to the 1963 H3N8 equine influenza virus lineage. Despite the nucleotide similarity, viruses from Chile were antigenically more closely related to avian viruses and transmitted effectively in chickens, suggesting adaptation to the avian host. These studies provide the initial demonstration that equine-like H3 hemagglutinin continues to circulate in a wild bird reservoir.
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Ferreri LM, Ortiz L, Geiger G, Barriga GP, Poulson R, Gonzalez-Reiche AS, Crum JA, Stallknecht D, Moran D, Cordon-Rosales C, Rajao D, Perez DR. Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. Ecol Evol 2019; 9:6534-6546. [PMID: 31236242 PMCID: PMC6580304 DOI: 10.1002/ece3.5232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
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Affiliation(s)
- Lucas M Ferreri
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.,Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Ginger Geiger
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Gonzalo P Barriga
- Laboratory of Emerging Viruses, Virology Program Institute of Biomedical Sciences, Faculty of Medicine Universidad de Chile Santiago Chile
| | - Rebecca Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | | | - Jo Anne Crum
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Moran
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Celia Cordon-Rosales
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Daniel R Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
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