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Viruses
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Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses
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Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 12870

Special Issue Editor

Prof. Dr. Sasan Fereidouni

E-Mail Website
Guest Editor
Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1a, 1160 Vienna, Austria
Interests: avian influenza ecology, surveillance, immunopathogenesis; virology; microbiology; eco-immunology; one-health

Special Issue Information

Dear Colleagues,

Avian influenza viruses, with the panzootic events of the highly pathogenic avian influenza viruses (HPAIs) (2000–2004), have become one of the most critical challenges for domestic poultry and wildlife conservation in terms of affected geographic areas and the number of infected species. The current panzootic is very special because of the high detection levels of HAPIVs in wild birds and even healthy animals; high mortality and economic loss in the poultry industry; the transmission of viruses to marine mammals, such as harbor seals, elephant seals, and sea lions, causing high mortality among them; the transmission of these viruses to seabirds especially gull species in Asia and Europe, causing several high-mortality outbreaks; their potential risks for biodiversity and sporadic infections in mammalian species such as lions, raccoons, skunks, foxes, and humans; the continuous evolution of the avian influenza viruses with high potential to change the preferential binding of the viruses from avian‐like receptors to mammalian-like receptors, increasing their zoonotic potential; change in the dynamics of HPAIVs to increase their range of hosts and pathogenicity; and their capacity to evolve as human pandemic pathogens.

Unfortunately, scientific publications about the current panzootic and the infectious HAPIVs are quite scattered; therefore, the Editors of this Special Issue invite all scientists, influenza experts, epidemiologists, and outbreak investigators to submit their manuscripts regarding molecular epidemiology, phylogeny, evolution, receptor binding affinity and antigenic cartography, intra- and cross-species transmission, and reports of outbreaks of avian influenza viruses with special emphasis on recent outbreaks and the current HPAI panzootic.

Prof. Dr. Sasan Fereidouni
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • avian influenza viruses
  • highly pathogenic avian influenza viruses (HPAIs)
  • molecular epidemiology
  • phylogeny
  • evolution
  • intra- and cross-species transmission

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Published Papers (8 papers)

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Research

Jump to: Review

15 pages, 2079 KiB  
Article
Genetic Characterization of Kazakhstan Isolates: Avian Influenza H9N2 Viruses Demonstrate Their Potential to Infect Mammals
by Barshagul Baikara, Kobey Karamendin, Yermukhammet Kassymbekov, Klara Daulbayeva, Temirlan Sabyrzhan, Sardor Nuralibekov, Yelizaveta Khan, Nurlan Sandybayev, Sasan Fereidouni and Aidyn Kydyrmanov
Viruses 2025, 17(5), 685; https://doi.org/10.3390/v17050685 - 8 May 2025
Viewed by 746
Abstract
Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment. Therefore, influenza monitoring studies, including [...] Read more.
Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment. Therefore, influenza monitoring studies, including those of H9N2 viruses, are crucial for understanding, evaluating, and mitigating the risks associated with avian infections, and have broader implications for global public health. Although H9N2 viruses are not considered enzootic in Kazakhstan, they have been repeatedly detected in wild waterfowls and domestic poultry. In this study, all eight gene segments of influenza A/H9N2 viruses isolated in various regions of Kazakhstan between 2014 and 2020 were sequenced and analyzed. Molecular characterization revealed the presence of genetic markers associated with mammalian infectivity and disease potential. Furthermore, their predicted receptor binding site sequences indicate their potential capacity to attach to human-type receptors. These findings highlight the importance of continued surveillance and molecular investigation to better understand the evolution and zoonotic potential of H9N2 viruses in Kazakhstan. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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30 pages, 7440 KiB  
Article
Exploring Avian Influenza Viruses in Yakutia—The Largest Breeding Habitat of Wild Migratory Birds in Northeastern Siberia
by Nikita Kasianov, Kirill Sharshov, Anastasiya Derko, Ivan Sobolev, Nikita Dubovitskiy, Arina Loginova, Evgeniy Shemyakin, Maria Vladimirtseva, Nikolay Egorov, Viacheslav Gabyshev, Yujin Kim, Sun-Hak Lee, Andrew Y. Cho, Deok-Hwan Kim, Tae-Hyeon Kim, Chang-Seon Song, Hyesung Jeong, Weonhwa Jheong, Yoonjee Hong, Junki Mine, Yuko Uchida, Ryota Tsunekuni, Takehiko Saito and Alexander Shestopalovadd Show full author list remove Hide full author list
Viruses 2025, 17(5), 632; https://doi.org/10.3390/v17050632 - 27 Apr 2025
Viewed by 395
Abstract
Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal [...] Read more.
Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal swab samples collected from 56 bird species. We identified 74 AIVs of H3N6, H3N8, H4N6, H5N3, H7N7, H10N3, and H11N9 subtypes in Anseriformes order. Phylogenetic analysis showed that the isolates belong to the Eurasian lineage and have genetic similarities with strains from East Asia, Europe, and North America. Cluster analysis has demonstrated the circulation of stable AIV genotypes for several years. We assume that Yakutia is an important territory for viral exchange on the migratory routes of migrating birds. In addition, several amino acid substitutions have been found to be associated with increased virulence and adaptation to mammalian hosts, highlighting the potential risk of interspecific transmission. These results provide a critical insight into the ecology of the AIV and highlight the importance of continued monitoring in this geographically significant region. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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20 pages, 2314 KiB  
Article
Perpetuation of Avian Influenza from Molt to Fall Migration in Wild Swan Geese (Anser cygnoides): An Agent-Based Modeling Approach
by John Y. Takekawa, Chang-Yong Choi, Diann J. Prosser, Jeffery D. Sullivan, Nyambayar Batbayar and Xiangming Xiao
Viruses 2025, 17(2), 196; https://doi.org/10.3390/v17020196 - 30 Jan 2025
Viewed by 1377
Abstract
Wild waterfowl are considered to be the reservoir of avian influenza, but their distinct annual life cycle stages and their contribution to disease dynamics are not well understood. Studies of the highly pathogenic avian influenza (HPAI) virus have primarily focused on wintering grounds, [...] Read more.
Wild waterfowl are considered to be the reservoir of avian influenza, but their distinct annual life cycle stages and their contribution to disease dynamics are not well understood. Studies of the highly pathogenic avian influenza (HPAI) virus have primarily focused on wintering grounds, where human and poultry densities are high year-round, compared with breeding grounds, where migratory waterfowl are more isolated. Few if any studies of avian influenza have focused on the molting stage where wild waterfowl congregate in a few selected wetlands and undergo the simultaneous molt of wing and tail feathers during a vulnerable flightless period. The molting stage may be one of the most important periods for the perpetuation of the disease in waterfowl, since during this stage, immunologically naïve young birds and adults freely intermix prior to the fall migration. Our study incorporated empirical data from virological field samplings and markings of Swan Geese (Anser cygnoides) on their breeding grounds in Mongolia in an integrated agent-based model (ABM) that included susceptible–exposed–infectious–recovered (SEIR) states. Our ABM results provided unique insights and indicated that individual movements between different molting wetlands and the transmission rate were the key predictors of HPAI perpetuation. While wetland extent was not a significant predictor of HPAI perpetuation, it had a large effect on the number of infections and associated death toll. Our results indicate that conserving undisturbed habitats for wild waterfowl during the molting stage of the breeding season could reduce the risk of HPAI transmission. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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17 pages, 3745 KiB  
Article
Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis
by Patil Tawidian, Mia K. Torchetti, Mary L. Killian, Kristina Lantz, Krista E. Dilione, Jourdan M. Ringenberg, Sarah N. Bevins, Julianna B. Lenoch and Hon S. Ip
Viruses 2024, 16(12), 1818; https://doi.org/10.3390/v16121818 - 22 Nov 2024
Cited by 1 | Viewed by 2492
Abstract
The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified [...] Read more.
The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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11 pages, 5907 KiB  
Article
Mass Mortality in Terns and Gulls Associated with Highly Pathogenic Avian Influenza Viruses in Caspian Sea, Kazakhstan
by Aidyn Kydyrmanov, Kobey Karamendin, Yermukhammet Kassymbekov, Klara Daulbayeva, Temirlan Sabyrzhan, Yelizaveta Khan, Sardor Nuralibekov, Barshagul Baikara and Sasan Fereidouni
Viruses 2024, 16(11), 1661; https://doi.org/10.3390/v16111661 - 24 Oct 2024
Cited by 2 | Viewed by 2157
Abstract
Mass mortality in Caspian terns (Hydroprogne caspia), Pallas’s gulls (Ichthyaetus ichthyaetus), and Caspian gulls (Larus cachinnans) was recorded on the northeastern shores of the Caspian Sea in June 2022. More than 5000 gulls and terns died due [...] Read more.
Mass mortality in Caspian terns (Hydroprogne caspia), Pallas’s gulls (Ichthyaetus ichthyaetus), and Caspian gulls (Larus cachinnans) was recorded on the northeastern shores of the Caspian Sea in June 2022. More than 5000 gulls and terns died due to the outbreak. The outbreak was investigated in the field, and representative numbers of samples were collected and analyzed using pathological, virological, and molecular methods. Highly pathogenic avian influenza A (H5N1) viruses were detected and isolated from samples collected from dead birds. Genetic and phylogenetic analyses indicated that the hemagglutinin (HA) genes belonged to the clade 2.3.4.4.b of the H5Nx HPAI viruses, B2 sub-lineage, and were closely related to the highly pathogenic influenza viruses, caused an outbreak in wild birds with a high mortality rate in the western part of the Caspian Sea. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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14 pages, 5516 KiB  
Article
Complex Evolutionary Dynamics of H5N8 Influenza A Viruses Revealed by Comprehensive Reassortment Analysis
by Egor Degtyarev, Sofia Feoktistova, Pavel Volchkov and Andrey Deviatkin
Viruses 2024, 16(9), 1405; https://doi.org/10.3390/v16091405 - 3 Sep 2024
Viewed by 1987
Abstract
Influenza A viruses (IAVs) circulate among different species and have the potential to cause significant pandemics in humans. This study focuses on reassortment events in the H5N8 subtype of IAV, which poses a serious threat to public health due to its high pathogenicity [...] Read more.
Influenza A viruses (IAVs) circulate among different species and have the potential to cause significant pandemics in humans. This study focuses on reassortment events in the H5N8 subtype of IAV, which poses a serious threat to public health due to its high pathogenicity in birds and potential for cross-species transmission. We retrieved 2359 H5N8 IAV sequences from GISAID, and filtered and analyzed 442 complete genomic sequences for reassortment events using pairwise distance deviation matrices (PDDMs) and pairwise distance correspondence plots (PDCPs). This detailed case study of specific H5N8 viruses revealed previously undescribed reassortment events, highlighting the complex evolutionary history and potential pandemic threat of H5N8 IAVs. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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Review

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27 pages, 326 KiB  
Review
Improving Influenza Nomenclature Based on Transmission Dynamics
by Jwee Chiek Er
Viruses 2025, 17(5), 633; https://doi.org/10.3390/v17050633 - 28 Apr 2025
Viewed by 325
Abstract
Influenza A viruses (IAVs) evolve rapidly, exhibit zoonotic potential, and frequently adapt to new hosts, often establishing long-term reservoirs. Despite advancements in genetic sequencing and phylogenetic classification, current influenza nomenclature systems remain static, failing to capture evolving epidemiological patterns. This rigidity has led [...] Read more.
Influenza A viruses (IAVs) evolve rapidly, exhibit zoonotic potential, and frequently adapt to new hosts, often establishing long-term reservoirs. Despite advancements in genetic sequencing and phylogenetic classification, current influenza nomenclature systems remain static, failing to capture evolving epidemiological patterns. This rigidity has led to delays or misinterpretations in public health responses, economic disruptions, and confusion in scientific communication. The existing nomenclature does not adequately reflect real-time transmission dynamics or host adaptations, limiting its usefulness for public health management. The 2009 H1N1 pandemic exemplified these limitations, as it was mischaracterized as “swine flu” despite sustained human-to-human transmission and no direct pig-to-human transmission reported. This review proposes a real-time, transmission-informed nomenclature system that prioritizes host adaptation and sustained transmissibility (R0 > 1) to align influenza classification with epidemiological realities and risk management. Through case studies of H1N1pdm09, H5N1, and H7N9, alongside a historical overview of influenza naming, we demonstrate the advantages of integrating transmission dynamics into naming conventions. Adopting a real-time, transmission-informed approach will improve pandemic preparedness, strengthen global surveillance, and enhance influenza classification for scientists, policymakers, and public health agencies. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
25 pages, 719 KiB  
Review
Diagnostic Assays for Avian Influenza Virus Surveillance and Monitoring in Poultry
by Shahan Azeem and Kyoung-Jin Yoon
Viruses 2025, 17(2), 228; https://doi.org/10.3390/v17020228 - 6 Feb 2025
Viewed by 1934
Abstract
Diagnostic testing plays a key role in a surveillance program as diagnostic testing aims to accurately determine the infection or disease status of an individual animal. Diagnostic assays for AIV can be categorized into four broad types: tests for detecting the virus, its [...] Read more.
Diagnostic testing plays a key role in a surveillance program as diagnostic testing aims to accurately determine the infection or disease status of an individual animal. Diagnostic assays for AIV can be categorized into four broad types: tests for detecting the virus, its antigen, its genomic material, and antibodies to the virus. Virus characterization almost always follows virus detection. The present article surveys the current literature on the goals, principles, test performance, advantages, and disadvantages of these diagnostic assays. Virus isolation can be achieved using embryonating eggs or cell cultures in a lab setting. Virus antigens can be detected by antigen-capturing immunoassays or tissue immunoassays. Viral RNA can be detected by PCR-based assays (gel-based reverse transcription–polymerase chain reaction (RT-PCR), or probe or SYBR® Green-based real-time RT-PCR), loop-mediated isothermal amplification, in situ hybridization, and nucleic acid sequence-based amplification. Antibodies to AIV can be detected by ELISA, agar gel immunodiffusion, hemagglutination inhibition, and microneutralization. Avian influenza virus can be characterized by hemagglutination inhibition, neuraminidase inhibition, sequencing (dideoxynucleotide chain-termination sequencing, next-generation sequencing), genetic sequence-based pathotype prediction, and pathogenicity testing. Novel and variant AIVs can be recognized by DNA microarrays, electron microscopy, mass spectroscopy, and Biological Microelectromechanical Systems. A variety of diagnostic tests are employed in AIV surveillance and monitoring. The choice of their use depends on the goal of testing (fit for purpose), the time of testing during the disease, the assay target, the sample matrix, assay performance, and the advantages and disadvantages of the assay. The article concludes with authors’ perspective of the use of diagnostic assays in the surveillance and monitoring of AIV in poultry. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses)
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