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Viruses
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Evolution and Adaptation of Avian Viruses
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Evolution and Adaptation of Avian Viruses

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

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 5096

Special Issue Editors

Dr. Giovanni Franzo

E-Mail Website
Guest Editor
Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy
Interests: avian viruses; molecular epidemiology; phylogenetics; phylodynamics; statistics; molecular diagnosis; vaccination
Special Issues, Collections and Topics in MDPI journals
Dr. Matteo Legnardi

E-Mail Website
Guest Editor
Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università, 16, 35020 Legnaro, Italy
Interests: molecular epidemiology; viral diseases; infectious bronchitis virus; infectious bursal disease virus
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The poultry industry is one of the leading sectors in animal production. It represents a significant source of profit in many high-income countries and a means of poverty alleviation through income generation and household food security in several rural communities. Poultry meat and eggs are also considered to be relatively affordable and more environmentally sustainable sources of high-quality protein compared to other livestock products. However, the profitability and efficiency of poultry farming are continually challenged by infectious diseases, which negatively impact animal productivity, welfare, and health. Rapidly evolving viruses pose a major threat due to their capability to adapt to new environmental conditions and farming systems and strategies.

Host jumps, vaccine escape, increased virulence, and diagnostic failures are just a few examples of how viral evolution can negatively impact animal production, both directly—by increasing animal losses and decreasing productivity—and indirectly—by increasing costs related to farm management, control strategies, and treatments. The need for more frequent antimicrobial treatment, which increases the risk of antimicrobial resistance emergence, cannot be neglected either.

Based on these premises, this Special Issue, titled “Evolution and Adaptation of Avian Viruses”, invites the submission of original research papers and reviews focused on avian virus epidemiology, molecular epidemiology, genetics, phylogenetics, evolution, virus–host interaction, interspecies transmission, diagnostics, treatment, vaccination, and control strategies. Experimental studies dealing with the molecular determinants and effects of evolution are also welcome. Under the One Health paradigm, collaboration between human health, animal health, environmental health, and food safety fields is particularly encouraged.

We look forward to receiving your submissions for this Special Issue.

Dr. Giovanni Franzo
Dr. Matteo Legnardi
Guest Editors

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

  • virus
  • poultry
  • evolution
  • genetics
  • diagnosis
  • host
  • epidemiology
  • control
  • vaccine

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Published Papers (4 papers)

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Research

22 pages, 36190 KiB  
Article
Phylogenetic Insights into H7Nx Influenza Viruses: Uncovering Reassortment Patterns and Geographic Variability
by Sofya G. Feoktistova, Alexandra O. Ivanova, Egor P. Degtyarev, Daria I. Smirnova, Pavel Yu. Volchkov and Andrei A. Deviatkin
Viruses 2024, 16(11), 1656; https://doi.org/10.3390/v16111656 - 23 Oct 2024
Viewed by 714
Abstract
Influenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of [...] Read more.
Influenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6, H7N7, H7N8, H7N9) viruses, which pose a significant pandemic risk due to the known cases of human infection and their potential for rapid genetic evolution and reassortment. The complete genome sequences of H7Nx influenza viruses (n = 3239) were compared between each other to investigate their phylogenetic relationships and reassortment patterns. For the selected viruses, phylogenetic trees were constructed for eight genome segments (PB2, PB1, PA, HA, NP, NA, M, NS) to assess the genetic diversity and geographic distribution of these viruses. Distinct phylogenetic clades with remarkable geographic patterns were found for the different segments. While the viruses were consistently grouped by subtype based on the NA segment sequences, the phylogeny of the other segment sequences, with the exception of the NS segment, showed distinct grouping patterns based on geographic origin rather than formal subtype assignment. Reassortment events leading to complex phylogenetic relationships were frequently observed. In addition, multiple cases of previously undescribed reassortments between subtypes were detected, emphasizing the fluidity of H7Nx virus populations. These results indicate a high degree of genetic diversity and reassortment within H7Nx influenza viruses. In other words, H7Nx viruses exist as constantly changing combinations of gene pools rather than stable genetic lineages. Full article
(This article belongs to the Special Issue Evolution and Adaptation of Avian Viruses)
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18 pages, 15192 KiB  
Article
Prevalence, Genotype Diversity, and Distinct Pathogenicity of 205 Gammacoronavirus Infectious Bronchitis Virus Isolates in China during 2019–2023
by Ting Xiong, Hangao Xie, Lin Li, Shijin Liang, Meizhen Huang, Chuanzhao Yu, Tingting Zhuang, Xuejing Liang, Dingxiang Liu and Ruiai Chen
Viruses 2024, 16(6), 930; https://doi.org/10.3390/v16060930 - 7 Jun 2024
Cited by 1 | Viewed by 944
Abstract
Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious disease in chickens and seriously endangers the poultry industry. The emergence and co-circulation of diverse IBV serotypes and genotypes with distinct pathogenicity worldwide pose a serious challenge to the development of effective intervention measures. [...] Read more.
Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious disease in chickens and seriously endangers the poultry industry. The emergence and co-circulation of diverse IBV serotypes and genotypes with distinct pathogenicity worldwide pose a serious challenge to the development of effective intervention measures. In this study, we report the epidemic trends of IBV in China from 2019 to 2023 and a comparative analysis on the antigenic characteristics and pathogenicity of isolates among major prevalent lineages. Phylogenetic and recombination analyses based on the nucleotide sequences of the spike (S) 1 gene clustered a total of 205 isolates into twelve distinct lineages, with GI-19 as a predominant lineage (61.77 ± 4.56%) exhibiting an overall increasing trend over the past five years, and demonstrated that a majority of the variants were derived from gene recombination events. Further characterization of the growth and pathogenic properties of six representative isolates from different lineages classified four out of the six isolates as nephropathogenic types with mortality rates in one-day-old SPF chickens varying from 20–60%, one as a respiratory type with weak virulence, and one as a naturally occurring avirulent strain. Taken together, our findings illuminate the epidemic trends, prevalence, recombination, and pathogenicity of current IBV strains in China, providing key information for further strengthening the surveillance and pathogenicity studies of IBV. Full article
(This article belongs to the Special Issue Evolution and Adaptation of Avian Viruses)
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10 pages, 867 KiB  
Communication
Assessment of Survival Kinetics for Emergent Highly Pathogenic Clade 2.3.4.4 H5Nx Avian Influenza Viruses
by Caroline J. Warren, Sharon M. Brookes, Mark E. Arnold, Richard M. Irvine, Rowena D. E. Hansen, Ian H. Brown, Ashley C. Banyard and Marek J. Slomka
Viruses 2024, 16(6), 889; https://doi.org/10.3390/v16060889 - 31 May 2024
Viewed by 1627
Abstract
High pathogenicity avian influenza viruses (HPAIVs) cause high morbidity and mortality in poultry species. HPAIV prevalence means high numbers of infected wild birds could lead to spill over events for farmed poultry. How these pathogens survive in the environment is important for disease [...] Read more.
High pathogenicity avian influenza viruses (HPAIVs) cause high morbidity and mortality in poultry species. HPAIV prevalence means high numbers of infected wild birds could lead to spill over events for farmed poultry. How these pathogens survive in the environment is important for disease maintenance and potential dissemination. We evaluated the temperature-associated survival kinetics for five clade 2.3.4.4 H5Nx HPAIVs (UK field strains between 2014 and 2021) incubated at up to three temperatures for up to ten weeks. The selected temperatures represented northern European winter (4 °C) and summer (20 °C); and a southern European summer temperature (30 °C). For each clade 2.3.4.4 HPAIV, the time in days to reduce the viral infectivity by 90% at temperature T was established (DT), showing that a lower incubation temperature prolonged virus survival (stability), where DT ranged from days to weeks. The fastest loss of viral infectivity was observed at 30 °C. Extrapolation of the graphical DT plots to the x-axis intercept provided the corresponding time to extinction for viral decay. Statistical tests of the difference between the DT values and extinction times of each clade 2.3.4.4 strain at each temperature indicated that the majority displayed different survival kinetics from the other strains at 4 °C and 20 °C. Full article
(This article belongs to the Special Issue Evolution and Adaptation of Avian Viruses)
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17 pages, 8724 KiB  
Article
The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus
by Giovanni Franzo, Giulia Faustini, Claudia Maria Tucciarone, Francesca Poletto, Francesca Tonellato, Mattia Cecchinato and Matteo Legnardi
Viruses 2024, 16(3), 481; https://doi.org/10.3390/v16030481 - 20 Mar 2024
Cited by 1 | Viewed by 1407
Abstract
The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the “Old World”. Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each [...] Read more.
The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the “Old World”. Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each with distinct production systems and control strategies. This study leverages this scenario to explore how different environments may influence virus evolution. Through the analysis of the complete S1 sequence, four datasets were identified, comprising strains of monophyletic clades circulating in different continents or countries (e.g., Asia vs. Europe and China vs. Thailand), indicative of single introduction events and independent evolution. The population dynamics and evolutionary rate variation over time, as well as the presence and intensity of selective pressures, were estimated and compared across these datasets. Since the lineage origin (approximately in the mid-20th century), a more persistent and stable viral population was estimated in Asia and China, while in Europe and Thailand, a sharp increase following the introduction (i.e., 2005 and 2007, respectively) of GI-19 was observed, succeeded by a rapid decline. Although a greater number of sites on the S1 subunit were under diversifying selection in the Asian and Chinese datasets, more focused and stronger pressures were evident in both the European (positions 2, 52, 54, 222, and 379 and Thai (i.e., positions 10, 12, 32, 56, 62, 64, 65, 78, 95, 96, 119, 128, 140, 182, 292, 304, 320, and 323) strains, likely reflecting a more intense and uniform application of vaccines in these regions. This evidence, along with the analysis of control strategies implemented in different areas, suggests a strong link between effective, systematic vaccine implementation and infection control. However, while the overall evolutionary rate was estimated at approximately 10−3 to 10−4, a significant inverse correlation was found between viral population size and the rate of viral evolution over time. Therefore, despite the stronger selective pressure imposed by vaccination, effectively constraining the former through adequate control strategies can efficiently prevent viral evolution and the emergence of vaccine-escaping variants. Full article
(This article belongs to the Special Issue Evolution and Adaptation of Avian Viruses)
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