Pathogenesis, Epidemiology, and Control of Animal Influenza Viruses—2nd Edition

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1389

Special Issue Editors


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Guest Editor
1. Balik Scientist Program, Department of Science and Technology, Bicutan, Taguig 1631, Philippines
2. Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA 30605, USA
Interests: respiratory viruses; influenza virus; virus evolution; next-generation sequencing

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Guest Editor
Assistant Professor, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
Interests: veterinary pathology; pathogenesis; virology; influenza virus
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Influenza viruses can be classified into four distinct virus species. Influenza B and C primarily infect humans, whereas influenza A and D viruses can affect non-human animal species. Among influenza viruses, influenza virus A has the broadest host range, which includes many species of birds and mammals.

Due to their broad host range, influenza viruses have a significant impact on multiple fields, including agriculture, public health, and wildlife health. To prevent and mitigate the consequences of influenza virus infections, it is imperative to better elucidate their epidemiology and mechanisms of disease progression and to further develop novel strategies for control and treatment in different hosts.

It is our pleasure to announce the launch of this Pathogens Special Issue on the “Pathogenesis, Epidemiology, and Control of Animal Influenza Viruses”. Our focus will be on influenza viruses of non-human animal species, especially those of poultry, swine, and equine, as well as those of wild migratory birds and marine mammals. Approaches that will be considered include classical virology, vaccinology, genomic analysis, case reports, epidemiology, and the ecology of animal influenza viruses. Multi-disciplinary research studies are especially welcome. Both original research and review articles will be considered for publication.

We look forward to receiving your submissions and to hearing about your exciting research.

Dr. Christina M. Leyson
Dr. Silvia Carnaccini
Guest Editors

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Keywords

  • avian influenza
  • swine influenza
  • equine influenza
  • animal influenza
  • influenza epidemiology
  • pathogenesis
  • influenza vaccines
  • influenza phylogenetics.

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Published Papers (2 papers)

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Research

25 pages, 1990 KiB  
Article
Fecal and Environmental Shedding of Influenza A Virus in Brazilian Swine: Genomic Evidence of Recent Human-to-Swine Transmission
by Nágila Rocha Aguilar, Beatriz Senra Alvares da Silva Santos, Bruno Zinato Carraro, Brenda Monique Magalhães Rocha, Jardelina de Souza Todao Bernardino, Ana Luiza Soares Fraiha, Alex Ranieri Jeronimo Lima, Gabriela Ribeiro, Alessandra Silva Dias, Renata Rezende Carvalho, Bruna Ferreira Sampaio Ribeiro, Marta Giovanetti, Luiz Carlos Júnior Alcântara, Sandra Coccuzzo Sampaio, Maria Carolina Quartim Barbosa Elias Sabbaga, Rafael Romero Nicolino, Zélia Inês Portela Lobato, Maria Isabel Maldonado Coelho Guedes, Cesar Rossas Mota Filho, Vincent Louis Viala, Bruna Coelho Lopes and Erica Azevedo Costaadd Show full author list remove Hide full author list
Pathogens 2025, 14(8), 753; https://doi.org/10.3390/pathogens14080753 - 31 Jul 2025
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Abstract
Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples [...] Read more.
Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples from naturally infected pigs in a commercial farm in Minas Gerais, Brazil. IAV RNA was detected in 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses from feces and effluent samples. Whole-genome sequencing revealed co-circulation of enzootic pH1N1 clade #2 (HA) and pN1 clade #4 (NA), alongside human-origin H3N2 sequences clustering within clade 3C.2a1b.2a.2a.1, and N2 segments related to pre-3C human lineages from 2001 to 2002. Phylogenetic and p-distance analyses support both recent reverse zoonosis and historical transmission events. Detection of complete HA/NA sequences from rectal swabs and treated effluent further emphasizes the surveillance value of non-respiratory matrices. The integration of respiratory and fecal/environmental sampling appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond. Full article
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23 pages, 4510 KiB  
Article
Identification and Characterization of Biosecurity Breaches on Poultry Farms with a Recent History of Highly Pathogenic Avian Influenza Virus Infection Determined by Video Camera Monitoring in the Netherlands
by Armin R. W. Elbers and José L. Gonzales
Pathogens 2025, 14(8), 751; https://doi.org/10.3390/pathogens14080751 - 30 Jul 2025
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Abstract
Biosecurity measures applied on poultry farms, with a recent history of highly pathogenic avian influenza virus infection, were monitored using 24 h/7 days-per-week video monitoring. Definition of biosecurity breaches were based on internationally acknowledged norms. Farms of four different production types (two broiler, [...] Read more.
Biosecurity measures applied on poultry farms, with a recent history of highly pathogenic avian influenza virus infection, were monitored using 24 h/7 days-per-week video monitoring. Definition of biosecurity breaches were based on internationally acknowledged norms. Farms of four different production types (two broiler, two layer, two breeder broiler, and one duck farm) were selected. Observations of entry to and exit from the anteroom revealed a high degree of biosecurity breaches in six poultry farms and good biosecurity practices in one farm in strictly maintaining the separation between clean and potentially contaminated areas in the anteroom. Hand washing with soap and water and/or using disinfectant lotion was rarely observed at entry to the anteroom and was almost absent at exit. Egg transporters did not disinfect fork-lift wheels when entering the egg-storage room nor change or properly disinfect footwear. The egg-storage room was not cleaned and disinfected after egg transport by the farmer. Similarly, footwear and trolley wheels were not disinfected when introducing young broilers or ducklings to the poultry unit. Biosecurity breaches were observed when introducing bedding material in the duck farm. This study shows a need for an engaging awareness and training campaign for poultry farmers and their co-workers as well as for transporters to promote good biosecurity practices. Full article
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