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Animals
Special Issues
Molecular Epidemiology of Animal-Associated Fungal and Viral Pathogens
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Molecular Epidemiology of Animal-Associated Fungal and Viral Pathogens

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Veterinary Clinical Studies".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 4128

Special Issue Editor

Dr. Fouad S. El-Mayet

E-Mail Website
Guest Editor
Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
Interests: veterinary virology; herpes virology; BoHV-1; HSV-1; viral latency; virus–host interaction; viral gene expression; duck hepatitis A viruses; astroviruses; FMDV

Special Issue Information

Dear Colleagues,

Molecular epidemiology is essential to understanding the evolution, transmission, and genetic diversity of animal-associated fungal and viral pathogens. As interactions between animals, humans, and the environment increase, these pathogens pose growing risks to both animal and public health.

This Special Issue highlights the advances in molecular tools and genomic approaches that reveal how these pathogens emerge and spread in domestic, wild, and aquatic animals. We invite original research, reviews, and communications focused on pathogen detection, genetic characterization, phylogenetics, host–pathogen interactions, resistance mechanisms, and molecular diagnostics.

Submissions with relevance to One Health, zoonotic threats, and transboundary disease control are especially encouraged. This issue aims to foster the development of effective surveillance and control strategies through interdisciplinary research at the intersection of animal, human, and environmental health.

Dr. Fouad S. El-Mayet
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 250 words) can be sent to the Editorial Office for assessment.

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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • molecular epidemiology
  • animal pathogens
  • fungal infections
  • viral infections
  • zoonotic diseases
  • genetic characterization
  • phylogenetic analysis
  • evolution

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

16 pages, 5731 KB  
Article
Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus
by Ibrahim Moharam, Julia Brüggemann, Ferdinand Schmitt, Benjamin Schade, Brigitte Böhm, Eva Kappe, Franziska Emmrich, Fares Z. Najar and Fouad S. El-Mayet
Animals 2026, 16(9), 1331; https://doi.org/10.3390/ani16091331 - 27 Apr 2026
Viewed by 154
Abstract
Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern [...] Read more.
Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting–stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Animal-Associated Fungal and Viral Pathogens)
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22 pages, 2661 KB  
Article
Molecular Diagnostics and Control of Zoonotic Dermatophytosis: First Detection of Trichophyton indotineae in a Dog in Africa
by Hend A. Zineldar, Wafaa M. El-Neshwy, Romeo T. Cristina, Nasser Z. Abouzeid, Mohammed I. Eisa, Florin Muselin, Eugenia Dumitrescu, Adel Abdelkhalek and Yasmine H. Tartor
Animals 2025, 15(17), 2622; https://doi.org/10.3390/ani15172622 - 7 Sep 2025
Cited by 3 | Viewed by 3127
Abstract
Fungal skin infections caused by dermatophytes are of significant veterinary and zoonotic concern. This study investigated the prevalence, risk factors, and treatment outcomes of dermatophytosis in dogs and cats with skin lesions. A total of 140 animals (90 dogs and 50 cats) that [...] Read more.
Fungal skin infections caused by dermatophytes are of significant veterinary and zoonotic concern. This study investigated the prevalence, risk factors, and treatment outcomes of dermatophytosis in dogs and cats with skin lesions. A total of 140 animals (90 dogs and 50 cats) that presented with skin lesions (alopecia, crusts, pruritus, and scales) were examined. Identification of dermatophyte isolates relied on both phenotypic characteristics and molecular techniques. The molecular approach involved PCR and sequencing of ribosomal DNA regions (ITS1, ITS2, and 5.8S rDNA), complemented by Restriction Fragment Length Polymorphism (RFLP). Treatment regimens included topical clotrimazole, systemic itraconazole, supportive therapy, and a dermatophyte vaccine. Of the 90 dog samples examined, 47 (52.22%) were positive for fungal culture (p = 0.65). In cats, 35 samples (70%) were positive (p < 0.0001). Microsporum canis was the most significant (p < 0.0001) prevalent isolate (60%), followed by Trichophyton mentagrophytes (20%). This study reported the first isolation of T. indotineae in Egypt. Younger animals (<1 year) exhibited a significantly (p < 0.05) higher risk of infection compared with adults (>1 year). Indoor/outdoor housing in cats significantly reduced the risk of infection when compared with indoor housing (p < 0.0001; odds ratio = 0.05). Combination therapy using itraconazole, clotrimazole, supportive treatment, and a dermatophyte vaccine resulted in the fastest clinical recovery (p < 0.0001). These findings underscore the importance of accurate diagnosis and effective treatment strategies for managing dermatophytosis in pets and preventing zoonotic transmission. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Animal-Associated Fungal and Viral Pathogens)
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