Hassanein, R. T., H. K. Abdelmegeed, D. A. Abdelwahed, A. G. Zaki, A. S. Saad, M. A. Shahein, A. F. Afify, and M. A. Rohaim, "Epidemiological and Genetic Insights of the Circulating Foot-and-Mouth Disease Virus Serotypes in Egypt.", Current microbiology, vol. 81, issue 12, pp. 435, 2024 Oct 30. Abstract

Foot-and-mouth disease virus (FMDV) remains a major threat to livestock in Egypt, with ongoing outbreaks involving serotypes A, O, and SAT2. This study aimed to improve the understanding of these circulating FMDV strains to improve control measures. Between 2022 and 2023, 134 cattle samples from across Egypt were analyzed, revealing a 67.9% positivity rate for Pan FMDV. Of these positive samples, 64 were identified as serotype A and 27 as serotype O. Genetic analysis indicated that serotype O strains clustered within the EA-3 topotype, suggesting endemic persistence and potential vaccine evasion, while serotype A strains were associated with the African topotype and linked to regions such as Ethiopia, Kenya, and Sudan. Notable amino acid mutations in the VP1 protein of both serotypes highlighted potential challenges to vaccine effectiveness. These findings underscore the need for enhanced surveillance, timely vaccine updates, and regional cooperation to effectively manage FMD outbreaks in Egypt and neighboring countries.

Alam, F., A. Ullah, M. A. Rohaim, M. Munir, and A. Hussain, "An automatic approach for the classification of lumpy skin disease in cattle.", Tropical animal health and production, vol. 57, issue 5, pp. 230, 2025 May 28. Abstract

Lumpy Skin Disease (LSD) presents significant risks and economic challenges to global cattle farming. Effective and accurate classification of LSD is essential for managing the disease and reducing its impacts. Manual diagnosis is time-consuming, labor-intensive, and requires experienced personnel. Automated classification methods provide advantages by reducing labor and improving accuracy. This study proposes an automated algorithm for LSD classification using machine learning. The method uses a carefully curated dataset of images from both LSD-infected cattle and healthy cattle. Inception V3 was employed to extract features from complex lesion patterns in infected cattle images, comparing them to healthy cattle images. Support Vector Machines (SVM) were used to classify the extracted features. The results show the model achieved an 84% accuracy rate, with precision at 80%, recall at 83%, and an F1 score of 82%. These results were compared with other machine learning models, including Logistic Regression, Random Forest, Decision Tree, and AdaBoost. SVM outperformed other models, demonstrating consistent evaluation precision at 0.84. For further enhancement, expanding the dataset with high-quality images and applying advanced machine learning algorithms like Vision Transformers (ViTs), MobileNetV2, and Visual Geometry Group (VGG) could refine automated LSD classification. The aim is to improve disease management practices in the livestock industry through better classification systems.

Abdelmonem, M., C. A. C. Abdullah, I. M. Bastawecy, A. M. A. Raof, A. F. Afify, R. E. F. Naggar, M. A. Rohaim, and M. Munir, "Antiviral Nanomedicine-Based Approaches against Epstein-Barr Virus Infection", Curr Treat Options Infect Dis, vol. 16, pp. 58–71, 2024. s40506-024-00271-4.pdf
Bastawecy, I. M., M. Abdelmonem, A. F. Afify, N. Saad, Y. Shirosaki, C. A. C. Abdullah, R. F El Naggar, M. A. Rohaim, and M. Munir, "Viral contamination in cell culture: analyzing the impact of Epstein Barr virus and Ovine Herpesvirus 2.", Frontiers in microbiology, vol. 16, pp. 1442321, 2025. Abstract

Cell culture techniques are increasingly favored over animal models due to rising costs, time constraints, and ethical concerns regarding animal use. These techniques serve critical roles in disease modeling, drug screening, drug discovery, and toxicity analysis. Notably, cell cultures facilitate primary virus isolation, infectivity assays, biochemical studies, and vaccine production. However, viral contamination in cell cultures poses significant challenges, particularly due to the necessity for complex and sophisticated detection methods. Among the prevalent viruses, Epstein Barr virus (EBV) is ubiquitous across human populations, infecting approximately 98% of individuals. Despite its prevalence, the detection of EBV is often not considered a safety priority, as its detection methods are well-established, including PCR assays that can identify both active and latent forms of the virus. Conversely, ovine herpesvirus 2 (OvHV-2), a relative of EBV, presents a critical concern due to its ability to infect a wide range of organs and species, including over 33 animal species and nearly all domestic sheep. This makes the detection of OvHV-2 crucial for the safety of cell cultures across various species. The literature reveals a gap in the comprehensive understanding of both EBV and OvHv-2 detection in cell culture systems, highlighting an urgent need for developing robust detection methodologies specific to EBV and OvHv-2 to ensure bioprocess safety.

Haider, A., Z. Abbas, A. Taqveem, A. Ali, M. Khurshid, R. F El Naggar, M. A. Rohaim, and M. Munir, "Lumpy Skin Disease: Insights into Molecular Pathogenesis and Control Strategies.", Veterinary sciences, vol. 11, issue 11, 2024. Abstract

Lumpy skin disease (LSD) is a viral infection that affects buffaloes and cattle across various regions, including both tropical and temperate climates. Intriguingly, the virus-carrying skin sores remain the primary source of infection for extended periods, exacerbated by the abundance of vectors in disease-endemic countries. Recent scientific advances have revealed the molecular aspects of LSD and offered improved vaccines and valuable antiviral targets. This review summarizes the molecular features of LSD and its effect on various livestock species. We then provide an extensive discussion on the transmission dynamics of LSD and the roles of vectors in its continued spread among livestock populations. Additionally, this review critically analyses the rationales behind, as well as the affordability and effectiveness, of current control strategies worldwide.

Afify, A. F., R. T. Hassanien, R. F El Naggar, M. A. Rohaim, and M. Munir, "Unmasking the ongoing challenge of equid herpesvirus- 1 (EHV-1): A comprehensive review.", Microbial pathogenesis, vol. 193, pp. 106755, 2024. Abstract

Equid herpesviruses (EHVs) are a group of highly impactful viral pathogens that affect horses, presenting a substantial risk to the global equine industry. Among these, equid herpesvirus-1 (EHV-1) primarily causes respiratory infections. However, its ability to spread to distant organs can lead to severe consequences such as abortion and neurological diseases. These viruses can enter a dormant phase, with minimal activity, and later reactivate to trigger active infections at any time. Recently, there has been a notable rise in the prevalence of a particularly devastating strains of EHV-1 known as equid herpesviral myeloencephalopathy (EHM). In the light of dynamic nature of EHV-1, this review provides a thorough overview of EHV-1 and explores how advances in viral biology affect the pathophysiology of viral infection. The information presented here is crucial for understanding the dynamics of EHV-1 infections and creating practical plans to stop the virus's global spread among equid populations.

Al-Natour, M. Q., M. A. Rohaim, R. F El Naggar, M. A. Abdelsabour, A. F. Afify, Y. M. Madbouly, and M. Munir, "Respiratory disease complex due to mixed viral infections in chicken in Jordan.", Poultry science, vol. 103, issue 4, pp. 103565, 2024. Abstract

The global distribution of avian respiratory viruses highlights the need for effective surveillance programs and international collaboration to monitor viral circulation and implement timely control measures. In the current study, we aim to provide a comprehensive overview of avian respiratory viral infections in the poultry flocks in Jordan, focusing on the major viruses involved, their epidemiology, clinical manifestations, and evolution based on viroinformatics that will be helpful to improve the diagnostic methods, and control strategies including vaccines in the region. In this research, various poultry broiler groups in Jordan experiencing respiratory symptoms were tested for respiratory viral pathogens from January 2021 to February 2022. The mortality rates observed in the examined groups varied between 6% and 40%. The identified strains were authenticated using the RT-qPCR assay. Furthermore, they underwent in-depth characterisation through the sequencing of the complete spike (S1) gene for infectious bronchitis virus (IBV) and the haemagglutinin (HA) gene for avian influenza virus (AIV) subtype H9N2. Co-infection of IBV and AIV H9N2 viruses was detected through molecular analysis. The IBV strains showed affiliation with the variant groups GI-16 (3 strains) and GI-23 (9 strains) and exhibited numerous mutations. Meanwhile, H9N2 avian influenza viruses displayed various changes in amino acids within the HA gene, suggesting the influence of antibody-driven selection pressure. The phylogenetic analysis revealed that the H9N2 viruses identified in this investigation shared close genetic ties with EG3 (3 strains) and the Middle East group (ME1; 8 strains). These strains have been recently found in Jordan and nearby countries in the Middle East. Moreover, their HA genes exhibited similarities to viruses belonging to the G1-like lineage. In conclusion, avian respiratory viral infections remain a significant concern for the poultry industry, requiring constant vigilance and proactive measures to minimise their impact. Continued surveillance, robust diagnostic methods, effective vaccines, and international cooperation are essential components of a comprehensive approach to combat avian respiratory viral infections (AI, IBV, ND and ILT 'viruses) and safeguard avian health and global poultry production.

Rohaim, M. A., E. L. Gardiner, R. F El Naggar, M. A. Abdelsabour, Y. M. Madbouly, M. O. Atasoy, K. A. Ahmed, M. M. El-Safty, and M. Munir, "Avian sarcoma/leukosis virus (RCAS)-mediated over-expression of IFITM3 protects chicks from highly pathogenic avian influenza virus subtype H5N1.", Microbes and infection, pp. 105231, 2023. Abstract

Broad-spectrum antiviral activities of interferon-induced transmembrane proteins (IFITMs) are primarily attributed to in vitro inhibition of viral entry. Here, we used an avian sarcoma-leukosis virus (RCAS)-based gene transfer system and successfully generated chicks that constitutively express chicken IFITM3 (chIFITM3). The chIFITM3-overexpressing chicks showed significant protection and disease tolerance against highly pathogenic avian influenza virus (HPAIV) H5N1 (Clade 2.2.1.2). The chicks, overexpressing chIFITM3, also showed delayed onset of clinical symptoms, reduced viral shedding, and alleviated histopathologic alterations compared to control and challenged chicks. These findings highlight that overexpression of chIFITM3 provide a substantial defense against zoonotic H5N1 in vivo.

Amoia, C. F., J. N. Hakizimana, N. K. Duggal, A. A. Chengula, M. A. Rohaim, M. Munir, J. Weger-Lucarelli, and G. Misinzo, "Genetic Diversity of Newcastle Disease Virus Involved in the 2021 Outbreaks in Backyard Poultry Farms in Tanzania.", Veterinary sciences, vol. 10, issue 7, pp. 477, 2023. Abstract

Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa in 2021. Reverse-transcription polymerase chain reaction (RT-PCR) based on fusion () gene amplification was conducted on 79 cloacal or tracheal swabs collected from chickens during a suspected ND outbreak. Our results revealed that 50 samples out 79 (50/79; 63.3%) were NDV-positive. Sequencing and phylogenetic analyses of the selected NDV isolates showed that 39 isolates belonged to subgenotype VII.2 and only one isolate belonged to subgenotype XIII.1.1. Nucleotide sequences of the NDV genes from Tanzania were closely related to recent NDV isolates circulating in southern Africa, suggesting that subgenotype VII.2 is the predominant subgenotype throughout Tanzania and southern Africa. Our data confirm the circulation of two NDV subgenotypes in Tanzania, providing important information to design genotype-matched vaccines and to aid ND surveillance. Furthermore, these results highlight the possibility of the spread and emergence of new NDV subgenotypes with the potential of causing future ND epizootics.

Vilela, J., M. A. Rohaim, and M. Munir, "Avian Orthoavulavirus Type-1 as Vaccine Vector against Respiratory Viral Pathogens in Animal and Human.", Vaccines, vol. 10, issue 2, 2022. Abstract

Avian orthoavulaviruses type-1 (AOaV-1) have recently transitioned from animal vaccine vector to a bona fide vaccine delivery vehicle in human. Owing to induction of robust innate and adaptive immune responses in mucus membranes in both birds and mammals, AOaVs offer an attractive vaccine against respiratory pathogens. The unique features of AOaVs include over 50 years of safety profile, stable expression of foreign genes, high infectivity rates in avian and mammalian hosts, broad host spectrum, limited possibility of recombination and lack of pre-existing immunity in humans. Additionally, AOaVs vectors allow the production of economical and high quantities of vaccine antigen in chicken embryonated eggs and several GMP-grade mammalian cell lines. In this review, we describe the biology of AOaVs and define protocols to manipulate AOaVs genomes in effectively designing vaccine vectors. We highlighted the potential and established portfolio of AOaV-based vaccines for multiple respiratory and non-respiratory viruses of veterinary and medical importance. We comment on the limitations of AOaV-based vaccines and propose mitigations strategies. The exploitation of AOaVs vectors is expanding at an exciting pace; thus, we have limited the scope to their use as vaccines against viral pathogens in both animals and humans.