Steven R. Fiddaman

Background/Objectives: Lumpy skin disease, a highly contagious Capripoxvirus infection, causes significant economic losses in cattle worldwide. In Ethiopia, diagnosis primarily relies on virus neutralization tests and PCR, highlighting the need for scalable serological tools suitable for large-volume surveillance. The objective of this study was to produce and functionally characterize egg-yolk-derived IgY antibodies against the lumpy skin disease virus (LSDV) vaccinal strain as a proof-of-concept for future serological assay development. Methods: An experimental study was conducted from January to May 2024 over 42 days. The vaccinal virus was adapted on the Vero cell line and titrated after two passages in Minimum Essential Medium. Chickens (n = 10) were allocated into two groups (six experimental and four control). The experimental group received the LSDV vaccinal strain with a booster on day 15, while the control group received a placebo. Weekly serum and egg samples were collected. IgY was extracted from egg yolk using polyethylene glycol precipitation followed by dialysis purification. The protein concentration, molecular weight, and functional activity were assessed using NanoDrop spectrophotometry, SDS-PAGE, and virus neutralization tests (VNTs), respectively. A statistical analysis was performed using linear regression, repeated-measures ANOVA, and a linear mixed-effects model in R (version 4.4.1), with p < 0.05 considered statistically significant. Results: Total protein concentration increased significantly over time (p = 0.0239), with significant differences observed across weeks (p < 0.0001). The virus neutralization assays demonstrated a significantly higher neutralizing activity of egg-yolk-derived IgY compared to serum-derived antibodies (p < 0.0002). Conclusions: This study demonstrates the feasibility of producing functionally active IgY antibodies against LSDV in egg yolk. However, as the protein quantification was based on total protein measurement and antigen-specific validation was not performed, further studies are required to confirm specificity and optimize their application in diagnostic assay development.

Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions of geographic and production-system factors to phenotypic diversity. Methods: Native chickens were sampled from 259 households across eight provinces in Indonesia. Household-level information on production systems and farmer selection practices was collected through structured surveys. Morphometric traits and HSV-derived plumage-colour variables were analysed using principal component analysis (PCA), permutational multivariate analysis of variance (PERMANOVA), and hierarchical variance partitioning to assess phenotypic variation across locations, provinces, and islands. Results: Substantial phenotypic variation was observed among sampled populations, with significant province- and island-level differences detected for several morphometric traits. However, extensive overlap among locations was evident in both morphometric and plumage-colour space, indicating diffuse rather than discrete structuring. Within-location variation accounted for the largest proportion of total phenotypic variance across most traits, consistent with decentralised smallholder management and continued human-mediated exchange. Conclusion: Geographic fragmentation and agroecological heterogeneity alone appear insufficient to generate strongly differentiated phenotypic groups when connectivity among populations is maintained. Whether this phenotypic connectivity corresponds to contemporary gene flow, retained ancestral variation, or convergent environmental responses remains to be tested using genomic data.

Marek's disease (MD) is common in chickens from small flocks, most of which are not vaccinated against this disease. However, little is known about the virulence of strains of Marek's disease virus (MDV) that are currently circulating in small flocks in England and Wales, and whether they pose any risk to commercial poultry. Between 2017 and 2025, 31 samples with histopathological lesions consistent with MD, submitted to the Animal and Plant Health Agency, were confirmed by real-time PCR at the Pirbright Institute's MDV Reference Laboratory. The age, gender, breed of chicken, flock size, MD vaccination status, clinical signs, and pathology due to MD were recorded. Sequencing of the MDV meq gene, which is closely associated with virulence, showed a range of Meq protein "isoforms" (standard, long, very long, and a previously unreported isoform designated very very long) with, respectively, 4, 7, 10, and 12 tetraproline repeat motifs. Phylogenetic analysis showed that British small flocks are a reservoir of MDV strains of diverse origins. While the majority of Meq sequences lie within well-established European MDV clades (including an ancient clade of low-virulence strains, and the very virulent plus (vv+) MDV Polen clade), 10 strains cluster phylogenetically with MDV from a diverse range of geographic locations, including Asia and South America.RESEARCH HIGHLIGHTS Molecular characterization of MDV strains from British small chicken flocks showed great diversity.Sequencing showed a variety of Meq protein isoforms: standard, long, very long, and very very long.Phylogenetic analysis identified MDV strains similar to those from diverse geographical regions, varying in predicted virulence.

Following their domestication, chickens were translocated around the world to novel environments. Through a combination of natural and artificial selection, chickens adapted to these local conditions, creating significant genetic diversity across populations worldwide. Studying this diversity in the context of local environmental conditions may offer insights into mechanisms of adaptation to environmental stressors. In this study, we analyzed genomic data from the Chicken Genomic Diversity Consortium, applying multiple statistical approaches, including fixation index (F _ST ), nucleotide diversity (π), Tajima’s D, and runs of homozygosity (ROH), to identify selective sweeps among indigenous chickens from Afghanistan, China, Indonesia, Iran and Pakistan, compared with White Leghorn chickens. We identified sweeps in 14 genes related to heat tolerance, associated with relevant gene ontology (GO) terms and located within ROH regions. These genes, such as CDH23 , NPSR1 , MCU , TRPV2 , TRPV1 , TRPV3 , ATP2B4 , CALM1 , CACNB2 , TRAT1 , BDNF , SCIN , WIPF3 , PRKD1 , and DNAJC10 play crucial roles in calcium signaling pathways, thermal sensation, and the plasticity of neurodevelopmental processes. These findings illustrate the significant role of selection in shaping genomic differentiation across chicken populations and provide insights into the genetic basis of adaptation to environmental stressors.

Avian alphaherpesviruses of the genus Mardivirus include several economically important pathogens, such as the tumour-causing Marek’s disease virus (MDV-1) of chickens. However, the diversity of related viruses in wild and non-model avian hosts remains poorly characterised. Here, we describe the genome of Pavonine herpesvirus 1 (PaHv1), a novel Mardivirus infecting peafowl ( Pavo spp.). Through de novo assembly of reads generated from whole-genome sequencing of 370 captive peafowl, we generated a single viral genomic scaffold of 134,149 bp in length and an estimated total genome size of ∼146 kbp following reconstruction of terminal repeat regions. PaHv1 exhibits canonical Mardivirus UL-IRL-IRS-US genomic architecture and encodes 169 open reading frames, of which 82 have clear orthologs in other Mardivirus species. Comparative genomic analyses revealed strong syntenic concordance between PaHv1, MDV-1, MDV-2 and Meleagrid alphaherpesvirus 1 (HVT), but with notable absences of the Meq oncogene, viral interleukin-8 (vIL8), and a truncated pp38 gene – genes known to underpin oncogenicity and virulence in MDV-1. Phylogenetic analysis places PaHv1 firmly within the Mardivirus genus as a sister to the poultry-associated MDV-1 and MDV-2 viruses, but distinct from a previously described Phasianid herpesvirus with a partial DNA terminase sequence. PaHv1 was detected predominantly in feather-derived samples, consistent with replication or persistence in the feather follicle epithelium. Taken together, these findings identify PaHv1 as a novel, likely non-oncogenic Mardivirus , expanding our understanding of herpesvirus diversity, evolution and host association in galliform birds. Importance: Herpesviruses cause several economically important diseases in domesticated birds, including Marek’s disease, duck plague and infectious laryngotracheitis. Despite this, our understanding of herpesviruses infecting wild and semi-wild birds remains limited. Here, we present the genome of Pavonine herpesvirus 1 (PaHv1), a virus in the Mardivirus genus which infects peafowl. Based on comparative genomics with other Mardivirus species, we note the absence of several genes important for the high virulence of Marek’s Disease Virus, such as the Meq oncogene, viral interleukin-8 and a truncated pp38. This, taken together with absence of clinical disease in preliminary observations, suggests that PaHv1 causes either a subclinical infection or one with mild symptoms. Our work expands the known evolutionary breadth of avian herpesviruses in the Mardivirus genus. In addition, PaHv1 may provide a useful starting point for the development of novel vaccine vectors for pathogenic herpesvirus infections.

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek’s disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested theMeqoncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into—and generate evolutionary hypotheses on—the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations. Abstract Reviewing current advances in our understanding of molecular evolution underpinning vertebrate immunity, we propose hypotheses to explain differences in selection modes across immune genes and discuss supporting evidence.

Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.

The ability of zinc finger antiviral protein (ZAP) to recognize and respond to RNA virus sequences with elevated frequencies of CpG dinucleotides has been proposed as a functional part of the vertebrate innate immune antiviral response. It has been further proposed that ZAP activity shapes compositions of cytoplasmic mRNA sequences to avoid self-recognition, particularly mRNAs for interferons (IFNs) and IFN-stimulated genes (ISGs) expressed during the antiviral state. We investigated whether restriction of the replication of mutants of influenza A virus (IAV) and the echovirus 7 (E7) replicon with high CpG and UpA frequencies varied in different species of mammals and birds. Cell lines from different bird orders showed substantial variability in restriction of CpG-high mutants of IAV and E7 replicons, whereas none restricted UpA-high mutants, in marked contrast to universal restriction of both mutants in mammalian cells. Dinucleotide representation in ISGs and IFN genes was compared with those of cellular transcriptomes to determine whether potential differences in inferred ZAP activity between species shaped dinucleotide compositions of highly expressed genes during the antiviral state. While mammalian type 1 IFN genes typically showed often profound suppression of CpG and UpA frequencies, there was no oversuppression of either in ISGs in any species, irrespective of their ability to restrict CpG- or UpA-high mutants. Similarly, genome sequences of mammalian and avian RNA viruses were compositionally equivalent, as were IAV strains recovered from ducks, chickens and humans. Overall, we found no evidence for host variability in inferred ZAP function shaping host or viral transcriptome compositions.