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Avian Influenza (AI) remains a critical threat to livestock production in Oceania, with recent outbreaks of Highly Pathogenic Avian Influenza (HPAI) H7 subtypes in Australia and New Zealand. Historically, AI detections in these countries were largely confined to wild birds. However, since 2024, multiple outbreaks in commercial poultry populations have been reported, with the emergence of HPAI H7N3, H7N8, and H7N9 in Australia and H7N6 in New Zealand. To investigate the epidemiological links of these outbreaks, we retrieved all publicly available H7 hemagglutinin (HA) gene sequences from animals in Oceania between 2014 and 2025 that were deposited in GISAID and NCBI databases. Phylogenetic reconstruction using maximum likelihood methods revealed distinct Australian and New Zealand clades, suggesting local viral evolution rather than recent transboundary introductions. The absence of phylogenetic clustering between Oceanian and Asian H7 sequences suggests limited recent gene flow between regions, particularly in the HA gene segment. These local viral mutations can pose a threat to the poultry industry; therefore, continuous genomic surveillance in commercial farms and wild bird reservoirs is crucial. Such efforts support the One Health framework by enabling early detection of pathogenic variants and reducing zoonotic spillover risks for animal and public health.

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

Key message We report success of host-induced gene silencing in downregulation of aflatoxin biosynthesis in Aspergillus flavus infecting maize transformed with a hairpin construct targeting transcription factor aflR . Infestation of crops by aflatoxin-producing fungi results in economic losses as well as negative human and animal health effects. Currently, the control strategies against aflatoxin accumulation are not effective to the small holder farming systems in Africa and this has led to widespread aflatoxin exposure especially in rural populations of sub-Saharan Africa that rely on maize as a staple food crop. A recent strategy called host-induced gene silencing holds great potential for developing aflatoxin-resistant plant germplasm for the African context where farmers are unable to make further investments other than access to the germplasm. We transformed maize with a hairpin construct targeting the aflatoxin biosynthesis transcription factor aflR . The developed transgenic maize were challenged with an aflatoxigenic Aspergillus flavus strain from Eastern Kenya, a region endemic to aflatoxin outbreaks. Our results indicated that aflR was downregulated in A. flavus colonizing transgenic maize. Further, maize kernels from transgenic plants accumulated significantly lower levels of aflatoxins (14-fold) than those from wild type plants. Interestingly, we observed that our silencing cassette caused stunting and reduced kernel placement in the transgenic maize. This could have been due to “off-target” silencing of unintended genes in transformed plants by aflR siRNAs. Overall, this work indicates that host-induced gene silencing has potential in developing aflatoxin-resistant germplasm.

Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) protein gene, including the cleavage site, of the obtained viruses. We aligned and compared study sequences with representative NDV of different genotypes from GenBank. The fusion protein cleavage site of all the study sequences had the motif 112RRQKRFV118 indicating their velogenic nature. Phylogenetic analysis revealed that the NDV from various sites in Kenya was highly similar genetically and that it clustered together with NDV of genotype V. The study samples were 96% similar to previous Ugandan and Kenyan viruses grouped in subgenotype Vd This study points to possible circulation of NDV of similar genetic characteristics between backyard poultry farms and live bird markets in Kenya. The study also suggests the possible spread of velogenic NDV between Kenya and Uganda possibly through cross-border live bird trade. Our study provides baseline information on the genetic characteristics of NDV circulating in the Kenyan poultry population. This highlights the need for the ND control programmes to place more stringent measures on cross-border trade of live bird markets and poultry products to prevent the introduction of new strains of NDV that would otherwise be more difficult to control.

We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.

This study aimed to investigate the signatures of selection in guineafowl and chicken genomes adapted to divergent climatic conditions across Africa, Asia, and Europe. We used whole genome sequence data of guineafowls and chicken from selected countries in these continents. To identify the signatures of selection, we employed three population genomics methods: FST, integrated Haplotype Score (iHS), and Cross-Population Extended Haplotype Homozygosity (XP-EHH). Our findings revealed enriched terms related to metabolic processes, response to stimulus, signaling, and developmental processes, all of which play a role in the stress response for both guineafowls and chickens. Several candidate genes such as CRYGN, BRAF, MAP3K2, ANGPT2, COL1A1, ATP13A4, and SLC66A1, were among the positively selected candidate genes. Most of the candidate genes selected and the significant pathways identified play various roles in stress response in these two poultry species. Examination of divergent populations has provided new insights into genes potentially under selection for tolerance to the populations indigenous environment, serving as a baseline for examining the genomic contributions to tolerance adaption. The knowledge gained from this research establishes a valuable foundation and guide for molecular breeding and conservation.Competing Interest StatementThe authors have declared no competing interest.Footnotes* https://docs.google.com/spreadsheets/d/15rKN3UER_eKaURKjjPEHrIrdQJ8WvWjt/edit?gid=634045355#gid=634045355