Xiaolong Wang

Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species— Spheniscus humboldti ( S. humboldti ), Pygoscelis papua ( P. papua ), Pygoscelis adeliae ( P. adeliae ), and Aptenodytes forsteri ( A. forsteri )—collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing S. humboldti , Microviridae were enriched in P. papua , Caliciviridae accounted for a substantial proportion in A. forsteri , and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti . Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses. IMPORTANCE: This study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.

Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.

Foot-and-mouth disease virus (FMDV) serotype SAT3 is a rarely studied serotype primarily circulating in southern Africa, with African buffalo (Syncerus caffer) serving as its key reservoir. In this study, we performed a comprehensive phylogenetic and phylodynamic analysis of SAT3 based on 81 full-length VP1 gene sequences collected between 1934 and 2018. Maximum likelihood and Bayesian analyses revealed five distinct topotypes, each with clear geographic and host associations. Notably, topotypes I, II and III were observed in both African buffalo and cattle (Bos taurus), while topotype IV appeared restricted to African buffalo. Likelihood mapping indicated moderate to strong phylogenetic signal, and the mean substitution rate was estimated at 3.709 × 10⁻³ substitutions/site/year under a relaxed molecular clock. The time to the most recent common ancestor (TMRCA) was traced back to 1875. Discrete phylogeographic reconstruction identified Zimbabwe as a major center, with multiple supported cross-border transmission routes. Host transition analysis further confirmed strong directional flow from buffalo to cattle (BF = 1631.09, pp = 1.0), highlighting the wildlife–livestock interface as a key driver of SAT3 persistence. Together, these results underscore the evolutionary complexity of SAT3 and the importance of integrating molecular epidemiology, spatial modeling, and host ecology to inform FMD control strategies in endemic regions.

[This corrects the article DOI: 10.1371/journal.pone.0311936.].

This study assesses the prevalence of bovine trypanosomes and the density of tsetse flies in the Yem Special District, Southern Ethiopia, highlighting the disease's significant impact on livestock health and agricultural productivity. Conducted between May 2022 and January 2023, the cross-sectional survey analyzed 960 blood samples for trypanosomes prevalence and tsetse fly density. Results revealed a 10.63% (9–12%) overall prevalence of bovine trypanosomes, with Trypanosoma congolense (5.83%) and Trypanosoma vivax (4.73%) as the predominant species, and 0.63% of mixed infection. Significant associations were found between trypanosomes and anemia, age, and sex, with higher prevalence rates observed in cattle with poor body condition scores and black-hair coats. The study identified three Glossina species, with Glossina morsitans submorsitans being the most prevalent. The findings underscore the need for integrated vector control strategies, community engagement in disease management, and further research using molecular techniques for deeper understanding and effective control measures. Collaboration among stakeholders is crucial for mitigating the disease's impact on livestock and human populations.

Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of “viral dark matter,” the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.

Foot-and-mouth disease (FMD) is a severe, highly contagious viral disease of livestock that has a significant economic impact on domestic animals and threatens wildlife survival in China and border countries. However, effective surveillance and prevention of this disease is often incomplete and unattainable due to the cost, the great diversity of wildlife hosts, the changing range and dynamics, and the diversity of FMDV. In this study, we used predictive models to reveal the spread and risk of FMD in anticipation of identifying key nodes to control its spread. For the first time, the spatial distribution of FMD serotype O was predicted in western China and border countries using a niche model, which is a combination of eco-geographic, human, topographic, and vegetation variables. The transboundary least-cost pathways (LCPs) model for ungulates in the study area were also calculated. Our study indicates that FMD serotype O survival is seasonal at low altitudes (March and June) and more sensitive to temperature differences at high altitudes. FMD serotype O risk was higher in Central Asian countries and both were highly correlated with the population variables. Ten LCPs were obtained representing Pakistan, Kazakhstan, Kyrgyzstan, and China.