The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral contigs closely related to mammals were assigned to 22 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.

The discovery of new viruses is important for predicting their potential threats to the health of humans and other animals. A novel picornavirus was identified from oral, throat, and anal swab samples collected from belugas (Delphinapterus leucas), from Dalian Sun Asia Tourism Holding Co., China, between January and December 2018, using a metagenomics approach. The genome of this novel PicoV-HMU-1 strain was 8197 nucleotides (nt) in length, with a open reading frame (from 1091 to 8074 nt) that encoded a polyprotein precursor of 2328 amino acids. Moreover, the genomic length and GC content of PicoV-HMU-1 were within the ranges found in other picornaviruses, and the genome organization was also similar. Nevertheless, PicoV-HMU-1 had a lower amino acid identity and distinct host species compared with other members of the Picornaviridae family. Phylogenetic trees were constructed based on the P1 and 3D amino acid sequences of PicoV-HMU-1 along with representative members of the Picornaviridae family, which showed that PicoV-HMU-1 was related to unclassified bat picornaviruses groups. These findings suggest that the PicoV-HMU-1 strain represents a potentially novel genus of picornavirus. These data can enhance our understanding of the picornavirus genetic diversity and evolution.

Throughout the COVID‐19 pandemic, rhinovirus (RV) remained notable persistence, maintaining its presence while other seasonal respiratory viruses were largely suppressed by pandemic restrictions during national lockdowns. This research explores the epidemiological dynamics of RV infections among pediatric populations on Hainan Island, China, specifically focusing on the impact before and after the zero‐COVID policy was lifted. From January 2021 to December 2023, 19 680 samples were collected from pediatric patients hospitalized with acute lower respiratory tract infections (ARTIs) at the Hainan Maternal and Child Health Hospital. The infection of RV was detected by tNGS. RV species and subtypes were identified in 32 RV‐positive samples representing diverse time points by analyzing the VP4/VP2 partial regions. Among the 19 680 pediatric inpatients with ARTIs analyzed, 21.55% were found to be positive for RV infection, with notable peaks observed in April 2021 and November 2022. A gradual annual decline in RV infections was observed, alongside a seasonal pattern of higher prevalence during the colder months. The highest proportion of RV infections was observed in the 0–1‐year age group. Phylogenetic analysis on 32 samples indicated a trend from RV‐A to RV‐C in 2022. This observation suggests potential evolving dynamics within the RV species although further studies are needed due to the limited sample size. The research emphasizes the necessity for ongoing surveillance and targeted management, particularly for populations highly susceptible to severe illnesses caused by RV infections.

Objective: Inner Mongolia, with its vast grasslands providing ideal habitats for ticks, has recently emerged as a hotspot of novel tick-borne virus (TBV) prevalence. However, the diversity of TBVs and their potential spillover risks remain to be elucidated. Methods: In 2021, we collected 500 Haemaphysalis longicornis, Ixodes persulcatus, and Dermacentor silvarum ticks from Hulunbuir, Inner Mongolia, and conducted virome analysis and viral surveillance to evaluate TBV exposure risk in Hulunbuir. Results: A total of 26 viral species belonging to nine families were identified, including four novel viruses (Yiliekede tick virus 1 [YLTV1, Rhabdoviridae], Meitian tick virus [MtTV, Phenuiviridae], Wunuer pestivirus, and Wunuer tick phlebovirus) and 11 new strains of human-pathogenic viruses (including Songling virus [SGLV], Beiji nairovirus [BJNV], and Nuomin virus [NOMV]), from three dominant tick species. Virome profiling revealed striking species-specific patterns: I. persulcatus exhibited the highest viral richness and abundance, dominated by Chuviridae (NOMV) and Phenuiviridae; D. silvarum uniquely carried Phenuiviridae (MtTV); and H. longicornis showed Nairoviridae predominance (SGLV, BJNV). Phylogenetic analyses demonstrated that MtTV clustered with human-pathogenic Tacheng tick virus 2, and NOMV-YL strains showed high similarity to clinical NOMV isolates from febrile patients. Regional surveillance demonstrated MtTV’s pan-regional circulation in D. silvarum across nine locations (MIR=4–8%), contrasting with localized Yiliekede foci for SGLV (MIR=0.6%), BJNV (0.4%), and NOMV (1.0%). Conclusions: This study not only mapped the landscape of TBVs in a key pastoral region, but also highlighted the potential spillover risk of TBVs, including MtTV, YLTV1, SGLV, BJNV, and NOMV. Our findings underscore the urgent need for One Health strategies for monitoring emerging TBVs at the tick-human-livestock interface in northern China.

Introduction: Papillomaviruses (PVs) can cause hyperplasia in the skin and mucous membranes of humans, mammals, and non-mammalian animals, and are a significant risk factor for cervical and genital cancers.Methods: Using next-generation sequencing (NGS), we identified two novel strains of papillomavirus, PV-HMU-1 and PV-HMU-2, in swabs taken from belugas (Delphinapterus leucas) at Polar Ocean Parks in Qingdao and Dalian.Results: We amplified the complete genomes of both strains and screened ten belugas and one false killer whale (Pseudorca crassidens) for the late gene (L1) to determine the infection rate. In Qingdao, 50% of the two sampled belugas were infected with PV-HMU-1, while the false killer whale was negative. In Dalian, 71% of the eight sampled belugas were infected with PV-HMU-2. In their L1 genes, PV-HMU-1 and PV-HMU-2 showed 64.99 and 68.12% amino acid identity, respectively, with other members of Papillomaviridae. Phylogenetic analysis of combinatorial amino acid sequences revealed that PV-HMU-1 and PV-HMU-2 clustered with other known dolphin PVs but formed distinct branches. PVs carried by belugas were proposed as novel species under Firstpapillomavirinae.Conclusion: The discovery of these two novel PVs enhances our understanding of the genetic diversity of papillomaviruses and their impact on the beluga population.