Introduction

Owing to economic globalisation and environmental changes, the risk of emerging infectious diseases (EID) is increasing globally, posing threats to human health, the economy, and society. Approximately 60.3% of human EIDs are caused by zoonotic pathogens, originating from rodents, bats, birds, and other wildlife [1-3], with viral or prion pathogens accounting for 25.4% of all EID events [1].Coronavirus Disease 2019 (COVID-19) and Ebola hemorrhagic fever (EBHF) bleong to EID events. Rodential is the largest mammalian group on Earth, with 35 families, 389 genera, and approximately 2700 species (~43% of all mammal species) worldwide [4]. Rodents are widely distributed, diverse in species, have a strong reproductive ability, migrate in groups, and are mostly concentrated in densely populated and humid and warm places such as Central and Southern China, providing them with many opportunities to interact with humans.
Rodents carry Yersinia pestis, Hantaviruses (HanVs), and Leptospira, which cause plague, haemorrhagic fever, and leptospirosis, respectively [5]. Moreover, several important zoonotic viruses carried by rodents are members of the Hantaviridae ,Flaviviridae ,Arenaviridae, Reoviridae ,Piconaviridae , and Togaviridae families [4-9]. Many of these family viruses include multiple agents associated with acute gastroenteritis or febrile illnesses that can cause severe diseases in humans. Lassa virus (LASV), lymphocytic choriomeningitis virus (LCMV), Tacaribe, Machupo, Junin, Guanarinto, Sabia, and the recently discovered White-water Arroyo and Lujo viruses are high-impact pathogens belonging to theArenaviridae family [10-13]. HanVs infect a wide range of mammalian hosts; Hanta, Seoul, Puumala, and Sin Nombre viruses are etiological agents of haemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome in humans [7]. Virus-host co-divergence and cross-species transmission have played an important role in the evolution and taxonomy of HanVs [7]. Additionally, rat hepatitis E is the causative agent of hepatitis in humans [14] and tick-borne encephalitis virus [15] causes human meningitis, encephalitis, and meningoencephalitis in the northern European subcontinent. Severe fever with thrombocytopenia syndrome [16], Crimean Congo haemorrhagic fever, and Omsk haemorrhagic fever viruses are transmitted by rodents to humans as vectors [5].
Next-generation sequencing (NGS), viral metagenomic analysis is rapidly evolving in the study of natural environments [17], humans, and animals [18]. Recently, metagenomic and meta-transcriptomic analyses have been increasingly used to investigate the composition of rodent virome. For example, the Aichi virus and novel circovirus have been detected in wild rodent faecal samples in the analysis of mouse enterovirus diversity [4]. The detection of multiple infectious viruses in rodent lungs in mainland Southeast Asia [18]. Hainan Island is a tropical island province that has been geographically isolated from mainland China for a long time; therefore, its ecological environment and microorganisms are independent to some degree. Owing to the unique climate and geographical environment of Hainan Island, it is rich in diverse mammalian species, especially rodents. The Hainan Province is an important free trade port in China; therefore, the spread of viral pathogens from this province is expected to increase through economic globalisation. In our previous studies, the Wenzhou virus (WENV) belonging toArenaviridae from Rattus norvegicus was detected in Daoke Village, Hainan, and a complete genome sequence was obtained [19]. The present study aimed to . We collected 588 throat and anal swabs from 326 rodents belonging to 6 species and grouped the swabs into 28 pools according to the rodent species, swab types, and sample locations. We sequenced the virome, revealed that coronaviruses, flaviviruses, parvoviruses, astroviruses, and papillomaviruses are carried by rodents, and revealed the viral abundance of each pool. The annotation and phylogenetic description of rodent-borne viruses will help us to explore their origin, spread mode, and evolutionary patterns.