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.