Dataset Information

A dataset of diversity and distribution of rodents and shrews in China.

ABSTRACT: The rodents and shrews are important reservoirs for a large number of zoonotic pathogens. Here by performing a literature review, we determined the occurrence and distribution of rodents and shrews in China at three scales including province, city, and county levels. The peer-reviewed papers published in English and Chinese were collected, standard procedures were applied in reference books, field surveys and websites to remove duplicates, and information on recorded locations of rodents and shrews was extracted. The dataset contains 13,911 records of geo-referenced occurrences for 364 rodents and shrews distributed over 1,663 locations distinguished. As pathogens continue to emerge from rodents and shrews, this dataset could assist efforts to put preliminary bounds around a variety of spatial analyses of rodents and shrews, facilitate a better understanding of the transmission risk of the pathogens they carry, and be helpful for assessing the risk of future emergence of rodent-borne zoonoses.

SUBMITTER: Chen JJ

PROVIDER: S-EPMC9200832 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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A dataset of diversity and distribution of rodents and shrews in China.

Chen Jin-Jin JJ Xu Qiang Q Wang Tao T Meng Fan-Fei FF Li Zhi-Wei ZW Fang Li-Qun LQ Liu Wei W Liu Wei W

Scientific data 20220615 1

The rodents and shrews are important reservoirs for a large number of zoonotic pathogens. Here by performing a literature review, we determined the occurrence and distribution of rodents and shrews in China at three scales including province, city, and county levels. The peer-reviewed papers published in English and Chinese were collected, standard procedures were applied in reference books, field surveys and websites to remove duplicates, and information on recorded locations of rodents and shr ...[more]

PMID: 35705563

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Project description:BackgroundWild rodents and shrews serve as vital sentinel species for monitoring zoonotic viruses due to their close interaction with human environments and role as natural reservoirs for diverse viral pathogens. Although several studies have explored viral diversity and assessed pathogenic risks in wild rodents and shrews, the full extent of this diversity remains insufficiently understood.ResultsWe conducted high-throughput sequencing on 1113 small mammals collected from 97 townships across seven cities in Hubei Province during 2021, supplemented by publicly available data from 2014 and 2016-2017. This analysis revealed a diverse array of novel viruses spanning several viral families, including Arenaviridae, Hepeviridae, Chuviridae, Paramyxoviridae, Arteriviridae, Nodaviridae, Rhabdoviridae, Dicistroviridae, Astroviridae, and Picornaviridae. Phylogenetic analysis and genome structure characterization highlighted the discovery of these novel viruses, enhancing our understanding of viral diversity and evolution. Key host species such as Chodsigoa smithii, Anourosorex squamipes, Niviventer niviventer, and Apodemus agrarius were identified as significant contributors to viral circulation, making them crucial targets for future surveillance. Additionally, the central Plain of Hubei Province was recognized as a critical geographic hub for viral transmission, underscoring its importance in monitoring and controlling viral spread. Machine learning models were employed to assess the zoonotic potential of the identified viruses, revealing that families such as Arenaviridae, Coronaviridae, Hantaviridae, Arteriviridae, Astroviridae, Hepeviridae, Lispiviridae, Nairoviridae, Nodaviridae, Paramyxoviridae, Rhabdoviridae, Picornaviridae, and Picobirnaviridae possess a high likelihood of infecting humans. Notably, rodent-derived Rotavirus A, HTNV, and SEOV displayed almost complete amino acid identity with their human-derived counterparts, indicating a significant risk for human outbreaks.ConclusionThis study provides a comprehensive virome landscape for wild rodents and shrews in Central China, highlighting novel viruses and the critical roles of specific host species and regions in viral transmission. By identifying key species and hotspots for viral spread and assessing the zoonotic potential of the discovered viruses, this research enhances our understanding of virus ecology and the factors driving zoonotic disease emergence. The findings emphasize the need for targeted surveillance and proactive strategies to mitigate the risks of zoonotic spillovers, contributing to global public health preparedness. Video Abstract.

Project description:BackgroundBartonella are intracellular bacteria that are transmitted via animal scratches, bites and hematophagous arthropods. Rodents and their associated fleas play a key role in the maintenance of Bartonella worldwide, with > 22 species identified in rodent hosts. No studies have addressed the occurrence and diversity of Bartonella species and vectors for small mammals in Arctic and Subarctic ecosystems, which are increasingly impacted by invasive species and climate change.MethodsIn this study, we characterized the diversity of rodent fleas using conventional PCR targeting the mitochondrial cytochrome c oxidase II gene (COII) and Bartonella species in rodents and shrews (n = 505) from northern Canada using conventional PCR targeting the ITS (intergenic transcribed spacer) region and gltA (citrate synthase) gene. Metagenomic sequencing of a portion of the gltA gene was completed on a subset of 42 rodents and four rodent flea pools.ResultsYear, total summer precipitation the year prior to sampling, average minimum spring temperature and small mammal species were significant factors in predicting Bartonella positivity. Occurrence based on the ITS region was more than double that of the gltA gene and was 34% (n = 349) in northern red-backed voles, 35% (n = 20) in meadow voles, 37% (n = 68) in deer mice and 31% (n = 59) in shrews. Six species of Bartonella were identified with the ITS region, including B. grahamii, B. elizabethae, B. washoensis, Candidatus B. rudakovii, B. doshiae, B. vinsonii subsp. berkhoffii and subsp. arupensis. In addition, 47% (n = 49/105) of ITS amplicons had < 97% identity to sequences in GenBank, possibly due to a limited reference library or previously unreported species. An additional Bartonella species (B. heixiaziensis) was detected during metagenomic sequencing of the gltA gene in 6/11 rodents that had ITS sequences with < 97% identity in GenBank, highlighting that a limited reference library for the ITS marker likely accounted for low sequence similarity in our specimens. In addition, one flea pool from a northern red-backed vole contained multiple species (B. grahamii and B. heixiaziensis).ConclusionOur study calls attention to the usefulness of a combined approach to determine the occurrence and diversity of Bartonella communities in hosts and vectors.

Dataset Information

A dataset of diversity and distribution of rodents and shrews in China.

Publications

A dataset of diversity and distribution of rodents and shrews in China.

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