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Distribution and characteristics of Beilong virus among wild rodents and shrews in China.

ABSTRACT: Beilong virus (BeiV), a member of the newly recognized genus Jeilongvirus of family Paramyxoviridae, has been reported with limited geographic and host scopes, only in Hongkong, China and from two rat species. Here, by next-generation sequencing (NGS) on dominant wild small animal species in 4 provinces in China, we obtained a complete sequence of BeiV strain from Rattus norvegicus in Guangdong, neighboring HongKong, China. We then made an expanded epidemiological investigation in 11 provinces to obtain the geographic distribution and genetic features of this virus. Altogether 7168 samples from 2005 animals (1903 rodents, 100 shrews, 2 mustelidaes) that belonged to 33 species of Cricetidae, Muridae, Sciuridae and Dipodidae family of Rodentia, 3 species of Soricidae family of Soricomorpha, 2 species of Mustelidae family of Carnivora were examined by RT-PCR and sequencing. A positive rate of 3.7% (266/7168) was obtained that was detected from 22 animal species, including 5 species of Cricetidae family, 12 species of Muridae family, 2 species of Sciuridae family and 3 species of Soricidae family. Phylogenetic analyses based on 154 partial Large gene sequences grouped the current BeiV into two lineages, that were related to their geographic regions and animal hosts. Our study showed the wide distribution of BeiV in common species of wild rodents and shrews in China, highlighting the necessity of epidemiological study in wider regions.

SUBMITTER: Chen JJ

PROVIDER: S-EPMC7335238 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Distribution and characteristics of Beilong virus among wild rodents and shrews in China.

Chen Jin-Jin JJ Zhang Xiao-Ai XA Fan Hang H Jiang Fa-Chun FC Jin Mu-Zi MZ Dai Ke K Wang Ning N Zhang Pan-He PH Li Xiao-Kun XK Li Hao H Shi Wenqiang W Yang Zhi-Cong ZC Fang Li-Qun LQ Zhou Hai-Sheng HS Wei Yue-Hong YH Liu Wei W

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 20200704

Beilong virus (BeiV), a member of the newly recognized genus Jeilongvirus of family Paramyxoviridae, has been reported with limited geographic and host scopes, only in Hongkong, China and from two rat species. Here, by next-generation sequencing (NGS) on dominant wild small animal species in 4 provinces in China, we obtained a complete sequence of BeiV strain from Rattus norvegicus in Guangdong, neighboring HongKong, China. We then made an expanded epidemiological investigation in 11 provinces t ...[more]

PMID: 32634600

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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:BackgroundThere is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.MethodsFifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.Resultscytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys.ConclusionThis study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

Dataset Information

Distribution and characteristics of Beilong virus among wild rodents and shrews in China.

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Distribution and characteristics of Beilong virus among wild rodents and shrews in China.

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