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Wang T, Du H, Feng N, Liu Y, Xu Y, Sun H, Peng P, Qin S, Zhang X, Liu Y, Yu M, Liang H, He B, Zhu G, Tu C, Tu Z. First complete genomic sequence analysis of canine distemper virus in wild boar. Virol Sin 2024:S1995-820X(24)00072-5. [PMID: 38768711 DOI: 10.1016/j.virs.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/29/2024] [Indexed: 05/22/2024] Open
Affiliation(s)
- Tong Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Haiying Du
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yuhang Liu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yu Xu
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Heting Sun
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Peng Peng
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Siyuan Qin
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Xiaotian Zhang
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Yan Liu
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Mingyuan Yu
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Hongrui Liang
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Guoqiang Zhu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| | - Changchun Tu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Zhongzhong Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
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Guo G, Wang M, Zhou D, He X, Han P, Chen G, Zeng J, Liu Z, Wu Y, Weng S, He J. Virome Analysis Provides an Insight into the Viral Community of Chinese Mitten Crab Eriocheir sinensis. Microbiol Spectr 2023; 11:e0143923. [PMID: 37358426 PMCID: PMC10433957 DOI: 10.1128/spectrum.01439-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Recent advances in viromics have led to the discovery of a great diversity of RNA viruses and the identification of a large number of viral pathogens. A systematic exploration of viruses in Chinese mitten crab (Eriocheir sinensis), one of the most important aquatic commercial species, is still lacking. Here, we characterized the RNA viromes of asymptomatic, milky disease (MD)-affected, and hepatopancreatic necrosis syndrome (HPNS)-affected Chinese mitten crabs collected from 3 regions in China. In total, we identified 31 RNA viruses belonging to 11 orders, 22 of which were first reported here. By comparing viral composition between samples, we observed high variation in viral communities across regions, with most of the viral species being region-specific. We proposed to establish several novel viral families or genera based on the phylogenetic relationships and genome structures of viruses discovered in this study, expanding our knowledge of viral diversity in brachyuran crustaceans. IMPORTANCE High-throughput sequencing and meta-transcriptomic analysis provide us with an efficient tool to discover unknown viruses and explore the composition of viral communities in specific species. In this study, we investigated viromes in asymptomatic and diseased Chinese mitten crabs collected from three distant locations. We observed high regional variation in the composition of viral species, highlighting the importance of multi-location sampling. In addition, we classified several novel and ICTV-unclassified viruses based on their genome structures and phylogenetic relationships, providing a new perspective on current viral taxa.
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Affiliation(s)
- Guangyu Guo
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Muhua Wang
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dandan Zhou
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xinyi He
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiyun Han
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Gongrui Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiamin Zeng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhi Liu
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yinqing Wu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Wang G, He Y, Yan X, Sun Y, Yi L, Tu C, He B. Virome Profiling of Chickens with Hepatomegaly Rupture Syndrome Reveals Coinfection of Multiple Viruses. Viruses 2023; 15:1249. [PMID: 37376549 DOI: 10.3390/v15061249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Liver diseases seriously challenge the health of chickens raised on scaled farms and cause tremendous economic losses to farm owners. The causative agents for liver diseases are still elusive, even though various pathogens, such as the hepatitis E virus, have been reported. In the winter of 2021, a liver disease was observed on a chicken farm in Dalian, China, which increased chicken mortality by up to 18%. We conducted panvirome profiling of the livers, spleens, kidneys, and recta of 20 diseased chickens. The viromic results revealed coinfection of multiple viruses, including pathogenic ones, in these organs. The viruses were highly identical to those detected in other provinces, and the vaccine and field strains of avian encephalomyelitis virus (AEV) and chicken infectious anemia virus (CIAV) cocirculated on the farm. In particular, the liver showed higher abundance of AEV and multiple fowl adenoviruses than other organs. Furthermore, the liver also contracted avian leukemia virus and CIAV. Experimental animals with infected liver samples developed minor to medium lesions of the liver and showed a virus abundance profile for AEV across internal organs similar to that in the original samples. These results suggest that coinfection with multiple pathogenic viruses influences the occurrence and development of infectious liver disease. The results also highlight that strong farm management standards with strict biosafety measures are needed to minimize the risk of pathogenic virus introduction to the farm.
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Affiliation(s)
- Guoshuai Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yaqi He
- Beijing Centre Biology Co., Ltd., Beijing 102600, China
| | - Xiaomin Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
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Liu Y, Guo L, Wang G, Gao F, Tu Z, Xu D, Sun L, Yi L, Zhu G, Tu C, He B. DNA virome of ticks in the Northeast and Hubei provinces of China reveals diverse single-stranded circular DNA viruses. Parasit Vectors 2023; 16:61. [PMID: 36759895 PMCID: PMC9912487 DOI: 10.1186/s13071-023-05684-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Ticks are medically important vectors capable of transmitting a variety of pathogens to and between host species. Although the spectrum of tick-borne RNA viruses has been frequently investigated, the diversity of tick-borne DNA viruses remains largely unknown. METHODS A total of 1571 ticks were collected from forests and infested animals, and the diversity of the viruses they harbored was profiled using a DNA-specific virome method. The viromic data were phylogenetically analyzed and validated by PCR assays. RESULTS Although diverse and abundant prokaryotic viruses were identified in the collected ticks, only eukaryotic DNA viruses with single-stranded circular genomes covering the anelloviruses and circular replication-associated (Rep) protein-encoding single-stranded (CRESS) DNA viruses were recovered from ticks. Anelloviruses were detected only in two tick pools, but CRESS DNA viruses were prevalent across these ticks except in one pool of Dermacentor spp. ticks. Phylogenetic analyses revealed that these tick-borne CRESS DNA viruses were related to viruses recovered from animal feces, tissues and even environmental samples, suggesting that their presence may be largely explained by environmental factors rather than by tick species and host blood meals. CONCLUSIONS Based on the results, tick-borne eukaryotic DNA viruses appear to be much less common than eukaryotic RNA viruses. Investigations involving a wider collection area and more diverse tick species are required to further support this speculation.
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Affiliation(s)
- Yuhang Liu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Lei Guo
- grid.454880.50000 0004 0596 3180Division of Wildlife and Plant Conservation, State Forestry and Grassland Administration, Changchun, Jilin China
| | - Guoshuai Wang
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Fei Gao
- Section of Wildlife Conservation, Greater Xing’an Mountains Forestry Group Corporation, Jiagedaqi, Heilongjiang China
| | - Zhongzhong Tu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Deming Xu
- Forestry Bureau of Linjiang City, Linjiang, Jilin China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke, Heilongjiang China
| | - Le Yi
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Guoqiang Zhu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China
| | - Changchun Tu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Biao He
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China. .,Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China.
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5
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Sun Y, Sun L, Sun S, Tu Z, Liu Y, Yi L, Tu C, He B. Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife. Pathogens 2023; 12:pathogens12020156. [PMID: 36839428 PMCID: PMC9959412 DOI: 10.3390/pathogens12020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Eastern roe deer (Capreolus pygargus) is a small ruminant and is widespread across China. This creature plays an important role in our ecological system. Although a few studies have been conducted to investigate pathogens harbored by this species, our knowledge of the virus diversity is still very sparse. In this study, we conducted the whole virome profiling of a rescue-failed roe deer, which revealed a kobuvirus (KoV), a bocaparvovirus (BoV), and multiple circular single-stranded viruses. These viruses were mainly recovered from the rectum, but PCR detection showed systematic infection of the KoV. Particularly, the KoV and BoV exhibited closely genetic relationships with bovine and canine viruses, respectively, highly suggesting the spillover of viruses from domestic animals to wildlife. Although these viruses were unlikely to have been responsible for the death of the animal, they provide additional data to understand the virus spectrum harbored by roe deer. The transmission of viruses between domestic animals and wildlife highlights the need for extensive investigation of wildlife viruses.
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Affiliation(s)
- Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke 164400, China
| | - Sheng Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zhongzhong Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
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Zhou D, Liu S, Guo G, He X, Xing C, Miao Q, Chen G, Chen X, Yan H, Zeng J, Zheng Z, Deng H, Weng S, He J. Virome Analysis of Normal and Growth Retardation Disease-Affected Macrobrachium rosenbergii. Microbiol Spectr 2022; 10:e0146222. [PMID: 36445118 PMCID: PMC9769563 DOI: 10.1128/spectrum.01462-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, is an important aquaculture species in China. Growth retardation disease (GRD) is a common contagious disease in M. rosenbergii, resulting in slow growth and precocious puberty in prawns, and has caused growing economic losses in the M. rosenbergii industry. To investigate the viral diversity of M. rosenbergii and identify potentially high-risk viruses linked to GRD, virome analysis of the GRD-affected and normal M. rosenbergii was carried out using next-generation sequencing (NGS). A total of 327 contigs (>500 bp) were related to viral sequences belonging to 23 families/orders and a group of unclassified viruses. The majority of the viral contigs in M. rosenbergii belonged to the order Picornavirales, with the Solinviviridae family being the most abundant in both the diseased and normal groups. Furthermore, 16 RNA viral sequences with nearly complete genomes were characterized and phylogenetically analyzed, belonging to the families Solinviviridae, Flaviviridae, Polycipiviridae, Marnaviridae, and Dicistroviridae as well as three new clades of the order Picornavirales. Notably, the cross-species transmission of a picorna-like virus was observed between M. rosenbergii and plants. The "core virome" seemed to be present in the diseased and normal prawns. Still, a clear difference in viral abundance was observed between the two groups. These results showed that the broad diversity of viruses is present in M. rosenbergii and that the association between viruses and disease of M. rosenbergii needs to be further investigated. IMPORTANCE Growth retardation disease (GRD) has seriously affected the development and economic growth of the M. rosenbergii aquaculture industry. Our virome analysis showed that diverse viral sequences were present in M. rosenbergii, significantly expanding our knowledge of viral diversity in M. rosenbergii. Some differences in viral composition were noted between the diseased and normal prawns, indicating that some viruses become more abundant in occurrences or outbreaks of diseases. In the future, more research will be needed to determine which viruses pose a risk for M. rosenbergii. Our study provides important baseline information contributing to disease surveillance and risk assessment in M. rosenbergii aquaculture.
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Affiliation(s)
- Dandan Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Liu
- School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Guangyu Guo
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyi He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Qijin Miao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Gongrui Chen
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaolin Chen
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongyu Yan
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiamin Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhenwen Zheng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hengwei Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis. mSystems 2022; 7:e0090722. [PMID: 36286492 PMCID: PMC9765019 DOI: 10.1128/msystems.00907-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Widespread in public databases, foreign contaminant sequences pose a substantial obstacle in genomic analyses. Such contamination in viral genome databases is also notorious but more complicated and often causes questionable results in various applications, particularly in virome-based virus detection. Here, we conducted comprehensive screening and identification of the foreign sequences hidden in the largest eukaryotic viral genome collections of GenBank and UniProt using a scrutiny pipeline, which enables us to rigorously detect those problematic viral sequences (PVSs) with origins in hosts, vectors, and laboratory components. As a result, a total of 766 nucleotide PVSs and 276 amino acid PVSs with lengths up to 6,605 bp were determined, which were widely distributed in 39 families with many involving highly public health-concerning viruses, such as hepatitis C virus, Crimean-Congo hemorrhagic fever virus, and filovirus. The majority of these PVSs are genomic fragments of hosts including humans and bacteria. However, they cannot simply be regarded as foreign contaminants, since parts of them are results of natural occurrence or artificial engineering of viruses. Nevertheless, they severely disturb such sequence-based analyses as genome annotation, taxonomic assignment, and virome profiling. Therefore, we provide a clean version of the eukaryotic viral reference data set by the removal of these PVSs, which allows more accurate virome analysis with less time consumed than with other comprehensive databases. IMPORTANCE High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline. We found hundreds of PVSs that are related to hosts, vectors, and laboratory components. By the removal of them, the resulting data set greatly improves the accuracy and efficiency of eukaryotic virome profiling. These results refresh our knowledge of the type and origin of PVSs and also have warning implications for viromic analysis. Viromic practitioners should be aware of these problems caused by PVSs and need to realize that a careful review of bioinformatic results is necessary for a reliable conclusion.
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Virome Profiling of an Amur leopard cat Reveals Multiple Anelloviruses and a Bocaparvovirus. Vet Sci 2022; 9:vetsci9110640. [DOI: 10.3390/vetsci9110640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
As a small top predator, Amur leopard cat (Prionailurus bengalensis euptilurus) is widely distributed in northeast Asia and plays an important role in the control of small rodent populations and in the maintenance of ecological equilibrium. However, the viruses harbored by this creature have been rarely investigated. Here, we report the DNA and RNA eukaryotic virome profiling of an injured Amur leopard cat followed by PCR validation, which revealed diverse anelloviruses in multiple organs and a bocaparvovirus in the lymph, but no RNA viruses. These anelloviruses have diverse genomic structures and are classified into four phylogroups with viruses of various felines, while the bocaparvovirus is extremely similar to those recovered from diarrheal domestic cats, illustrating the transmission of the virus between domestic animals and wildlife. These data provide the first insight into the genetic diversity of Amur leopard cat viruses, highlighting the need for further investigation of wild animals.
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Detection and Characterization of a Reassortant Mammalian Orthoreovirus Isolated from Bats in Xinjiang, China. Viruses 2022; 14:v14091897. [PMID: 36146702 PMCID: PMC9504886 DOI: 10.3390/v14091897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Mammalian orthoreoviruses (MRVs) are increasingly reported to cause various diseases in humans and other animals, with many possibly originating from bats, highlighting the urgent need to investigate the diversity of bat-borne MRVs (BtMRVs). Here, we report the detection and characterization of a reassortant MRV that was isolated from a bat colony in Xinjiang, China. The BtMRV showed a wide host and organ tropism and can efficiently propagate the cell lines of different animals. It caused mild damage in the lungs of the experimentally inoculated suckling mice and was able to replicate in multiple organs for up to three weeks post-inoculation. Complete genome analyses showed that the virus was closely related to MRVs in a wide range of animals. An intricate reassortment network was revealed between the BtMRV and MRVs of human, deer, cattle, civet and other bat species. Specifically, we found a bat-specific clade of segment M1 that provides a gene source for the reassortment of human MRVs. These data provide important insights to understand the diversity of MRVs and their natural circulation between bats, humans, and other animals. Further investigation and surveillance of MRV in bats and other animals are needed to control and prevent potential MRV-related diseases.
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