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Lan D, Fu W, Ji W, Mipam TD, Xiong X, Ying S, Xiong Y, Sheng P, Ni J, Bai L, Shan T, Kong X, Li J. Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 2024; 15:64. [PMID: 38706000 DOI: 10.1186/s40104-024-01027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes. RESULTS We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations. CONCLUSIONS The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.
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Affiliation(s)
- Daoliang Lan
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
| | - Wei Fu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Wenhui Ji
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Tserang-Donko Mipam
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Xianrong Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Shi Ying
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yan Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Peng Sheng
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Jiangping Ni
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Lijun Bai
- Chengdu Genepre Technology Co., Ltd., Chengdu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Jian Li
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Chukwudozie KI, Wang H, Wang X, Lu C, Xue J, Zhang W, Shan T. Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard ( Panthera uncia). Heliyon 2024; 10:e29799. [PMID: 38681641 PMCID: PMC11053277 DOI: 10.1016/j.heliyon.2024.e29799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.
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Affiliation(s)
- Kingsley Ikechukwu Chukwudozie
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
- Department of Microbiology, University of Nigeria, Zip code: 410001, PR China
| | - Haoning Wang
- Heilongjiang cold Region Wetland Ecology and Environment Research key laboratory, school of geography and tourism, Harbin university, 109 zhongxing Road, Harbin, 150086, Heilongjiang province, PR China
- School of Geography and Tourism, Harbin University, Harbin 150086, Heilongjiang province, PR China
| | - Xiaolong Wang
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province. Zip code: 154100, PR China
| | - Chunying Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Jiaxin Xue
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
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Wang X, Tong W, Yang X, Zhai H, Qin W, Liu C, Zheng H, Yu H, Tong G, Zhang Z, Kong N, Shan T. RBM14 inhibits the replication of porcine epidemic diarrhea virus by recruiting p62 to degrade nucleocapsid protein through the activation of autophagy and interferon pathway. J Virol 2024; 98:e0018224. [PMID: 38411947 PMCID: PMC10949495 DOI: 10.1128/jvi.00182-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) results in PED, which is an infectious intestinal disease with the representative features of diarrhea, vomiting, and dehydration. PEDV infects neonatal piglets, causing high mortality rates. Therefore, elucidating the interaction between the virus and host in preventing and controlling PEDV infection is of immense significance. We found a new antiviral function of the host protein, RNA-binding motif protein 14 (RBM14), which can inhibit PEDV replication via the activation of autophagy and interferon (IFN) signal pathways. We found that RBM14 can recruit cargo receptor p62 to degrade PEDV nucleocapsid (N) protein through the RBM14-p62-autophagosome pathway. Furthermore, RBM14 can also improve the antiviral ability of the hosts through interacting with mitochondrial antiviral signaling protein to induce IFN expression. These results highlight the novel mechanism underlying RBM14-induced viral restriction. This mechanism leads to the degradation of viral N protein via the autophagy pathway and upregulates IFN for inhibiting PEDV replication; thus, offering new ways for preventing and controlling PED.IMPORTANCEPorcine epidemic diarrhea virus (PEDV) is a vital reason for diarrhea in neonatal piglets, which causes high morbidity and mortality rates. There is currently no effective vaccine or drug to treat and prevent infection with the PEDV. During virus infection, the host inhibits virus replication through various antiviral factors, and at the same time, the virus antagonizes the host's antiviral reaction through its own encoded protein, thus completing the process of virus replication. Our study has revealed that the expression of RNA-binding motif protein 14 (RBM14) was downregulated in PEDV infection. We found that RBM14 can recruit cargo receptor p62 to degrade PEDV N protein via the RBM14-p62-autophagosome pathway and interacted with mitochondrial antiviral signaling protein and TRAF3 to activate the interferon signal pathway, resulting in the inhibition of PEDV replication.
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Affiliation(s)
- Xiaoquan Wang
- Jiangsu University of Science and Technology, Zhenjiang, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhendong Zhang
- Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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4
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Hameed M, Wahaab A, Shan T, Wang X, Khan S, Di D, Xiqian L, Zhang JJ, Anwar MN, Nawaz M, Li B, Liu K, Shao D, Qiu Y, Wei J, Ma Z. Corrigendum: A metagenomic analysis of mosquito virome collected from different animal farms at Yunnan-Myanmar border of China. Front Microbiol 2024; 15:1393495. [PMID: 38567077 PMCID: PMC10986897 DOI: 10.3389/fmicb.2024.1393495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2020.591478.].
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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5
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Qian L, Zhuang Z, Lu J, Wang H, Wang X, Yang S, Ji L, Shen Q, Zhang W, Shan T. Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea. Heliyon 2024; 10:e25616. [PMID: 38375275 PMCID: PMC10875384 DOI: 10.1016/j.heliyon.2024.e25616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.
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Affiliation(s)
- Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Zi Zhuang
- Center of Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Soochow University, Suzhou, Jiangsu, 215000, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
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6
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Wang J, Yan J, Wang S, Chen R, Xing Y, Liu Q, Gao S, Zhu Y, Li J, Zhou Y, Shan T, Tong W, Zheng H, Kong N, Jiang Y, Liu C, Tong G, Yu H. An Expeditious Neutralization Assay for Porcine Reproductive and Respiratory Syndrome Virus Based on a Recombinant Virus Expressing Green Fluorescent Protein. Curr Issues Mol Biol 2024; 46:1047-1063. [PMID: 38392184 PMCID: PMC10887926 DOI: 10.3390/cimb46020066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024] Open
Abstract
Due to the extensive genetic and antigenic variation in Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), as well as its rapid mutability and evolution, PRRS prevention and control can be challenging. An expeditious and sensitive neutralization assay for PRRSV is presented to monitor neutralizing antibodies (NAbs) in serum during vaccine research. Here, a PRRSV expressing eGFP was successfully rescued with reverse genetics based on the infectious clone HuN4-F112-eGFP which we constructed. The fluorescent protein expressions of the reporter viruses remained stable for at least five passages. Based on this reporter virus, the neutralization assay can be easily used to evaluate the level of NAbs by counting cells with green fluorescence. Compared with the classical CPE assay, the newly developed assay increases sensitivity by one- to four-fold at the early antibody response stage, thus saving 2 days of assay waiting time. By using this assay to unveil the dynamics of neutralizing antibodies against PRRSV, priming immunity through either a single virulent challenge or only vaccination could produce limited NAbs, but re-infection with PRRSV would induce a faster and stronger NAb response. Overall, the novel HuN4-F112-eGFP-based neutralization assay holds the potential to provide a highly efficient platform for evaluating the next generation of PRRS vaccines.
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Affiliation(s)
- Juan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jiecong Yan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shuaiyong Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Ronglin Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yanru Xing
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Qingyan Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shuolei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yuxiang Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jiannan Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
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7
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Yang X, Kong N, Qin W, Zhai X, Song Y, Tong W, Li L, Liu C, Zheng H, Yu H, Zhang W, Tong G, Shan T. PGAM5 degrades PDCoV N protein and activates type I interferon to antagonize viral replication. J Virol 2023; 97:e0147023. [PMID: 37882521 PMCID: PMC10688367 DOI: 10.1128/jvi.01470-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE As a member of the δ-coronavirus family, porcine deltacoronavirus (PDCoV) is a vital reason for diarrhea in piglets, which can contribute to high morbidity and mortality rates. Initially identified in Hong Kong in 2012, the virus has rapidly spread worldwide. During PDCoV infection, the virus employs evasion mechanisms to evade host surveillance, while the host mounts corresponding responses to impede viral replication. Our research has revealed that PDCoV infection down-regulates the expression of PGAM5 to promote virus replication. In contrast, PGAM5 degrades PDCoV N through autophagy by interacting with the cargo receptor P62 and the E3 ubiquitination ligase STUB1. Additionally, PGAM5 interacts with MyD88 and TRAF3 to activate the IFN signal pathway, resulting in the inhibition of viral replication.
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Affiliation(s)
- Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yiyi Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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Hu Y, Wang A, Yan W, Li J, Meng X, Chen L, Li S, Tong W, Kong N, Yu L, Yu H, Shan T, Xu J, Tong G, Zheng H. Identification of Linear Epitopes in the C-Terminal Region of ASFV p72 Protein. Microorganisms 2023; 11:2846. [PMID: 38137990 PMCID: PMC10746095 DOI: 10.3390/microorganisms11122846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/24/2023] Open
Abstract
African swine fever, which is induced by the African swine fever virus (ASFV), poses a significant threat to the global pig industry due to its high lethality in domestic pigs and wild boars. Despite the severity of the disease, there is a lack of effective vaccines and drugs against the ASFV. The p72 protein, constituting 31 to 33% of the total virus particle mass, serves as the primary capsid protein of ASFV. It is a crucial antigen for the development of ASF subunit vaccines and serological diagnostic methods. In this investigation, 27 monoclonal antibodies (mAbs) were generated through mouse immunization with the truncated C-terminal p72 protein expressed by Escherichia coli. Among these, six mAbs exhibited binding to the p72 trimer, with their respective recognized epitopes identified as 542VTAHGINLIDKF553, 568GNAIKTP574, and 584FALKPREEY592. All three epitopes were situated within the interval sequences of functional units of the C-terminal jelly-roll barrel of p72. Notably, two epitopes, 568GNAIKTP574 and 584FALKPREEY592, were internal to the p72 trimer, while the epitope 542VTAHGINLIDKF553 was exposed on the surface of the trimer and consistently conserved across all ASFV genotypes. These findings enhance our comprehension of the antigenic function and structure of the p72 protein, facilitating the utilization of p72 in the development of diagnostic techniques for ASFV.
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Affiliation(s)
- Yifan Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Anchen Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
- College of Life Sciences, Anhui Agricultural University, Hefei 230031, China;
| | - Wanwan Yan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Junbo Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Xin Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Lingchao Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Songnan Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Jiaping Xu
- College of Life Sciences, Anhui Agricultural University, Hefei 230031, China;
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.H.); (A.W.); (W.Y.); (J.L.); (X.M.); (L.C.); (S.L.); (W.T.); (N.K.); (L.Y.); (H.Y.); (T.S.); (G.T.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
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9
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Jiang X, Liu J, Xi Y, Zhang Q, Wang Y, Zhao M, Lu X, Wu H, Shan T, Ni B, Zhang W, Ma X. Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health. mSphere 2023; 8:e0034523. [PMID: 37724888 PMCID: PMC10597464 DOI: 10.1128/msphere.00345-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.
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Affiliation(s)
- Xiaojie Jiang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yongshun Wang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiang Lu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Bin Ni
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
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10
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Pan J, Ji L, Wu H, Wang X, Wang Y, Wu Y, Yang S, Shen Q, Liu Y, Zhang W, Zhang K, Shan T. Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau. BMC Genomics 2023; 24:568. [PMID: 37749507 PMCID: PMC10521573 DOI: 10.1186/s12864-023-09646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. RESULTS By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. CONCLUSIONS This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.
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Grants
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
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Affiliation(s)
- Jiamin Pan
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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11
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Zhai H, Qin W, Dong S, Yang X, Zhai X, Tong W, Liu C, Zheng H, Yu H, Kong N, Tong G, Shan T. PEDV N protein capture protein translation element PABPC1 and eIF4F to promote viral replication. Vet Microbiol 2023; 284:109844. [PMID: 37572396 DOI: 10.1016/j.vetmic.2023.109844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Porcine epidemic diarrhea (PED) is an acute, highly infectious intestinal disease caused by the porcine epidemic diarrhea virus (PEDV), which seriously endangers the healthy development of the pig industry. PEDV N protein is the most abundant viral structural protein, which can be combined with viral genomic RNA to form ribonucleoprotein complexes, thereby participating in the transcription and replication of the virus. However, how PEDV hijacks the host transcription translation system to promote viral proliferation remains unclear. In this study, we found that there is an interaction between PEDV N, polyadenylate-binding protein cytoplasmic 1 (PABPC1) and eukaryotic initiation factor 4F (eIF4F) proteins through coimmunoprecipitation, GST pulldown and fluorescence microscopy experiments. PABPC1 could bind to the poly(A) tail of the mRNA, and eIF4F could bind to the 5' end cap structure of the mRNA, so the interaction of PABPC1 and eIF4F could facilitate mRNA forming a circular shape to promote translation to the proteins. To further explore the effect of N protein capture protein translation element PABPC1 and eIF4F on PEDV replication, we overexpressed PABPC1, eIF4F (containing eIF4A, eIF4E and eIF4G) separately on Vero cells and LLC-PK1 cells, and we found that the PABPC1 and eIF4F protein could promote PEDV replication. Taken together, our data suggested that PEDV N protein promoted cyclization of viral mRNA carried by N protein through binding with PABPC1 and eIF4F proteins, thus promoting viral transcription and facilitating viral replication.
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Affiliation(s)
- Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
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12
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Zhai X, Kong N, Zhang Y, Song Y, Qin W, Yang X, Ye C, Ye M, Tong W, Liu C, Zheng H, Yu H, Zhang W, Yang X, Zhang G, Tong G, Shan T. N protein of PEDV plays chess game with host proteins by selective autophagy. Autophagy 2023; 19:2338-2352. [PMID: 36861818 PMCID: PMC10351448 DOI: 10.1080/15548627.2023.2181615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
Macroautophagy/autophagy is a cellular degradation and recycling process that maintains the homeostasis of organisms. The protein degradation role of autophagy has been widely used to control viral infection at multiple levels. In the ongoing evolutionary arms race, viruses have developed various ways to hijack and subvert autophagy in favor of its replication. It is still unclear exactly how autophagy affects or inhibits viruses. In this study, we have found a novel host restriction factor, HNRNPA1, that could inhibit PEDV replication by degrading viral nucleocapsid (N) protein. The restriction factor activates the HNRNPA1-MARCHF8/MARCH8-CALCOCO2/NDP52-autophagosome pathway with the help of transcription factor EGR1 targeting the HNRNPA1 promoter. HNRNPA1 could also promote the expression of IFN to facilitate the host antiviral defense response for antagonizing PEDV infection through RIGI protein interaction. During viral replication, we found that PEDV can, in contrast, degrade the host antiviral proteins HNRNPA1 and others (FUBP3, HNRNPK, PTBP1, and TARDBP) through its N protein through the autophagy pathway. These results reveal the dual function of selective autophagy in PEDV N and host proteins, which could promote the ubiquitination of viral particles and host antiviral proteins and degradation both of the proteins to regulate the relationship between virus infection and host innate immunity.Abbreviations: 3-MA: 3-methyladenine; ATG: autophagy related; Baf A1: bafilomycin A1; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4',6-diamidino-2-phenylindole; GPI: glycosyl-phosphatidylinositol; hpi: hours post infection; MARCHF8/MARCH8: membrane-associated ring-CH-type finger 8; MOI: multiplicity of infection; N protein: nucleocapsid protein; PEDV: porcine epidemic diarrhea virus; siRNA: small interfering RNA; TCID50: 50% tissue culture infectious doses.
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Affiliation(s)
- Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yu Zhang
- Department of Preventive Dentistry, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiyi Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenqian Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Manqing Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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13
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Qin W, Kong N, Zhang Y, Wang C, Dong S, Zhai H, Zhai X, Yang X, Ye C, Ye M, Tong W, Liu C, Yu L, Zheng H, Yu H, Zhang W, Lan D, Tong G, Shan T. PTBP1 suppresses porcine epidemic diarrhea virus replication via inducing protein degradation and IFN production. J Biol Chem 2023; 299:104987. [PMID: 37392846 PMCID: PMC10407749 DOI: 10.1016/j.jbc.2023.104987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/03/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes severe morbidity and mortality among newborn piglets. It significantly threatens the porcine industry in China and around the globe. To accelerate the developmental pace of drugs or vaccines against PEDV, a deeper understanding of the interaction between viral proteins and host factors is crucial. The RNA-binding protein, polypyrimidine tract-binding protein 1 (PTBP1), is crucial for controlling RNA metabolism and biological processes. The present work focused on exploring the effect of PTBP1 on PEDV replication. PTBP1 was upregulated during PEDV infection. The PEDV nucleocapsid (N) protein was degraded through the autophagic and proteasomal degradation pathways. Moreover, PTBP1 recruits MARCH8 (an E3 ubiquitin ligase) and NDP52 (a cargo receptor) for N protein catalysis and degradation through selective autophagy. Furthermore, PTBP1 induces the host innate antiviral response via upregulating the expression of MyD88, which then regulates TNF receptor-associated factor 3/ TNF receptor-associated factor 6 expression and induces the phosphorylation of TBK1 and IFN regulatory factor 3. These processes activate the type Ⅰ IFN signaling pathway to antagonize PEDV replication. Collectively, this work illustrates a new mechanism related to PTBP1-induced viral restriction, where PTBP1 degrades the viral N protein and induces type Ⅰ IFN production to suppress PEDV replication.
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Affiliation(s)
- Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; College of Animal & Verterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yu Zhang
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenqian Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Manqing Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Daoliang Lan
- College of Animal & Verterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
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14
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Xi Y, Jiang X, Xie X, Zhao M, Zhang H, Qin K, Wang X, Liu Y, Yang S, Shen Q, Ji L, Shang P, Zhang W, Shan T. Viromics Reveals the High Diversity of Viruses from Fishes of the Tibet Highland. Microbiol Spectr 2023; 11:e0094623. [PMID: 37219423 PMCID: PMC10269613 DOI: 10.1128/spectrum.00946-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Aquaculture is important for food security and nutrition. The economy has recently been significantly threatened and the risk of zoonoses significantly increased by aquatic diseases, and the ongoing introduction of new aquatic pathogens, particularly viruses, continues to represent a hazard. Yet, our knowledge of the diversity and abundance of fish viruses is still limited. Here, we conducted a metagenomic survey of different species of healthy fishes caught in the Lhasa River, Tibet, China, and sampled intestinal contents, gills, and tissues. To be more precise, by identifying and analyzing viral genomes, we aim to determine the abundance, diversity, and evolutionary relationships of viruses in fish with other potential hosts. Our analysis identified 28 potentially novel viruses, 22 of which may be associated with vertebrates, across seven viral families. During our research, we found several new strains of viruses in fish, including papillomavirus, hepadnavirus, and hepevirus. Additionally, we discovered two viral families, Circoviridae and Parvoviridae, which were prevalent and closely related to viruses that infect mammals. These findings further expand our understanding of highland fish viruses and highlight the emerging view that fish harbor large, unknown viruses. IMPORTANCE The economy and zoonoses have recently been significantly threatened by aquatic diseases. Yet, our knowledge of the diversity and abundance of fish viruses is still limited. We identified the wide genetic diversity of viruses that these fish were harboring. Since there are currently few studies on the virome of fish living in the Tibet highland, our research adds to the body of knowledge. This discovery lays the groundwork for future studies on the virome of fish species and other highland animals, preserving the ecological equilibrium on the plateau.
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Affiliation(s)
- Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaojie Jiang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinrui Xie
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
| | - Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Han Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Kailin Qin
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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15
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Lu J, Wang H, Wang C, Zhao M, Hou R, Shen Q, Yang S, Ji L, Liu Y, Wang X, Liu S, Shan T, Zhang W. Gut phageome of the giant panda ( Ailuropoda melanoleuca) reveals greater diversity than relative species. mSystems 2023:e0016123. [PMID: 37272702 DOI: 10.1128/msystems.00161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals.IMPORTANCEGut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.
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Affiliation(s)
- Juan Lu
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang, China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Min Zhao
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Quan Shen
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wen Zhang
- 1Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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Zhuang Z, Qian L, Lu J, Zhang X, Mahmood A, Cui L, Wang H, Wang X, Yang S, Ji L, Shan T, Shen Q, Zhang W. Comparison of viral communities in the blood, feces and various tissues of wild brown rats ( Rattus norvegicus). Heliyon 2023; 9:e17222. [PMID: 37389044 PMCID: PMC10300334 DOI: 10.1016/j.heliyon.2023.e17222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
Viral diseases caused by new outbreaks of viral infections pose a serious threat to human health. Wild brown rats (Rattus norvegicus), considered one of the world's largest and most widely distributed rodents, are host to various zoonotic pathogens. To further understand the composition of the virus community in wild brown rats and explore new types of potentially pathogenic viruses, viral metagenomics was conducted to investigate blood, feces, and various tissues of wild brown rats captured from Zhenjiang, China. Results indicated that the composition of the virus community in different samples showed significant differences. In blood and tissue samples, members of the Parvoviridae and Anelloviridae form the main body of the virus community. Picornaviridae, Picobirnaviridae, and Astroviridae made up a large proportion of fecal samples. Several novel genome sequences from members of different families, including Anelloviridae, Parvoviridae, and CRESS DNA viruses, were detected in both blood and other samples, suggesting that they have the potential to spread across organs to cause viremia. These viruses included not only strains closely related to human viruses, but also a potential recombinant virus. Multiple dual-segment picornaviruses were obtained from fecal samples, as well as virus sequences from the Astroviridae and Picornaviridae. Phylogenetic analysis showed that these viruses belonged to different genera, with multiple viruses clustered with other animal viruses. Whether they have pathogenicity and the ability to spread across species needs further study.
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Affiliation(s)
- Zi Zhuang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaodan Zhang
- Department of Clinical Laboratory, Zhenjiang Center for Disease Prevention and Control, Zhenjiang, 212002, China
| | - Asif Mahmood
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lei Cui
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Huiying Wang
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
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17
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Xu Z, Hu Y, Li J, Wang A, Meng X, Chen L, Wei J, Tong W, Kong N, Yu L, Yu H, Shan T, Tong G, Wang G, Zheng H. Screening and identification of the dominant antigens of the African swine fever virus. Front Vet Sci 2023; 10:1175701. [PMID: 37215478 PMCID: PMC10192620 DOI: 10.3389/fvets.2023.1175701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 05/24/2023] Open
Abstract
African swine fever is a highly lethal contagious disease of pigs for which there is no vaccine. Its causative agent African swine fever virus (ASFV) is a highly complex enveloped DNA virus encoding more than 150 open reading frames. The antigenicity of ASFV is still unclear at present. In this study, 35 proteins of ASFV were expressed by Escherichia coli, and ELISA was developed for the detection of antibodies against these proteins. p30, p54, and p22 were presented as the major antigens of ASFV, positively reacting with all five clinical ASFV-positive pig sera, and 10 pig sera experimentally infected by ASFV. Five proteins (pB475L, pC129R, pE199L, pE184L, and pK145R) reacted well with ASFV-positive sera. The p30 induced a rapid and strong antibody immune response during ASFV infection. These results will promote the development of subunit vaccines and serum diagnostic methods against ASFV.
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Affiliation(s)
- Zhaoyang Xu
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
- College of Veterinary Medicine of Shandong Agricultural University, Tai'an, China
| | - Yifan Hu
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Junbo Li
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Ancheng Wang
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xin Meng
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Lingchao Chen
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai Yu
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guihua Wang
- College of Veterinary Medicine of Shandong Agricultural University, Tai'an, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
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18
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Zhao M, Bao S, Xu D, He J, Zhang H, Ji L, Yang S, Wang X, Shen Q, Liu J, Zhang Q, Ma X, Zhang W, Shan T. Virome of wild rats (Rattus norvegicus) captured far from pig farms in Jiangsu province of China reveals novel porcine circovirus type 2d (PCV2d) sequences. Virol J 2023; 20:46. [PMID: 36894948 PMCID: PMC9997004 DOI: 10.1186/s12985-023-02005-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Porcine circovirus type 2 (PCV2) has caused great economic losses in the global pig industry. There have been published records of wild rats acting as the reservoirs of PCV2 (only PCV2a and PCV2b), but almost all of which were related to the PCV2-infected swine herds. RESULTS In this study, we carried out the detection, amplification, and characterization of novel PCV2 strains in wild rats that were captured far from pig farms. Nested PCR assay demonstrated that the kidney, heart, lung, liver, pancreas, and large and small intestines of rats were screened positive for PCV2. We subsequently sequenced two full genomes of PCV2 in positive sample pools, designated as js2021-Rt001 and js2021-Rt002. Genome sequence analysis indicated that they had the highest similarity to nucleotide sequences of porcine-origin PCV2 isolates in Vietnam. Phylogenetically, js2021-Rt001 and js2021-Rt002 were a part of the PCV2d genotype cluster, which is a predominant genotype circulating worldwide in recent years. The antibody recognition regions, immunodominant decoy epitope, and heparin sulfate binding motif of the two complete genome sequences coincided with those previously reported. CONCLUSIONS Our research reported the genomic characterization of two novel PCV2 strains (js2021-Rt001 and js2021-Rt002) and provided the first supported evidence that PCV2d could naturally infect wild rats in China. However, whether the newly identified strains have potential for circulating in nature in vertical and horizontal transmission or inter-species jumping between rats and pigs needs further research.
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Affiliation(s)
- Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Siwen Bao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Diandian Xu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jingxian He
- School of Medicine, Suzhou University, Suzhou, 215031, Jiangsu, China
| | - Han Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, 811602, Qinghai, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, 811602, Qinghai, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, 811602, Qinghai, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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19
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Yang Z, Wang H, Yang S, Wang X, Shen Q, Ji L, Zeng J, Zhang W, Gong H, Shan T. Virome diversity of ticks feeding on domestic mammals in China. Virol Sin 2023; 38:208-221. [PMID: 36781125 PMCID: PMC10176445 DOI: 10.1016/j.virs.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 107) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.
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Affiliation(s)
- Zijun Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
| | - Haiyan Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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20
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Dai Z, Wang H, Wu H, Zhang Q, Ji L, Wang X, Shen Q, Yang S, Ma X, Shan T, Zhang W. Parvovirus dark matter in the cloaca of wild birds. Gigascience 2023; 12:7025321. [PMID: 36734170 PMCID: PMC9896142 DOI: 10.1093/gigascience/giad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
With the development of viral metagenomics and next-generation sequencing technology, more and more novel parvoviruses have been identified in recent years, including even entirely new lineages. The Parvoviridae family includes a different group of viruses that can infect a wide variety of animals. In this study, systematic analysis was performed to identify the "dark matter" (datasets that cannot be easily attributed to known viruses) of parvoviruses and to explore their genetic diversity from wild birds' cloacal swab samples. We have tentatively defined this parvovirus "dark matter" as a highly divergent lineage in the Parvoviridae family. All parvoviruses showed several characteristics, including 2 major protein-coding genes and similar genome lengths. Moreover, we observed that the novel parvo-like viruses share similar genome organizations to most viruses in Parvoviridae but could not clustered with the established subfamilies in phylogenetic analysis. We also found some new members associated with the Bidnaviridae family, which may be derived from parvovirus. This suggests that systematic analysis of domestic and wild animal samples is necessary to explore the genetic diversity of parvoviruses and to mine for more of this potential dark matter.
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Affiliation(s)
| | | | | | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | | | - Tongling Shan
- Correspondence address. Tongling Shan, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 224001, China. E-mail:
| | - Wen Zhang
- Correspondence address. Wen Zhang, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China. E-mail:
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21
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Yang S, Mao Q, Wang Y, He J, Yang J, Chen X, Xiao Y, He Y, Zhao M, Lu J, Yang Z, Dai Z, Liu Q, Yao Y, Lu X, Li H, Zhou R, Zeng J, Li W, Zhou C, Wang X, Shen Q, Xu H, Deng X, Delwart E, Shan T, Zhang W. Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal. Environ Microbiome 2022; 17:58. [PMID: 36437477 PMCID: PMC9703751 DOI: 10.1186/s40793-022-00453-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. RESULTS We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common. CONCLUSIONS Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.
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Affiliation(s)
- Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingqing Mao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jingxian He
- Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xu Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuqing Xiao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zijun Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qi Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuxin Yao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hong Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rui Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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22
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Wang K, Tian X, Shan T, Wang C. Simulation of Material Movement in the Process of Catalytic Pyrolysis of Waste Tires. Russ J Phys Chem B 2022. [DOI: 10.1134/s1990793122050116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Dong S, Kong N, Shen H, Li Y, Qin W, Zhai H, Zhai X, Yang X, Ye C, Ye M, Liu C, Yu L, Zhen H, Tong W, Yu H, Zhang W, Tong G, Shan T. KLF16 inhibits PEDV replication by activating the type I IFN signaling pathway. Vet Microbiol 2022; 274:109577. [DOI: 10.1016/j.vetmic.2022.109577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 10/31/2022]
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24
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Dong S, Kong N, Qin W, Zhai H, Zhai X, Yang X, Ye C, Ye M, Liu C, Yu L, Zheng H, Tong W, Yu H, Zhang W, Li Y, Tong G, Shan T. ATG4B hinders porcine epidemic diarrhea virus replication through interacting with TRAF3 and activating type-I IFN signaling. Vet Microbiol 2022; 273:109544. [PMID: 36049346 DOI: 10.1016/j.vetmic.2022.109544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 10/15/2022]
Abstract
Autophagy-related 4B (ATG4B) is found to exert a vital function in viral replication, although the mechanism through which ATG4B activates type-I IFN signaling to hinder viral replication remains to be explained, so far. The current work revealed that ATG4B was downregulated in porcine epidemic diarrhea virus (PEDV)-infected LLC-PK1 cells. In addition, ATG4B overexpression inhibited PEDV replication in both Vero cells and LLC-PK1 cells. On the contrary, ATG4B knockdown facilitated PEDV replication. Moreover, ATG4B was observed to hinder PEDV replication by activating type-I IFN signaling. Further detailed analysis revealed that the ATG4B protein targeted and upregulated the TRAF3 protein to induce IFN expression via the TRAF3-pTBK1-pIRF3 pathway. The above data revealed a novel mechanism underlying the ATG4B-mediated viral restriction, thereby providing novel possibilities for preventing and controlling PEDV.
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Affiliation(s)
- Sujie Dong
- College of Animal Science, Tarim University, Xinjiang, China; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenqian Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Manqing Ye
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Youwen Li
- College of Animal Science, Tarim University, Xinjiang, China.
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
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25
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Sun D, Kong N, Dong S, Chen X, Qin W, Wang H, Jiao Y, Zhai H, Li L, Gao F, Yu L, Zheng H, Tong W, Yu H, Zhang W, Tong G, Shan T. 2AB protein of Senecavirus A antagonizes selective autophagy and type I interferon production by degrading LC3 and MARCHF8. Autophagy 2022; 18:1969-1981. [PMID: 34964697 PMCID: PMC9450971 DOI: 10.1080/15548627.2021.2015740] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Senecavirus A (SVA), an important emerging porcine virus, has outbreaks in different regions and countries each year, becoming a virus with global prevalence. SVA infection has been reported to induce macroautophagy/autophagy; however, the molecular mechanisms of autophagy induction and the effect of SVA on autophagy remain unknown. This study showed that SVA infection induced the autophagy process in the early stage of SVA infection, and the rapamycin-induced autophagy inhibited SVA replication by degrading virus 3 C protein. To counteract this, SVA utilized 2AB protein inhibiting the autophagy process from promoting viral replication in the late stage of SVA infection. Further study showed that SVA 2AB protein interacted with MARCHF8/MARCH8 and LC3 to degrade the latter and inhibit the autophagy process. In addition, we found that MARCHF8 was a positive regulator of type I IFN (IFN-I) signaling. During the autophagy process, the SVA 2AB protein targeted MARCHF8 and MAVS forming a large complex for degradation to deactivate IFN-I signaling. Together, our study reveals the molecular mechanisms of selective autophagy in the host against viruses and reveals potential viral strategies to evade the autophagic process and IFN-I signaling for successful pathogenesis.Abbreviations: Baf A1: bafilomycin A1; Co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4',6-diamidino-2-phenylindole; hpi: hours post-infection; IFN: interferon; ISG: IFN-stimulated gene; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARCHF8/MARCH8: membrane associated ring-CH-type finger 8; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; Rapa: rapamycin; RT: room temperature; siRNA: small interfering RNA; SVA: Senecavirus A; TCID50: 50% tissue culture infectious doses.
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Affiliation(s)
- Dage Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyong Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Hua Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Yajuan Jiao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, PR China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China,CONTACT Guangzhi Tong ; Tongling Shan
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
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26
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Abstract
The concept of extrafibrillar demineralization involves selective removal of apatite crystallites from the extrafibrillar spaces of mineralized dentin without disturbing the intrafibrillar minerals within collagen. This helps avoiding activation of endogenous proteases and enables air-drying of partially demineralized dentin without causing collapse of completely demineralized collagen matrix that adversely affects resin infiltration. The objective of the present study was to evaluate the potential of quaternized carboxymethyl chitosan (QCMC)-based extrafibrillar demineralization in improving resin-dentin bond durability. Isothermal titration calorimetry indicated that QCMC synthesized by quaternization of O-carboxymethyl chitosan had moderate affinity for Ca2+ (binding constant: 8.9 × 104 M-1). Wet and dry bonding with the QCMC-based demineralization produced tensile bond strengths equivalent to the phosphoric acid (H3PO4)-based etch-and-rinse technique. Those bond strengths were maintained after thermocycling. Amide I and PO43- mappings of QCMC-conditioned dentin were performed with atomic force microscope-infrared spectroscopy (AFM-IR). Whereas H3PO4-etched dentin exhibited an extensive reduction in PO43- signals corresponding to apatite depletion, QCMC-conditioned dentin showed scattered dark areas and bright PO43- streak signals. The latter were consistent with areas identified as collagen fibrils in the amide I mapping and were suggestive of the presence of intrafibrillar minerals in QCMC-conditioned dentin. Young's modulus mapping of QCMC-demineralized dentin obtained by AFM-based amplitude modulation-frequency modulation recorded moduli that were the same order of magnitude as those in mineralized dentin and at least 1 order higher than H3PO4-etched dentin. In situ zymography of the gelatinolytic activity within hybrid layers created with QCMC conditioning revealed extremely low signals before and after thermocycling, compared with H3PO4-etched dentin for both wet and dry bonding. Confocal laser scanning microscopy identified the antibacterial potential of QCMC against Streptococcus mutans and Enterococcus faecalis biofilms. Taken together, the QCMC-based demineralization retains intrafibrillar minerals, preserves the elastic modulus of collagen fibrils, reduces endogenous proteolytic activity, and inhibits bacteria biofilms to extend dentin bond durability.
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Affiliation(s)
- T Shan
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - L Huang
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - F R Tay
- Department of Endodontics, The Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - L Gu
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
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27
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Chen X, Shan T, Sun D, Zhai H, Dong S, Kong N, Zheng H, Tong W, Tong G. Host Zinc-finger CCHC-type containing protein 3 inhibits pseudorabies virus proliferation by regulating type I interferon signaling. Gene X 2022; 827:146480. [PMID: 35390445 DOI: 10.1016/j.gene.2022.146480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 11/04/2022] Open
Abstract
Zinc finger CCHC-type containing protein 3 (ZCCHC3) acts as an antiviral factor that interacts with RIG-I and cGAS to modulate innate signaling against viral infections. Here, we investigated the role of porcine ZCCHC3 during pseudorabies virus (PRV) proliferation. We found that porcine ZCCHC3 plays an inhibitory role in the proliferation of PRV by regulating cellular innate immune responses. Further, overexpression of ZCCHC3 inhibited gB protein levels and viral titers, whereas knockdown of ZCCHC3 promoted viral growth. ZCCHC3 overexpression increased IFN-β expression to upregulate downstream gene expression, thus leading to the suppression of viral replication. However, PRV infection reduced the endogenous expression of ZCCHC3 in permissive cells. Importantly, PRV-encoded UL13 and UL24 proteins were identified to inhibit the expression of ZCCHC3, thus antagonizing its antiviral effect. Collectively, our data underscore the important role of ZCCHC3 against PRV infection and promote understandings of viral proteins in PRV pathogenesis.
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Affiliation(s)
- Xiaoyong Chen
- Institute of Animal Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou, Zhejiang, PR China; Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Dage Sun
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Huanjie Zhai
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Sujie Dong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Ning Kong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Hao Zheng
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, Jiangsu, PR China.
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28
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Zhao M, Yue C, Yang Z, Li Y, Zhang D, Zhang J, Yang S, Shen Q, Su X, Qi D, Ma R, Xiao Y, Hou R, Yan X, Li L, Zhou Y, Liu J, Wang X, Wu W, Zhang W, Shan T, Liu S. Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem. Sci Total Environ 2022; 820:153317. [PMID: 35066043 DOI: 10.1016/j.scitotenv.2022.153317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Cross-species transmission events were commonplace, with numerous cases of host-switching during the viral evolutionary history, but relatively little evidence for onward transmission in different species living in the same ecosystem. For understanding the communications of viruses in giant pandas (Ailuropoda melanoleuca) and their associated organisms, based on a large size of samples (N = 2305) collected between 2015 and 2020 from giant panda (N = 776) and other four giant panda-associated organisms in the same ecosystem, red pandas (N = 700), stray cats (N = 32), wild rats (N = 42), and mosquitoes (N = 755), viromics was used for the virus identification and subsequent virus traceability. The results showed that a feline panleukopenia virus (FPV) was found in giant pandas with clinical signs of vomiting and mild diarrhea. Meanwhile, the same FPV strain was also prevalent in the healthy red panda (Ailurus fulgens) population. From the viromes of the five different organisms, 250 virus genomes were determined. Our data revealed that besides FPV, other putative pathogenic viruses, such as red panda amdoparvoviruses (RPAVs) and Getah viruses (GETVs) were responsible for previous disease or death of some red pandas. We also demonstrated that a number of viruses were involved in potential interspecies jumping events between giant pandas and their associated species. Collectively, our results shed light on the genetic diversity and relationship of diverse viral pathogens in 'Giant pandas-Associated animals-Arthropods' and report some cases of possible viral host-switching among these host species living in the same ecosystem.
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Affiliation(s)
- Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chanjuan Yue
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Zijun Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yunli Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dongsheng Zhang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Ju Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaoyan Su
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xia Yan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Lin Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Yanshan Zhou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Jiabin Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Wei Wu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, Sichuan, China.
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29
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Shan T, Yang S, Wang H, Wang H, Zhang J, Gong G, Xiao Y, Yang J, Wang X, Lu J, Zhao M, Yang Z, Lu X, Dai Z, He Y, Chen X, Zhou R, Yao Y, Kong N, Zeng J, Ullah K, Wang X, Shen Q, Deng X, Zhang J, Delwart E, Tong G, Zhang W. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. Microbiome 2022; 10:60. [PMID: 35413940 PMCID: PMC9001828 DOI: 10.1186/s40168-022-01246-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/16/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. RESULTS Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). CONCLUSIONS The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.
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Affiliation(s)
- Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, 150886, Heilongjiang, China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, 150886, Heilongjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Ju Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaolong Wang
- Wildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry University, Harbin, 150006, Heilongjiang, China
| | - Juan Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Min Zhao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Zijun Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ziyuan Dai
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Rui Zhou
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yuxin Yao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Kalim Ullah
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Jianmin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
- International Center for Genomics Research, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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30
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Lu J, Yang S, Wang C, Wang H, Gong G, Xi Y, Pan J, Wang X, Zeng J, Zhang J, Li P, Shen Q, Shan T, Zhang W. Gut Virome of the World's Highest-Elevation Lizard Species ( Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses. Microbiol Spectr 2022; 10:e0187221. [PMID: 35196818 PMCID: PMC8865479 DOI: 10.1128/spectrum.01872-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/29/2022] [Indexed: 12/27/2022] Open
Abstract
The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.
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Affiliation(s)
- Juan Lu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Wang
- The Affiliated Huai’an Hospital, Xuzhou Medical University, Huai’an, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jiamin Pan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ju Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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31
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Zhang Y, Wang C, Zhu C, Ye W, Gu Q, Shu C, Feng X, Chen X, Zhang W, Shan T. Redondoviridae infection regulates circRNAome in periodontitis. J Med Virol 2022; 94:2537-2547. [PMID: 35075668 DOI: 10.1002/jmv.27624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 11/08/2022]
Abstract
Redondoviridae is a recently identified family of DNA viruses associated with periodontitis. Circular RNAs (circRNAs) are novel endogenous, conserved noncoding RNAs contributing to the virus-related immune-inflammatory response. The present study aimed to analyze the expression profiles of circRNAs in the gingival tissues of periodontitis patients with and without Redondoviridae-infection and healthy controls using high-throughput RNA sequencing combined with experimental validation. Out of 17819 circRNAs, 175 were dysregulated. Functional annotation and enrichment analysis of the differential circRNA host genes demonstrated potential alterations in the molecular and cellular components and metabolism in individuals suffering from periodontitis with Redondoviridae infection. Moreover, "axon guidance", "lysine biosynthesis", and "vascular endothelial growth factor signaling pathways" were significantly enriched in Redondoviridae-infected gingivitis tissues. Furthermore, the key circRNAs (circCOL1A1, circAASS, circPTK2, circATP2B4, circDOCK1, circTTBK2, and circMCTP2) associated with the pathobiology of Redondoviridae-related periodontitis were identified by constructing circRNA-miRNA-mRNA networks. Bioinformatics analyses demonstrated that abnormally expressed circRNAs might contribute to the etiopathogenesis and development of Redondoviridae-related periodontitis. The present study's findings have enhanced the current understanding ofthe Redondoviridae-related periodontitis mechanism and provide insights into further applications for diagnostic markers and therapeutic uses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Zhang
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Ce Zhu
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Wei Ye
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Qin Gu
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Chenbin Shu
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Xiping Feng
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Xi Chen
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,National Clinical Research Center for Oral Diseases, Shanghai, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, PR China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, PR China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
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Zhou Y, Zhou W, Xiao T, Chen Y, Lv T, Wang Y, Zhang S, Cai H, Chi X, Kong X, Zhou K, Shen P, Shan T, Xiao Y. Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China. Emerg Microbes Infect 2021; 10:2244-2255. [PMID: 34756150 PMCID: PMC8648027 DOI: 10.1080/22221751.2021.2005453] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.
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Affiliation(s)
- Yanzi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Shuntian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Hongliu Cai
- Department of Intensive Care Unit, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Xiaoyang Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, and Second Clinical Medical College, Jinan University, Shenzhen, China, 518000
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
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Jiao Y, Kong N, Wang H, Sun D, Dong S, Chen X, Zheng H, Tong W, Yu H, Yu L, Huang Y, Wang H, Sui B, Zhao L, Liao Y, Zhang W, Tong G, Shan T. PABPC4 Broadly Inhibits Coronavirus Replication by Degrading Nucleocapsid Protein through Selective Autophagy. Microbiol Spectr 2021; 9:e0090821. [PMID: 34612687 PMCID: PMC8510267 DOI: 10.1128/spectrum.00908-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Emerging coronaviruses (CoVs) can cause severe diseases in humans and animals, and, as of yet, none of the currently available broad-spectrum drugs or vaccines can effectively control these diseases. Host antiviral proteins play an important role in inhibiting viral proliferation. One of the isoforms of cytoplasmic poly(A)-binding protein (PABP), PABPC4, is an RNA-processing protein, which plays an important role in promoting gene expression by enhancing translation and mRNA stability. However, its function in viruses remains poorly understood. Here, we report that the host protein, PABPC4, could be regulated by transcription factor SP1 and broadly inhibits the replication of CoVs, covering four genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus) of the Coronaviridae family by targeting the nucleocapsid (N) protein through the autophagosomes for degradation. PABPC4 recruited the E3 ubiquitin ligase MARCH8/MARCHF8 to the N protein for ubiquitination. Ubiquitinated N protein was recognized by the cargo receptor NDP52/CALCOCO2, which delivered it to the autolysosomes for degradation, resulting in impaired viral proliferation. In addition to regulating gene expression, these data demonstrate a novel antiviral function of PABPC4, which broadly suppresses CoVs by degrading the N protein via the selective autophagy pathway. This study will shed light on the development of broad anticoronaviral therapies. IMPORTANCE Emerging coronaviruses (CoVs) can cause severe diseases in humans and animals, but none of the currently available drugs or vaccines can effectively control these diseases. During viral infection, the host will activate the interferon (IFN) signaling pathways and host restriction factors in maintaining the innate antiviral responses and suppressing viral replication. This study demonstrated that the host protein, PABPC4, interacts with the nucleocapsid (N) proteins from eight CoVs covering four genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus) of the Coronaviridae family. PABPC4 could be regulated by SP1 and broadly inhibits the replication of CoVs by targeting the nucleocapsid (N) protein through the autophagosomes for degradation. This study significantly increases our understanding of the novel host restriction factor PABPC4 against CoV replication and will help develop novel antiviral strategies.
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Affiliation(s)
- Yajuan Jiao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Hua Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Dage Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Xiaoyong Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yaowei Huang
- College of Animal Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Huan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Baokun Sui
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Ling Zhao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
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Cheng Y, Chen Y, Liu Y, Guo Y, Zhou Y, Xiao T, Zhang S, Xu H, Chen Y, Shan T, Xiao Y, Zhou K. Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris. Emerg Microbes Infect 2021; 9:1843-1852. [PMID: 32731802 PMCID: PMC7473080 DOI: 10.1080/22221751.2020.1803769] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new resistance mechanism of tigecycline. In this study, a novel chromosome-encoded tigecycline resistance gene, tet(X14), was identified in a tigecycline-resistant and colistin-resistant Empedobacter stercoris strain ES183 recovered from a pig fecal sample in China. Tet(X14) shows 67.14-96.39% sequence identity to the other variants [Tet(X) to Tet(X13)]. Overexpression of Tet(X14) in Escherichia coli confers 16-fold increase in tigecycline MIC (from 0.125 to 2 mg/L), which is lower than that of Tet(X3), Tet(X4) and Tet(X6). Structural modelling predicted that Tet(X14) shared a high homology with the other 12 variants with RMSD value from 0.003 to 0.055, and Tet(X14) can interact with tetracyclines by a similar pattern as the other Tet(X)s. tet(X14) and two copies of tet(X2) were identified on a genome island with abnormal GC content carried by the chromosome of ES183, and no mobile genetic elements were found surrounding, suggesting that tet(X14) might be heterologously obtained by ES183 via recombination. Blasting in Genbank revealed that Tet(X14) was exclusively detected on the chromosome of Riemerella anatipestifer, mainly encoded on antimicrobial resistance islands. E. stercoris and R. anatipestifer belong to the family Flavobacteriaceae, suggesting that the members of Flavobacteriaceae maybe the major reservoir of tet(X14). Our study reports a novel chromosome-encoded tigecycline resistance gene tet(X14). The expanded members of Tet(X) family warrants the potential large-scale dissemination and the necessity of continuous surveillance for tet(X)-mediated tigecycline resistance.
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Affiliation(s)
- Yingying Cheng
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, People's Republic of China.,The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Yong Chen
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, People's Republic of China.,The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Yang Liu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, People's Republic of China.,The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Yuqi Guo
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, People's Republic of China.,The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Yanzi Zhou
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Tingting Xiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Shuntian Zhang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yunbo Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yonghong Xiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, People's Republic of China.,The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, People's Republic of China
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Chen X, Sun D, Dong S, Zhai H, Kong N, Zheng H, Tong W, Li G, Shan T, Tong G. Host Interferon-Stimulated Gene 20 Inhibits Pseudorabies Virus Proliferation. Virol Sin 2021; 36:1027-1035. [PMID: 33830434 DOI: 10.1007/s12250-021-00380-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/23/2021] [Indexed: 12/30/2022] Open
Abstract
Host interferon-stimulated gene 20 (ISG20) exerts antiviral effects on viruses by degrading viral RNA or by enhancing IFN signaling. Here, we examined the role of ISG20 during pseudorabies virus (PRV) proliferation. We found that ISG20 modulates PRV replication by enhancing IFN signaling. Further, ISG20 expression was upregulated following PRV infection and poly(I:C) treatment. Ectopic expression of ISG20 inhibited PRV proliferation in PK15 cells, whereas knockdown of ISG20 promoted PRV proliferation. In addition, ISG20 expression upregulated IFN-β expression and enhanced IFN downstream signaling during PRV infection. Notably, PRV UL24 suppressed the transcription of ISG20, thus antagonizing its antiviral effect. Further domain mapping analysis showed that the N terminus (amino acids 1-90) of UL24 was responsible for the inhibition of ISG20 transcription. Collectively, these findings characterize the role of ISG20 in suppressing PRV replication and increase the understanding of host-PRV interplay.
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Affiliation(s)
- Xiaoyong Chen
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Dage Sun
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Sujie Dong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Huanjie Zhai
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Ning Kong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China
| | - Hao Zheng
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China
| | - Guoxin Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China.
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China.
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36
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Hameed M, Wahaab A, Shan T, Wang X, Khan S, Di D, Xiqian L, Zhang JJ, Anwar MN, Nawaz M, Li B, Liu K, Shao D, Qiu Y, Wei J, Ma Z. A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan-Myanmar Border of China. Front Microbiol 2021; 11:591478. [PMID: 33628201 PMCID: PMC7898981 DOI: 10.3389/fmicb.2020.591478] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Metagenomic analysis of mosquito-borne and mosquito-specific viruses is useful to understand the viral diversity and for the surveillance of pathogens of medical and veterinary importance. Yunnan province is located at the southwest of China and has rich abundance of mosquitoes. Arbovirus surveillance is not conducted regularly in this province particularly at animal farms, which have public health as well as veterinary importance. Here, we have analyzed 10 pools of mosquitoes belonging to Culex tritaeniorhyncus, Aedes aegypti, Anopheles sinensis, and Armigeres subalbatus species, collected from different animal farms located at Yunnan province of China by using metagenomic next-generation sequencing technique. The generated viral metagenomic data reveal that the viral community matched by the reads was highly diverse and varied in abundance among animal farms, which contained more than 19 viral taxonomic families, specific to vertebrates, invertebrates, fungi, plants, protozoa, and bacteria. Additionally, a large number of viral reads were related to viruses that are non-classified. The viral reads related to animal viruses included parvoviruses, anelloviruses, circoviruses, flaviviruses, rhabdoviruses, and seadornaviruses, which might be taken by mosquitoes from viremic animal hosts during blood feeding. Notably, the presence of viral reads matched with Japanese encephalitis virus, Getah virus, and porcine parvoviruses in mosquitoes collected from different geographic sites suggested a potential circulation of these viruses in their vertebrate hosts. Overall, this study provides a comprehensive knowledge of diverse viral populations present at animal farms of Yunnan province of China, which might be a potential source of diseases for humans and domestic animals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Li C, Shan T, Chen Z, Zhou J, Li H, Tong G, Liu G. Isolation and complete genome analysis of a novel duck picornavirus in China. Vet Microbiol 2020; 253:108950. [PMID: 33341468 DOI: 10.1016/j.vetmic.2020.108950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/02/2020] [Indexed: 01/13/2023]
Abstract
A novel duck picornavirus, designated as duck/AH15/CHN/2015, was isolated and identified from Cherry Valley ducks with short beak and dwarfism syndrome in 2015 in Anhui province of China. Duck/AH15/CHN/2015 has the highest degree of amino acid sequence identity (approximately 43 %) with duck hepatitis A viruses (DHAV) Complete genome analysis revealed that duck/AH15/CHN/2015 possesses a typical picornavirus-like genomic organization, 5' UTR-L-P1 (VP0-VP3-VP1)-P2 (2A1-2A2- 2B-2C)-P3 (3A-3B-3C-3D)-3'UTR-poly (A). The 5'UTR contains a potential type IV internal ribosome entry site, while a conserved "barbell"-like structure is found at the 3'UTR, which is similar to DHAV. Compared to the closest related DHAVs, two unrelated 2A proteins were predicted in duck/AH15/CHN/2015, while three unrelated 2A proteins were presented in DHAVs. Based on the amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3CD (3C and 3D), duck/AH15/CHN/2015 was closely related to but distinct from DHAVs, and it was proposed to be a member of a novel species in the genus Avihepatovirus of the family Picornaviridae.
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Affiliation(s)
- Chuanfeng Li
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Tongling Shan
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Zongyan Chen
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Jiewen Zhou
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Hang Li
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Guangzhi Tong
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China.
| | - Guangqing Liu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China.
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Abstract
Artificial intelligence (AI) is a technology that utilizes machines to mimic intelligent human behavior. To appreciate human-technology interaction in the clinical setting, augmented intelligence has been proposed as a cognitive extension of AI in health care, emphasizing its assistive and supplementary role to medical professionals. While truly autonomous medical robotic systems are still beyond reach, the virtual component of AI, known as software-type algorithms, is the main component used in dentistry. Because of their powerful capabilities in data analysis, these virtual algorithms are expected to improve the accuracy and efficacy of dental diagnosis, provide visualized anatomic guidance for treatment, simulate and evaluate prospective results, and project the occurrence and prognosis of oral diseases. Potential obstacles in contemporary algorithms that prevent routine implementation of AI include the lack of data curation, sharing, and readability; the inability to illustrate the inner decision-making process; the insufficient power of classical computing; and the neglect of ethical principles in the design of AI frameworks. It is necessary to maintain a proactive attitude toward AI to ensure its affirmative development and promote human-technology rapport to revolutionize dental practice. The present review outlines the progress and potential dental applications of AI in medical-aided diagnosis, treatment, and disease prediction and discusses their data limitations, interpretability, computing power, and ethical considerations, as well as their impact on dentists, with the objective of creating a backdrop for future research in this rapidly expanding arena.
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Affiliation(s)
- T Shan
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - F R Tay
- The Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - L Gu
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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Xiao Y, Wang H, Feng L, Pan J, Chen Z, Wang H, Yang S, Shen Q, Wang X, Shan T, Zhang W. Fecal, oral, blood and skin virome of laboratory rabbits. Arch Virol 2020; 165:2847-2856. [PMID: 33034764 PMCID: PMC7546134 DOI: 10.1007/s00705-020-04808-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022]
Abstract
Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we detected a novel polyomavirus (RabPyV), and phylogenetic analysis based on the large T antigen, VP1 and VP2 regions indicated that the novel strain might have undergone a recombination event. Recombination analysis based on related genomes confirmed that RabPyV is a multiple recombinant between rodent-like and avian-like polyomaviruses. In fecal samples, three partial or complete genome sequences of viruses belonging to the families Picobirnaviridae, Parvoviridae, Microviridae and Coronaviridae were characterized, and phylogenetic trees were constructed based on the predicted amino acid sequences of viral proteins. This study increases the amount of genetic information on viruses present in laboratory rabbits.
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Affiliation(s)
- Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Lei Feng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jiamin Pan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zeyu Chen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huiling Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Yang S, Shan T, Xiao Y, Zhang H, Wang X, Shen Q, Wang Y, Yao Y, Liu Q, Wang H, Zhang W. Digging metagenomic data of pangolins revealed SARS-CoV-2 related viruses and other significant viruses. J Med Virol 2020; 93:1786-1791. [PMID: 32940906 DOI: 10.1002/jmv.26524] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/02/2023]
Abstract
Pangolin metagenomic data obtained from public databases were used to assemble partial or complete viral genomes showing genetic relationship to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sendai virus, flavivirus, picornavirus, parvovirus, and genomovirus, respectively. Most of these virus genomes showed genomic recombination signals. Phylogeny based on the SARS-CoV-2-related virus sequences assembled in this study and those recently published indicated that pangolin SARS-CoV-2-related viruses were clustered into two sub-lineages according to geographic sampling sites. These findings suggest the need for further pangolin samples, from different countries, to be collected and analyzed for coronavirus to elucidate whether pangolins are intermittent hosts for SARS-CoV-2.
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Affiliation(s)
- Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Heteng Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuxin Yao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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Shan T, Fu R, Xie Y, Chen Q, Wang Y, Li Z, Song X, Li P, Wang B. Regulatory Mechanism of Maize (Zea mays L.) miR164 in Salt Stress Response. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420070133] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bai Y, Li L, Shan T, Zhang Y, Chen X, Gao F, Jiang Y, Zhou Y, Li G, Yu L, Kong N, Ma Z, Tong G. Proteasomal degradation of nonstructural protein 12 by RNF114 suppresses porcine reproductive and respiratory syndrome virus replication. Vet Microbiol 2020; 246:108746. [PMID: 32605740 DOI: 10.1016/j.vetmic.2020.108746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/31/2020] [Accepted: 05/31/2020] [Indexed: 11/20/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant threat to the swine industry worldwide, and the development of effective and sustainable measures to control PRRSV transmission remains a pressing problem. The function of PRRSV nonstructural protein 12 (Nsp12), which might play essential roles in viral replication and production, remains unknown. In this study, we identified a new host-restricted factor, porcine RING finger protein 114 (RNF114), as an inhibitor of PRRSV replication through its degradation of viral Nsp12. Western blot, quantitative real-time polymerase chain reaction, and viral titer assays indicated that RNF114 overexpression suppressed PRRSV replication, whereas RNF114 knockdown increased viral titer and nucleocapsid protein levels. Additionally, we observed that PPRSV infection led to increased RNF114 levels during the middle and late phases of infection in both porcine alveolar macrophages and MARC-145 cells. Moreover, screening of PRRSV Nsps showed that RNF114 interacted with viral Nsp12, and that RNF114-specific anti-PRRSV effects were associated with its ubiquitin ligase activity, which involves K27-linked polyubiquitination and degradation of Nsp12 through a proteasome-dependent pathway. These findings identified RNF114 as a critical regulator of PRRSV replication and offer insights into the roles of Nsp12 in PRRSV pathogenesis.
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Affiliation(s)
- Yuanzhe Bai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Yujiao Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Xiaoyong Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China.
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Liu J, Nong Q, Wang J, Chen W, Xu Z, You W, Xie J, Wang Y, Shan T. Breed difference and regulatory role of CRTC3 in porcine intramuscular adipocyte. Anim Genet 2020; 51:521-530. [PMID: 32400010 DOI: 10.1111/age.12945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 12/17/2022]
Abstract
The cAMP responsive element binding protein (CREB)-regulated transcription coactivator 3 (CRTC3) is a member of the CRTC protein family and plays an important role in energy metabolism. The aim of this study was to determine if the expression of porcine CRTC3 is related to intramuscular fat (IMF) deposition and meat quality in Heigai pigs (a local fatty breed in China) and Duroc × Landrace × Yorkshire (DLY) pigs (a lean crossbred pig widely cultured in China). In addition, the effect of ectopic expression of CRTC3 on gene expression in porcine IMF adipocytes was also examined. Our results showed that Heigai pigs had lower lean percentage, thicker back fat thickness and smaller loin muscle area than DLY pigs. Compared with DLY pigs, Heigai pigs had higher marbling scores, better meat color and higher IMF contents and triglyceride concentrations. Higher levels of oxidative metabolic enzyme and expression of the slow oxidative muscle fiber-related genes were observed in longissimus dorsi muscle and psoas major muscle (P < 0.05) from Heigai pigs. Notably, CRTC3 and adipocyte-specific marker genes were highly expressed in muscle tissues of Heigai pigs. The expression of lipolysis-related genes ATGL and HSL were lower in Heigai muscles. Moreover, forced expression of CRTC3 promoted lipid accumulation and increased the expression of PPARγ, C/EBPα, leptin and FABP4 (P < 0.05), whereas it decreased the expression of ATGL and HSL in IMF adipocytes. These results suggest that CRTC3 expression is associated with lipid accumulation and IMF deposition in pigs.
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Affiliation(s)
- J Liu
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - Q Nong
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - J Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - W Chen
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - Z Xu
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - W You
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - J Xie
- Shandong Chunteng Food Co. Ltd, Zaozhuang, Shandong, 277500, China
| | - Y Wang
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - T Shan
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
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Cai Z, Fan Y, Zhang Z, Lu C, Zhu Z, Jiang T, Shan T, Peng Y. VirusCircBase: a database of virus circular RNAs. Brief Bioinform 2020; 22:2182-2190. [PMID: 32349124 DOI: 10.1093/bib/bbaa052] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11 924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.
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Kong N, Meng Q, Jiao Y, Wu Y, Zuo Y, Wang H, Sun D, Dong S, Zhai H, Tong W, Zheng H, Yu H, Tong G, Xu Y, Shan T. Identification of a novel B-cell epitope in the spike protein of porcine epidemic diarrhea virus. Virol J 2020; 17:46. [PMID: 32245493 PMCID: PMC7119268 DOI: 10.1186/s12985-020-01305-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/26/2020] [Indexed: 01/02/2023] Open
Abstract
Background Porcine epidemic diarrhea virus (PEDV) infection causes an acute enteric tract infectious disease characterized by vomiting, anorexia, dehydration, weight loss and high mortality in neonatal piglets. During PEDV infection, the spike protein (S) is a major virion structural protein interacting with receptors and inducing neutralizing antibodies. However, the neutralizing B-cell epitopes within PEDV S protein have not been well studied. Methods To accurately identify the important immunodominant region of S1, the purified truncated S1 proteins (SA, SB, SC, SD and SE) were used to immunize BALB/c mice to prepare polyclonal antibodies. The antisera titers were determined by indirect ELISA, western blot and IFA after four immunizations to find the important immunodominant region of S1, and then purified the immunodominant region of S1 protein and immunized mice to generate the special antibodies, and then used recombinant peptides to determine the B-cell epitopes of monoclonal antibodies. Results Five antisera of recombinant proteins of the spike protein region of PEDV were generated and we found that only the polyclonal antibody against part of the S1 region (signed as SE protein, residues 666–789) could recognize the native PEDV. Purified SE protein was used to immunize BALB/c mice and generate mAb 2E10. Pepscan of the SE protein demonstrated that SE16 (722SSTFNSTREL731) is the minimal linear epitope required for reactivity with the mAb 2E10. Further investigation indicated that the epitope SE16 was localized on the surface of PEDV S protein in the 3D structure. Conclusions A mAb 2E10 that is specifically bound to PEDV was generated and identified a specific linear B-cell epitope (SE16, 722SSTFNSTREL731) of the mAb. The epitope region of PEDV S1 localized in the different regions in comparison with the earlier identified epitopes. These findings enhance the understanding of the PEDV spike protein structure for vaccine design and provide a potential use for developing diagnostic methods to detect PEDV.
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Affiliation(s)
- Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Qiong Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,College of Life Science, Xinyang Normal University, Xinyang, China
| | - Yajuan Jiao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yongguang Wu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yewen Zuo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Hua Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Dage Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Yongjie Xu
- College of Life Science, Xinyang Normal University, Xinyang, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China.
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Zhao T, Gong H, Shen X, Zhang W, Shan T, Yu X, Wang SJ, Cui L. Comparison of Viromes in Ticks from Different Domestic Animals in China. Virol Sin 2020; 35:398-406. [PMID: 32157603 DOI: 10.1007/s12250-020-00197-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/11/2019] [Indexed: 11/24/2022] Open
Abstract
Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock. This study aimed to investigate the geographical distribution of tick species and tick-associated viruses in central and eastern China. Total 573 ticks from domestic animals including dogs, sheep and cattle were collected in 2017. Two genera of ticks were identified including Rhipicephalus and Haemaphysalis. Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations. Following trimming, 13,640 reads were obtained and annotated to 19 virus families. From these sequences, above 37.74% of the viral reads were related to the RNA viruses. Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera. The viral diversity of R. microplus was significantly different from that of other Rhipicephalus species. On the other hand, substantial overlap in viral species was observed between the same genera. In addition, we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes. Rather, the geographic location seems to significantly influence the viral families. Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses. In conclusion, the present study provides a baseline for comparing viruses detected in ticks, according to species, natural hosts, and geographic locations.
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Affiliation(s)
- Tingting Zhao
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haiyan Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiaojuan Shen
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 2012013, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiangqian Yu
- Shanghai Pudong New District Center for Animal Diseases Control and Prevention, Shanghai, 201299, China
| | - Seong Jin Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Li Cui
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Jiang W, Ren Y, Han X, Xue J, Shan T, Chen Z, Liu Y, Wang Q. Recombinase polymerase amplification-lateral flow (RPA-LF) assay combined with immunomagnetic separation for rapid visual detection of Vibrio parahaemolyticus in raw oysters. Anal Bioanal Chem 2020; 412:2903-2914. [PMID: 32128642 DOI: 10.1007/s00216-020-02532-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 12/20/2022]
Abstract
This study was the first attempt to optimize a recombinase polymerase amplification (RPA) and lateral flow (LF) assay combined with immunomagnetic separation (IMS) for the detection of Vibrio parahaemolyticus in raw oysters. The newly developed IMS-RPA-LF assay effectively combines sample preparation, amplification, and detection into a single platform. Under optimal conditions, the average capture efficiency (CE) for 104 colony forming units (CFU)/mL of four V. parahaemolyticus strains with 0.4 mg of immunomagnetic beads within 45 min was 80.3%. After optimization, the RPA-LF assay was able to detect V. parahaemolyticus within 15 min, comprising DNA amplification with RPA for 10 min at 37 °C and visualization of the amplicons through LF strips for 5 min. The RPA-LF assay exhibited good specificity by showing a test line for eight V. parahaemolyticus strains with different serotypes but no cross-reaction with 12 non-V. parahaemolyticus bacteria. RPA-LF assay was found to be sensitive and detected as low as 10 pg genomic DNA of V. parahaemolyticus. For spiked oyster samples, the detection sensitivity of V. parahaemolyticus was improved to 2 CFU/g by IMS-RPA-LF after enrichment for 4 h; in contrast, the IMS-PCR method required 8 h. Hence, even when V. parahaemolyticus was present in very low numbers in samples, the IMS-RPA-LF assay could be completed within half a workday. Because of the high sensitivity, specificity, and speed of the IMS-RPA-LF assay, this newly developed method opens a novel pathway for rapid diagnostic screening of V. parahaemolyticus in seafood, which is an increasingly important health issue worldwide. Graphical abstract.
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Affiliation(s)
- Wei Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang, Shanghai, 200241, China
| | - Yaling Ren
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiangan Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang, Shanghai, 200241, China
| | - Junxin Xue
- Shanghai Customs, Shanghai, 200135, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang, Shanghai, 200241, China
| | - Zhaoguo Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang, Shanghai, 200241, China
| | - Yongjie Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Quan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang, Shanghai, 200241, China.
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Kong N, Shan T, Wang H, Jiao Y, Zuo Y, Li L, Tong W, Yu L, Jiang Y, Zhou Y, Li G, Gao F, Yu H, Zheng H, Tong G. BST2 suppresses porcine epidemic diarrhea virus replication by targeting and degrading virus nucleocapsid protein with selective autophagy. Autophagy 2019; 16:1737-1752. [PMID: 31868081 DOI: 10.1080/15548627.2019.1707487] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Interferon-induced BST2 (bone marrow stromal cell antigen 2) inhibits viral replication by tethering enveloped virions to the cell surface to restrict viral release and by inducing the NFKB-dependent antiviral immune response. However, the mechanism by which BST2 uses the selective autophagy pathway to inhibit viral replication is poorly understood. In this study, we showed that BST2 expression was significantly increased during porcine epidemic diarrhea virus (PEDV) infection of Vero cells by IRF1 targeting its promoter. We also showed that BST2 suppressed PEDV replication by binding and degrading the PEDV-encoded nucleocapsid (N) protein. The downregulation of N protein was blocked by macroautophagy/autophagy inhibitors but not a proteasome inhibitor, implying that the N protein was degraded via the selective autophagy pathway. Both the BST2 and N protein interacted with the E3 ubiquitin ligase MARCHF8/MARCH8 and the cargo receptor CALCOCO2/NDP52, and the ubiquitination of N protein was necessary for the degradation of N mediated by the BST2-MARCHF8 axis. The knockdown of MARCHF8 or ATG5 with small interfering RNAs blocked the selective autophagy pathway, rescued the protein abundance of PEDV N in 293T cells, and prevented the inhibition of PEDV replication by BST2 in Vero cells. Together, our data demonstrate the novel mechanism of BST2-mediated virus restriction, in which BST2 recruits MARCHF8 to catalyze the ubiquitination of the PEDV N protein. The ubiquitinated N protein is then recognized by CALCOCO2/NDP52, which delivers it to autolysosome for degradation through the selective autophagy pathway. Abbreviations: 3MA: 3-methyladenine; ATG: autophagy-related; Baf A1: bafilomycin A1; BST2: bone marrow stromal cell antigen 2; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CC: coiled-coil; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; CQ: chloroquine; CT: cytoplasmic tail; DAPI: 4',6-diamidino-2-phenylindole; GPI: glycosyl-phosphatidylinositol; hpi: hours post infection; IRF1: interferon regulatory factor 1; ISG: IFN-stimulated gene; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARCHF8/MARCH8: membrane-associated ring-CH-type finger 8; MOI: multiplicity of infection; N protein: nucleocapsid protein; PED: porcine epidemic diarrhea; PEDV: porcine epidemic diarrhea virus; RT: room temperature; siRNA: small interfering RNA; STAT: signal transducer and activator of transcription; TCID50: 50% tissue culture infectious doses; TM: transmembrane.
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Affiliation(s)
- Ning Kong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Hua Wang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China
| | - Yajuan Jiao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China
| | - Yewen Zuo
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China
| | - Liwei Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Lingxue Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Yifeng Jiang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Yanjun Zhou
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Guoxin Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Fei Gao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Hai Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Hao Zheng
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Shanghai, PR China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University , Yangzhou, PR China
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Li L, Zhao K, Gao F, Jiang Y, Shan T, Tong W, Zheng H, Yu L, Li G, Ma Z, Tong G. Restriction of porcine reproductive and respiratory syndrome virus replication by galectin-1. Vet Microbiol 2019; 235:310-318. [PMID: 31383318 DOI: 10.1016/j.vetmic.2019.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 01/07/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes great economic losses to the swine industry globally; however, effective control measures for this virus are limited. Here, we screened a porcine alveolar macrophage (PAM) cDNA library with a yeast two-hybrid system to reveal that galectin-1 (Gal-1), an endogenous innate immune protein encoded by LGALS1, interacts with nonstructural protein 11 (Nsp11) of PRRSV. Western blotting and viral titer assays indicated that Gal-1 overexpression suppressed replication in multiple PRRSV strains (P < 0.001), whereas Gal-1 knockdown or knockout increased viral titer and nucleocapsid protein expression. The Gal-1-specific anti-PRRSV effect was associated with the endoribonuclease domain of Nsp11 through inactivation of interferon-antagonist function and stimulation of interferon-stimulated gene expression. Additionally, Gal-1 interacted with PRRSV E protein but not with PRRSV glycoproteins, and recombinant Gal-1 treatment inhibited PRRSV in PAMs and MARC-145 cells. Furthermore, Gal-1 inhibited replication in multiple viruses, including equine arteritis virus, porcine epidemic diarrhea virus, pseudorabies virus, Japanese encephalitis virus, and classical swine fever virus, suggesting its potential broad application for antiviral strategies. Our findings provide insight into the important role of Gal-1 in PRRSV pathogenesis and its potential use as a novel therapeutic target against PRRSV infection.
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Affiliation(s)
- Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Kuan Zhao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, PR China.
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50
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Wang H, Ling Y, Shan T, Yang S, Xu H, Deng X, Delwart E, Zhang W. Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae. Virus Evol 2019; 5:vez013. [PMID: 31191981 PMCID: PMC6555873 DOI: 10.1093/ve/vez013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nineteen families of phages infecting bacteria or archaea are currently recognized by the International Committee on Taxonomy of Viruses (ICTV). Of these, only two have single-stranded DNA genomes, namely Inoviridae and Microviridae. The distribution, genetic characteristics, and ecological roles of Microviridae remain largely under explored. Here, using viral metagenomics, we investigate the intestinal virome from human and twenty-four species of animals, as well as freshwater samples, containing abundant sequence reads showing similarity to the Microviridae. Eight hundred and sixty complete or near complete Microviridae-related genomes were generated, showing high levels of co-infections and sequence divergence. Sequence comparison and phylogenetic analysis showed that the Microviridae subfamily Gokushovirinae was highly prevalent and that some strains may qualify as new subfamilies. This study significantly augments our knowledge of the genetic diversity, genome evolution, and distribution in animal species of members of the family Microviridae.
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Affiliation(s)
- Hao Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Yu Ling
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, 438 Jiefang Road, Zhenjiang, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, 270 masonic avenue, San Francisco, CA, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 masonic avenue, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, 270 masonic avenue, San Francisco, San Francisco CA, USA
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
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