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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Liu J, Jiang X, Lei W, Xi Y, Zhang Q, Cai H, Ma X, Liu Y, Wang W, Liu N, Zhang X, Ma W, Zhao C, Ni B, Zhang W, Wang Y. Differences between the intestinal microbial communities of healthy dogs from plateau and those of plateau dogs infected with Echinococcus. Virol J 2024; 21:116. [PMID: 38783310 PMCID: PMC11112841 DOI: 10.1186/s12985-024-02364-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
OBJECTIVE Cystic echinococcosis (CE) represents a profoundly perilous zoonotic disease. The advent of viral macrogenomics has facilitated the exploration of hitherto uncharted viral territories. In the scope of this investigation, our objective is to scrutinize disparities in the intestinal microbiotic ecosystems of canines dwelling in elevated terrains and those afflicted by Echinococcus infection, employing the tool of viral macrogenomics. METHODS In this study, we collected a comprehensive total of 1,970 fecal samples from plateau dogs infected with Echinococcus, as well as healthy control plateau dogs from the Yushu and Guoluo regions in the highland terrain of China. These samples were subjected to viral macrogenomic analysis to investigate the viral community inhabiting the canine gastrointestinal tract. RESULTS Our meticulous analysis led to the identification of 136 viral genomic sequences, encompassing eight distinct viral families. CONCLUSION The outcomes of this study hold the potential to enhance our comprehension of the intricate interplay between hosts, parasites, and viral communities within the highland canine gut ecosystem. Through the examination of phage presence, it may aid in early detection or assessment of infection severity, providing valuable insights into Echinococcus infection and offering prospects for potential treatment strategies.
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Affiliation(s)
- Jia Liu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Xiaojie Jiang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Wen Lei
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Qing Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Huixia Cai
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Xiao Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Yufang Liu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Wei Wang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Na Liu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Xiongying Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Wanli Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Cunzhe Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China
| | - Bin Ni
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Yongshun Wang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, 811602, China.
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Bhagchandani T, Haque MMU, Sharma S, Malik MZ, Ray AK, Kaur US, Rai A, Verma A, Sawlani KK, Chaturvedi R, Dandu H, Kumar A, Tandon R. Plasma Virome of HIV-infected Subjects on Suppressive Antiretroviral Therapy Reveals Association of Differentially Abundant Viruses with Distinct T-cell Phenotypes and Inflammation. Curr Genomics 2024; 25:105-119. [PMID: 38751600 PMCID: PMC11092910 DOI: 10.2174/0113892029279786240111052824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 05/18/2024] Open
Abstract
Background The plasma virome represents the overall composition of viral sequences present in it. Alteration in plasma virome has been reported in treatment naïve and immunocompromised (CD4 count < 200) people with HIV (PWH). However, the effect of ART on virome composition in PWH on ART with preserved CD4 counts is poorly understood. Objectives We aimed to assess the alterations in plasma virome in PWH on ART in comparison to HIV-negative uninfected controls and to further investigate possible associations of plasma viruses with inflammation and immune dysfunction, namely, immunosenescence and immune exhaustion. Methods Plasma viral DNA from PWH on ART and controls was used for sequencing on the Illumina Nextseq500 platform, followed by the identification of viral sequences using an automated pipeline, VIROMATCH. Multiplex cytokine assay was performed to measure the concentrations of various cytokines in plasma. Immunophenotyping was performed on PBMCs to identify T cell markers of immunosenescence and immune exhaustion. Results In our observational, cross-sectional pilot study, chronically infected PWH on ART had significantly different viral species compositions compared to controls. The plasma virome of PWH showed a significantly high relative abundance of species Human gammaherpesvirus 4, also known as Epstein-Barr virus (EBV). Moreover, EBV emerged as a significant viral taxon differentially enriched in PWH on ART, which further correlated positively with the exhaustion phenotype of T cells and significantly increased TNF-α in PWH on ART. Additionally, a significantly increased proportion of senescent T cells and IL-8 cytokine was detected in PWH on ART. Conclusion Altered plasma virome influenced the inflammatory response and T-cell phenotype in PWH on ART.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad M. Ul Haque
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shilpa Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- Host-Pathogen Interaction Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ashwini K. Ray
- Laboratory of Metabolic Disorder and Environmental Biotechnology, Department of Environmental Studies, Faculty of Science, University of Delhi, New Delhi, India
| | - Urvinder S. Kaur
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Kamal K. Sawlani
- Department of Medicine, King George’s Medical University, Lucknow, India
| | - Rupesh Chaturvedi
- Host-Pathogen Interaction Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Special Centre for System Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Himanshu Dandu
- Department of Medicine, King George’s Medical University, Lucknow, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore; India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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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] [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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Pourkarim MR. Navigating Evolving Challenges in Blood Safety. Viruses 2024; 16:123. [PMID: 38257823 PMCID: PMC10821029 DOI: 10.3390/v16010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Blood safety remains a paramount public health concern, and health authorities maintain a high level of vigilance to prevent transfusion-transmitted infections (TTIs) [...].
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Affiliation(s)
- Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion, Tehran 14665-1157, Iran
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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] [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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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] [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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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] [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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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] [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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10
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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] [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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11
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Bao S, Wang H, Li W, Wu H, Lu C, Yong L, Zhang Q, Lu X, Zhao M, Lu J, Liu J, Ikechukwu CK, Xu J, Ni P, Xiong Y, Zhang W, Zhou C. Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection. Gut Microbes 2023; 15:2234653. [PMID: 37448101 DOI: 10.1080/19490976.2023.2234653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.
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Affiliation(s)
- Siwen Bao
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | - Chunying Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Liang Yong
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Qing Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, China
| | | | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Ying Xiong
- Department of Pharmacy, Yancheng Third People's Hospital, Yancheng, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
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12
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Hu H, Ling Y, Wang X, Wang H, Zhu N, Li Y, Xu H. Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues. Pathogens 2022; 11:pathogens11121452. [PMID: 36558785 PMCID: PMC9781650 DOI: 10.3390/pathogens11121452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01.
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Affiliation(s)
- Huimin Hu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
- Department of Dermatology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian 223002, China
| | - Yu Ling
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing 210004, China
| | - Xuan Wang
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Hao Wang
- Department of Dermatology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian 223002, China
| | - Niannan Zhu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Yumei Li
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Hui Xu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
- Correspondence: ; Tel.: +86-051185026785
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13
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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. ENVIRONMENTAL 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] [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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14
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Slavov SN. Viral Metagenomics for Identification of Emerging Viruses in Transfusion Medicine. Viruses 2022; 14:v14112448. [PMID: 36366546 PMCID: PMC9699440 DOI: 10.3390/v14112448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Viral metagenomics has revolutionized our understanding for identification of unknown or poorly characterized viruses. For that reason, metagenomic studies gave been largely applied for virus discovery in a wide variety of clinical samples, including blood specimens. The emerging blood-transmitted virus infections represent important problem for public health, and the emergence of HIV in the 1980s is an example for the vulnerability of Blood Donation systems to such infections. When viral metagenomics is applied to blood samples, it can give a complete overview of the viral nucleic acid abundance, also named "blood virome". Detailed characterization of the blood virome of healthy donors could identify unknown (emerging) viral genomes that might be assumed as hypothetic transfusion threats. However, it is impossible only by application of viral metagenomics to assign that one viral agent could impact blood transfusion. That said, this is a complex issue and will depend on the ability of the infectious agent to cause clinically important infection in blood recipients, the viral stability in blood derivatives and the presence of infectious viruses in blood, making possible its transmission by transfusion. This brief review summarizes information regarding the blood donor virome and some important challenges for use of viral metagenomics in hemotherapy for identification of transfusion-transmitted viruses.
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Affiliation(s)
- Svetoslav Nanev Slavov
- Department of Cellular and Molecular Therapy (NuCeL), Butantan Institute, São Paulo 05503-900, SP, Brazil; ; Tel.: +55-(16)-2101-9300 (ext. 9365)
- Laboratory of Bioinformatics, Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Rua Tenente Catão Roxo 2501, Ribeirão Preto CEP 14051-140, SP, Brazil
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15
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Mao Q, Sun G, Qian Y, Qian Y, Li W, Wang X, Shen Q, Yang S, Zhou C, Wang H, Zhang W. Viral metagenomics of pharyngeal secretions from children with acute respiratory diseases with unknown etiology revealed diverse viruses. Virus Res 2022; 321:198912. [PMID: 36058285 DOI: 10.1016/j.virusres.2022.198912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/21/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
Acute respiratory tract infections are a major public health problem and the leading cause of morbidity in children younger than 5 years old. This study investigated the potential reasons of unexplained acute respiratory infections in children in Xuzhou and its environs during 2018-2019.We collected pharyngeal swab samples from 411 children under the age of five who presented with symptoms of unexplained acute respiratory infection and were negative for bacteria, mycoplasma, and influenza viruses. Using viral metagenomic techniques, viral nucleic acids were extracted, enriched, and sequenced from the samples. Results indicated that Picornaviridae, Parvoviridae, Paramyxoviridae, Coronaviridae, and Anelloviridae were the five virus families with the highest relative content of sequence reads. And we detected 35 HBoV-positive and 12 HEV-positive samples out of 411 samples by the polymerase chain reaction (PCR). Partial or nearly complete genome sequences of viruses belonging to the families Picornaviridae, Parvoviridae, and Anelloviridae were characterized, and phylogenetic trees were constructed based on the nucleic acid or amino acid sequences of the predicted viral open reading frames (ORFs), as well as genotyping of the viruses. In addition, we observed recombination events in the Saffold virus and Coxsackievirus A9 by analyzing the genetic characteristics of the viruses revealed in this study. This study provides vital information for the prevention and treatment of acute respiratory infections in children younger than five years old.
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Affiliation(s)
- Qingqing Mao
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212013, China; School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Guangming Sun
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou 221009, Jiangsu, China
| | - Yu Qian
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yuchen Qian
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital, Nanjing Medical University, Taizhou, Jiangsu 225300, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital, Nanjing Medical University, Taizhou, Jiangsu 225300, China.
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China.
| | - Wen Zhang
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212013, China; School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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16
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Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs. Microbiol Resour Announc 2022; 11:e0068122. [PMID: 35972248 PMCID: PMC9476932 DOI: 10.1128/mra.00681-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The genome sequences of three anelloviruses (genus Alphatorquevirus), a genomovirus (genus Gemykolovirus), and an unclassified papillomavirus were identified in four human nasopharyngeal swabs, and one was positive for influenza A and one for influenza B virus. The influenza B virus-positive sample had a coinfection with an anellovirus and a papillomavirus.
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17
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Virome of Giant Panda-Infesting Ticks Reveals Novel Bunyaviruses and Other Viruses That Are Genetically Close to Those from Giant Pandas. Microbiol Spectr 2022; 10:e0203422. [PMID: 35916407 PMCID: PMC9430136 DOI: 10.1128/spectrum.02034-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tick infestations have been reported as one of the factors threatening the health of giant pandas, but studies of viral pathogens carried by ticks feeding on the blood of giant pandas are limited. To assess whether blood-sucking ticks of giant pandas can carry viral pathogens and if so, whether the viruses in ticks are associated with those previously detected in giant panda hosts, we determined the viromes of ticks detached from giant pandas in a field stocking area in Sichuan Province, southwest China. Using viral metagenomics we identified 32 viral species in ticks, half of which (including anellovirus [n = 9], circovirus [n = 3], and gemycircularvirus [n = 4]) showed homology to viruses carried by giant pandas and their associated host species (such as red pandas and mosquitoes) in the same living domain. Remarkably, several viruses in this study phylogenetically assigned as bunyavirus, hepe-like virus, and circovirus were detected with relatively high abundance, but whether these newly identified tick-associated viruses can replicate in ticks and then transmit to host animals during a blood meal will require further investigation. These findings further expand our understanding of the role of giant panda-infesting ticks in the local ecosystem, especially related to viral acquisition and transmission, and lay a foundation to assess the risk for giant panda exposure to tick-borne viruses. IMPORTANCE Ticks rank only second to mosquitoes as blood-feeding arthropods, capable of spreading pathogens (including viruses, bacteria, and parasites) to hosts during a blood meal. To better understand the relationship between viruses carried by ticks and viruses that have been reported in giant pandas, it is necessary to analyze the viromes of giant panda-parasitic blood-sucking ticks. This study collected 421 ticks on the body surface of giant pandas in Sichuan Province, China. We characterized the extensive genetic diversity of viruses harbored by these ticks and reported frequent communication of viruses between giant pandas and their ticks. While most of the virome discovered here are nonpathogenic viruses from giant pandas and potentially tick-specific viruses, we revealed some possible tick-borne viruses, represented by novel bunyaviruses. This research contributes to the literature because currently there are few studies on the virome of giant panda-infesting ticks.
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18
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Taylo LJ, Keeler EL, Bushman FD, Collman RG. The enigmatic roles of Anelloviridae and Redondoviridae in humans. Curr Opin Virol 2022; 55:101248. [PMID: 35870315 DOI: 10.1016/j.coviro.2022.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/26/2022]
Abstract
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded DNA genomes that are common components of the human virome. Despite their small genome size of less than 5000 bases, they are remarkably successful - anelloviruses colonize over 90% of adult humans, while the recently discovered redondoviruses have been found at up to 80% prevalence in some populations. Anelloviruses are present in blood and many organs, while redondoviruses are found mainly in the ororespiratory tract. Despite their high prevalence, little is known about their biology or pathogenic potential. In this review, we discuss anelloviruses and redondoviruses and explore their enigmatic roles in human health and disease.
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Affiliation(s)
- Louis J Taylo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Bao S, Wang H, Li W, Ji L, Wang X, Shen Q, Yang S, Zhou C, Zhang W. Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection. J Med Virol 2022; 94:4959-4969. [PMID: 35718835 DOI: 10.1002/jmv.27946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/10/2022]
Abstract
The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases. Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection.
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Affiliation(s)
- Siwen Bao
- Department of Microbiology, Jiangsu University, Zhenjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Likai Ji
- Department of Microbiology, Jiangsu University, Zhenjiang, China
| | - Xiaochun Wang
- Department of Microbiology, Jiangsu University, Zhenjiang, China
| | - Quan Shen
- Department of Microbiology, Jiangsu University, Zhenjiang, China
| | - Shixing Yang
- Department of Microbiology, Jiangsu University, Zhenjiang, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Wen Zhang
- Department of Microbiology, Jiangsu University, Zhenjiang, China
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20
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153317. [PMID: 35066043 DOI: 10.1016/j.scitotenv.2022.153317] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [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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21
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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] [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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22
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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] [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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23
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Li X, Liu Q, Chen X, Xiao Y, Yang S, Zhang W, Chen J. The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin. Future Virol 2022. [DOI: 10.2217/fvl-2020-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.
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Affiliation(s)
- Xinlin Li
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Qi Liu
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
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Lu J, Yang S, Zhang X, Tang X, Zhang J, Wang X, Wang H, Shen Q, Zhang W. Metagenomic Analysis of Viral Community in the Yangtze River Expands Known Eukaryotic and Prokaryotic Virus Diversity in Freshwater. Virol Sin 2022; 37:60-69. [PMID: 35234628 PMCID: PMC8922420 DOI: 10.1016/j.virs.2022.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource. First insight into viral community composition in large river ecosystem. Virus hallmark genes present both diverse and conservative characteristics. The composition of viral communities is similar on the whole. Slight regional variation of virome is existed in individual areas.
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Baylis SA, Adlhoch C, Childs L. An Evaluation of Hepatitis E Virus Molecular Typing Methods. Clin Chem 2021; 68:181-191. [PMID: 34969109 DOI: 10.1093/clinchem/hvab186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Hepatitis E virus (HEV) is a major cause of acute viral hepatitis. Better understanding of HEV subtypes involved in hepatitis E infections is essential. Investigation of sources and routes of transmission and the identification of potential clusters/outbreaks rely upon molecular typing of viral strains. A study was carried out to evaluate the ability of laboratories to undertake molecular typing with genotype and subtype determination. METHODS A blinded panel of 11 different Orthohepevirus A strains was distributed to 28 laboratories performing HEV sequence analysis. Laboratories used their routine HEV sequencing and genotyping methods. RESULTS Results were returned by 25 laboratories. Overall, 93% samples were assigned to the correct genotype and 81% were assigned to the correct subtype. Fragments amplified for typing ranged in size and the sequencing assays targeted both the structural and non-structural protein-coding regions. There was good agreement between the reported sequences where methods targeted overlapping fragments. In some cases, incorrect genotypes/subtypes were reported, including those not contained in the panel, and in one case, a genotype was reported for a blinded control sample containing Zika virus; collectively these data indicate contamination problems. CONCLUSIONS In general, identification of genotypes was good; however, in a small number of cases, there was a failure to generate sequences from some of the samples. There was generally broad agreement between the use of online typing tools such as the one provided by HEVnet and curated lists of published HEV reference sequences; however, going forward harmonization between these resources is essential.
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Affiliation(s)
- Sally A Baylis
- Viral Safety Section, Paul-Ehrlich-Institut, Langen, Germany
| | - Cornelia Adlhoch
- Disease Programmes Unit, European Centre for Disease Prevention and Control, Solna, Sweden
| | - Liam Childs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
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26
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Tochetto C, Cibulski SP, Muterle Varela AP, Cerva C, Alves de Lima D, Fumaco Teixeira T, Quoos Mayer F, Roehe PM. A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs. J Gen Virol 2021; 102. [PMID: 34928204 DOI: 10.1099/jgv.0.001706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named 'Suismacovirus', comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses' genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.
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Affiliation(s)
- Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristine Cerva
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Diane Alves de Lima
- Laboratório de Microbiologia do Centro Clínico Veterinário, Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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27
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Ning SY, Zhou MM, Yang J, Zeng J, Wang JP. Viral metagenomics reveals two novel anelloviruses in feces of experimental rats. Virol J 2021; 18:252. [PMID: 34930331 PMCID: PMC8686219 DOI: 10.1186/s12985-021-01723-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models, and a history of pathogenic infections in these animals will directly affect the animal trial results. The pathogenicity of Anellovirus (AV) remains poorly understood due to the lack of a suitable model cell line or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique. METHODS Fecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline and two novel anelloviruses (AVs) were identified from fecal sample of experimental rats. The prevalence of these two viruses was investigated by conventional PCR. RESULTS The complete genomic sequence of these two AVs were determined and fully characterized, with strain name ratane153-zj1 and ratane153-zj2. The circular genomes of ratane153-zj1 and ratane153-zj2 are 2785 nt and 1930 nt in length, respectively, and both include three ORFs. Ratane153-zj1 closely clustered with members within the genus Wawtorquevirus and formed a separate branch based on the phylogenetic tree constructed over the amino acid sequence of ORF1 of the two AVs identified in this study and other related AVs. While the complete amino acid sequences of ORF1 of ratane153-zj2 (nt 335 to 1390) had the highest sequence identity with an unclassified AV (GenBank No. ATY37438) from Chinchilla lanigera, and they clustered with one AV (GenBank No. QYD02305) belonging to the genus Etatorquevirus from Lynx rufus. Conventional PCR with two sets of specific primers designed based on the two genomes, respectively, showed that they were detectable at a low frequency in cohorts of experimental rats. CONCLUSION Our study expanded the genome diversity of AVs and provided genetic background information of viruses existed in experimental rats.
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Affiliation(s)
- Song-Yi Ning
- Joint Institute of Molecular Etiology Diagnosis, Donghai County People's Hospital, Jiangsu University, Donghai, 222300, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ming-Ming Zhou
- School of Nursing, Taihu University of Wuxi, Wuxi, 214063, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jia-Ping Wang
- Department of Clinical Laboratory, Donghai County People's Hospital, Donghai, 222300, Jiangsu, China.
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Yang Z, Zhang J, Yang S, Wang X, Shen Q, Sun G, Wang H, Zhang W. Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence. Virol J 2021; 18:163. [PMID: 34372876 PMCID: PMC8351423 DOI: 10.1186/s12985-021-01632-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Ticks (class Arachnida, subclass Acari) are vectors of transmitting a broad range of pathogenic microorganisms, protozoa, and viruses affecting humans and animals. Liaoning Province is rich in forests where different animals and, abundant Haemaphysalis longicornis ticks exist. Methods Using viral metagenomics, we analyzed the virome in 300 Haemaphysalis longicornis ticks collected from June to August 2015 in the forested region of Liaoning Province, China. Results From the 300 ticks, 1,218,388 high-quality reads were generated, of which 5643 (0.463%) reads showed significant sequence identity to known viruses. Sequence and phylogenetic analysis revealed that viral sequences showing a close relationship with Dabieshan tick virus, Aleutian mink disease virus, adeno-associated virus, Gokushovirus, avian gyrovirus 2 were present in the virome of these ticks. However, the significance of these viruses to human and animal health requires further investigation. Notably, an hepe-like virus, named tick-borne hepe-like virus sequence, was obtained and was highly prevalent in these ticks with a rate of 50%. Nevertheless, one constraint of our study was the limited geographical distribution of the sampled ticks. Conclusion Our study offers an overview of the virome in ticks from a forest region of Liaoning Province and provides further awareness of the viral diversity of ticks. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01632-x.
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Affiliation(s)
- Zijun Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, 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
| | - Xiaochun Wang
- 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
| | - Guangming Sun
- Xuzhou Central Hospital, 131 Huanchen Road, Xuzhou, 221009, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, Jiangsu, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Abstract
The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France.
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30
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Yang J, Wang H, Zhang X, Yang S, Xu H, Zhang W. Viral metagenomic identification of a novel anellovirus in blood sample of a child with atopic dermatitis. J Med Virol 2021; 93:4038-4041. [PMID: 33058155 DOI: 10.1002/jmv.26603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
Here, using viral metagenomics, a novel anellovirus with strain name HuAV-zj-ad1 was detected in blood sample from a child with atopic dermatitis. The complete genome sequence of HuAV-zj-ad1 was determined and fully characterized. The circular genome of HuAV-zj-ad1 is 2841 nt in length and includes four polyprotein ORFs. Phylogenetic analysis and pairwise sequence comparisons based on the amino acid sequences of ORF1, ORF2, ORF3, ORF4 indicated that HuAV-zj-ad1 belonged to a novel species within the genus Betatorquevirus. Polymerase chain reaction screening results showed this anellovirus was not present 50 blood samples from normal children. Whether this novel species of anellovirus has association with a certain disease needs further study.
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Affiliation(s)
- Jie Yang
- Department of Dermatology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- 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
| | - Xiaodan Zhang
- Zhenjiang Center for Disease Prevention and Control, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hui Xu
- Department of Dermatology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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31
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Cordey S, Laubscher F, Hartley MA, Junier T, Keitel K, Docquier M, Guex N, Iseli C, Vieille G, Le Mercier P, Gleizes A, Samaka J, Mlaganile T, Kagoro F, Masimba J, Said Z, Temba H, Elbanna GH, Tapparel C, Zanella MC, Xenarios I, Fellay J, D'Acremont V, Kaiser L. Blood virosphere in febrile Tanzanian children. Emerg Microbes Infect 2021; 10:982-993. [PMID: 33929935 PMCID: PMC8171259 DOI: 10.1080/22221751.2021.1925161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.Trial registration: ClinicalTrials.gov identifier: NCT02225769.
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Affiliation(s)
- Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mary-Anne Hartley
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland.,Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas Junier
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristina Keitel
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland.,Department of Paediatric Emergency Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Gael Vieille
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Anne Gleizes
- SwissProt group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | | | - Frank Kagoro
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - John Masimba
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Zamzam Said
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Gasser H Elbanna
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Marie-Celine Zanella
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, Geneva, Switzerland.,Agora Center, University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valérie D'Acremont
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland.,Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
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32
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Valença IN, Santos RBD, Peronni KC, Sauvage V, Vandenbogaert M, Caro V, Silva Junior WAD, Covas DT, Silva-Pinto AC, Laperche S, Kashima S, Slavov SN. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Rev Inst Med Trop Sao Paulo 2021; 63:e40. [PMID: 34037156 PMCID: PMC8149102 DOI: 10.1590/s1678-9946202163040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/18/2021] [Indexed: 11/22/2022] Open
Abstract
To date, blood banks apply routine diagnosis to a specific spectrum of
transfusion-transmitted viruses. Even though this measure is considered highly
efficient to control their transmission, the threat imposed by emerging viruses
is increasing globally, which can impact transfusion safety, especially in the
light of the accelerated viral discovery by novel sequencing technologies. One
of the most important groups of patients, who may indicate the presence of
emerging viruses in the field of blood transfusion, is the group of individuals
who receive multiple transfusions due to hereditary hemoglobinopathies. It is
possible that they harbor unknown or unsuspected parenterally-transmitted
viruses. In order to elucidate this, nucleic acids from 30 patients with
beta-thalassemia were analyzed by Illumina next-generation sequencing and
bioinformatics analysis. Three major viral families:
Anelloviridae, Flaviviridae and
Hepadnaviridae were identified. Among
them, anelloviruses were the most representative, being detected with high
number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C),
Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV
and HCV detection was expected due to the high seroprevalence in patients with
beta thalassemia. Our results do not confirm the presence of emerging or
unsuspected viruses threatening the transfusion safety at present, but can be
used to actively search for viruses that threaten blood transfusion safety. We
believe that the application of viral metagenomics in multiple-transfused
patients is highly useful to monitor possible viral transfusion threats and for
the annotation of their virome composition.
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Affiliation(s)
- Ian Nunes Valença
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Bezerra Dos Santos
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Kamila Chagas Peronni
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Virginie Sauvage
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Valérie Caro
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Wilson Araújo da Silva Junior
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
| | - Ana Cristina Silva-Pinto
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Syria Laperche
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Simone Kashima
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
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33
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Smith K, Fielding R, Schiavone K, Hall KR, Reid VS, Boyea D, Smith EL, Schmidlin K, Fontenele RS, Kraberger S, Varsani A. Circular DNA viruses identified in short-finned pilot whale and orca tissue samples. Virology 2021; 559:156-164. [PMID: 33892449 DOI: 10.1016/j.virol.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Members of the Delphinidae family are widely distributed across the world's oceans. We used a viral metagenomic approach to identify viruses in orca (Orcinus orca) and short-finned pilot whale (Globicephala macrorhynchus) muscle, kidney, and liver samples from deceased animals. From orca tissue samples (muscle, kidney, and liver), we identified a novel polyomavirus (Polyomaviridae), three cressdnaviruses, and two genomoviruses (Genomoviridae). In the short-finned pilot whale we were able to identify one genomovirus in a kidney sample. The presence of unclassified cressdnavirus within two samples (muscle and kidney) of the same animal supports the possibility these viruses might be widespread within the animal. The orca polyomavirus identified here is the first of its species and is not closely related to the only other dolphin polyomavirus previously discovered. The identification and verification of these viruses expands the current knowledge of viruses that are associated with the Delphinidae family.
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Affiliation(s)
- Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Russell Fielding
- HTC Honors College, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Kelsie Schiavone
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Katharine R Hall
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Vincent S Reid
- Barrouallie Whaler's Project, Saint Vincent and the Grenadines
| | | | - Emma L Smith
- Department of Chemical & Biological Sciences, University of the West Indies-Cave Hill, Barbados
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700, Cape Town, South Africa.
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34
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Cai HZ, Zhang H, Yang J, Zeng J, Wang H. Preliminary assessment of viral metagenome from cancer tissue and blood from patients with lung adenocarcinoma. J Med Virol 2021; 93:5126-5133. [PMID: 33595122 DOI: 10.1002/jmv.26887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022]
Abstract
In this study, using a viral metagenomic method, we investigated the composition of virome in blood and cancer tissue samples that were collected from 25 patients with lung adenocarcinoma. Results indicated that virus sequences showing similarity to human pegivirus (HPgV), anellovirus, human endogenous retrovirus (HERV), and polyomavirus were recovered from this cohort. Three different complete genomes of HPgV were acquired from the blood samples and one complete genome of polyomavirus was determined from the cancer tissue sample. Phylogenetic analysis indicated that the three HPgV strains belonged to genotype 3 and the polyomavirus showed the highest sequence identity (99.73%) to trichodysplasia spinulosa-associated polyomavirus. PCR screening results indicated that the three HPgVs were present in 5 out of the 25 blood samples and the polyomavirus only existed in a cancer tissue sample pool. Whether infections with viruses have an association with lung cancer needs further study with a larger size of sampling.
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Affiliation(s)
- Hua-Zhong Cai
- Department of Emergency, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Heteng Zhang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jie Yang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian Zeng
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
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35
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Zhang HT, Wang H, Wu HS, Zeng J, Yang Y. Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis. Virol J 2021; 18:11. [PMID: 33407663 PMCID: PMC7789296 DOI: 10.1186/s12985-020-01482-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. METHODS To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. RESULTS Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. CONCLUSION Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.
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Affiliation(s)
- He-Teng Zhang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China
- 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
| | - Hai-Sheng Wu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 810021, Qinghai, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Yang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China.
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36
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Chen XU, He Y, Li W, Kalim U, Xiao Y, Yang J, Wang X, Yang S, Zhang W. Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China. Pol J Microbiol 2020; 69:471-478. [PMID: 33574875 PMCID: PMC7812366 DOI: 10.33073/pjm-2020-051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/17/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Porcine astroviruses (PAstVs) have wide distribution in swine herds worldwide. At present, five porcine astrovirus genotypes have been identified. In this study, using viral metagenomics, a novel PAstV strain (designated as Ahast) was identified in fecal samples from pigs in Anhui of China, and the complete genomic sequence of Ahast was obtained by assembling and PCR amplification. Genomic structural analysis indicated that Ahast had a typical ribosomal frameshifting signal, and some conserve amino acid motifs were also found in virally encoded proteins. Phylogenetic analysis and sequence comparison indicated that this virus belonged to porcine astrovirus genotype 4 (PAstV4), which formed a clade clustered with other PAstV4. Multiple recombinant events were confirmed by recombination analysis and indicated that Ahast was a potential recombinant. Epidemiological investigation indicated that PAstV4 has a 10.7% prevalence in this pig farm. The new recombinant identified in this study will be beneficial to comprehend the origin, genetic diversity, and evolution of porcine astroviruses in Anhui of China.
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Affiliation(s)
- X U Chen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yumin He
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Weina Li
- Pharmacy Department, People's Hospital of Rizhao, Rizhao, China
| | - Ullah Kalim
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jie Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, China
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37
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Wang XC, Wang H, Tan SD, Yang SX, Shi XF, Zhang W. Viral metagenomics reveals diverse anelloviruses in bone marrow specimens from hematologic patients. J Clin Virol 2020; 132:104643. [PMID: 32961430 DOI: 10.1016/j.jcv.2020.104643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients. METHODS A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones. RESULTS Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples. CONCLUSIONS Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.
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Affiliation(s)
- Xiao-Chun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an 223002, China.
| | - Shi-Dong Tan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Shi-Xing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Xiao-Feng Shi
- Department of Hematology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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Thi Kha Tu N, Thi Thu Hong N, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, van Doorn HR, Dang Trung Nghia H, Thao Huong D, An Han D, Thi Thu Ha L, Deng X, Thwaites G, Delwart E, Virtala AMK, Vapalahti O, Baker S, Van Tan L. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020; 12:E960. [PMID: 32872469 PMCID: PMC7552073 DOI: 10.3390/v12090960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
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Affiliation(s)
- Nguyen Thi Kha Tu
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Nguyen Thi Thu Hong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ha Noi 8000, Vietnam;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Duong An Han
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Luu Thi Thu Ha
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Xutao Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Anna-Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Olli Vapalahti
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Virology and Immunology, HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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Liu Q, Wang H, Ling Y, Yang SX, Wang XC, Zhou R, Xiao YQ, Chen X, Yang J, Fu WG, Zhang W, Qi GL. Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer. Virol J 2020; 17:61. [PMID: 32334626 PMCID: PMC7183601 DOI: 10.1186/s12985-020-01332-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/16/2020] [Indexed: 01/08/2023] Open
Abstract
Background Musk deer can produce musk which has high medicinal value and is closely related to human health. Viruses in forest musk deer both threaten the health of forest musk deer and human beings. Methods Using viral metagenomics we investigated the virome in 85 faeces samples collected from forest musk deer. Results In this article, eight novel CRESS-DNA viruses were characterized, whole genomes were 2148 nt–3852 nt in length. Phylogenetic analysis indicated that some viral genomes were part of four different groups of CRESS-DNA virus belonging in the unclassified CRESS-DNA virus, Smacoviridae, pCPa-like virus and pPAPh2-like virus. UJSL001 (MN621482), UJSL003 (MN621469) and UJSL017 (MN621476) fall into the branch of unclassified CRESS-DNA virus (CRESSV1–2), UJSL002 (MN621468), UJSL004 (MN621481) and UJSL007 (MN621470) belong to the cluster of Smacoviridae, UJSL005 (MN604398) showing close relationship with pCPa-like (pCRESS4–8) clusters and UJSL006 (MN621480) clustered into the branch of pPAPh2-like (pCRESS9) virus, respectively. Conclusion The virome in faeces samples of forest musk deer from Chengdu, Sichuan province, China was revealed, which further characterized the diversity of viruses in forest musk deer intestinal tract.
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Affiliation(s)
- Qi Liu
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.,Agricultural Engineering Research Institute, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hao Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Yu Ling
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Shi-Xing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Xiao-Chun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Rui Zhou
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Yu-Qing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Xu Chen
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Jie Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Wei-Guo Fu
- Agricultural Engineering Research Institute, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
| | - Gui-Lan Qi
- Institute of Animal Husbandry, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, Sichuan 611130, China.
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Identification of a novel bovine copiparvovirus in pooled fetal bovine serum. Virus Genes 2020; 56:522-526. [PMID: 32306155 PMCID: PMC7329774 DOI: 10.1007/s11262-020-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/03/2020] [Indexed: 01/12/2023]
Abstract
A novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~ 50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to the Copiparvovirus genus, being most closely related to bovine parvovirus 2 (BPV2) with 41% identity with the non-structural protein NS1 and 47% identity with the virus capsid protein of BPV2. A screen of individual and pooled bovine sera identified a closely related variant of the novel virus in a second serum pool. For classification purposes, the novel virus has been designated bovine copiparvovirus species 3 isolate JB9 (bocopivirus 3-JB9).
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Fahsbender E, Charlys da-Costa A, Elise Gill D, Augusto de Padua Milagres F, Brustulin R, Julio Costa Monteiro F, Octavio da Silva Rego M, Soares D’Athaide Ribeiro E, Cerdeira Sabino E, Delwart E. Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus. PLoS One 2020; 15:e0229993. [PMID: 32134963 PMCID: PMC7058308 DOI: 10.1371/journal.pone.0229993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.
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Affiliation(s)
- Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
| | - Antonio Charlys da-Costa
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Danielle Elise Gill
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | | | | | | | - Ester Cerdeira Sabino
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
- * E-mail:
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Human Tibroviruses: Commensals or Lethal Pathogens? Viruses 2020; 12:v12030252. [PMID: 32106547 PMCID: PMC7150972 DOI: 10.3390/v12030252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022] Open
Abstract
Rhabdoviruses are a large and ecologically diverse family of negative-sense RNA viruses (Mononegavirales: Rhabdoviridae). These viruses are capable of infecting an unexpectedly wide variety of plants, vertebrates, and invertebrates distributed over all human-inhabited continents. However, only a few rhabdoviruses are known to infect humans: a ledantevirus (Le Dantec virus), several lyssaviruses (in particular, rabies virus), and several vesiculoviruses (e.g., Chandipura virus, vesicular stomatitis Indiana virus). Recently, several novel rhabdoviruses have been discovered in the blood of both healthy and severely ill individuals living in Central and Western Africa. These viruses—Bas-Congo virus, Ekpoma virus 1, and Ekpoma virus 2—are members of the little-understood rhabdoviral genus Tibrovirus. Other than the basic genomic architecture, tibroviruses bear little resemblance to well-studied rhabdoviruses such as rabies virus and vesicular stomatitis Indiana virus. These three human tibroviruses are quite divergent from each other, and each of them clusters closely with tibroviruses currently known only from biting midges or healthy cattle. Seroprevalence studies suggest that human tibrovirus infections may be common but are almost entirely unrecognized. The pathogenic potential of this diverse group of viruses remains unknown. Although certain tibroviruses may be benign and well-adapted to humans, others could be newly emerging and produce serious disease. Here, we review the current knowledge of tibroviruses and argue that assessing their impact on human health should be an urgent priority.
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Li W, Dong S, Xu J, Zhou X, Han J, Xie Z, Gong Q, Peng H, Zhou C, Lin M. Viral metagenomics reveals sapoviruses of different genogroups in stool samples from children with acute gastroenteritis in Jiangsu, China. Arch Virol 2020; 165:955-958. [PMID: 32048042 PMCID: PMC7131977 DOI: 10.1007/s00705-020-04549-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/13/2020] [Indexed: 11/26/2022]
Abstract
Sapoviruses (SAVs), including several genogroups (GI to GV), are one of the causes of acute gastroenteritis (AGE). In this study, viral metagenomics revealed the presence of sapoviruses of different genogroups in stool from children with AGE. Eight different complete SAV genomes were determined, of which five belonged to GI and the other three belonged to GII, GIV and GV, respectively. Although they were highly similar to published sequences, the GIV and GV were the first complete genome sequences of these SAVs found in China. In a prevalence investigation, 19% of subjects with AGE were positive for SAVs, while none of the control group was positive.
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Affiliation(s)
- Wang Li
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Surong Dong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Juan Xu
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Xiaobin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Junling Han
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Zhaqing Xie
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Qin Gong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Hailin Peng
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
| | - Mei Lin
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
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Wang Y, Cui X, Chen X, Yang S, Ling Y, Song Q, Zhu S, Sun L, Li C, Li Y, Deng X, Delwart E, Zhang W. A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus. Arch Virol 2020; 165:703-707. [PMID: 31982944 PMCID: PMC7087231 DOI: 10.1007/s00705-019-04488-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.
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Affiliation(s)
- Yan Wang
- College of Animal Sciences and Technologies, Anhui Agricultural University, Hefei, 230036, China.,School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Xuejiao Cui
- College of Animal Sciences and Technologies, Anhui Agricultural University, Hefei, 230036, China
| | - Xu Chen
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Yu Ling
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Qianben Song
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Su Zhu
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Luying Sun
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Chuang Li
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China
| | - Yu Li
- College of Animal Sciences and Technologies, Anhui Agricultural University, Hefei, 230036, China.
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 941187, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 941187, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, 94143, USA
| | - Wen Zhang
- School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, 202103, Jiangsu, China.
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Gao L, Rong X, He M, Zhang L, Li T, Wang W, Candotti D, Allain JP, Fu Y, Li C. Metagenomic analysis of potential pathogens from blood donors in Guangzhou, China. Transfus Med 2019; 30:61-69. [PMID: 31845424 DOI: 10.1111/tme.12657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/25/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVES This study aimed to identify the emerging/reemerging pathogens in blood donation samples. BACKGROUND A metagenomic analysis has previously been used to look for pathogens but in this study, the relationship with aminotransferase (ALT) is described. METHODS/MATERIALS Excluding samples reactive to hepatitis B virus, hepatitis C virus, human immunodeficiency syndrome virus or syphilis and plasma samples were stratified into three groups of ALT levels (IU/L): A ≤ 50, B 51 to 69 and C ≥ 70, respectively. Each group was mixed in a pool of 100 samples, from which DNA and cDNA libraries were established for next generation sequencing and analysis. Pathogens of interest were identified by immunoassays, nested-polymerase chain reaction, phylogenetic analysis and pathogen detection in follow-up donors. RESULTS Several new or reemerging transfusion-transmitted pathogens were identified; Streptococcus suis, Babesia species and Toxoplasma gondii were found in the three ALT groups, Epstein-Barr virus (EBV) only in group C. Ten S. suis nucleic acid positive samples were detected, all closely phylogenetically related to reference strains. A donor in group A carried both S. suis genome and specific IgM in follow-up samples. This strain was identified as nontoxic S. suis. Five samples contained a short fragment of Babesia species SpeI-AvaI gene, while T. gondii was identified in 20 samples as a short fragment of 18S rDNA gene. In group C, two samples contained EBV genome. CONCLUSIONS Blood donations that contained S. suis, Babesia species and T. gondii sequences might represent potential transfusion risks. EBV, a potential cause of elevated ALT, was detected. Metagenomic analysis might be a useful technology for monitoring blood safety.
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Affiliation(s)
- Lei Gao
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Xia Rong
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Ling Zhang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Tingting Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wenjing Wang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Daniel Candotti
- Department of Blood Transmitted Agents, National Institute of Blood Transfusion, Paris, France
| | - Jean-Pierre Allain
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Division of Transfusion Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yongshui Fu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
| | - Chengyao Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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Li G, Zhou Z, Yao L, Xu Y, Wang L, Fan X. Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels. Transfusion 2019; 59:3177-3185. [PMID: 31393615 DOI: 10.1111/trf.15476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/14/2019] [Accepted: 07/20/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND A serum alanine aminotransferase (ALT) test is currently demanded for blood donation in China. One of the major reasons to include such a test is possible etiology of known or unknown hepatotropic viruses. However, this hypothesis has never been examined convincingly. STUDY DESIGN AND METHODS The study recruited 90 Chinese blood donors that were divided into three groups based on their ALT values. Serum virome from these donors was explored using a metagenomics approach with enhanced sensitivity resolved at single sequencing reads. RESULTS Anellovirus and pegivirus C (GBV-C) were detected among these donors. None of them were found solely in donors with abnormal liver enzyme. Anellovirus was highly prevalent (93.3%) and the co-infection with multiple genera (alpha, beta, and gammatorquevirus) were more common in the donors with normal ALT values in comparison to those with elevated ALT (single/double/triple Anellovirus genera, 1/3/24 vs. 7/7/14 or 6/7/13, p = 0.009). For unmapped reads that accounted for 15 ± 14.9% of the data, similarity-based (BLASTN, BLASTP, and HMMER3) and similarity-independent (k-mer frequency) analysis identified several circular rep encoding ssDNA (CRESS-DNA) genomes. Direct PCR testing indicated these genomes were likely reagent contaminants. CONCLUSION Viral etiology is not responsible for elevated ALT levels in Chinese blood donors. The ALT test, if not abandoned, should be adjusted for its cutoff in response to donor shortage in China.
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Affiliation(s)
- Gang Li
- Wuhan Blood Center, Wuhan, China
| | | | - Li Yao
- Wuhan Blood Center, Wuhan, China
| | - Yanjuan Xu
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Lan Wang
- Wuhan Blood Center, Wuhan, China
| | - Xiaofeng Fan
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri.,Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, Missouri
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Ye SH, Siddle KJ, Park DJ, Sabeti PC. Benchmarking Metagenomics Tools for Taxonomic Classification. Cell 2019; 178:779-794. [PMID: 31398336 PMCID: PMC6716367 DOI: 10.1016/j.cell.2019.07.010] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/17/2023]
Abstract
Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
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Affiliation(s)
- Simon H Ye
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Systems Biology, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Systems Biology, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
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Li J, Cui L, Deng X, Yu X, Zhang Z, Yang Z, Delwart E, Zhang W, Hua X. Canine bufavirus in faeces and plasma of dogs with diarrhoea, China. Emerg Microbes Infect 2019; 8:245-247. [PMID: 30866778 PMCID: PMC6455112 DOI: 10.1080/22221751.2018.1563457] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Jingjiao Li
- a Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology , Shanghai Jiao Tong University , Shanghai , People's Republic of China.,b Department of Microbiology, School of Medicine , Jiangsu University , Zhenjiang , People's Republic of China
| | - Li Cui
- a Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology , Shanghai Jiao Tong University , Shanghai , People's Republic of China
| | - Xutao Deng
- c Blood Systems Research Institute , San Francisco , CA , USA
| | - Xiangqian Yu
- d Shanghai Pudong New Area Center for Animal Disease Prevention and Control , Shanghai , People's Republic of China
| | - Zhonghai Zhang
- d Shanghai Pudong New Area Center for Animal Disease Prevention and Control , Shanghai , People's Republic of China
| | - Zhibiao Yang
- a Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology , Shanghai Jiao Tong University , Shanghai , People's Republic of China
| | - Eric Delwart
- c Blood Systems Research Institute , San Francisco , CA , USA.,e Department of Laboratory Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Wen Zhang
- b Department of Microbiology, School of Medicine , Jiangsu University , Zhenjiang , People's Republic of China
| | - Xiuguo Hua
- a Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology , Shanghai Jiao Tong University , Shanghai , People's Republic of China
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Zur Hausen H, Bund T, de Villiers EM. Infectious Agents in Bovine Red Meat and Milk and Their Potential Role in Cancer and Other Chronic Diseases. Curr Top Microbiol Immunol 2019; 407:83-116. [PMID: 28349283 DOI: 10.1007/82_2017_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Red meat and dairy products have frequently been suggested to represent risk factors for certain cancers, chronic neurodegenerative diseases, and autoimmune and cardiovascular disorders. This review summarizes the evidence and investigates the possible involvement of infectious factors in these diseases. The isolation of small circular single-stranded DNA molecules from serum and dairy products of Eurasian Aurochs (Bos taurus)-derived cattle, obviously persisting as episomes in infected cells, provides the basis for further investigations. Gene expression of these agents in human cells has been demonstrated, and frequent infection of humans is implicated by the detection of antibodies in a high percentage of healthy individuals. Epidemiological observations suggest their relationship to the development multiple sclerosis, to heterophile antibodies, and to N-glycolylneuraminic acid (Neu5Gc) containing cell surface receptors.
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Affiliation(s)
- Harald Zur Hausen
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Timo Bund
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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