1
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Chen X, Zou T, Zeng Q, Chen Y, Zhang C, Jiang S, Ding G. Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries. J Dent 2024; 146:105059. [PMID: 38801939 DOI: 10.1016/j.jdent.2024.105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVES Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC. METHODS Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software. RESULTS 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome. CONCLUSIONS Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC. CLINICAL SIGNIFICANCE The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.
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Affiliation(s)
- Xin Chen
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China
| | - Ting Zou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China
| | - Qinglu Zeng
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Yubing Chen
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Chengfei Zhang
- Endodontology, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, PR China
| | - Shan Jiang
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China.
| | - Guicong Ding
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China.
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2
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Zhao X, Dai C, Qian S, Tang Q, Li L, Hao Y, Zhou Z, Ge X, Gong C, Yuan J. Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis). Microbiol Spectr 2023; 11:e0081023. [PMID: 37265414 PMCID: PMC10434060 DOI: 10.1128/spectrum.00810-23] [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: 02/24/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.
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Affiliation(s)
- Xin Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Caijiao Dai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Shiyu Qian
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qing Tang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhijian Zhou
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xingyi Ge
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Cheng Gong
- Tian-e-zhou National Reserve for Lipotes Vexillifer, Shishou, People’s Republic of China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
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3
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First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing. Viruses 2023; 15:v15030750. [PMID: 36992458 PMCID: PMC10056474 DOI: 10.3390/v15030750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.
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4
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Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach. JOURNAL OF TROPICAL ECOLOGY 2023. [DOI: 10.1017/s0266467423000019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Abstract
During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.
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5
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Zoghi S, Masoudi MS, Taheri R. The Evolving Role of Next Generation Sequencing in Pediatric Neurosurgery: a Call for Action for Research, Clinical Practice, and Optimization of Care. World Neurosurg 2022; 168:232-242. [PMID: 36122859 DOI: 10.1016/j.wneu.2022.09.056] [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: 07/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
NGS (Next-Generation Sequencing) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it appears that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to employ it in its routine practice and guidelines. In this review, we briefly summarized the developments that lead to the establishment of NGS technology, reviewed the current applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and lastly discuss the steps we need to take to better harness NGS in pediatric neurosurgery.
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Affiliation(s)
- Sina Zoghi
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Reza Taheri
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran.
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6
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Liu Z, Ding X, Haider MS, Ali F, Yu H, Chen X, Tan S, Zu Y, Liu W, Ding B, Zheng A, Zheng J, Qian Z, Ashfaq H, Yu D, Li K. A metagenomic insight into the Yangtze finless porpoise virome. Front Vet Sci 2022; 9:922623. [PMID: 36118360 PMCID: PMC9478467 DOI: 10.3389/fvets.2022.922623] [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: 04/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.
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Affiliation(s)
- Zhigang Liu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
- Zhigang Liu
| | - Xin Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | | | - Farah Ali
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Han Yu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Xin Chen
- College of Life Science, Anqing Normal University, Anqing, China
| | - Shuaishuai Tan
- College of Life Science, Anqing Normal University, Anqing, China
| | - Yuan Zu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Wenlong Liu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Bangzhi Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | - Aifang Zheng
- College of Life Science, Anqing Normal University, Anqing, China
| | - Jinsong Zheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengyi Qian
- Hubei Yangtze River Ecological Protection Foundation, Wuhan, China
| | - Hassan Ashfaq
- Institute of Continuing Education and Extension, University of Veterinary Animal Sciences, Lahore, Pakistan
| | - Daoping Yu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Li
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7
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Wang X, Carrai M, Van Brussel K, Feng S, Beatty JA, Shi M, Holmes EC, Li J, Barrs VR. Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak. Viruses 2022; 14:v14071412. [PMID: 35891392 PMCID: PMC9325248 DOI: 10.3390/v14071412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterised the diversity of these Carnivore protoparvovirus 1 variants in 18 faecal samples collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of >10,000 × coverage per site. All samples comprised FPV alone. Compared with the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were nonsynonymous, including 9 in nonstructural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit interhost diversity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intrahost diversity at all polymorphic positions was low, with subconsensus variant frequencies (SVF) of <1% except for two positions (2108 and 3208) in two samples with SVF of 1.1−1.3%. Intrahost nucleotide diversity was measured across the whole genome (0.7−1.5%) and for each gene and was highest in the NS2 gene of four samples (1.2−1.9%). Overall, intrahost viral genetic diversity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.
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Affiliation(s)
- Xiuwan Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; (X.W.); (S.F.); (J.L.)
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Maura Carrai
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China; (M.C.); (J.A.B.)
- Centre for Animal Health and Welfare, City University of Hong Kong, Hong Kong, China
| | - Kate Van Brussel
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
- School of Life and Environmental Sciences and School of Medical Sciences, Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW 2006, Australia;
| | - Shuo Feng
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; (X.W.); (S.F.); (J.L.)
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Julia A. Beatty
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China; (M.C.); (J.A.B.)
- Centre for Animal Health and Welfare, City University of Hong Kong, Hong Kong, China
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou 510275, China;
| | - Edward C. Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW 2006, Australia;
| | - Jun Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; (X.W.); (S.F.); (J.L.)
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Centre for Animal Health and Welfare, City University of Hong Kong, Hong Kong, China
| | - Vanessa R. Barrs
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China; (M.C.); (J.A.B.)
- Centre for Animal Health and Welfare, City University of Hong Kong, Hong Kong, China
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence:
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8
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Lim HGM, Hsiao SH, Lee YCG. Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. BIOLOGY 2021; 10:biology10101023. [PMID: 34681121 PMCID: PMC8533344 DOI: 10.3390/biology10101023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 10/24/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently become a novel pandemic event following the swine flu that occurred in 2009, which was caused by the influenza A virus (H1N1 subtype). The accurate identification of the huge number of samples during a pandemic still remains a challenge. In this study, we integrate two technologies, next-generation sequencing and cloud computing, into an optimized workflow version that uses a specific identification algorithm on the designated cloud platform. We use 182 samples (92 for COVID-19 and 90 for swine flu) with short-read sequencing data from two open-access datasets to represent each pandemic and evaluate our workflow performance based on an index specifically created for SARS-CoV-2 or H1N1. Results show that our workflow could differentiate cases between the two pandemics with a higher accuracy depending on the index used, especially when the index that exclusively represented each dataset was used. Our workflow substantially outperforms the original complete identification workflow available on the same platform in terms of time and cost by preserving essential tools internally. Our workflow can serve as a powerful tool for the robust identification of cases and, thus, aid in controlling the current and future pandemics.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Shih-Hsin Hsiao
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Correspondence:
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9
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Oluniyi PE, Ajogbasile F, Oguzie J, Uwanibe J, Kayode A, Happi A, Ugwu A, Olumade T, Ogunsanya O, Eromon PE, Folarin O, Frost SDW, Heeney J, Happi CT. VGEA: an RNA viral assembly toolkit. PeerJ 2021; 9:e12129. [PMID: 34567846 PMCID: PMC8428259 DOI: 10.7717/peerj.12129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/17/2021] [Indexed: 12/11/2022] Open
Abstract
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user's choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License.
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Affiliation(s)
- Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Fehintola Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Judith Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Jessica Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Adeyemi Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Alphonsus Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Testimony Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Olusola Ogunsanya
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Philomena Ehiaghe Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Onikepe Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Simon D W Frost
- Microsoft Research, Redmond, WA, United States of America.,London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jonathan Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
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10
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Shi Y, Tao J, Li B, Shen X, Cheng J, Liu H. The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus. Front Vet Sci 2021; 8:695088. [PMID: 34307533 PMCID: PMC8292670 DOI: 10.3389/fvets.2021.695088] [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] [Received: 04/14/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.
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Affiliation(s)
- Ying Shi
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Jie Tao
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Benqiang Li
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Xiaohui Shen
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Huili Liu
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
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11
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Caruso G, Giammanco A, Virruso R, Fasciana T. Current and Future Trends in the Laboratory Diagnosis of Sexually Transmitted Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:1038. [PMID: 33503917 PMCID: PMC7908473 DOI: 10.3390/ijerph18031038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022]
Abstract
Sexually transmitted infections (STIs) continue to exert a considerable public health and social burden globally, particularly for developing countries. Due to the high prevalence of asymptomatic infections and the limitations of symptom-based (syndromic) diagnosis, confirmation of infection using laboratory tools is essential to choose the most appropriate course of treatment and to screen at-risk groups. Numerous laboratory tests and platforms have been developed for gonorrhea, chlamydia, syphilis, trichomoniasis, genital mycoplasmas, herpesviruses, and human papillomavirus. Point-of-care testing is now a possibility, and microfluidic and high-throughput omics technologies promise to revolutionize the diagnosis of STIs. The scope of this paper is to provide an updated overview of the current laboratory diagnostic tools for these infections, highlighting their advantages, limitations, and point-of-care adaptability. The diagnostic applicability of the latest molecular and biochemical approaches is also discussed.
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Affiliation(s)
- Giorgia Caruso
- U.O.C. of Microbiology and Virology, ARNAS “Civico, Di Cristina and Benfratelli”, 90127 Palermo, Italy
| | - Anna Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (A.G.); (T.F.)
| | - Roberta Virruso
- U.O.C. of Microbiology, Virology and Parassitology, A.O.U.P. “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Teresa Fasciana
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (A.G.); (T.F.)
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12
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Lu C, Zhang Z, Cai Z, Zhu Z, Qiu Y, Wu A, Jiang T, Zheng H, Peng Y. Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics. BMC Biol 2021; 19:5. [PMID: 33441133 PMCID: PMC7807511 DOI: 10.1186/s12915-020-00938-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.
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Affiliation(s)
- Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zheng Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zhaozhong Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Heping Zheng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China.
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13
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Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P. A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep 2020; 10:11194. [PMID: 32641704 PMCID: PMC7343800 DOI: 10.1038/s41598-020-68159-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/16/2020] [Indexed: 01/22/2023] Open
Abstract
The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p < 0.0001), and the results were highly specific for the spiked pathogens. In clinical samples, the diagnostic accuracy, sensitivity and specificity of the mNGS with reference to conventional methods were 100%, 95% and 96%, respectively. The clinical application of mNGS holds promise to benefit patients with CNS infections of unknown etiology.
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Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Level 2M, Office H2M-24093, PO BOX 26999, Doha, Qatar. .,Weill Cornell Medical College in Qatar, Doha, Qatar. .,Sidra Medicine, Doha, Qatar.
| | | | - Patrick Tang
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Kin-Ming Tsui
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Andres Perez Lopez
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Mohammad Janahi
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Rusung Tan
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Peter Tilley
- British Columbia Children's Hospital, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
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14
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in both the USA and the world. Recent research has demonstrated the involvement of the gut microbiota in CRC development and progression. Microbial biomarkers of disease have focused primarily on the bacterial component of the microbiome; however, the viral portion of the microbiome, consisting of both bacteriophages and eukaryotic viruses, together known as the virome, has been lesser studied. Here we review the recent advancements in high-throughput sequencing (HTS) technologies and bioinformatics, which have enabled scientists to better understand how viruses might influence the development of colorectal cancer. We discuss the contemporary findings revealing modulations in the virome and their correlation with CRC development and progression. While a variety of challenges still face viral HTS detection in clinical specimens, we consider herein numerous next steps for future basic and clinical research. Clinicians need to move away from a single infectious agent model for disease etiology by grasping new, more encompassing etiological paradigms, in which communities of various microbial components interact with each other and the host. The reporting and indexing of patient health information, socioeconomic data, and other relevant metadata will enable identification of predictive variables and covariates of viral presence and CRC development. Altogether, the virome has a more profound role in carcinogenesis and cancer progression than once thought, and viruses, specific for either human cells or bacteria, are clinically relevant in understanding CRC pathology, patient prognosis, and treatment development.
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15
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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica). Viruses 2019; 11:v11110979. [PMID: 31652964 PMCID: PMC6893680 DOI: 10.3390/v11110979] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.
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16
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Abstract
Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.
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Affiliation(s)
- Yong-Zhen Zhang
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Xin-Chen Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
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17
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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18
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Kuehn R, Stoeckle BC, Young M, Popp L, Taeubert JE, Pfaffl MW, Geist J. Identification of a piscine reovirus-related pathogen in proliferative darkening syndrome (PDS) infected brown trout (Salmo trutta fario) using a next-generation technology detection pipeline. PLoS One 2018; 13:e0206164. [PMID: 30346982 PMCID: PMC6197672 DOI: 10.1371/journal.pone.0206164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/08/2018] [Indexed: 01/02/2023] Open
Abstract
The proliferative darkening syndrome (PDS) is an annually recurring disease that causes species-specific die-off of brown trout (Salmo trutta fario) with a mortality rate of near 100% in pre-alpine rivers of central Europe. So far the etiology and causation of this disease is still unclear. The objective of this study was to identify the cause of PDS using a next-generation technology detection pipeline. Following the hypothesis that PDS is caused by an infectious agent, brown trout specimens were exposed to water from a heavily affected pre-alpine river with annual occurrence of the disease. Specimens were sampled over the entire time period from potential infection through death. Transcriptomic analysis (microarray) and RT-qPCR of brown trout liver tissue evidenced strong gene expression response of immune-associated genes. Messenger RNA of specimens with synchronous immune expression profiles were ultra-deep sequenced using next-generation sequencing technology (NGS). Bioinformatic processing of generated reads and gap-filling Sanger re-sequencing of the identified pathogen genome revealed strong evidence that a piscine-related reovirus is the causative organism of PDS. The identified pathogen is phylogenetically closely related to the family of piscine reoviruses (PRV) which are considered as the causation of different fish diseases in Atlantic and Pacific salmonid species such as Salmo salar and Onchorhynchus kisutch. This study also highlights that the approach of first screening immune responses along a timeline in order to identify synchronously affected stages in different specimens which subsequently were ultra-deep sequenced is an effective approach in pathogen detection. In particular, the identification of specimens with synchronous molecular immune response patterns combined with NGS sequencing and gap-filling re-sequencing resulted in the successful pathogen detection of PDS.
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Affiliation(s)
- Ralph Kuehn
- Unit of Molecular Zoology, Department of Zoology, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM, United States of America
| | - Bernhard C Stoeckle
- Unit of Molecular Zoology, Department of Zoology, Technical University of Munich, Freising, Germany.,Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany
| | - Marc Young
- Unit of Molecular Zoology, Department of Zoology, Technical University of Munich, Freising, Germany
| | - Lisa Popp
- Unit of Molecular Zoology, Department of Zoology, Technical University of Munich, Freising, Germany
| | - Jens-Eike Taeubert
- Fachberatung für Fischerei Niederbayern, Bezirk Niederbayern, Landshut, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Juergen Geist
- Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany
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19
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Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus. Virology 2018; 521:77-91. [PMID: 29886344 DOI: 10.1016/j.virol.2018.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022]
Abstract
The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.
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20
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Nooij S, Schmitz D, Vennema H, Kroneman A, Koopmans MPG. Overview of Virus Metagenomic Classification Methods and Their Biological Applications. Front Microbiol 2018; 9:749. [PMID: 29740407 PMCID: PMC5924777 DOI: 10.3389/fmicb.2018.00749] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.
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Affiliation(s)
- Sam Nooij
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Dennis Schmitz
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Harry Vennema
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Annelies Kroneman
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marion P G Koopmans
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
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21
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Abstract
PURPOSE OF REVIEW With the advent of novel massively parallel sequencing technologies and bioinformatic processing capabilities, clinical applications of metagenomic studies are rapidly being integrated into medicine. Through this paper, we hope to introduce this powerful new tool to clinicians caring for children. RECENT FINDINGS Very few studies have looked at metagenomic applications in children. The ability to perform these types of massive sequencing projects was not possible as little as 7 years ago. SUMMARY Metagenomics is defined as the study of all genetic material within a given sample. Novel sequencing and analysis approaches allow for unbiased assays to identify pathogens missed by targeted sequencing and culture methods. Although not widely available yet, metagenomic studies have been used to diagnose pediatric infections, identify resistance genes in clinical samples, and characterize outbreaks. Although cost and turnaround time have limited its application in clinical laboratories to date, novel platforms and increasing comfort with these techniques continue to push diagnostic metagenomics into clinical pediatric medicine. Much work in this field is yet to be done. That being said, we feel that pediatric clinicians will be using metagenomic techniques in the care of children with increasing frequency in the near future.
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22
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Greninger AL. A decade of RNA virus metagenomics is (not) enough. Virus Res 2018; 244:218-229. [PMID: 29055712 PMCID: PMC7114529 DOI: 10.1016/j.virusres.2017.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022]
Abstract
It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.
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Affiliation(s)
- Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, United States; Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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23
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Mourani PM, Sontag MK. Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm. Pediatr Clin North Am 2017; 64:1039-1056. [PMID: 28941534 DOI: 10.1016/j.pcl.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Ventilator-associated pneumonia (VAP) is a serious complication of critical illness. Surveillance definitions have undergone revisions for more objective and consistent reporting. The 1 organism-1 disease paradigm for microbial involvement may not adequately apply to many cases of VAP, in which pathogens are introduced to a pre-existing and often complex microbial community that facilitates or hinders the potential pathogen, consequently determining whether progression to VAP occurs. As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment.
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Affiliation(s)
- Peter M Mourani
- Section of Critical Care, Department of Pediatrics, University of Colorado Denver, School of Medicine, Children's Hospital Colorado, 13121 East 17th Avenue, MS8414, Aurora, CO 80045, USA.
| | - Marci K Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver Anschutz Medical Campus, 13001 East 17th, B119, Aurora, CO 80045, USA
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24
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Kujiraoka M, Kuroda M, Asai K, Sekizuka T, Kato K, Watanabe M, Matsukiyo H, Saito T, Ishii T, Katada N, Saida Y, Kusachi S. Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach. Front Microbiol 2017; 8:685. [PMID: 28473817 PMCID: PMC5397476 DOI: 10.3389/fmicb.2017.00685] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/04/2017] [Indexed: 12/16/2022] Open
Abstract
Acute cholecystitis (AC), which is strongly associated with retrograde bacterial infection, is an inflammatory disease that can be fatal if inappropriately treated. Currently, bacterial culture testing, which is basically recommended to detect the etiological agent, is a time-consuming (4–6 days), non-comprehensive approach. To rapidly detect a potential pathogen and predict its antimicrobial susceptibility, we undertook a metagenomic approach to characterize the bacterial infection associated with AC. Six patients (P1–P6) who underwent cholecystectomy for AC were enrolled in this study. Metagenome analysis demonstrated possible single or multiple bacterial infections in four patients (P1, P2, P3, and P4) with 24-h experimental procedures; in addition, the CTX-M extended-spectrum ß-lactamase (ESBL) gene was identified in two bile samples (P1 and P4). Further whole genome sequencing of Escherichia coli isolates suggested that CTX-M-27-producing ST131 and CTX-M-14-producing novel-ST were identified in P1 and P4, respectively. Metagenome analysis of feces and saliva also suggested some imbalance in the microbiota for more comprehensive assessment of patients with AC. In conclusion, metagenome analysis was useful for rapid bacterial diagnostics, including assessing potential antimicrobial susceptibility, in patients with AC.
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Affiliation(s)
- Manabu Kujiraoka
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan.,Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Koji Asai
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Kengo Kato
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Manabu Watanabe
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Hiroshi Matsukiyo
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Tomoaki Saito
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Tomotaka Ishii
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Natsuya Katada
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Yoshihisa Saida
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
| | - Shinya Kusachi
- Department of Surgery, Toho University Ohashi Medical CenterTokyo, Japan
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25
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Yang X, Xu P, Graham RI, Yuan H, Wu K. Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm. J Vis Exp 2017:55534. [PMID: 28448051 PMCID: PMC5564690 DOI: 10.3791/55534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Many novel viruses have been discovered in animal hosts using next-generation sequencing technologies. Previously, we reported a mutualistic virus, Helicoverpa armigera densovirus (HaDV2), in a lepidopteran species, the cotton bollworm, Helicoverpa armigera (Hubner). Here, we describe the protocols that are currently used to study the effect of HaDV2 on its host. First, we establish a HaDV2-free cotton bollworm colony from a single breeding pair. Then, we orally inoculate some neonate larval offspring with HaDV2-containing filtered liquid to produce two colonies with the same genetic background: one HaDV2-infected, the other uninfected. A protocol to compare life table parameters (e.g., larval, pupal, and adult periods and fecundity) between the HaDV2-infected and -uninfected individuals is also presented, as are the protocols for determining the host-tissue distribution and transmission efficiency of HaDV2. These protocols would also be suitable for investigating the effects of other orally transmitted viruses on their insect hosts, lepidopteran hosts in particular.
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Affiliation(s)
- Xianming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences
| | | | - He Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences;
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26
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Bartenhagen C, Fischer U, Korn K, Pfister SM, Gombert M, Chen C, Okpanyi V, Hauer J, Rinaldi A, Bourquin JP, Eckert C, Hu J, Ensser A, Dugas M, Borkhardt A. Infection as a cause of childhood leukemia: virus detection employing whole genome sequencing. Haematologica 2017; 102:e179-e183. [PMID: 28154091 DOI: 10.3324/haematol.2016.155382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Klaus Korn
- Institute for Clinical and Molecular Virology, University Hospital, Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Cai Chen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.,Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Vera Okpanyi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Anna Rinaldi
- Pediatric Oncology, University Children's Hospital Zurich, Switzerland
| | | | - Cornelia Eckert
- Department of Pediatrics, Division of Oncology and Hematology, Charité Berlin, Germany
| | - Jianda Hu
- Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital, Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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27
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VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology 2017; 503:21-30. [PMID: 28110145 DOI: 10.1016/j.virol.2017.01.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 01/21/2023]
Abstract
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
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28
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Bullman S, Meyerson M, Kostic AD. Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 12:217-244. [PMID: 27959634 DOI: 10.1146/annurev-pathol-012615-044305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Established infectious agents continue to be a major cause of human morbidity and mortality worldwide. However, the causative agent remains unknown for a wide range of diseases; many of these are suspected to be attributable to yet undiscovered microorganisms. The advent of unbiased high-throughput sequencing and bioinformatics has enabled rapid identification and molecular characterization of known and novel infectious agents in human disease. An exciting era of microbe discovery, now under way, holds great promise for the improvement of global health via the development of antimicrobial therapies, vaccination strategies, targeted public health measures, and probiotic-based preventions and therapies. Here, we review the history of pathogen discovery, discuss improvements and clinical applications for the detection of microbially associated diseases, and explore the challenges and strategies for establishing causation in human disease.
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Affiliation(s)
- Susan Bullman
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215; , .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215; , .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.,Harvard Medical School, Boston, Massachusetts 02115
| | - Aleksandar D Kostic
- Research Division, Joslin Diabetes Center, Boston, Massachusetts 02215; .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
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29
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Fawaz M, Vijayakumar P, Mishra A, Gandhale PN, Dutta R, Kamble NM, Sudhakar SB, Roychoudhary P, Kumar H, Kulkarni DD, Raut AA. Duck gut viral metagenome analysis captures snapshot of viral diversity. Gut Pathog 2016; 8:30. [PMID: 27284287 PMCID: PMC4899906 DOI: 10.1186/s13099-016-0113-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/30/2016] [Indexed: 11/18/2022] Open
Abstract
Background Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. Methods To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. Result In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. Conclusion This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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Affiliation(s)
- Mohammed Fawaz
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Periyasamy Vijayakumar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Anamika Mishra
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Pradeep N Gandhale
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Rupam Dutta
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Nitin M Kamble
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Shashi B Sudhakar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Parimal Roychoudhary
- College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Aizawl, Mizoram India
| | - Himanshu Kumar
- Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Diwakar D Kulkarni
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Ashwin Ashok Raut
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
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30
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Alves JMP, de Oliveira AL, Sandberg TOM, Moreno-Gallego JL, de Toledo MAF, de Moura EMM, Oliveira LS, Durham AM, Mehnert DU, Zanotto PMDA, Reyes A, Gruber A. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. Front Microbiol 2016; 7:269. [PMID: 26973638 PMCID: PMC4777721 DOI: 10.3389/fmicb.2016.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.
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Affiliation(s)
- João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - André L de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Tatiana O M Sandberg
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - Marcelo A F de Toledo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Elisabeth M M de Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Liliane S Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São PauloSão Paulo, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São PauloSão Paulo, Brazil
| | - Alan M Durham
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo São Paulo, Brazil
| | - Dolores U Mehnert
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Paolo M de A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los AndesBogotá, Colombia; Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint LouisMO, USA
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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31
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Abstract
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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32
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Kajon AE, Lamson D. 31st annual meeting of the Pan American Society for Clinical Virology and Clinical Virology Symposium, Daytona Beach, FL, USA, 26–29 April 2015. Future Virol 2015. [DOI: 10.2217/fvl.15.89] [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
The 31st annual meeting of the Pan American Society for Clinical Virology and Clinical Virology Symposium was held in Daytona Beach, FL, USA on 26–29 April 2015. This year the symposium was jointly cosponsored by the American Society for Microbiology, the France Foundation and the Pan American Society for Clinical Virology. The event was chaired by Steven Specter and Richard Hodinka.
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Affiliation(s)
- Adriana E Kajon
- Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr., SE, Albuquerque, NM 87108–5127, USA
| | - Daryl Lamson
- Wadsworth Center, New York State Department of Health (NYSDOH), David Axelrod Institute, 120 New Scotland Ave., Albany, NY 12208, USA
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33
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Abstract
Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.
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34
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Rosseel T, Ozhelvaci O, Freimanis G, Van Borm S. Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 2015; 222:72-80. [PMID: 26025457 DOI: 10.1016/j.jviromet.2015.05.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/28/2015] [Accepted: 05/22/2015] [Indexed: 12/27/2022]
Abstract
Viral metagenomic approaches are increasingly being used for viral discovery. Various strategies are applied to enrich viral sequences, but there is often a lack of knowledge about their effective influence on the viral discovery sensitivity. We evaluate some convenient and widely used approaches for RNA virus discovery in clinical samples in order to reveal their sensitivity and potential bias introduced by the enrichment or amplifications steps. An RNA virus was artificially spiked at a fixed titer in serum and lung tissue, respectively, low and high nucleic acid content matrices. For serum, a simple DNase treatment on the RNA extract gave the maximum gain in proportion of viral sequences (83×), and a subsequent ribosomal RNA removal nearly doubled once more the proportion of viral sequences. For lung tissue, a ribosomal RNA depletion step on the RNA extract had the biggest gain in proportion of viral sequences (32×). We show also that direct sequencing of cDNA is recommended above an extra random PCR amplification step, and a that the virion enrichment strategy (filtration and nuclease treatment) has a beneficial effect for sequencing-based virus discovery. Our findings provide sample-dependent guidelines for targeted virus discovery strategies.
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Affiliation(s)
- Toon Rosseel
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Orkun Ozhelvaci
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium
| | - Graham Freimanis
- The Pirbright Institute, Ash Rd, Woking GU24 0NF, United Kingdom
| | - Steven Van Borm
- Veterinary and Agrochemical Research Centre CODA/CERVA, Groeselenberg 99, Brussels Belgium.
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35
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Jensen RH, Mollerup S, Mourier T, Hansen TA, Fridholm H, Nielsen LP, Willerslev E, Hansen AJ, Vinner L. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS One 2015; 10:e0122636. [PMID: 25853649 PMCID: PMC4390369 DOI: 10.1371/journal.pone.0122636] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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Affiliation(s)
- Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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36
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Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 2014; 213:139-46. [PMID: 25497414 PMCID: PMC4344864 DOI: 10.1016/j.jviromet.2014.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/29/2022]
Abstract
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Edward T Mee
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Sophie Collot-Teixeira
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Rob Anderson
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Silke Schepelmann
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Philip D Minor
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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Taboada B, Espinoza MA, Isa P, Aponte FE, Arias-Ortiz MA, Monge-Martínez J, Rodríguez-Vázquez R, Díaz-Hernández F, Zárate-Vidal F, Wong-Chew RM, Firo-Reyes V, del Río-Almendárez CN, Gaitán-Meza J, Villaseñor-Sierra A, Martínez-Aguilar G, Salas-Mier MDC, Noyola DE, Pérez-Gónzalez LF, López S, Santos-Preciado JI, Arias CF. Is there still room for novel viral pathogens in pediatric respiratory tract infections? PLoS One 2014; 9:e113570. [PMID: 25412469 PMCID: PMC4239085 DOI: 10.1371/journal.pone.0113570] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/24/2014] [Indexed: 11/30/2022] Open
Abstract
Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Marco A. Espinoza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Fernando E. Aponte
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | | | | | | | - Rosa María Wong-Chew
- Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., Mexico
| | | | | | - Jesús Gaitán-Meza
- Nuevo Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | | | | | | | - Daniel E. Noyola
- Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- * E-mail:
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Reconceptualizing major depressive disorder as an infectious disease. BIOLOGY OF MOOD & ANXIETY DISORDERS 2014; 4:10. [PMID: 25364500 PMCID: PMC4215336 DOI: 10.1186/2045-5380-4-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/09/2014] [Indexed: 12/11/2022]
Abstract
In this article, I argue for a reconceptualization of major depressive disorder (major depression) as an infectious disease. I suggest that major depression may result from a parasitic, bacterial, or viral infection and present examples that illustrate possible pathways by which these microorganisms could contribute to the etiology of major depression. I also argue that the reconceptualization of the human body as an ecosystem for these microorganisms and the human genome as a host for non-human exogenous sequences may greatly amplify the opportunity to discover genetic links to the illness. Deliberately speculative, this article is intended to stimulate novel research approaches and expand the circle of researchers taking aim at this vexing illness.
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Takeuchi F, Sekizuka T, Yamashita A, Ogasawara Y, Mizuta K, Kuroda M. MePIC, metagenomic pathogen identification for clinical specimens. Jpn J Infect Dis 2014; 67:62-5. [PMID: 24451106 DOI: 10.7883/yoken.67.62] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Next-generation DNA sequencing technologies have led to a new method of identifying the causative agents of infectious diseases. The analysis comprises three steps. First, DNA/RNA is extracted and extensively sequenced from a specimen that includes the pathogen, human tissue and commensal microorganisms. Second, the sequenced reads are matched with a database of known sequences, and the organisms from which the individual reads were derived are inferred. Last, the percentages of the organisms' genomic sequences in the specimen (i.e., the metagenome) are estimated, and the pathogen is identified. The first and last steps have become easy due to the development of benchtop sequencers and metagenomic software. To facilitate the middle step, which requires computational resources and skill, we developed a cloud-computing pipeline, MePIC: "Metagenomic Pathogen Identification for Clinical specimens." In the pipeline, unnecessary bases are trimmed off the reads, and human reads are removed. For the remaining reads, similar sequences are searched in the database of known nucleotide sequences. The search is drastically sped up by using a cloud-computing system. The webpage interface can be used easily by clinicians and epidemiologists. We believe that the use of the MePIC pipeline will promote metagenomic pathogen identification and improve the understanding of infectious diseases.
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Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F. A survey of overlooked viral infections in biological experiment systems. PLoS One 2014; 9:e105348. [PMID: 25144530 PMCID: PMC4140767 DOI: 10.1371/journal.pone.0105348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/23/2014] [Indexed: 12/04/2022] Open
Abstract
It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
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Affiliation(s)
- Yajing Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Hui Wang
- NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kunhan Xu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Peixiang Ni
- BGI-Tianjin, Airport Economic Area, Tianjin, China
| | - Huan Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Jinmin Ma
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
| | - Huanming Yang
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Feng Xu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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Elevated levels of circulating DNA in cardiovascular disease patients: metagenomic profiling of microbiome in the circulation. PLoS One 2014; 9:e105221. [PMID: 25133738 PMCID: PMC4136842 DOI: 10.1371/journal.pone.0105221] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/19/2014] [Indexed: 01/21/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide. An expanding body of evidence supports the role of human microbiome in the establishment of CVDs and, this has gained much attention recently. This work was aimed to study the circulating human microbiome in CVD patients and healthy subjects. The levels of circulating cell free DNA (circDNA) was higher in CVD patients (n = 80) than in healthy controls (n = 40). More specifically, the relative levels of circulating bacterial DNA and the ratio of 16S rRNA/β-globin gene copy numbers were higher in the circulation of CVD patients than healthy individuals. In addition, we found a higher circulating microbial diversity in CVD patients (n = 3) in comparison to healthy individuals (n = 3) by deep shotgun sequencing. At the phylum level, we observed a dominance of Actinobacteria in CVD patients, followed by Proteobacteria, in contrast to that in healthy controls, where Proteobacteria was predominantly enriched, followed by Actinobacteria. The circulating virome in CVD patients was enriched with bacteriophages with a preponderance of Propionibacterium phages, followed by Pseudomonas phages and Rhizobium phages in contrast to that in healthy individuals, where a relatively greater abundance of eukaryotic viruses dominated by Lymphocystis virus (LCV) and Torque Teno viruses (TTV) was observed. Thus, the release of bacterial and viral DNA elements in the circulation could play a major role leading to elevated circDNA levels in CVD patients. The increased circDNA levels could be either the cause or consequence of CVD incidence, which needs to be explored further.
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Zhang B, Tang C, Yue H, Ren Y, Song Z. Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 2014; 95:1603-1611. [DOI: 10.1099/vir.0.063743-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.
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Affiliation(s)
- Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Yupeng Ren
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Zhigang Song
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
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Abstract
We recently introduced the concept of the infectome as a means of studying all infectious factors which contribute to the development of autoimmune disease. It forms the infectious part of the exposome, which collates all environmental factors contributing to the development of disease and studies the sum total of burden which leads to the loss of adaptive mechanisms in the body. These studies complement genome-wide association studies, which establish the genetic predisposition to disease. The infectome is a component which spans the whole life and may begin at the earliest stages right up to the time when the first symptoms manifest, and may thus contribute to the understanding of the pathogenesis of autoimmunity at the prodromal/asymptomatic stages. We provide practical examples and research tools as to how we can investigate disease-specific infectomes, using laboratory approaches employed from projects studying the “immunome” and “microbiome”. It is envisioned that an understanding of the infectome and the environmental factors that affect it will allow for earlier patient-specific intervention by clinicians, through the possible treatment of infectious agents as well as other compounding factors, and hence slowing or preventing disease development.
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PhyloFlu, a DNA microarray for determining the phylogenetic origin of influenza A virus gene segments and the genomic fingerprint of viral strains. J Clin Microbiol 2013; 52:803-13. [PMID: 24353006 DOI: 10.1128/jcm.03134-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recent evidence suggests that most influenza A virus gene segments can contribute to the pathogenicity of the virus. In this regard, the hemagglutinin (HA) subtype of the circulating strains has been closely surveyed, but the reassortment of internal gene segments is usually not monitored as a potential source of an increased pathogenicity. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origins of the eight segments of the influenza virus genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 neuraminidase (NA) subtypes. Viral genetic material was amplified by reverse transcription-PCR (RT-PCR) with primers specific to the conserved 5' and 3' ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3 labeling. The microarray unambiguously determined the clades for all eight influenza virus genes in 74% (28/38) of the samples. The microarray was validated with reference strains from different animal origins, as well as from human, swine, and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed for the determination of the time and place that strains with the same genomic pattern were previously reported. PhyloFlu is useful for characterizing and surveying the genetic diversity and variation of animal viruses circulating in different environmental niches and for obtaining a more detailed surveillance and follow up of reassortant events that can potentially modify virus pathogenicity.
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Li L, McGraw S, Zhu K, Leutenegger CM, Marks SL, Kubiski S, Gaffney P, Dela Cruz FN, Wang C, Delwart E, Pesavento PA. Circovirus in tissues of dogs with vasculitis and hemorrhage. Emerg Infect Dis 2013; 19:534-41. [PMID: 23628223 PMCID: PMC3647419 DOI: 10.3201/eid1904.121390] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We characterized the complete genome of a novel dog circovirus (DogCV) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. DogCV was detected by PCR in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. Co-infection with other canine pathogens was detected for 13/19 (68%) DogCV-positive dogs with diarrhea. DogCV capsid proteins from different dogs varied by up to 8%. In situ hybridization and transmission electron microscopy detected DogCV in the lymph nodes and spleens of 4 dogs with vascular compromise and histiocytic inflammation. The detection of a circovirus in tissues of dogs expands the known tropism of these viruses to a second mammalian host. Our results indicate that circovirus, alone or in co-infection with other pathogens, might contribute to illness and death in dogs.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, California, USA
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Routh A, Johnson JE. Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data. Nucleic Acids Res 2013; 42:e11. [PMID: 24137010 PMCID: PMC3902915 DOI: 10.1093/nar/gkt916] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5' end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3' end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
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Affiliation(s)
- Andrew Routh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Wang H, Xie J, Shreeve TG, Ma J, Pallett DW, King LA, Possee RD. Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera). PLoS One 2013; 8:e74508. [PMID: 24058580 PMCID: PMC3776811 DOI: 10.1371/journal.pone.0074508] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/02/2013] [Indexed: 12/23/2022] Open
Abstract
We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees (Bombuspascuorum) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroadestructor virus-1 (VDV1) and Deformed wing virus (DWV) genomic sequences were obtained for A. mellifera but not B. pascuorum. Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5’-DWV-VDV1-DWV-3’. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt) in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences) and within-population (dataset of this study) levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10%) were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.
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Affiliation(s)
- Hui Wang
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
- * E-mail:
| | - Jiazheng Xie
- Beijing Genome Institute, Yantian District, Shenzhen, China
| | - Tim G. Shreeve
- Department of Biological and Medical Sciences, Oxford Brooks University, Oxford, United Kingdom
| | - Jinmin Ma
- Beijing Genome Institute, Yantian District, Shenzhen, China
| | - Denise W. Pallett
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
| | - Linda A. King
- Department of Biological and Medical Sciences, Oxford Brooks University, Oxford, United Kingdom
| | - Robert D. Possee
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
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Karlsson OE, Hansen T, Knutsson R, Löfström C, Granberg F, Berg M. Metagenomic Detection Methods in Biopreparedness Outbreak Scenarios. Biosecur Bioterror 2013; 11 Suppl 1:S146-57. [DOI: 10.1089/bsp.2012.0077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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50
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Affiliation(s)
- Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
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