151
|
Song H, Lim Y, Im H, Bae JM, Kang GH, Ahn J, Baek D, Kim TY, Yoon SS, Koh Y. Interpretation of EBV infection in pan-cancer genome considering viral life cycle: LiEB (Life cycle of Epstein-Barr virus). Sci Rep 2019; 9:3465. [PMID: 30837539 PMCID: PMC6401378 DOI: 10.1038/s41598-019-39706-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
We report a novel transcriptomic analysis workflow called LiEB (Life cycle of Epstein-Barr virus) to characterize distributions of oncogenic virus, Epstein-Barr virus (EBV) infection in human tumors. We analyzed 851 The Cancer Genome Atlas whole-transcriptome sequencing (WTS) data to investigate EBV infection by life cycle information using three-step LiEB workflow: 1) characterize virus infection generally; 2) align transcriptome sequences against a hybrid human-EBV genome, and 3) quantify EBV gene expression. Our results agreed with EBV infection status of public cell line data. Analysis in stomach adenocarcinoma identified EBV-positive cases involving PIK3CA mutations and/or CDKN2A silencing with biologically more determination, compared to previous reports. In this study, we found that a small number of colorectal adenocarcinoma cases involved with EBV lytic gene expression. Expression of EBV lytic genes was also observed in 3% of external colon cancer cohort upon WTS analysis. Gene set enrichment analysis showed elevated expression of genes related to E2F targeting and interferon-gamma responses in EBV-associated tumors. Finally, we suggest that interpretation of EBV life cycle is essential when analyzing its infection in tumors, and LiEB provides high capability of detecting EBV-positive tumors. Observation of EBV lytic gene expression in a subset of colon cancers warrants further research.
Collapse
Affiliation(s)
- Hyojin Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yoojoo Lim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hogune Im
- Genome Opinion, Ansan, Gyeonggi-do, Republic of Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Junhak Ahn
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Daehyun Baek
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Youngil Koh
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| |
Collapse
|
152
|
Pichon M, Burucoa C. Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases. Healthcare (Basel) 2019; 7:E34. [PMID: 30813360 PMCID: PMC6473412 DOI: 10.3390/healthcare7010034] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori is a bacterium that selectively infects the gastric epithelium of half of the world population. The microbiome, community of microorganisms gained major interest over the last years, due to its modification associated to health and disease states. Even if most of these descriptions have focused on chronic disorders, this review describes the impact of the intestinal bacterial microbiome on host response to Helicobacter associated diseases. Microbiome has a direct impact on host cells, major barrier of the gastro-intestinal tract, but also an indirect impact on immune system stimulation, by enhancing or decreasing non-specific or adaptive response. In microbial infections, especially in precancerous lesions induced by Helicobacter pylori infection, these modifications could lead to different outcome. Associated to data focusing on the microbiome, transcriptomic analyses of the eukaryote response would lead to a complete understanding of these complex interactions and will allow to characterize innovative biomarkers and personalized therapies.
Collapse
Affiliation(s)
- Maxime Pichon
- Bacteriology and Infection Control Laboratory, Infectious Agents Department, University Hospital of Poitiers, 86021 Poitiers, France.
- Laboratoire Inflammation, Tissus Épithéliaux et Cytokines, EA 4331, Faculté de Médecine et de Pharmacie, University of Poitiers, 86022 Poitiers, France.
| | - Christophe Burucoa
- Bacteriology and Infection Control Laboratory, Infectious Agents Department, University Hospital of Poitiers, 86021 Poitiers, France.
- Laboratoire Inflammation, Tissus Épithéliaux et Cytokines, EA 4331, Faculté de Médecine et de Pharmacie, University of Poitiers, 86022 Poitiers, France.
| |
Collapse
|
153
|
Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, Porter N, Martens E, O'Connell R, Jacob V, Scherl E, Crawford C, Stephens WZ, Casjens SR, Longman RS, Round JL. Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis. Cell Host Microbe 2019; 25:285-299.e8. [PMID: 30763538 PMCID: PMC6885004 DOI: 10.1016/j.chom.2019.01.008] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/23/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023]
Abstract
Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.
Collapse
Affiliation(s)
- Lasha Gogokhia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kate Buhrke
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rickesha Bell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Brenden Hoffman
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - D Garrett Brown
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Christin Hanke-Gogokhia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John F Valentine
- Department of Internal Medicine, Division of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nathan Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ryan O'Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Vinita Jacob
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ellen Scherl
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Carl Crawford
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sherwood R Casjens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Randy S Longman
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| |
Collapse
|
154
|
Calvario A, Foti C, Scarasciulli M, Romita P, Eliassen E, Marzullo A, Colacicco AM, Miragliotta G. Leukocytoclastic Vasculitis Associated with HHV6-A/ciHHV6-A and HHV6-B Coinfection in an Immunocompetent Woman. Endocr Metab Immune Disord Drug Targets 2019; 19:221-225. [DOI: 10.2174/1871530318666181106153758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 09/19/2018] [Accepted: 10/26/2018] [Indexed: 01/08/2023]
Abstract
Background and Objective: Leukocytoclastic vasculitis (LCV) is a small vessel vasculitis that can be limited to the skin but may also affect other organs. Often, its cause is unknown. LCV has previously been reported to occur with the reactivation of human herpesvirus 6 (HHV-6). Here, we report a second instance of HHV-6 reactivation in a 43-year-old woman with idiopathic cutaneous LCV. </P><P> Case Description: In this case, the patient was immunocompetent, and testing revealed that she had inherited chromosomally integrated human herpesvirus 6 variant A (iciHHV6-A) with a parallel skin infection of HHV-6B. The integrated ciHHV-6A strain was found to be transcriptionally active in the blood, while HHV-6B late antigen was detected in a skin biopsy. The patient’s rash was not accompanied by fever nor systemic symptoms and resolved over four weeks without any therapeutic intervention.Conclusion:In light of the transcriptional activity documented in our case, further examination of a possible role for HHV-6 in the etiology of LCV is warranted.
Collapse
Affiliation(s)
- Agata Calvario
- Microbiology and Virology Unit, Policlinico University Hospital of Bari, Italy
| | - Caterina Foti
- Dermatological Clinic, Department of Biomedical Science and Human Oncology, University of Bari, Italy
| | - Maria Scarasciulli
- Microbiology and Virology Unit, Policlinico University Hospital of Bari, Italy
| | - Paolo Romita
- Dermatological Clinic, Department of Biomedical Science and Human Oncology, University of Bari, Italy
| | - Eva Eliassen
- HHV-6 Foundation, Santa Barbara, CA, United States
| | - Andrea Marzullo
- Department of Emergency and Transplant Organ, University of Bari, Italy
| | | | | |
Collapse
|
155
|
Cladel NM, Jiang P, Li JJ, Peng X, Cooper TK, Majerciak V, Balogh KK, Meyer TJ, Brendle SA, Budgeon LR, Shearer DA, Munden R, Cam M, Vallur R, Christensen ND, Zheng ZM, Hu J. Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models. Emerg Microbes Infect 2019; 8:1108-1121. [PMID: 31340720 PMCID: PMC6713970 DOI: 10.1080/22221751.2019.1637072] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/20/2019] [Indexed: 12/13/2022]
Abstract
Human papillomaviruses (HPV) contribute to most cervical cancers and are considered to be sexually transmitted. However, papillomaviruses are often found in cancers of internal organs, including the stomach, raising the question as to how the viruses gain access to these sites. A possible connection between blood transfusion and HPV-associated disease has not received much attention. Here we show, in rabbit and mouse models, that blood infected with papillomavirus yields infections at permissive sites with detectable viral DNA, RNA transcripts, and protein products. The rabbit skin tumours induced via blood infection displayed decreased expression of SLN, TAC1, MYH8, PGAM2, and APOBEC2 and increased expression of SDRC7, KRT16, S100A9, IL36G, and FABP9, as seen in tumours induced by local infections. Furthermore, we demonstrate that blood from infected mice can transmit the infection to uninfected animals. Finally, we demonstrate the presence of papillomavirus infections and virus-induced hyperplasia in the stomach tissues of animals infected via the blood. These results indicate that blood transmission could be another route for papillomavirus infection, implying that the human blood supply, which is not screened for papillomaviruses, could be a potential source of HPV infection as well as subsequent cancers in tissues not normally associated with the viruses.
Collapse
Affiliation(s)
- Nancy M. Cladel
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pengfei Jiang
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, National Cancer Institute, NIH, Frederick, MD, USA
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Jingwei J. Li
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Xuwen Peng
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA , USA
| | - Timothy K. Cooper
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, Frederick, MD, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, National Cancer Institute, NIH, Frederick, MD, USA
| | - Karla K. Balogh
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Thomas J. Meyer
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sarah A. Brendle
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lynn R. Budgeon
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Debra A. Shearer
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Regina Munden
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA , USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Raghavan Vallur
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Neil D. Christensen
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, National Cancer Institute, NIH, Frederick, MD, USA
| | - Jiafen Hu
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| |
Collapse
|
156
|
Van Belleghem JD, Dąbrowska K, Vaneechoutte M, Barr JJ, Bollyky PL. Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Viruses 2018; 11:E10. [PMID: 30585199 PMCID: PMC6356784 DOI: 10.3390/v11010010] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023] Open
Abstract
The human body is host to large numbers of bacteriophages (phages)⁻a diverse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the diverse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.
Collapse
Affiliation(s)
- Jonas D Van Belleghem
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland.
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
157
|
Abstract
Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus (Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of known Gamma HPV types and suggest that WHIM syndrome patients are uniquely susceptible to Gamma HPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusual Gamma HPV skin warts observed in WHIM patients. Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samples from 48 patients with rare genetic immunodeficiencies, including patients with warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, or epidermodysplasia verruciformis (EV). Their profiles were compared with the profiles of swabs from 14 healthy adults and warts from 6 immunologically normal children. Individual patients were typically infected with multiple HPV types; up to 26 different types were isolated from a single patient (multiple anatomical sites, one time point). Among these, we identified the complete genomes of 83 previously unknown HPV types and 35 incomplete genomes representing possible additional new types. HPV types in the genus Gammapapillomavirus were common in WHIM patients, whereas EV patients mainly shed HPVs from the genus Betapapillomavirus. Preliminary evidence based on three WHIM patients treated with plerixafor, a leukocyte mobilizing agent, suggest that longer-term therapy may correlate with decreased HPV diversity and increased predominance of HPV types associated with childhood skin warts. IMPORTANCE Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus (Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of known Gamma HPV types and suggest that WHIM syndrome patients are uniquely susceptible to Gamma HPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusual Gamma HPV skin warts observed in WHIM patients.
Collapse
|
158
|
Proal A, Marshall T. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity. Front Pediatr 2018; 6:373. [PMID: 30564562 PMCID: PMC6288442 DOI: 10.3389/fped.2018.00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.
Collapse
Affiliation(s)
- Amy Proal
- Autoimmunity Research Foundation, Thousand Oaks, CA, United States
| | | |
Collapse
|
159
|
Møller-Olsen C, Ho SFS, Shukla RD, Feher T, Sagona AP. Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells. Sci Rep 2018; 8:17559. [PMID: 30510202 PMCID: PMC6277420 DOI: 10.1038/s41598-018-35859-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/09/2018] [Indexed: 01/13/2023] Open
Abstract
Bacterial infections can be treated with bacteriophages that show great specificity towards their bacterial host and can be genetically modified for different applications. However, whether and how bacteriophages can kill intracellular bacteria in human cells remains elusive. Here, using CRISPR/Cas selection, we have engineered a fluorescent bacteriophage specific for E. coli K1, a nosocomial pathogen responsible for urinary tract infections, neonatal meningitis and sepsis. By confocal and live microscopy, we show that engineered bacteriophages K1F-GFP and E. coli EV36-RFP bacteria displaying the K1 capsule, enter human cells via phagocytosis. Importantly, we show that bacteriophage K1F-GFP efficiently kills intracellular E. coli EV36-RFP in T24 human urinary bladder epithelial cells. Finally, we provide evidence that bacteria and bacteriophages are degraded by LC3-associated phagocytosis and xenophagy.
Collapse
Affiliation(s)
| | - Siu Fung Stanley Ho
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Ranti Dev Shukla
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamas Feher
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
| |
Collapse
|
160
|
Greninger AL, Naccache SN. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 2018; 3:643-653. [PMID: 31639732 DOI: 10.1373/jalm.2018.026120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today. CONTENT Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation. SUMMARY Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.
Collapse
Affiliation(s)
| | - Samia N Naccache
- Department of Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| |
Collapse
|
161
|
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management. Viruses 2018; 10:v10110633. [PMID: 30441786 PMCID: PMC6266913 DOI: 10.3390/v10110633] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.
Collapse
|
162
|
Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
Collapse
Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
| |
Collapse
|
163
|
Abstract
Ambitious efforts to catalog viruses across the globe may facilitate our understanding of viral communities and ecology, boost infectious disease diagnostics and surveillance, and spur new therapeutics. Charles Schmidt investigates.
Collapse
|
164
|
Characterization of dog serum virome from Northeastern Brazil. Virology 2018; 525:192-199. [PMID: 30292963 DOI: 10.1016/j.virol.2018.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 11/24/2022]
Abstract
Domestic dogs share habitats with human, a fact that makes them a potential source of zoonotic viruses. Moreover, knowledge regarding possible bloodborne pathogens is important due to the increasing application of blood transfusion in dogs. In the present study, we evaluated the serum virome of 520 dogs using throughput sequencing (HTS). The serum samples were pooled and sequenced using an Illumina MiSeq platform. Our unbiased method identified prevalent canine pathogens as canine protoparvovirus 1 (canine parvovirus 2), undersearched agents as canine bocaparvovirus 1 (minute virus of canines) and canine circovirus, circular viruses closely related to viruses recently found in human samples, and new parvovirus and anelloviruses. The dog virome described in the present work furthers the knowledge concerning the viral population in domestic animals. The present data includes information regarding viral agents that are potentially transmitted through blood transfusion among dogs.
Collapse
|
165
|
Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, Liu Q, Walters RG, Lin K, Ju J, Korneliussen T, Yang MA, Fu Q, Wang J, Zhou L, Krogh A, Zhang H, Wang W, Chen Z, Cai Z, Yin Y, Yang H, Mao M, Shendure J, Wang J, Albrechtsen A, Jin X, Nielsen R, Xu X. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell 2018; 175:347-359.e14. [DOI: 10.1016/j.cell.2018.08.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/12/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023]
|
166
|
Colson P, Ominami Y, Hisada A, La Scola B, Raoult D. Giant mimiviruses escape many canonical criteria of the virus definition. Clin Microbiol Infect 2018; 25:147-154. [PMID: 30267933 DOI: 10.1016/j.cmi.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/10/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND The discovery of mimivirus in 2003 prompted the quest for other giant viruses of amoebae. Mimiviruses and their relatives were found to differ considerably from other viruses. Their study led to major advances in virology and evolutionary biology. AIMS We summarized the widening gap between mimiviruses and other viruses. SOURCES We collected data from articles retrieved from PubMed using as keywords 'giant virus', 'mimivirus' and 'virophage', as well as quoted references from these articles. CONTENT Data accumulated during the last 15 years on mimiviruses and other giant viruses highlight that there is a quantum leap between these infectious agents, the complexity of which is similar to that of intracellular microorganisms, and classical viruses. Notably, in addition to their giant structures and genomes, giant viruses have abundant gene repertoires with genes unique in the virosphere, including a tremendous set of translation components. The viruses contain hundreds of proteins and many transcripts. They share a core of central and ancient proteins but their genome sequences display a substantial level of mosaicism. Finally, mimiviruses have a specific mobilome, including virophages that can integrate into their genomes, and against which they can defend themselves through integration of short fragments of the DNA of these invaders. IMPLICATIONS Mimiviruses and subsequently discovered giant viruses have changed the virus paradigm and contradict many virus definition criteria delineated for classical viruses. The major cellular hallmark that is still lacking in giant viruses is the ribosome, including both ribosomal protein and RNA encoding genes, which makes them bona fide microbes without ribosomes.
Collapse
Affiliation(s)
- P Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Y Ominami
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, Minato-ku, Tokyo, Japan
| | - A Hisada
- Hitachi Ltd, Research & Development Group, Saitama, Japan
| | - B La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - D Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
| |
Collapse
|
167
|
Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality. mSystems 2018; 3:mSystems00081-18. [PMID: 30271878 PMCID: PMC6156273 DOI: 10.1128/msystems.00081-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022] Open
Abstract
Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status. Epstein-Barr virus (EBV) is convincingly associated with gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. To test the hypothesis that there are additional cancer types with high prevalence of EBV, we determined EBV viral expression in all the Cancer Genome Atlas Project (TCGA) mRNA sequencing (mRNA-seq) samples (n = 10,396) from 32 different tumor types. We found that EBV was present in gastric adenocarcinoma and lymphoma, as expected, and was also present in >5% of samples in 10 additional tumor types. For most samples, EBV transcript levels were low, which suggests that EBV was likely present due to infected infiltrating B cells. In order to determine if there was a difference in the B-cell populations, we assembled B-cell receptors for each sample and found B-cell receptor abundance (P ≤ 1.4 × 10−20) and diversity (P ≤ 8.3 × 10−27) were significantly higher in EBV-positive samples. Moreover, diversity was independent of B-cell abundance, suggesting that the presence of EBV was associated with an increased and altered B-cell population. IMPORTANCE Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status.
Collapse
|
168
|
Evaluation of the serum virome in calves persistently infected with Pestivirus A, presenting or not presenting mucosal disease. Virus Genes 2018; 54:768-778. [PMID: 30218293 DOI: 10.1007/s11262-018-1599-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/04/2018] [Indexed: 01/20/2023]
Abstract
Bovine viral diarrhea virus 1, reclassified as Pestivirus A, causes an economically important cattle disease that is distributed worldwide. Pestivirus A may cause persistent infection in that calves excrete the virus throughout their lives, spreading the infection in the herd. Many persistently infected (PI) calves die in the first 2 years of life from mucosal disease (MD) or secondary infections, probably as a consequence of virus-induced immune depression. Here, high-throughput sequencing (HTS) was applied for evaluation of the total virome in sera of (i) PI calves displaying clinically apparent MD (n = 8); (ii) PI calves with no signs of MD (n = 8); and (iii) control, Pestivirus A-free calves (n = 8). All the groups were collected at the same time and from the same herd. Serum samples from calves in each of the groups were pooled, submitted to viral RNA/DNA enrichment, and sequenced by HTS. Viral genomes of Pestivirus A, Ungulate erythroparvovirus 1, bosavirus (BosV), and hypothetical circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses were identified. Specific real-time PCR assays were developed to determine the frequency of occurrence of such viruses in each of the groups. The absolute number of distinct viral genomes detected in both PI calf groups was higher than in the control group, as revealed by higher number of reads, contigs, and genomes, representing a wider range of taxons. Genomes representing members of the family Parvoviridae, such as U. erythroparvovirus 1 and BosV, were most frequently detected in all the three groups of calves. Only in MD-affected PI calves, we found two previously unreported Hypothetical single-stranded DNA genomes clustered along with CRESS-DNA viruses. These findings reveal that parvoviruses were the most frequently detected viral genomes in cattle serum; its frequency of detection bears no statistical correlation with the status of calves in relation to Pestivirus A infection, since clinically normal or MD-affected/non-affected PI calves were infected with similar U. erythroparvovirus 1 genome loads. Moreover, MD-affected PI calves were shown to support viremia of CRESS-DNA viral genomes; however, the meaning of such correlation remains to be established.
Collapse
|
169
|
Affiliation(s)
- Giorgio Gallinella
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| |
Collapse
|
170
|
Cuypers L, Pérez AB, Chueca N, Aldamiz-Echevarría T, Alados JC, Martínez-Sapiña AM, Merino D, Pineda JA, Téllez F, Espinosa N, Salméron J, Rivero-Juarez A, Vivancos MJ, Hontañón V, Vandamme AM, García F. Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis. PLoS One 2018; 13:e0201268. [PMID: 30044871 PMCID: PMC6059487 DOI: 10.1371/journal.pone.0201268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
Despite high response rates associated to hepatitis C virus (HCV) treatment, no protective immunity is acquired, allowing for reinfection and continued infectiousness. Distinguishing between relapse and reinfection is crucial for patient counselling and to choose the most appropriate retreatment. Here, refined phylogenetic analysis using multiple genes served to assess genotype and reinfection for 53 patients for whom the virus was sampled before start of therapy and at time of sustained virological response evaluation at week 12. At baseline, genotypes were determined as HCV1a (41.5%), HCV1b (24.5%), HCV4 (18.9%) and HCV3a (15.1%), while six cases revealed to be discordantly assigned by phylogeny and commercial assays. Overall, 60.4% was co-infected with HIV. The large majority was classified as people who inject drugs (78.6%), often co-infected with HIV. Transmission was sexual in seven cases, of which five in HIV-positive men-who-have-sex-with-men. Overall, relapse was defined for 44 patients, while no conclusion was drawn for four patients. Five patients were reinfected with a different HCV strain, of which three with a different genotype, showing that phylogeny is needed not only to determine the genotype, but also to distinguish between relapse and intra-subtype reinfection. Of note, phylogenies are more reliable when longer fragments of the viral genome are being sequenced.
Collapse
Affiliation(s)
- Lize Cuypers
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Belén Pérez
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | - Natalia Chueca
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | | | | | | | - Dolores Merino
- Clinical Microbiology, Hospital Infanta Elena, Huelva, Spain
| | | | - Francisco Téllez
- UGC Enfermedades Infecciosas y Microbiología, Hospital La Línea, AGS Campo de Gibraltar, Cadiz, Spain
| | - Nuria Espinosa
- Clinical Microbiology, Hospital Virgen del Rocío, Sevilla, Spain
| | - Javier Salméron
- Hepatology Unit, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. CIBERehd, Granada, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC). Hospital Universitario Reina Sofía de Córdoba. Universidad de Córdoba, Córdoba, Spain
| | | | - Víctor Hontañón
- Clinical Microbiology, University Hospital La Paz, Madrid, Spain
| | - Anne-Mieke Vandamme
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Féderico García
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| |
Collapse
|
171
|
Abstract
Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined. Polar bears in captivity can be exposed to opportunistic pathogens not present in their natural environments. A 4-month-old polar bear (Ursus maritimus) living in an isolated enclosure with his mother in the Tierpark Berlin, Berlin, Germany, was suffering from severe abdominal pain, mild diarrhea, and loss of appetite and died in early 2017. Histopathology revealed severe hepatic degeneration and necrosis without evidence of inflammation or inclusion bodies, although a viral infection had been suspected on the basis of the clinical signs. We searched for nucleic acids of pathogens by shotgun high-throughput sequencing (HTS) from genomic DNA and cDNA extracted from tissue and blood. We identified a novel Mastadenovirus and assembled a nearly complete genome from the shotgun sequences. Quantitative PCR (qPCR) revealed that viral DNA was present in various concentrations in all tissues examined and that the highest concentrations were found in blood. Viral culture did not yield cytopathic effects, but qPCR suggested that virus replication was sustained for up to three passages. Positive immunofluorescence staining confirmed that the virus was able to replicate in the cells during early passage. Phylogenetic analysis demonstrated that the virus is highly divergent compared to other previously identified Mastadenovirus members and basal to most known viral clades. The virus was found only in the 4-month-old bear and not in other captive polar bears tested. We surmised, therefore, that the polar bear was infected from an unknown reservoir, illustrating that adenoviral diversity remains underestimated and that cross-species transmission of viruses can occur even under conditions of relative isolation. IMPORTANCE Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined.
Collapse
|
172
|
Identification of a novel torque teno mini virus in cerebrospinal fluid from a child with encephalitis. Virol Sin 2018; 32:541-544. [PMID: 29047018 DOI: 10.1007/s12250-017-4042-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Anelloviruses are single-strand circular DNA viruses and ubiquitous within the human population. Although there is no direct evidence, many studies have suggested the anelloviruses may be associated with a variety of diseases. In this study, a novel torque teno mini virus (TTMV) was detected in a child with unexplained encephalitis. The detected virus had a circular genome of 2943 nt in length and 3 open reading frames. It shared 45.4% - 35.9% nucleotide identities with known TTMV species and < 35% with the other species of anellovirus, which suggested it might belong to a new species within the genus Betatorquevirus. Phylogenetic analysis based on the amino acid sequences of ORF1 showed that this virus represented a distinct branch within the diversity of anellovirus. Whether this novel anellovirus strain is associated with encephalitis requires further study.
Collapse
|
173
|
Brito F, Cordey S, Delwart E, Deng X, Tirefort D, Lemoine-Chaduc C, Zdobnov E, Lecompte T, Kaiser L, Waldvogel-Abramowski S, Preynat-Seauve O. Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank. Vox Sang 2018; 113:10.1111/vox.12695. [PMID: 30022500 PMCID: PMC6338525 DOI: 10.1111/vox.12695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/28/2018] [Accepted: 06/25/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND OBJECTIVES Platelet concentrates are frequently transfused to patients with reduced immunity. An exhaustive description of their viral content is needed to prevent unwanted infection. MATERIAL AND METHODS To track viral sequences, a shotgun metagenomics approach was used on a bank of 300 platelets concentrates. Sequences were analysed through the diagnostics-oriented pipeline ezVIR. RESULTS We only observed viruses commonly described in healthy individuals. CONCLUSION Herein is reported the first viral landscape of a platelet concentrates bank.
Collapse
Affiliation(s)
- Francisco Brito
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospitals of Geneva, Switzerland
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA
| | - Diderik Tirefort
- Department of Internal Medicine of Medical Specialties, Faculty of Medicine of Geneva, Switzerland
| | | | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Thomas Lecompte
- Department of Internal Medicine of Medical Specialties, Faculty of Medicine of Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospitals of Geneva, Switzerland
| | - Sophie Waldvogel-Abramowski
- Department of Internal Medicine of Medical Specialties, Faculty of Medicine of Geneva, Switzerland
- Blood Transfusion Center, University Hospitals of Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Internal Medicine of Medical Specialties, Faculty of Medicine of Geneva, Switzerland
| |
Collapse
|
174
|
Lim ES, Rodriguez C, Holtz LR. Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community. MICROBIOME 2018; 6:87. [PMID: 29751830 PMCID: PMC5946436 DOI: 10.1186/s40168-018-0475-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/06/2018] [Indexed: 05/29/2023]
Abstract
Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the existence of an intra-amniotic microbial community and the importance of understanding how the infant gut is populated, we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies using next-generation sequencing methods. Contrary to expectations, the bacterial microbiota of amniotic fluid was indistinguishable from contamination controls. Viral reads were sparse in the amniotic fluid, and we found no evidence of a core viral community across samples.
Collapse
Affiliation(s)
- Efrem S. Lim
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287 USA
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8208, St. Louis, MO 63110 USA
| | - Lori R. Holtz
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8208, St. Louis, MO 63110 USA
| |
Collapse
|
175
|
Freer G, Maggi F, Pifferi M, Di Cicco ME, Peroni DG, Pistello M. The Virome and Its Major Component, Anellovirus, a Convoluted System Molding Human Immune Defenses and Possibly Affecting the Development of Asthma and Respiratory Diseases in Childhood. Front Microbiol 2018; 9:686. [PMID: 29692764 PMCID: PMC5902699 DOI: 10.3389/fmicb.2018.00686] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/23/2018] [Indexed: 12/13/2022] Open
Abstract
The microbiome, a thriving and complex microbial community colonizing the human body, has a broad impact on human health. Colonization is a continuous process that starts very early in life and occurs thanks to shrewd strategies microbes have evolved to tackle a convoluted array of anatomical, physiological, and functional barriers of the human body. Cumulative evidence shows that viruses are part of the microbiome. This part, called virome, has a dynamic composition that reflects what we eat, how and where we live, what we do, our genetic background, and other unpredictable variables. Thus, the virome plays a chief role in shaping innate and adaptive host immune defenses. Imbalance of normal microbial flora is thought to trigger or exacerbate many acute and chronic disorders. A compelling example can be found in the respiratory apparatus, where early-life viral infections are major determinants for the development of allergic diseases, like asthma, and other non-transmissible diseases. In this review, we focus on the virome and, particularly, on Anelloviridae, a recently discovered virus family. Anelloviruses are major components of the virome, present in most, if not all, human beings, where they are acquired early in life and replicate persistently without causing apparent disease. We will discuss how modulation of innate and adaptive immune systems by Anelloviruses can influence the development of respiratory diseases in childhood and provide evidence for the use of Anelloviruses as useful and practical molecular markers to monitor inflammatory processes and immune system competence.
Collapse
Affiliation(s)
- Giulia Freer
- Retrovirus Center, Department of Translational Research, University of Pisa, Pisa, Italy
| | | | - Massimo Pifferi
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Maria E Di Cicco
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Diego G Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Retrovirus Center, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Unit, University Hospital of Pisa, Pisa, Italy
| |
Collapse
|
176
|
Tang KW, Larsson E. Tumour virology in the era of high-throughput genomics. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0265. [PMID: 28893932 PMCID: PMC5597732 DOI: 10.1098/rstb.2016.0265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
With the advent of massively parallel sequencing, oncogenic viruses in tumours can now be detected in an unbiased and comprehensive manner. Additionally, new viruses or strains can be discovered based on sequence similarity with known viruses. Using this approach, the causative agent for Merkel cell carcinoma was identified. Subsequent studies using data from large collections of tumours have confirmed models built during decades of hypothesis-driven and low-throughput research, and a more detailed and comprehensive description of virus-tumour associations have emerged. Notably, large cohorts and high sequencing depth, in combination with newly developed bioinformatical techniques, have made it possible to rule out several suggested virus-tumour associations with a high degree of confidence. In this review we discuss possibilities, limitations and insights gained from using massively parallel sequencing to characterize tumours with viral content, with emphasis on detection of viral sequences and genomic integration events.This article is part of the themed issue 'Human oncogenic viruses'.
Collapse
Affiliation(s)
- Ka-Wei Tang
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| |
Collapse
|
177
|
Strano E, Viana MP, Sorichetta A, Tatem AJ. Mapping road network communities for guiding disease surveillance and control strategies. Sci Rep 2018; 8:4744. [PMID: 29549364 PMCID: PMC5856805 DOI: 10.1038/s41598-018-22969-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/26/2018] [Indexed: 01/19/2023] Open
Abstract
Human mobility is increasing in its volume, speed and reach, leading to the movement and introduction of pathogens through infected travelers. An understanding of how areas are connected, the strength of these connections and how this translates into disease spread is valuable for planning surveillance and designing control and elimination strategies. While analyses have been undertaken to identify and map connectivity in global air, shipping and migration networks, such analyses have yet to be undertaken on the road networks that carry the vast majority of travellers in low and middle income settings. Here we present methods for identifying road connectivity communities, as well as mapping bridge areas between communities and key linkage routes. We apply these to Africa, and show how many highly-connected communities straddle national borders and when integrating malaria prevalence and population data as an example, the communities change, highlighting regions most strongly connected to areas of high burden. The approaches and results presented provide a flexible tool for supporting the design of disease surveillance and control strategies through mapping areas of high connectivity that form coherent units of intervention and key link routes between communities for targeting surveillance.
Collapse
Affiliation(s)
- Emanuele Strano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- German Aerospace Center (DLR), German Remote Sensing Data Center (DFD), Oberpfaffenhofen, D-82234, Wessling, Germany.
| | | | - Alessandro Sorichetta
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Andrew J Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK.
- Flowminder Foundation, Stockholm, Sweden.
| |
Collapse
|
178
|
Abstract
Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagenome sequencing data was successfully generated for samples from 49 participants. Although 16S rDNA sequencing was more sensitive, metagenome sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by metagenome sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses suggested cases of infection with potential pathogens that are often missed during routine urine culture due to species specific growth requirements. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to more comprehensively and quantitatively describe the urinary microbiome.
Collapse
|
179
|
Cao J, Li D. Searching for human oncoviruses: Histories, challenges, and opportunities. J Cell Biochem 2018; 119:4897-4906. [PMID: 29377246 DOI: 10.1002/jcb.26717] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 01/05/2023]
Abstract
Oncoviruses contribute significantly to cancer burden. A century of tumor virological studies have led to the discovery of seven well-accepted human oncoviruses, cumulatively responsible for approximately 15% of human cancer cases. Virus-caused cancers are largely preventable through vaccination. Identifying additional oncoviruses and virus-caused tumors will advance cancer prevention and precision medicine, benefiting affected individuals, and society as a whole. The historic success of finding human oncoviruses has provided a unique lesson for directing new research efforts in the post-sequencing era. Combing the experiences from these pioneer studies with emerging high-throughput techniques will certainly accelerate new discovery and advance our knowledge of the remaining human oncoviruses.
Collapse
Affiliation(s)
- Jian Cao
- Department of Pathology, Yale University, New Haven, Connecticut
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont.,Department of Computer Science, University of Vermont, Burlington, Vermont.,Neuroscience, Behavior, Health Initiative, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, University of Vermont, Burlington, Vermont
| |
Collapse
|
180
|
Zhou C, Liu S, Song W, Luo S, Meng G, Yang C, Yang H, Ma J, Wang L, Gao S, Wang J, Yang H, Zhao Y, Wang H, Zhou X. Characterization of viral RNA splicing using whole-transcriptome datasets from host species. Sci Rep 2018; 8:3273. [PMID: 29459752 PMCID: PMC5818608 DOI: 10.1038/s41598-018-21190-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/31/2018] [Indexed: 01/16/2023] Open
Abstract
RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses.
Collapse
Affiliation(s)
- Chengran Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Wenhui Song
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shiqi Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chentao Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hua Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Liang Wang
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Shan Gao
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Hui Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,The Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China. .,National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
181
|
Roperto S, Russo V, Corrado F, Munday JS, De Falco F, Roperto F. Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries). Transbound Emerg Dis 2018; 65:758-764. [PMID: 29330926 DOI: 10.1111/tbed.12800] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Indexed: 12/13/2022]
Abstract
Blood samples from 65 sheep were tested for the presence of bovine Deltapapillomavirus (δPVs) DNA. The sheep were divided into three groups. Sheep in groups 1 and 2 were from Sardinia and Campania, respectively, and were in contact with cattle and grazed on lands contaminated with bracken fern. Sheep in Group 3 lived in closed pens and had no contact with cattle. These sheep were fed hay that did not contain bracken fern. Bovine δPV E5 DNA was detected in blood from 24 of 27 (89%) sheep in Group 1. A single bovine δPV type was detected in the blood from nine (33%) sheep, including the detection of bovine δPV-1 DNA in four sheep, bovine δPV-2 in four and δPV-13 in one sheep. Two δPV types were detected in 33% of the sheep, and three bovine δPV types were detected in 22% of the sheep. Bovine δPVs were detected in 17 of 20 (85%) sheep from Group 2. The detection rate by a single δPV type was 40% with just δPV-1 DNA amplified from two, just δPV-2 DNA from four, and just δPV-13 DNA from two sheep. Two and three δPVs were detected in 30% and 15%, respectively. All sequenced amplicons showed a 100% identity with papillomaviral E5 DNA deposited in GenBank. Bovine δPV-14 DNA sequences were not detected from any sheep. No bovine δPV DNA was revealed in blood samples from sheep in Group 3. The detection of bovine δPV DNA in the blood of sheep means that sheep may be able to be infected by these PVs. This suggests that bovine δPVs could potentially be a previously unrecognized cause of disease in sheep. Furthermore, it is possible that sheep could act as a reservoir for these viruses.
Collapse
Affiliation(s)
- S Roperto
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Napoli, Italia
| | - V Russo
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Napoli, Italia
| | - F Corrado
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici (Na), Italia
| | - J S Munday
- Pathobiology, Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - F De Falco
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università di Napoli Federico II, Napoli, Italia
| | - F Roperto
- Dipartimento di Biologia, Università di Napoli Federico II, Napoli, Italia
| |
Collapse
|
182
|
Viral Concentration and Amplification from Human Serum Samples Prior to Application of Next-Generation Sequencing Analysis. Methods Mol Biol 2018; 1838:173-188. [PMID: 30128997 DOI: 10.1007/978-1-4939-8682-8_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The protocol presented here allows the isolation, purification, nucleic acid extraction, and amplification of DNA/RNA from viruses present in human sera samples. The method allows the random amplification of the viral genomes present by using a Sequence-Independent, Single-Primer Amplification (SISPA) approach enabling the study of both DNA/RNA viruses. An amplification step is needed, as the concentration of viral DNA/RNA in serum samples is low for direct library preparation. The application of the described protocol guarantees enough randomly amplified double-strand DNA for further library preparation using Nextera XT kit from Illumina.
Collapse
|
183
|
Xu M, Yang Y, Zhou Y, Liu Z, Liu Y, He M. Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens. Transfusion 2017; 58:633-637. [PMID: 29250787 DOI: 10.1111/trf.14455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Many emerging infectious pathogens are well known for existing in healthy blood donors and could be transmitted via blood transfusion or plasma derivatives usage. Therefore, there is an urgent need to discover the pathogens in qualified blood donation to avoid potential threats to blood safety. STUDY DESIGN AND METHODS The objective of this study was to investigate the microbiome that existed in pooled plasma from different manufacturers in Chengdu and Guiyang. Random polymerase chain reaction, large-scale clone sequencing, and bioinformatics were used to investigate the metagenomics and microbiome structure of pooled plasma. Among detected microbiomes, potential pathogens were subsequently identified. RESULT After host DNA cleaning, 551 clones were classified as bacteria; 88 clones were classified as viruses, and four clones were considered to be parasites, respectively. Thirteen kinds of bacteria and two kinds of parasites that might potentially threaten blood safety were identified along with six kinds of nonpathogenic viruses. The infection status of one identified pathogen Coxiella burnetii was evaluated in 1638 plasma samples. The reactive rate of immunoglobulin (Ig)G1 was 1.10% (18/1638), the reactive rate of IgG2 was 0.85% (14/1638), and the reactive rate of IgM was 0.98% (16/1638). CONCLUSION Some pathogens that were already considered as threats to blood safety were discovered in those pooled plasma such as C. burnetii, Orientia tsutsugamushi, and Plasmodium sp. As a result, we should initiate some specific tests in the endemic area on plasma donors to enhance the blood safety in China.
Collapse
Affiliation(s)
- Min Xu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| | - Yashan Yang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| | - Ya Zhou
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| | - Zhiyang Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| | - Yu Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and the Sichuan Blood Safety and Blood Substitute International Science and Technology Cooperation Base, Chengdu, China
| |
Collapse
|
184
|
Hindawi SI, Hashem AM, Damanhouri GA, El-Kafrawy SA, Tolah AM, Hassan AM, Azhar EI. Inactivation of Middle East respiratory syndrome-coronavirus in human plasma using amotosalen and ultraviolet A light. Transfusion 2017; 58:52-59. [PMID: 29239484 PMCID: PMC7169686 DOI: 10.1111/trf.14422] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Middle East respiratory syndrome‐coronavirus (MERS‐CoV) is a novel zoonotic pathogen. Although the potential for MERS‐CoV transmission through blood transfusion is not clear, MERS‐CoV was recognized as a pathogen of concern for the safety of the blood supply especially after its detection in whole blood, serum, and plasma of infected individuals. Here we investigated the efficacy of amotosalen and ultraviolet A light (UVA) to inactivate MERS‐CoV in fresh‐frozen plasma (FFP). STUDY DESIGN AND METHODS Pooled FFP units were spiked with a recent clinical MERS‐CoV isolate. Infectious and genomic viral titers were determined in plasma before and after inactivation with amotosalen/UVA treatment by plaque assay and reverse transcription–quantitative polymerase chain reaction, respectively. In addition, residual replicating or live virus after inactivation was examined by passaging in the permissive Vero E6 cells. RESULTS The mean MERS‐CoV infectious titer in pretreatment samples was 4.67 ± 0.25 log plaque‐forming units (pfu)/mL, which was reduced to undetectable levels after inactivation with amotosalen/UVA demonstrating a mean log reduction of more than 4.67 ± 0.25 pfu/mL. Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/mL in all three passages. CONCLUSION Our data show that amotosalen/UVA treatment is a potent and effective way to inactivate MERS‐CoV infectious particles in FFP to undetectable levels and to minimize the risk of any possible transfusion‐related MERS‐CoV transmission.
Collapse
Affiliation(s)
- Salwa I Hindawi
- Blood Transfusion Services, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghazi A Damanhouri
- Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Clinical Pathology Department, National Liver Institute, Menoufiya University, Shebin El-Kom, Egypt
| | - Ahmed M Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
185
|
Signorini L, Villani S, Ticozzi R, Ambrogi F, Dolci M, Boldorini R, Ciotti M, Ferrante P, Delbue S. Merkel cell polyomavirus DNA in the blood of patients with neurological diseases and healthy controls. Future Virol 2017. [DOI: 10.2217/fvl-2017-0078] [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
Aim: Merkel cell polyomavirus (MCPyV) is the etiological agent of Merkel cell carcinoma. Its genome has been detected in anatomic districts from healthy and ill subjects. Data regarding the MCPyV DNAemia in neurological patients are lacking. Materials & methods: Blood was obtained from 129 neurological patients and 181 controls (HIV positive or negative). Real-time polymerase chain reaction (Q-PCR) was conducted to quantify MCPyV loads in blood specimens. Results: MCPyV DNA was detected in 17.1% of cases and 11.0% of controls in <1% of cells. No association between MCPyV DNA presence and HIV status was observed. Conclusion: Blood cells may be a reservoir for MCPyV. The presence of MCPyV genome in blood of healthy subjects might be relevant for transfusion medicine.
Collapse
Affiliation(s)
- Lucia Signorini
- Department of Medicine & Surgery, Via Cadore, 48, University of Milano Bicocca, 20900 Monza, Italy
| | - Sonia Villani
- Department of Biomedical, Surgical & Dental Sciences, Via Pascal, 36, University of Milano, 20133 Milano, Italy
| | - Rosalia Ticozzi
- Department of Biomedical, Surgical & Dental Sciences, Via Pascal, 36, University of Milano, 20133 Milano, Italy
| | - Federico Ambrogi
- Department of Clinical Sciences & Community Health, Medical Statistics, Biometry and Bioinformatics, University of Milan, 20133 Milan, Italy
| | - Maria Dolci
- Department of Biomedical, Surgical & Dental Sciences, Via Pascal, 36, University of Milano, 20133 Milano, Italy
| | - Renzo Boldorini
- Unit of Pathology, Department of Health Sciences, University of Eastern Piedmont Novara, Corso Giuseppe Mazzini, 18, 28100 Novara, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, 00173 Rome, Italy
| | - Pasquale Ferrante
- Department of Biomedical, Surgical & Dental Sciences, Via Pascal, 36, University of Milano, 20133 Milano, Italy
| | - Serena Delbue
- Department of Biomedical, Surgical & Dental Sciences, Via Pascal, 36, University of Milano, 20133 Milano, Italy
| |
Collapse
|
186
|
Mazzoni E, Rotondo JC, Marracino L, Selvatici R, Bononi I, Torreggiani E, Touzé A, Martini F, Tognon MG. Detection of Merkel Cell Polyomavirus DNA in Serum Samples of Healthy Blood Donors. Front Oncol 2017; 7:294. [PMID: 29238698 PMCID: PMC5712532 DOI: 10.3389/fonc.2017.00294] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/16/2017] [Indexed: 12/27/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) has been detected in 80% of Merkel cell carcinomas (MCC). In the host, the MCPyV reservoir remains elusive. MCPyV DNA sequences were revealed in blood donor buffy coats. In this study, MCPyV DNA sequences were investigated in the sera (n = 190) of healthy blood donors. Two MCPyV DNA sequences, coding for the viral oncoprotein large T antigen (LT), were investigated using polymerase chain reaction (PCR) methods and DNA sequencing. Circulating MCPyV sequences were detected in sera with a prevalence of 2.6% (5/190), at low-DNA viral load, which is in the range of 1–4 and 1–5 copies/μl by real-time PCR and droplet digital PCR, respectively. DNA sequencing carried out in the five MCPyV-positive samples indicated that the two MCPyV LT sequences which were analyzed belong to the MKL-1 strain. Circulating MCPyV LT sequences are present in blood donor sera. MCPyV-positive samples from blood donors could represent a potential vehicle for MCPyV infection in receivers, whereas an increase in viral load may occur with multiple blood transfusions. In certain patient conditions, such as immune-depression/suppression, additional disease or old age, transfusion of MCPyV-positive samples could be an additional risk factor for MCC onset.
Collapse
Affiliation(s)
- Elisa Mazzoni
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - John C Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - Luisa Marracino
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - Rita Selvatici
- Department of Medical Sciences, Section of Microbiology and Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Ilaria Bononi
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - Elena Torreggiani
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - Antoine Touzé
- UMR INRA 1282 ISP, Faculté des Sciences Pharmaceutiques, Université Francois Rabelais, Tours, France
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| | - Mauro G Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Ferrara, Italy
| |
Collapse
|
187
|
Abstract
Bacterial viruses are among the most numerous biological entities within the human body. These viruses are found within regions of the body that have conventionally been considered sterile, including the blood, lymph, and organs. However, the primary mechanism that bacterial viruses use to bypass epithelial cell layers and access the body remains unknown. Here, we used in vitro studies to demonstrate the rapid and directional transcytosis of diverse bacteriophages across confluent cell layers originating from the gut, lung, liver, kidney, and brain. Bacteriophage transcytosis across cell layers had a significant preferential directionality for apical-to-basolateral transport, with approximately 0.1% of total bacteriophages applied being transcytosed over a 2-h period. Bacteriophages were capable of crossing the epithelial cell layer within 10 min with transport not significantly affected by the presence of bacterial endotoxins. Microscopy and cellular assays revealed that bacteriophages accessed both the vesicular and cytosolic compartments of the eukaryotic cell, with phage transcytosis suggested to traffic through the Golgi apparatus via the endomembrane system. Extrapolating from these results, we estimated that 31 billion bacteriophage particles are transcytosed across the epithelial cell layers of the gut into the average human body each day. The transcytosis of bacteriophages is a natural and ubiquitous process that provides a mechanistic explanation for the occurrence of phages within the body. Bacteriophages (phages) are viruses that infect bacteria. They cannot infect eukaryotic cells but can penetrate epithelial cell layers and spread throughout sterile regions of our bodies, including the blood, lymph, organs, and even the brain. Yet how phages cross these eukaryotic cell layers and gain access to the body remains unknown. In this work, epithelial cells were observed to take up and transport phages across the cell, releasing active phages on the opposite cell surface. Based on these results, we posit that the human body is continually absorbing phages from the gut and transporting them throughout the cell structure and subsequently the body. These results reveal that phages interact directly with the cells and organs of our bodies, likely contributing to human health and immunity.
Collapse
|
188
|
Abstract
The emergence of novel zoonotic pathogens is one of the greatest challenges to global health security. The advent of increasingly sophisticated diagnostics tools has revolutionized our capacity to detect and respond to these health threats more rapidly than ever before. Yet, no matter how sophisticated these tools become, the initial identification of emerging infectious diseases begins at the local community level. It is here that the initial human or animal case resides, and it is here that early pathogen detection would have maximum benefit. Unfortunately, many areas at highest risk of zoonotic disease emergence lack sufficient infrastructure capacity to support robust laboratory diagnostic systems. Multiple factors are essential for pathogen detection networks, including an understanding of the complex sociological and ecological factors influencing disease transmission risk, community engagement, surveillance along high-risk human-animal interfaces, and a skilled laboratory workforce. Here we discuss factors relevant to the emerging disease paradigm, recent technical advances in diagnostic methods, and strategies for comprehensive and sustainable approaches to rapid zoonotic disease detection.
Collapse
Affiliation(s)
- Brian H Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Jonna A K Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| |
Collapse
|
189
|
Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection. Vaccines (Basel) 2017; 5:vaccines5040040. [PMID: 29099809 PMCID: PMC5748607 DOI: 10.3390/vaccines5040040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022] Open
Abstract
Viruses are responsible for most of both upper and lower acute respiratory infections (ARIs). The microbiome—the ecological community of microorganisms sharing the body space, which has gained considerable interest over the last decade—is modified in health and disease states. Even if most of these disturbances have been previously described in relation to chronic disorders of the gastrointestinal microbiome, after a short reminder of microbiome characteristics and methods of characterization, this review will describe the impact of the microbiome (mainly respiratory) on host responses to viral ARIs. The microbiome has a direct environmental impact on the host cells but also an indirect impact on the immune system, by enhancing innate or adaptive immune responses. In microbial infections, especially in viral infections, these dramatic modifications could lead to a dramatic impact responsible for severe clinical outcomes. Studies focusing on the microbiome associated with transcriptomic analyses of the host response and deep characterization of the pathogen would lead to a better understanding of viral pathogenesis and open avenues for biomarker development and innovative therapeutics.
Collapse
|
190
|
Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
|
191
|
Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres. J Virol 2017; 91:JVI.01137-17. [PMID: 28835501 PMCID: PMC5660504 DOI: 10.1128/jvi.01137-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 01/31/2023] Open
Abstract
The genomes of human herpesvirus 6A (HHV-6A) and HHV-6B have the capacity to integrate into telomeres, the essential capping structures of chromosomes that play roles in cancer and ageing. About 1% of people worldwide are carriers of chromosomally integrated HHV-6 (ciHHV-6), which is inherited as a genetic trait. Understanding the consequences of integration for the evolution of the viral genome, for the telomere, and for the risk of disease associated with carrier status is hampered by a lack of knowledge about ciHHV-6 genomes. Here, we report an analysis of 28 ciHHV-6 genomes and show that they are significantly divergent from the few modern nonintegrated HHV-6 strains for which complete sequences are currently available. In addition, ciHHV-6B genomes in Europeans are more closely related to each other than to ciHHV-6B genomes from China and Pakistan, suggesting regional variation of the trait. Remarkably, at least one group of European ciHHV-6B carriers has inherited the same ciHHV-6B genome, integrated in the same telomere allele, from a common ancestor estimated to have existed 24,500 ± 10,600 years ago. Despite the antiquity of some, and possibly most, germ line HHV-6 integrations, the majority of ciHHV-6B (95%) and ciHHV-6A (72%) genomes contain a full set of intact viral genes and therefore appear to have the capacity for viral gene expression and full reactivation. IMPORTANCE Inheritance of HHV-6A or HHV-6B integrated into a telomere occurs at a low frequency in most populations studied to date, but its characteristics are poorly understood. However, stratification of ciHHV-6 carriers in modern populations due to common ancestry is an important consideration for genome-wide association studies that aim to identify disease risks for these people. Here, we present full sequence analysis of 28 ciHHV-6 genomes and show that ciHHV-6B in many carriers with European ancestry most likely originated from ancient integration events in a small number of ancestors. We propose that ancient ancestral origins for ciHHV-6A and ciHHV-6B are also likely in other populations. Moreover, despite their antiquity, all of the ciHHV-6 genomes appear to retain the capacity to express viral genes, and most are predicted to be capable of full viral reactivation. These discoveries represent potentially important considerations in immunocompromised patients, in particular in organ transplantation and in stem cell therapy.
Collapse
|
192
|
Parvovirus B19 in the Context of Hematopoietic Stem Cell Transplantation: Evaluating Cell Donors and Recipients. Transplant Direct 2017; 3:e217. [PMID: 29184906 PMCID: PMC5682762 DOI: 10.1097/txd.0000000000000731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 01/07/2023] Open
Abstract
Background Parvovirus B19 (B19V) is a common human pathogen, member of the family Parvoviridae. Typically, B19V has been found to infect erythroid progenitors and cause hematological disorders, such as anemia and aplastic crisis. However, the persistence of genomic deoxyribonucleic acid (DNA) has been demonstrated in tonsils, liver, skin, brain, synovial, and testicular tissues as well as bone marrow, for both symptomatic and asymptomatic subjects. Although the molecular and cellular mechanisms of persistence remain undefined, it raises questions about potential virus transmissibility and its effects in the context of allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. Methods With this aim, we retrospectively screened allogeneic stem cell donors from 173 patients admitted for allo-HSCT from January 2008 to May 2013 using a seminested polymerase chain reaction approach. Results We found 8 positive donor samples, yielding a 4.6% of parvovirus prevalence (95% confidence interval, 2.36-8.85). Pre- and post-HSCT samples (n = 51) from the 8 recipients of the positive donors were also investigated, and 1 case exhibited B19V DNA in the post-HSCT follow-up (D + 60). Direct DNA sequencing was performed to determine the genotype of isolates and classification, performed by phylogenetic reconstruction, showed a predominance of genotype 1a, whereas the rare genotype 3b was detected in 2 additional patients. By molecular cloning, different B19V 1a substrains polymorphisms were evidenced in the single case in which donor and its recipient were B19V+. Conclusions Our results suggest that HSCT allografts are not a main source for B19V transmission, pointing to potential events of reinfection or endogenous viral reactivation.
Collapse
|
193
|
Bua G, Gallinella G. How does parvovirus B19 DNA achieve lifelong persistence in human cells? Future Virol 2017. [DOI: 10.2217/fvl-2017-0079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Gloria Bua
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgio Gallinella
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, Italy
- S.Orsola-Malpighi Hospital – Microbiology, Via Massarenti, 9, I-40138 Bologna, Italy
| |
Collapse
|
194
|
Denner J. The porcine virome and xenotransplantation. Virol J 2017; 14:171. [PMID: 28874166 PMCID: PMC5585927 DOI: 10.1186/s12985-017-0836-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/27/2017] [Indexed: 12/29/2022] Open
Abstract
The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context. Xenotransplantation using pig cells, tissues or organs is under development in order to alleviate the shortage of human transplants. Here for the first time published data describing the viromes in different pigs and their relevance for the virus safety of xenotransplantation is analysed. In conclusion, the analysis of the porcine virome has resulted in numerous new viruses being described, although their impact on xenotransplantation is unclear. Most importantly, viruses with known or suspected zoonotic potential were often not detected by next generation sequencing, but were revealed by more sensitive methods.
Collapse
Affiliation(s)
- Joachim Denner
- Robert Koch Fellow, Robert Koch Institute, Nordufer, 20, Berlin, Germany.
| |
Collapse
|
195
|
Nikolich-Zugich J, Goodrum F, Knox K, Smithey MJ. Known unknowns: how might the persistent herpesvirome shape immunity and aging? Curr Opin Immunol 2017; 48:23-30. [PMID: 28780492 DOI: 10.1016/j.coi.2017.07.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/08/2017] [Accepted: 07/12/2017] [Indexed: 12/11/2022]
Abstract
The microbial community that colonizes all living organisms is gaining appreciation for its contributions to both physiologic and pathogenic processes. The virome, a subset of the overall microbiome, large and diverse, including viruses that persistently inhabit host cells, endogenous viral elements genomically or epigenomically integrated into cells, and viruses that infect the other (bacterial, protozoan, fungal, and archaeal) microbiome phylla. These viruses live in the organism for its life, and therefore are to be considered part of the aging process experienced by the organism. This review considers the impact of the persistent latent virome on immune aging. Specific attention will be devoted to the role of herpesviruses, and within them, the cytomegalovirus, as the key modulators of immune aging.
Collapse
Affiliation(s)
- Janko Nikolich-Zugich
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States.
| | - Felicia Goodrum
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States
| | - Kenneth Knox
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States; University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, United States
| | - Megan J Smithey
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States.
| |
Collapse
|
196
|
Viruses as vectors of horizontal transfer of genetic material in eukaryotes. Curr Opin Virol 2017; 25:16-22. [DOI: 10.1016/j.coviro.2017.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/18/2017] [Accepted: 06/13/2017] [Indexed: 01/04/2023]
|
197
|
Colson P, La Scola B, Raoult D. Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes. Annu Rev Virol 2017; 4:61-85. [PMID: 28759330 DOI: 10.1146/annurev-virology-101416-041816] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.
Collapse
Affiliation(s)
- Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| |
Collapse
|
198
|
Sauvage V, Gomez J, Boizeau L, Laperche S. The potential of viral metagenomics in blood transfusion safety. Transfus Clin Biol 2017; 24:218-222. [PMID: 28694025 DOI: 10.1016/j.tracli.2017.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 02/08/2023]
Abstract
Thanks to the significant advent of high throughput sequencing in the last ten years, it is now possible via metagenomics to define the spectrum of the microbial sequences present in human blood samples. Therefore, metagenomics sequencing appears as a promising approach for the identification and global surveillance of new, emerging and/or unexpected viruses that could impair blood transfusion safety. However, despite considerable advantages compared to the traditional methods of pathogen identification, this non-targeted approach presents several drawbacks including a lack of sensitivity and sequence contaminant issues. With further improvements, especially to increase sensitivity, metagenomics sequencing should become in a near future an additional diagnostic tool in infectious disease field and especially in blood transfusion safety.
Collapse
Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France.
| | - J Gomez
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
| | - L Boizeau
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
| | - S Laperche
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
| |
Collapse
|
199
|
Bovo S, Mazzoni G, Ribani A, Utzeri VJ, Bertolini F, Schiavo G, Fontanesi L. A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections. PLoS One 2017; 12:e0179462. [PMID: 28662150 PMCID: PMC5491021 DOI: 10.1371/journal.pone.0179462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022] Open
Abstract
Shot-gun next generation sequencing (NGS) on whole DNA extracted from specimens collected from mammals often produces reads that are not mapped (i.e. unmapped reads) on the host reference genome and that are usually discarded as by-products of the experiments. In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. Bioinformatic analyses were carried out to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. In silico analyses included read mapping and sequence assembly approaches for a viral metagenomic analysis using the NCBI Viral Genome Resource. Our approach identified sequences matching several viruses of the Parvoviridae family: porcine parvovirus 2 (PPV2), PPV4, PPV5 and PPV6 and porcine bocavirus 1-H18 isolate (PBoV1-H18). The presence of these viruses was confirmed by PCR and Sanger sequencing of individual DNA samples. PPV2, PPV4, PPV5, PPV6 and PBoV1-H18 were all identified in samples collected in 1998-2007, 1998-2000, 1997-2000, 1998-2004 and 2003, respectively. For most of these viruses (PPV4, PPV5, PPV6 and PBoV1-H18) previous studies reported their first occurrence much later (from 5 to more than 10 years) than our identification period and in different geographic areas. Our study provided a retrospective evaluation of apparently asymptomatic parvovirus infected pigs providing information that could be important to define occurrence and prevalence of different parvoviruses in South Europe. This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.
Collapse
Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Biocomputing Group, University of Bologna, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anisa Ribani
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Animal Science, Iowa State University, Iowa, United States of America
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- * E-mail:
| |
Collapse
|