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Zou S, Chen Z, Tan Y, Tan M, Guo W, Wu S, Liu J, Song S, Peng Y, Wang M, Liang K. Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection. HIV Med 2024; 25:794-804. [PMID: 38515324 DOI: 10.1111/hiv.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/02/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated. METHODS We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups. RESULTS Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001). CONCLUSION CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.
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Affiliation(s)
- Shi Zou
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhong Chen
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Yuting Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Miao Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Guo
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Songjie Wu
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Liu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Shihui Song
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongquan Peng
- Graduate Collaborative Training Base of the First Hospital of Changsha, Hengyang Medical School, Uni-versity of South China, Hengyang, China
| | - Min Wang
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Ke Liang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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2
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Gu Y, Wang Z, Xia X, Zhao G. Nocardia farcinica brain abscess with torque teno virus co-infection: A case report. Heliyon 2024; 10:e28632. [PMID: 38590894 PMCID: PMC11000006 DOI: 10.1016/j.heliyon.2024.e28632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Background Brain abscesses caused by Nocardia are rare and difficult to diagnose. Nocardia farcinica is among the most common species; however, the conventional diagnosis of N. farcinica infection consists of cerebrospinal fluid (CSF) and blood culture and Gram staining. These procedures prolong the time to diagnosis and initiating treatment. Case presentation A 69-year-old woman with diabetes mellitus presented with headaches and dizziness persisting for 2 weeks, which was initially diagnosed as a brain abscess. Due to the unusual presentation and rapid progression of symptoms, she underwent surgical resection of the brain abscess. No pathogens were detected in blood or CSF cultures. However, metagenomic next-generation sequencing (mNGS) identified N. farcinica and Torque teno virus in pus extracted from the abscesses. The patient received appropriate antibiotic therapy and recovered fully without any residual neurological deficits. Conclusion mNGS useful for prompt diagnosis and selection of antibiotic therapy for brain abscesses caused by Nocardia. Surgical intervention is necessary in some cases.
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Affiliation(s)
- Yuting Gu
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Zide Wang
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaohua Xia
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
| | - Guang Zhao
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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3
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Ceccarani C, Gaspari V, Morselli S, Djusse ME, Venturoli S, Camboni T, Severgnini M, Foschi C, Consolandi C, Marangoni A. Chlamydia trachomatis and Neisseria gonorrhoeae rectal infections: Interplay between rectal microbiome, HPV infection and Torquetenovirus. PLoS One 2024; 19:e0301873. [PMID: 38578759 PMCID: PMC10997096 DOI: 10.1371/journal.pone.0301873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/22/2024] [Indexed: 04/07/2024] Open
Abstract
Men having sex with men (MSM) represent a key population, in which sexually transmitted rectal infections (STIs) caused by Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and high-risk HPV (HR-HPV) are very common and linked to significant morbidity. Investigating the anorectal microbiome associated with rectal STIs holds potential for deeper insights into the pathogenesis of these infections and the development of innovative control strategies. In this study, we explored the interplay at the rectal site between C. trachomatis, N. gonorrhoeae, HR-HPV infection, and the anorectal microbiome in a cohort of 92 MSM (47 infected by CT and/or NG vs 45 controls). Moreover, we assessed the presence of Torquetenovirus (TTV), a non-pathogenic endogenous virus, considered as a possible predictor of immune system activation. We found a high prevalence of HR-HPV rectal infections (61%), especially in subjects with a concurrent CT/NG rectal infection (70.2%) and in people living with HIV (84%). In addition, we observed that TTV was more prevalent in subjects with CT/NG rectal infections than in non-infected ones (70.2% vs 46.7%, respectively). The anorectal microbiome of patients infected by CT and/or NG exhibited a reduction in Escherichia, while the presence of TTV was significantly associated with higher levels of Bacteroides. We observed a positive correlation of HR-HPV types with Escherichia and Corynebacterium, and a negative correlation with the Firmicutes phylum, and with Prevotella, Oscillospira, Sutterella. Our findings shed light on some of the dynamics occurring within the rectal environment involving chlamydial/gonococcal infections, HPV, TTV, and the anorectal microbiome. These data could open new perspectives for the control and prevention of STIs in MSM.
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Affiliation(s)
- Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Valeria Gaspari
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Morselli
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Marielle Ezekielle Djusse
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Simona Venturoli
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Claudio Foschi
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Antonella Marangoni
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
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Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep 2023; 13:8319. [PMID: 37221274 PMCID: PMC10205716 DOI: 10.1038/s41598-023-34730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023] Open
Abstract
Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
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Affiliation(s)
- Spyridon Megremis
- University of Manchester, Manchester, UK.
- University of Leicester, Leicester, UK.
| | | | | | | | | | | | - Susetta Finotto
- Friedrich Alexander University Erlangen-Nurnberg, Erlangen, Germany
| | - Tuomas Jartti
- University of Turku, Turku, Finland
- University of Oulu, Oulu, Finland
| | | | | | | | | | - Nikolaos G Papadopoulos
- University of Manchester, Manchester, UK.
- National and Kapodistrian University of Athens, Athens, Greece.
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5
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Rabelo NN, Yoshikawa MH, Telles JPM, Coelho G, de Souza CS, de Oliveira NPG, Mendoza TRT, Braz-Silva PH, Boechat AL, Teixeira MJ, Figueiredo EG. Torque Teno virus DNA is found in the intracranial aneurysm wall-Is there a causative role? Front Med (Lausanne) 2023; 10:1047310. [PMID: 36744144 PMCID: PMC9894622 DOI: 10.3389/fmed.2023.1047310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
Objective Torque Teno virus (TTV) is a recently discovered virus with high prevalence worldwide, that has been associated with vascular diseases. The aim of this study is to investigate the prevalence of TTV molecular DNA in the intracranial aneurysm (IA) artery walls. Method Samples of IA walls were collected after microsurgical clipping from 35 patients with IA (22 ruptured/13 unruptured cases). The samples were submitted to molecular DNA extraction using the EasyMag automatized extractor and performed with Qiagen DNA extraction Minikit 250. The samples underwent PCR examination with primers for β-globin as internal control using the Nanodrop ® 2000 spectrophotometer. A quantitative (real-time) PCR with TTV-specific primers was performed. Clinical and radiological data of patients included was collected. Results TTV was detected in 15 (42.85%) cases, being 10 (45.4%) ruptured and 5 (38.4%) unruptured (p = 0.732) lesions. Multiple IAs accounted for 14 (40%) cases. Five cases (17.2%) had TTV+ and multiple aneurysms (p = 0.73). Association between presence of virus and aneurysm rupture was not statistically significant (p = 0.96). Conclusion This study demonstrated a relatively high prevalence of viral DNA in the walls of IAs. This is the first study to identify the presence of TTV DNA in IA's samples, which was found more often in ruptured lesions. This is an exploratory study, therefore, larger studies are required to clarify the relationships between inflammation, viral infection, IA formation and rupture.
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Affiliation(s)
- Nícollas Nunes Rabelo
- Department of Neurosurgery, University of São Paulo, São Paulo, SP, Brazil,*Correspondence: Nícollas Nunes Rabelo,
| | | | | | - Giselle Coelho
- Department of Neurosurgery, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Paulo Henrique Braz-Silva
- Laboratory of Virology (LIM-52), University of São Paulo, São Paulo, SP, Brazil,Department of Stomatology, University of São Paulo, São Paulo, SP, Brazil
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6
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Spezia PG, Focosi D, Baj A, Novazzi F, Ferrante FD, Carletti F, Minosse C, Matusali G, Maggi F. TTV and other anelloviruses: The astonishingly wide spread of a viral infection. ASPECTS OF MOLECULAR MEDICINE 2023; 1:None. [PMID: 37398508 PMCID: PMC10308510 DOI: 10.1016/j.amolm.2023.100006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 07/04/2023]
Abstract
The broad family of viruses known as anelloviruses (AV) infects both humans and numerous animal species. They have a tiny, covalently closed single-stranded DNA genome and the astonishing capacity to infect a very high percentage of healthy and ill people with chronic infections that could last a lifetime. AV, and particularly the prototype Torquetenovirus, have established a successful interaction with the host's immune system and the rate at which they replicate is a gauge to measure overall immune function, even though many aspects of their life cycle and pathogenesis are still poorly understood.
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Affiliation(s)
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Federica Novazzi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Fabrizio Carletti
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Claudia Minosse
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
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Virome Profiling of an Amur leopard cat Reveals Multiple Anelloviruses and a Bocaparvovirus. Vet Sci 2022; 9:vetsci9110640. [DOI: 10.3390/vetsci9110640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
As a small top predator, Amur leopard cat (Prionailurus bengalensis euptilurus) is widely distributed in northeast Asia and plays an important role in the control of small rodent populations and in the maintenance of ecological equilibrium. However, the viruses harbored by this creature have been rarely investigated. Here, we report the DNA and RNA eukaryotic virome profiling of an injured Amur leopard cat followed by PCR validation, which revealed diverse anelloviruses in multiple organs and a bocaparvovirus in the lymph, but no RNA viruses. These anelloviruses have diverse genomic structures and are classified into four phylogroups with viruses of various felines, while the bocaparvovirus is extremely similar to those recovered from diarrheal domestic cats, illustrating the transmission of the virus between domestic animals and wildlife. These data provide the first insight into the genetic diversity of Amur leopard cat viruses, highlighting the need for further investigation of wild animals.
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Integrated Immunologic Monitoring in Solid Organ Transplantation: The Road Toward Torque Teno Virus-guided Immunosuppression. Transplantation 2022; 106:1940-1951. [PMID: 35509090 PMCID: PMC9521587 DOI: 10.1097/tp.0000000000004153] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Potent immunosuppressive drugs have been introduced into clinical care for solid organ transplant recipients. It is now time to guide these drugs on an individual level to optimize their efficacy. An ideal tool simultaneously detects overimmunosuppression and underimmunosuppression, is highly standardized, and is straightforward to implement into routine. Randomized controlled interventional trials are crucial to demonstrate clinical value. To date, proposed assays have mainly focused on the prediction of rejection and were based on the assessment of few immune compartments. Recently, novel tools have been introduced based on a more integrated approach to characterize the immune function and cover a broader spectrum of the immune system. In this respect, the quantification of the plasma load of a highly prevalent and apathogenic virus that might reflect the immune function of its host has been proposed: the torque teno virus (TTV). Although TTV control is driven by T cells, other major immune compartments might contribute to the hosts' response. A standardized in-house polymerase chain reaction and a conformité européenne-certified commercially available polymerase chain reaction are available for TTV quantification. TTV load is associated with rejection and infection in solid organ transplant recipients, and cutoff values for risk stratification of such events have been proposed for lung and kidney transplantation. Test performance of TTV load does not allow for the diagnosis of rejection and infection but is able to define at-risk patients. Hitherto TTV load has not been used in interventional settings, but two interventional randomized controlled trials are currently testing the safety and efficacy of TTV-guided immunosuppression.
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Human Virome in Cervix Controlled by the Domination of Human Papillomavirus. Viruses 2022; 14:v14092066. [PMID: 36146871 PMCID: PMC9503738 DOI: 10.3390/v14092066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 12/24/2022] Open
Abstract
Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related.
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Morselli S, Foschi C, Laghi L, Zagonari S, Patuelli G, Camboni T, Ceccarani C, Consolandi C, Djusse ME, Pedna MF, Marangoni A, Severgnini M, Sambri V. Torquetenovirus in pregnancy: Correlation with vaginal microbiome, metabolome and pro-inflammatory cytokines. Front Microbiol 2022; 13:998849. [PMID: 36160242 PMCID: PMC9501707 DOI: 10.3389/fmicb.2022.998849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Torquetenovirus (TTV) is a negative sense, single-stranded DNA virus present in many body fluids of apparently healthy individuals. At present, it is considered a non-pathogenic endogenous virus. TTV can be detected in the vagina of pregnant women, its abundance being modulated with the extent of immune system activation. Until now, there is only scarce information regarding the association between TTV and the composition of the vaginal environment. Therefore, this study aimed to assess the presence of TTV in the vaginal ecosystem of a cohort of white women with a normal pregnancy (n = 60) at different gestational stages (first, second and third trimester) and in 9 subjects suffering a first trimester miscarriage. For each woman, we determined (i) the presence and titer of TTV, (ii) the vaginal bacterial composition by means of Nugent score and 16S rRNA gene sequencing, (iii) the vaginal metabolic profiles through 1H-NMR spectroscopy, and (iv) the vaginal concentration of two pro-inflammatory cytokines (IL-6 and IL-8). More than one third of women were found negative for TTV at all gestational stages. Although not statistically significant, the positivity for TTV dropped from 53.3% in the first to 36.6% in the third trimester. TTV loads varied greatly among vaginal samples, ranging between 2 × 101 and 2 × 105 copies/reaction. No difference in TTV prevalence and loads was observed between women with normal pregnancies and miscarriages. The presence of TTV was more common in women with a higher vaginal leucocyte count (p = 0.02). The levels of IL-6 (p = 0.02), IL-8 (p = 0.03), propionate (p = 0.001) and cadaverine (p = 0.006) were significantly higher in TTV-positive samples. TTV titer was positively correlated with the concentrations of 4-hydroxyphenyllactate (p < 0.0001), isoleucine (p = 0.01) and phenylalanine (p = 0.04). TTV-positive samples were characterized by a higher relative abundance of Sneathia (p = 0.04) and Shuttleworthia (p = 0.0009). In addition, a trend toward a decrease of Lactobacillus crispatus and Lactobacillus jensenii, and an increase of Lactobacillus iners was observed for TTV-positive samples. In conclusion, we found that TTV is quite common in women with normal pregnancy outcomes, representing a possible predictor of local immune status.
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Affiliation(s)
- Sara Morselli
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences (DISTAL), Centre of Foodomics, University of Bologna, Cesena, Italy
- Interdepartmental Centre for Agri-Food Industrial Research (CIRI Agrifood), University of Bologna, Cesena, Italy
| | | | | | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Marielle Ezekielle Djusse
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Federica Pedna
- Great Romagna Hub Laboratory, Unit of Microbiology, Pievesestina di Cesena, Italy
| | - Antonella Marangoni
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- *Correspondence: Antonella Marangoni
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Vittorio Sambri
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- Great Romagna Hub Laboratory, Unit of Microbiology, Pievesestina di Cesena, Italy
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11
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Hoek RAS, Verschuuren EAM, de Vries RD, Vonk JM, van Baarle D, van der Heiden M, van Gemert JP, Gore EJ, Niesters HGM, Erasmus M, Hellemons ME, Scherbeijn SMJ, Wijbenga N, Mahtab EA, GeurtsvanKessel CH, Buter CVL. High torque tenovirus (TTV) load before first vaccine dose is associated with poor serological response to COVID-19 vaccination in lung transplant recipients. J Heart Lung Transplant 2022; 41:765-772. [PMID: 35606065 PMCID: PMC8924026 DOI: 10.1016/j.healun.2022.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Serological responses to COVID-19 vaccination are diminished in recipients of solid organ transplants, especially in lung transplant recipients (LTR), probably as result of immunosuppressive treatment. There is currently no marker of immunosuppression that can be used to predict the COVID-19 vaccination response. Here, we study whether torque tenovirus (TTV), a highly prevalent virus can be used as an indicator of immunosuppression. METHODS The humoral response to the mRNA 1273 vaccine was assessed in 103 LTR, who received a transplant between 4 and 237 months prior to vaccination, by measuring Spike (S)-specific IgG levels at baseline, 28 days after first, and 28 days after the second vaccination. TTV loads were determined by RT-PCR and Pearson's correlation coefficient was calculated to correlate serological responses to TTV load. RESULTS Humoral responses to COVID-19 vaccination were observed in 41 of 103 (40%) LTR at 28 days after the second vaccination. Sixty-two of 103 (60%) were non-responders. Lower TTV loads at baseline (significantly) correlated with higher S-specific antibodies and a higher percentage of responders. Lower TTV loads also strongly correlated with longer time since transplantation, indicating that participants with lower TTV loads were longer after transplantation. CONCLUSIONS This study shows a better humoral response to the SARS-CoV-2 vaccine in subjects with a lower TTV load pre-vaccination. In addition, TTV load correlates with the time after transplantation. Further studies on the use of TTV load in vaccination efficacy studies in immunocompromised cohorts should provide leads for the potential use of this marker for optimizing vaccination response.
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Affiliation(s)
- Rogier AS Hoek
- Department of Pulmonary Medicine, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Erik AM Verschuuren
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Judith M. Vonk
- Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marieke van der Heiden
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Johanna P van Gemert
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Edmund J Gore
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Hubert GM Niesters
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Michiel Erasmus
- Department of Thoracic Surgery, University of Groningen, University Medical Center Groningen, Netherlands
| | - Merel E. Hellemons
- Department of Pulmonary Medicine, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Nynke Wijbenga
- Department of Pulmonary Medicine, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Edris A.F. Mahtab
- Department of Cardiothoracic Surgery, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Coretta Van Leer Buter
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands,Reprint requests: Coretta Crista Van Leer Buter, MD, PhD, Medical Microbiology, University Medical Centre Groningen: Universitair Medisch Centrum Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands
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12
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Huang AL, Hendren N, Carter S, Larsen C, Garg S, La Hoz R, Farr M. Biomarker-Based Assessment for Infectious Risk Before and After Heart Transplantation. Curr Heart Fail Rep 2022; 19:236-246. [PMID: 35597863 PMCID: PMC9124010 DOI: 10.1007/s11897-022-00556-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
Purpose of Review Survival outcomes for heart transplant recipients have improved in recent decades, but infection remains a significant cause of morbidity and mortality. In this review, we discuss several biological markers, or biomarkers, that may be used to monitor immunologic status in this patient population. Recent Findings While modest, data on the utility of immune biomarkers in heart transplant recipients suggest correlation between low level of immune response and increased infection risk. More novel assays, such as the detection of circulating levels of pathogen cell-free DNA in plasma and the use of Torque teno virus load as a surrogate for net state of immunosuppression, have potential to be additional important biomarkers. Summary Biomarker approaches to individualize immunosuppression therapy among heart transplant recipients is a promising area of medicine. However, additional studies are needed to inform the optimal protocol in which to incorporate these biomarkers into clinical practice.
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Affiliation(s)
- Athena L. Huang
- Parkland Memorial Hospital, Dallas, TX USA
- Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Jr. Blvd, Dallas, TX 75235 USA
| | - Nicholas Hendren
- Parkland Memorial Hospital, Dallas, TX USA
- Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Jr. Blvd, Dallas, TX 75235 USA
| | - Spencer Carter
- Parkland Memorial Hospital, Dallas, TX USA
- Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Jr. Blvd, Dallas, TX 75235 USA
| | - Christian Larsen
- Division of Infectious Diseases and Geography Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Sonia Garg
- Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Jr. Blvd, Dallas, TX 75235 USA
| | - Ricardo La Hoz
- Division of Infectious Diseases and Geography Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Maryjane Farr
- Division of Cardiology, University of Texas Southwestern Medical Center, 5959 Harry Hines Jr. Blvd, Dallas, TX 75235 USA
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13
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Cordey S, Laubscher F, Hartley MA, Junier T, Keitel K, Docquier M, Guex N, Iseli C, Vieille G, Le Mercier P, Gleizes A, Samaka J, Mlaganile T, Kagoro F, Masimba J, Said Z, Temba H, Elbanna GH, Tapparel C, Zanella MC, Xenarios I, Fellay J, D’Acremont V, Kaiser L. Blood virosphere in febrile Tanzanian children. Emerg Microbes Infect 2021; 10:982-993. [PMID: 33929935 PMCID: PMC8171259 DOI: 10.1080/22221751.2021.1925161] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.Trial registration: ClinicalTrials.gov identifier: NCT02225769.
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Affiliation(s)
- Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mary-Anne Hartley
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas Junier
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristina Keitel
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
- Department of Paediatric Emergency Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Gael Vieille
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Anne Gleizes
- SwissProt group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | | | - Frank Kagoro
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - John Masimba
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Zamzam Said
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Gasser H. Elbanna
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Marie-Celine Zanella
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, Geneva, Switzerland
- Agora Center, University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valérie D’Acremont
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
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14
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Gromova OA, Torshin IY, Semenov VA, Putilina MV, Chuchalin AG. Direct and Indirect Neurological Signs of COVID-19. NEUROSCIENCE AND BEHAVIORAL PHYSIOLOGY 2021; 51:856-866. [PMID: 34751196 PMCID: PMC8566113 DOI: 10.1007/s11055-021-01144-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 01/05/2023]
Abstract
Objective. To systematize the neurological manifestations of COVID-19. Materials and methods. A systematic computerized analysis of all currently available publications on the neurological manifestations of COVID-19 was undertaken (2374 reports in PubMed) by topological data analysis. Results. A set of interactions between infection with SARS-CoV-2, metabolic impairments affecting neurotransmitters (acetylcholine, dopamine, serotonin, and GABA), enkephalins, and neurotrophins, micronutrients, chronic and acute inflammation, encephalopathy, cerebral ischemia, and neurodegeneration (including demyelination) was described. The most typical neurological manifestations of COVID-19 were anosmia/ageusia due to ischemia, neurodegeneration, and/or systematic increases in proinflammatory cytokine levels. COVID-19 provoked ischemic stroke, Guillain-Barré syndrome, polyneuropathy, encephalitis, meningitis, and parkinsonism. Coronavirus infection increased the severity of multiple sclerosis and myopathies. The possible roles of the human virome in the pathophysiology of COVID-19 are considered. A clinical case of a patient with neurological complications of COVID-19 is described. Conclusions. In the long-term perspective, COVID-19 promotes increases in neurodegenerative changes, which requires special neurological rehabilitation programs. Use of cholinergic drugs and antihypoxic agents compatible with COVID-19 therapy is advised.
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Affiliation(s)
- O. A. Gromova
- Institute of Pharmacoinformatics, “Informatics and Control” Federal Research Center, Russian Academy of Sciences, Moscow, Russia
- Big Data Storage and Analysis Center, Moscow State University, Moscow, Russia
| | - I. Yu. Torshin
- Institute of Pharmacoinformatics, “Informatics and Control” Federal Research Center, Russian Academy of Sciences, Moscow, Russia
- Big Data Storage and Analysis Center, Moscow State University, Moscow, Russia
| | - V. A. Semenov
- Kemorovo State Medical University, Russian Ministry of Health, Kemerovo, Russia
| | - M. V. Putilina
- Pirogov Russian National Research Medical University, Russian Ministry of Health, Moscow, Russia
| | - A. G. Chuchalin
- Pirogov Russian National Research Medical University, Russian Ministry of Health, Moscow, Russia
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15
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Li G, Zhou D, Zhao M, Liu Q, Hao X, Yan T, Yuan S, Zhang S, Cheng Z. Kinetic analysis of pathogenicity and tissue tropism of gyrovirus 3 in experimentally infected chickens. Vet Res 2021; 52:120. [PMID: 34526128 PMCID: PMC8442313 DOI: 10.1186/s13567-021-00990-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Gyrovirus 3 (GyV3), the third novel emerging species of the genus Gyrovirus of the Anelloviridae family, has been described in multiple hosts. Epidemiologically, there are suggestions that GyV3 is associated with diarrhea/proventriculitis, however, no direct causal evidence exists between GyV3 infection and specific clinical diseases. Herein, we infected special pathogen-free (SPF) chickens with GyV3, and then assessed the pathogenicity and tissue tropism. The results revealed that GyV3 induced persistent infection characterized by diarrhea, aplastic anemia, immunosuppression, and persistent systemic lymphocytic inflammation. Clinically, the infected chickens presented ruffled feathers, diarrhea, anemia, and weight loss. Aplastic anemia was characterized by progressive depletion of hematopoietic cells in the bone marrow, immunosuppression was associated with atrophy of the thymus, spleen, and bursa of Fabricious, progressive lymphocytic inflammations were characterized by proventriculitis, adrenalitis, pancreatitis, hepatitis, nephritis, and bronchitis. Viral loads of GyV3 in tissues exhibited “M”, “N”, “W” or “V” type dynamic changes. The highest level of viral loads was reported in bone marrow at 7dpi, followed by the adrenal gland at 2 dpi, the sciatic nerve at 7 dpi, and bile at 35 dpi. The bone marrow and kidney demonstrate the strongest immunostaining of GyV3-VP1 antigen and were suggested as the target tissues of GyV3. Collectively, GyV3 is an immunosuppressive pathogenic virus that targets the bone marrow and kidney in chickens. Exploring the pathogenicity and tissue tropism of GyV3 will guide the basic understanding of the biology of GyV3 and its pathogenesis in chickens.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Manda Zhao
- Department of Animal Science and Technology, Vocational-Technical School of Husbandry and Veterinary Medicine, Weifang, China
| | - Qing Liu
- Service Center of Jinan Zoo, Jinan, China
| | - Xiaojing Hao
- Qindao Husbandry and Veterinary Institute, Qingdao, China
| | - Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Shiyu Yuan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Shicheng Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.
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16
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van Lieverloo GGA, Wieske L, van Schaik IN, Deijs M, van der Hoek L, Eftimov F. Virus discovery in chronic inflammatory demyelinating polyneuropathy. J Neuroimmunol 2021; 358:577668. [PMID: 34325344 DOI: 10.1016/j.jneuroim.2021.577668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/22/2021] [Accepted: 07/18/2021] [Indexed: 11/18/2022]
Abstract
The events triggering and/or sustaining the auto-immune response underlying chronic inflammatory demyelinating polyneuropathy (CIDP) are unknown. Similar to Guillain-Barré syndrome (GBS), a viral infection might play a role in CIDP. In this study, an virus detection method (VIDISCA-next generation sequencing) capable of detecting known and unknown viruses, was used to analyze the virome in serum of 47 CIDP patients at different time points of the disease and, when available, in cerebrospinal fluid (CSF) samples (N: 17). Serum samples of GBS patients (N:24) and healthy controls (N:114) were used for comparisons. In 5/47 (10.6%; 95% CI: 4-23) CIDP samples, 10/24 (42%; 95% CI: 22-63) GBS samples and 32/114 (28.1%; 95% CI: 20-37) healthy controls samples, anelloviruses were detected, generally regarded as a non-pathogenic species. Parvovirus B19 and GB virus C were found in two CIDP samples (4%). Parvovirus B19, HIV-1 and GB virus C were found in three GBS samples (13%). In 2/17 CIDP CSF samples, an anellovirus and polyomavirus were detected, probably due to contamination during lumbar puncture. No sequences of other viruses were detected in serum or CSF. A (persistent) viral infection sustaining the auto-immune response in CIDP seems therefore unlikely.
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Affiliation(s)
| | - L Wieske
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands
| | - I N van Schaik
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands; Spaarne Gasthuis, Haarlem, the Netherlands
| | - M Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - L van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - F Eftimov
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands
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17
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Grinde B. Viruses belonging to Anelloviridae or Circoviridae as a possible cause of chronic fatigue. J Transl Med 2020; 18:485. [PMID: 33317538 PMCID: PMC7734913 DOI: 10.1186/s12967-020-02666-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
Chronic fatigue often starts with an acute viral infection-as witnessed in the case of SARS-CoV-2-but indirect consequences of these infections are presumably the actual cause of the condition. As recently reviewed in this journal, the culprit could be a virus already present in the patient. The review covers several types of viruses, but concludes that the question is still open. The focus is on well known, pathogenic viruses for which there are ample diagnostic tools. I argue that there is one lesser-known group of viruses, the related anello- and circoviruses, which ought to be investigated. More or less everyone harbours at least one strain of these viruses in the blood, while not in the spinal fluid. They normally replicate at a low level, but their activity increases in an immune suppressed host; and there are cases where they do reach the brain. The initial infection could facilitate their access to the brain.
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Affiliation(s)
- Bjørn Grinde
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Skøyen, PO Box 222, 0213, Oslo, Norway.
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18
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Neri L, Spezia PG, Suraci S, Macera L, Scribano S, Giusti B, Focosi D, Maggi F, Giannecchini S. Torque teno virus microRNA detection in cerebrospinal fluids of patients with neurological pathologies. J Clin Virol 2020; 133:104687. [PMID: 33176237 DOI: 10.1016/j.jcv.2020.104687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host. OBJECTIVE To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases. STUDY DESIGN Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses. RESULTS TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region. CONCLUSIONS These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.
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Affiliation(s)
- Lorenzo Neri
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy
| | - Stefano Scribano
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, and Laboratory of Clinical Microbiology, ASST dei Sette Laghi, Varese, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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19
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Brundin PM, Landgren BM, Fjällström P, Johansson AF, Nalvarte I. Blood hormones and torque teno virus in peripheral blood mononuclear cells. Heliyon 2020; 6:e05535. [PMID: 33294681 PMCID: PMC7691539 DOI: 10.1016/j.heliyon.2020.e05535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/04/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022] Open
Abstract
Men and women respond differently to infectious diseases. Women show less morbidity and mortality, partially due to the differences in sex hormone levels which can influence the immune response. Torque teno virus (TTV) is non-pathogenic and ubiquitously present in serum from a large proportion (up to 90%) of adult humans with virus levels correlating with the status of the host immune response. The source of TTV replication is unknown, but T-lymphocytes have been proposed. In this study we investigated the presence and levels of TTV in peripheral blood mononuclear cells (PBMCs) in premenopausal (pre-MP) women, post-menopausal (post-MP) women, and men, and determined their serum sex hormone levels. Of the examined subjects (n = 27), we found presence of TTV in PMBC from 17.6% pre-MP (n = 17), 25.0% post-MP (n = 4) and 50.0% men (n = 6). The levels of TTV/μg DNA were lower among TTV-positive men and post-MP women compared to pre-MP women. All the positive pre-MP women were either anovulatory, hypothyroid, or both. In addition, the TTV-positive pre-MP women had significantly lower progesterone levels compared to TTV-negative pre-MP women. Although our study was performed on a limited number of subjects, the data suggests that TTV in PBMC is associated with an anovulatory menstrual cycle with low progesterone levels, and possibly with male sex.
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Affiliation(s)
- Peik M.A. Brundin
- Department of Clinical Microbiology, Infection and Immunology, The Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57, Huddinge, Sweden
- S:t Görans Hospital, Dept of Medicine, Unit of Infectious Diseases, 112 81, Stockholm, Sweden
| | | | - Peter Fjällström
- Department of Clinical Microbiology, Infection and Immunology, The Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
| | - Anders F. Johansson
- Department of Clinical Microbiology, Infection and Immunology, The Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
| | - Ivan Nalvarte
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57, Huddinge, Sweden
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20
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St.Hilaire M, Austin S, Landis RC, Steininger C. Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission. Pathogens 2020; 9:E686. [PMID: 32839419 PMCID: PMC7559857 DOI: 10.3390/pathogens9090686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022] Open
Abstract
Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and Culex pipiens complex), from different geographic locations and environments (central Europe and the Caribbean) for highly sensitive next-generation sequencing-based virome characterization. We found a rich virus community associated with a great diversity of host species. Among those, we detected a large diversity of novel virus sequences that we could predominately assign to circular Rep-encoding single-stranded (CRESS) DNA viruses, including the full-length genome of a yet undescribed Gemykrogvirus species. Moreover, we report for the first time the detection of a potentially zoonotic CRESS-DNA virus (Cyclovirus VN) in mosquito vectors. This study expands the knowledge on virus diversity in medically important mosquito vectors, especially for CRESS-DNA viruses that have previously been shown to easily recombine and jump the species barrier.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Nicolas Rascovan
- Department of Genomes & Genetics, Institut Pasteur, 75015 Paris, France;
| | - Anna Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, 8036 Graz, Austria;
| | - Carina Zittra
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
- Unit Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, 1010 Vienna, Austria
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
| | - Thea Scantlebury-Manning
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Marquita Gittens-St.Hilaire
- Faculty of Medical Sciences, University of the West Indies, Queen Elizabeth Hospital, St. Michael BB14004, Barbados;
| | - Shane Austin
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Robert Clive Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown BB11115, Barbados;
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
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Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China. Virol Sin 2020; 36:25-32. [PMID: 32488409 PMCID: PMC7973343 DOI: 10.1007/s12250-020-00232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/07/2020] [Indexed: 11/08/2022] Open
Abstract
Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.
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22
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Torquetenovirus Serum Load and Long-Term Outcomes in Renal Transplant Recipients. J Clin Med 2020; 9:jcm9020440. [PMID: 32041187 PMCID: PMC7073853 DOI: 10.3390/jcm9020440] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/23/2020] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Following transplantation, patients must take immunosuppressive medication for life. Torquetenovirus (TTV) is thought to be marker for immunosuppression, and TTV–DNA levels after organ transplantation have been investigated, showing high TTV levels, associated with increased risk of infections, and low TTV levels associated with increased risk of rejection. However, this has been investigated in studies with relatively short follow-up periods. We hypothesized that TTV levels can be used to assess long term outcomes after renal transplantation. Serum samples of 666 renal transplant recipients were tested for TTV DNA. Samples were taken at least one year after renal transplantation, when TTV levels are thought to be relatively stable. Patient data was reviewed for graft failure, all-cause mortality and death due to infectious causes. Our data indicates that high TTV levels, sampled more than one year post-transplantation, are associated with all-cause mortality with a hazard ratio (HR) of 1.12 (95% CI, 1.02–1.23) per log10 increase in TTV viral load, (p = 0.02). Additionally, high TTV levels were also associated with death due to infectious causes (HR 1.20 (95% CI 1.01–1.43), p = 0.04). TTV levels decrease in the years following renal transplantation, but remain elevated longer than previously thought. This study shows that TTV level may aid in predicting long-term outcomes, all-cause mortality and death due to an infectious cause in renal transplant patients sampled over one year post-transplantation.
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23
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Detection of Torque Teno Virus (TTV) and TTV-Like Minivirus in patients with presumed infectious endophthalmitis in India. PLoS One 2020; 15:e0227121. [PMID: 31910220 PMCID: PMC6946165 DOI: 10.1371/journal.pone.0227121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/11/2019] [Indexed: 12/04/2022] Open
Abstract
Human anelloviruses (Torque Teno Virus (TTV) and TTV Like Mini Virus (TLMV)) are now being reported at a high prevalence across the world, with a controversial disease-inducing potential. The aim of this study was to investigate the role of these anellovirus in vitreous of patients with presumed infectious endophthalmitis. After informed consent, vitreous fluid from patients with endophthalmitis (n = 103) and non-infectious pathologies (n = 102) were analyzed for the presence of TTV and TLMV DNA by qPCR with the limit of quantification defined as 100 copies per reaction. Among the patients clinically diagnosed with endophthalmitis, 29 of the 40 culture proven samples (72.5%) and 42 out of 63 (66.6%) of culture-negative samples were positive for presence of TTV/TLMV. Interestingly, 51 of the 102 (50%) samples in the control group were also positive for TTV/TLMV. Comparing the clinical outcome among patients diagnosed with endophthalmitis, we observed no significant association in the final visual acuity of patients who were positive for presence of TTV/TLMV, however, these patients had significantly higher repeat antibiotic injections (p = 0.03). Further evidence is however needed to correlate TTV / TLMV with a particular pathology or group of pathologies in the eye.
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24
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Gromova O, Torshin I, Semenov V, Putilina M, Chuchalin A. Direct and indirect neurological manifestations of COVID-19. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:11-21. [DOI: 10.17116/jnevro202012011111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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25
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Schibler M, Brito F, Zanella MC, Zdobnov EM, Laubscher F, L'Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L. Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease. Genes (Basel) 2019; 10:genes10080625. [PMID: 31431002 PMCID: PMC6723360 DOI: 10.3390/genes10080625] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Meningitis, encephalitis, and myelitis are various forms of acute central nervous system (CNS) inflammation, which can coexist and lead to serious sequelae. Known aetiologies include infections and immune-mediated processes. Despite advances in clinical microbiology over the past decades, the cause of acute CNS inflammation remains unknown in approximately 50% of cases. High-throughput sequencing was performed to search for viral sequences in cerebrospinal fluid (CSF) samples collected from 26 patients considered to have acute CNS inflammation of unknown origin, and 10 patients with defined causes of CNS diseases. In order to better grasp the clinical significance of viral sequence data obtained in CSF, 30 patients without CNS disease who had a lumbar puncture performed during elective spinal anaesthesia were also analysed. One case of human astrovirus (HAstV)-MLB2-related meningitis and disseminated infection was identified. No other viral sequences that can easily be linked to CNS inflammation were detected. Viral sequences obtained in all patient groups are discussed. While some of them reflect harmless viral infections, others result from reagent or sample contamination, as well as index hopping. Altogether, this study highlights the potential of high-throughput sequencing in identifying previously unknown viral neuropathogens, as well as the interpretation issues related to its application in clinical microbiology.
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Affiliation(s)
- Manuel Schibler
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland.
| | - Francisco Brito
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Marie-Céline Zanella
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Evgeny M Zdobnov
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Arnaud G L'Huillier
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Juan Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Noémie Wagner
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Klara M Posfay-Barbe
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1206 Geneva, Switzerland
| | - Eduardo Schiffer
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Georges L Savoldelli
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Roxane Fournier
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Lauriane Lenggenhager
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
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26
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Freer G, Maggi F, Pistello M. Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. Curr Med Chem 2019; 26:1027-1044. [PMID: 28982318 DOI: 10.2174/0929867324666171005112921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/06/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND The virome is a network of viruses normally inhabiting humans. It forms a conspicuous portion of the so-called microbiome, once generically referred to as resident flora. Indeed, viruses infecting humans without leading to clinical disease are increasingly recognized as part of the microbiome and have an impact on the development of our immune system. In addition, they activate inflammasomes, multiprotein complexes that assemble in cells and that are responsible for the downstream effects of sensing pathogens. OBJECTIVE This review aims at summarizing the evidence on the role of the virome in modulating inflammation and emphasizes evidence for Anelloviruses as useful molecular markers to monitor inflammatory processes and immune system competence. METHOD We carried out a review of the literature published in the last 5 years and summarized older literature to take into account ground-breaking discoveries concerning inflammasome assembly and virome. RESULTS A massive amount of data recently emerging demonstrate that the microbiome closely reflects what we eat, and many other unexpected variables. Composition, location, and amount of the microbiome have an impact on innate and adaptive immune defences. Viruses making up the virome contribute to shaping the immune system. Anelloviruses, the best known of such viruses, are present in most human beings, persistently without causing apparent disease. Depending on their interplay with such viruses, inflammasomes instruct host defences to tolerate or forfeit a specific microorganism. CONCLUSION The virome plays an important role in shaping human immune defences and contributes to inflammatory processes by quenching or increasing them.
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Affiliation(s)
- Giulia Freer
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | | | - Mauro Pistello
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Unit, Pisa University Hospital, Pisa, Italy
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27
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Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res 2019; 29:831-842. [PMID: 30992304 PMCID: PMC6499319 DOI: 10.1101/gr.238170.118] [Citation(s) in RCA: 335] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Messacar
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Elizabeth Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Becky Fung
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | | | - Danielle Ingebrigtsen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Walter Lorizio
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Sandra M Paff
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - John A Leake
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Rick Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Roberta DeBiasi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC 20010, USA
- Department of Pediatrics, Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine, Washington, DC 20037, USA
| | - Samuel Dominguez
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA
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28
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Macera L, Spezia PG, Medici C, Rofi E, Del Re M, Focosi D, Mazzetti P, Navarro D, Antonelli G, Danesi R, Pistello M, Maggi F. Comparative evaluation of molecular methods for the quantitative measure of torquetenovirus viremia, the new surrogate marker of immune competence. J Med Virol 2019; 94:491-498. [PMID: 31002743 DOI: 10.1002/jmv.25488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/31/2019] [Accepted: 04/14/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Torquetenovirus (TTV) viremia is emerging as a promising tool to assess functional immune competence, to predict posttransplant immune-related complications, and eventually to customize immunosuppression. METHODS In this study, 327 blood samples were tested using two real-time PCR (rtPCR) assays both targeted to the untranslated region of the TTV genome. The first assay was an in-house rtPCR developed by our group, the second one was the recently marketed TTV R-GENE assay. RESULTS In the validation study, the TTV R-GENE showed good performances in precision and reproducibility, and sensitivity as low as 12 TTV DNA copies/mL, like previously reported for the in-house rtPCR. The Bland-Altman analysis showed that the mean difference between the two methods was -0.3 log copies/mL. In the comparison study, 69% and 72% of samples were detected positive by rtPCR and TTV R-GENE, respectively (94% concordance, κ = 0.88). Performances did not differ between the two rtPCRs by type of TTV group examined. When a newly-developed in-house digital droplet PCR was applied for TTV quantification and used as an alternative method of comparison on 94 samples, the results strongly correlated with those obtained by the two rtPCR methods (99% concordance). CONCLUSION In summary, all the molecular methods assayed are highly sensitive and accurate in quantitation of TTV DNA in blood samples.
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Affiliation(s)
- Lisa Macera
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | | | - Chiara Medici
- Virology Division, Pisa University Hospital, Pisa, Italy
| | - Eleonora Rofi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank Division, Pisa University Hospital, Pisa, Italy
| | - Paola Mazzetti
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - David Navarro
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Romano Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
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29
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Eibach D, Hogan B, Sarpong N, Winter D, Struck NS, Adu-Sarkodie Y, Owusu-Dabo E, Schmidt-Chanasit J, May J, Cadar D. Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana. Sci Rep 2019; 9:2360. [PMID: 30787417 PMCID: PMC6382885 DOI: 10.1038/s41598-019-38975-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
The cause of acute encephalitis/meningoencephalitis in pediatric patients remains often unexplained despite extensive investigations for large panel of pathogens. To explore a possible viral implication, we investigated the virome of cerebrospinal fluid specimens of 70 febrile pediatric inpatients with clinical compatible encephalitis/meningoencephalitis. Using viral metagenomics, we detected and genetically characterized three novel human Torque teno mini virus (TTMV) species (TTMV-G1-3). Phylogenetically, TTMV-G1-3 clustered in three novel monophyletic lineages within genus Betatorquevirus of the Anelloviridae family. TTMV-G1-3 were highly prevalent in diseased children, but absent in the healthy cohort which may indicate an association of TTMV species with febrile illness. With 2/3 detected malaria co-infection, it remains unclear if these novel anellovirus species are causative agents or increase disease severity by interaction with malaria parasites. The presence of the viruses 28 days after initiating antimalarial and/or antibiotic treatment suggests a still active viral infection likely as effect of parasitic and/or bacterial co-infection that may have initiated a modulated immune system environment for viral replication or a defective virus clearance. This study increases the current knowledge on the genetic diversity of TTMV and strengthens that human anelloviruses can be considered as biomarkers for strong perturbations of the immune system in certain pathological conditions.
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Affiliation(s)
- Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Nicole S Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, 40080, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Jonas Schmidt-Chanasit
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany.,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Daniel Cadar
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany. .,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.
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30
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High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal. Clin Microbiol Infect 2019; 25:422-430. [PMID: 30641229 PMCID: PMC7129948 DOI: 10.1016/j.cmi.2018.12.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
Abstract
Background Viral aetiologies are the most common cause of central nervous system (CNS) infections. Approximately one-half of CNS infections remain of undetermined origin. High-throughput sequencing (HTS) brought new perspectives to CNS infection investigations, allowing investigation of viral aetiologies with an unbiased approach. HTS use is still limited to specific clinical situations. Objectives The aim of this review was to evaluate the contribution and pitfalls of HTS for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis in CNS patient samples. Sources PubMed was searched from 1 January 2008 to 2 August 2018 to retrieve available studies on the topic. Additional publications were included from a review of full-text sources. Content Among 366 studies retrieved, 29 used HTS as a diagnostic technique. HTS was performed in cerebrospinal fluid and brain biopsy samples of 307 patients, including immunocompromised, immunocompetent paediatric, and adult cases. HTS was performed retrospectively in 18 studies and prospectively in 11. HTS led to the identification of a potential causal virus in 41 patients, with 11 viruses known and ten not expected to cause CNS infections. Various HTS protocols were used. Implications The additional value of HTS is difficult to quantify because of various biases. Nevertheless, HTS led to the identification of a viral cause in 13% of encephalitis, meningoencephalitis, and meningitis cases in which various assays failed to identify the cause. HTS should be considered early in clinical management as a complement to routine assays. Standardized strategies and systematic studies are needed for the integration of HTS in clinical management.
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31
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Martelli F, Macera L, Spezia PG, Medici C, Pistello M, Guasti D, Romagnoli P, Maggi F, Giannecchini S. Torquetenovirus detection in exosomes enriched vesicles circulating in human plasma samples. Virol J 2018; 15:145. [PMID: 30236130 PMCID: PMC6149034 DOI: 10.1186/s12985-018-1055-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Torquetenovirus (TTV) belongs to Anelloviridae family, infects nearly all people indefinitely without causing overt disease establishing a fine and successful interaction with the host. Increasing evidence have shown some human viruses exploit extracellular vesicles thereby helping viral persistence in the host. Here, the presence of TTV in extracellular vesicles circulating in human plasma was investigated. METHODS TTV DNA was quantified in plasma-derived exosomes from 122 samples collected from 97 diseased patients and 25 healthy donors. Exosomes enriched vesicles (EEVs) were extracted from plasma and characterized by Nanoparticle tracking analysis, by western blot for presence of tetraspanin CD63, CD81 and annexin II protein and, finally, by electron microscopy (EM). Presence and quantitation of TTV DNA were assessed with an universal single step real-time TaqMan PCR assay. RESULTS Preliminary investigation showed that the human plasma extracted extracellular vesicles exhibited a main size of 70 nm, had concentration of 2.5 × 109/ml, and scored positive for tetraspanin CD63, CD81 and annexin II, typical characteristic of the exosomes vesicles. EEVs extracted from pooled plasma with TTV DNA viremia of 9.7 × 104 copies/ml showed to contain 6.3 × 102 TTV copies/ml, corresponding to 0.65% of total viral load. Important, TTV yield changed significantly following freezing/thawing, detergents and DNAse treatment of plasma before EEVs extraction. EEVs purified by sucrose-density gradient centrifugation and analysis of gradient fraction positive for exosomes marker CD63 harbored 102 TTV copies/ml. Moreover, EM evidenced the presence of TTV-like particles in EEVs. Successive investigation of plasma EEVs from 122 subjects (37 HIV-positive, 20 HCV infected, 20 HBV infected, 20 kidney transplant recipients, and 25 healthy) reported TTV DNA detection in 42 (34%) of the viremic samples (37 were from diseased patients and 5 from healthy people) at a mean level of 4.8 × 103 copies/ml. The examination of EEVs selected samples reported the presence of TTV genogroup 1, 3, 4 and 5, with genogroup 3 highly observed. CONCLUSIONS Collectively, although these observations should be confirmed by further studies, circulation of TTV particles in EEVs opens new avenues and mechanistic insights on the molecular strategies adopted by anelloviruses to persist in the host.
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Affiliation(s)
- Francesco Martelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | - Lisa Macera
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Pietro Giorgio Spezia
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Chiara Medici
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | - Mauro Pistello
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Daniele Guasti
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | - Paolo Romagnoli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | | | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy.
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32
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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.
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33
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Vu DL, Cordey S, Simonetta F, Brito F, Docquier M, Turin L, van Delden C, Boely E, Dantin C, Pradier A, Roosnek E, Chalandon Y, Zdobnov EM, Masouridi-Levrat S, Kaiser L. Human pegivirus persistence in human blood virome after allogeneic haematopoietic stem-cell transplantation. Clin Microbiol Infect 2018; 25:225-232. [PMID: 29787887 DOI: 10.1016/j.cmi.2018.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/11/2018] [Accepted: 05/01/2018] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Because commensal viruses are defined by the immunologic tolerance afforded to them, any immunomodulation, such as is received during haematopoietic stem-cell transplantation, may shift the demarcation between innocuous viral resident and disease-causing pathogen. METHODS We analysed by deep-sequencing the plasma virome of 40 allogeneic haematopoietic stem-cell transplantation patients 1 month after transplantation. Because human pegivirus (HPgV) was highly prevalent, we performed a 1-year screening of 122 plasma samples by specific real-time reverse transcription PCR assay. We used the log-rank test and the Gray test to assess association with outcomes, and the Mann-Whitney test and multivariable linear regression model to assess association with T-cell reconstitution. RESULTS Polyomaviruses (PyV) (20/40 patients), anelloviruses (16/40), pegiviruses (14/40) and herpesviruses (14/40) were most frequently identified, including ten cytomegalovirus; three Epstein-Barr virus; two herpes simplex virus type 1; one human herpesvirus 6b and one human herpesvirus 7; 18 Merkel cell-PyV; two BK-PyV; three PyV-6; and one JC-PyV. Papillomavirus and adenovirus were identified in 11 and two patients, respectively. The HPgV specific real-time reverse transcription PCR screening identified 51 of 122 positive samples, high virus loads and persistent infections up to 1 year after transplantation. Comparison between patients with or without HPgV infection at time of transplantation did not reveal a significant difference in infections, engraftment, survival, graft vs. host disease, relapse or immune reconstitution. CONCLUSIONS The blood virome after allogeneic haematopoietic stem-cell transplantation includes several DNA viruses, notably herpesviruses and PyV. Among RNA viruses, HPgV is highly prevalent and persists for several months, and it thus may deserve special attention in further research on immune reconstitution.
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Affiliation(s)
- D-L Vu
- Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland; Swiss Transplant Cohort Study, Basel, Switzerland.
| | - S Cordey
- Laboratory of Virology, Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland; Faculty of Medicine, Geneva, Switzerland
| | - F Simonetta
- Division of Haematology, University of Geneva Hospitals, Geneva, Switzerland
| | - F Brito
- Faculty of Medicine, Geneva, Switzerland; Swiss Institute of Bioinformatics, Faculty of Medicine, Geneva, Switzerland
| | - M Docquier
- Faculty of Medicine, Geneva, Switzerland
| | - L Turin
- Laboratory of Virology, Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland; Faculty of Medicine, Geneva, Switzerland
| | - C van Delden
- Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland; Faculty of Medicine, Geneva, Switzerland; Swiss Transplant Cohort Study, Basel, Switzerland
| | - E Boely
- Swiss Transplant Cohort Study, Basel, Switzerland
| | - C Dantin
- Division of Haematology, University of Geneva Hospitals, Geneva, Switzerland
| | - A Pradier
- Division of Haematology, University of Geneva Hospitals, Geneva, Switzerland
| | - E Roosnek
- Faculty of Medicine, Geneva, Switzerland
| | - Y Chalandon
- Faculty of Medicine, Geneva, Switzerland; Division of Haematology, University of Geneva Hospitals, Geneva, Switzerland
| | - E M Zdobnov
- Faculty of Medicine, Geneva, Switzerland; Swiss Institute of Bioinformatics, Faculty of Medicine, Geneva, Switzerland
| | - S Masouridi-Levrat
- Division of Haematology, University of Geneva Hospitals, Geneva, Switzerland
| | - L Kaiser
- Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland; Faculty of Medicine, Geneva, Switzerland
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34
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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.
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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
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35
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Abstract
Circular single-stranded DNA viruses infect archaea, bacteria, and eukaryotic organisms. The relatively recent emergence of single-stranded DNA viruses, such as chicken anemia virus (CAV) and porcine circovirus 2 (PCV2), as serious pathogens of eukaryotes is due more to growing awareness than to the appearance of new pathogens or alteration of existing pathogens. In the case of the ubiquitous human circular single-stranded DNA virus family Anelloviridae, there is still no convincing direct causal relation to any specific disease. However, infections may play a role in autoimmunity by changing the homeostatic balance of proinflammatory cytokines and the human immune system, indirectly affecting the severity of diseases caused by other pathogens. Infections with CAV (family Anelloviridae, genus Gyrovirus) and PCV2 (family Circoviridae, genus Circovirus) are presented here because they are immunosuppressive and affect health in domesticated animals. CAV shares genomic organization, genomic orientation, and common features of major proteins with human anelloviruses, and PCV2 DNA may be present in human food and vaccines.
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Affiliation(s)
- L M Shulman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel; .,Laboratory of Environmental Virology, Central Virology Laboratory, Sheba Medical Center Public Health Services, Israel Ministry of Health, Tel Hashomer, 52621, Israel
| | - I Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, 50250, Israel;
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36
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Lempp C, Jungwirth N, Grilo ML, Reckendorf A, Ulrich A, van Neer A, Bodewes R, Pfankuche VM, Bauer C, Osterhaus ADME, Baumgärtner W, Siebert U. Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany. PLoS One 2017; 12:e0175469. [PMID: 28399176 PMCID: PMC5388480 DOI: 10.1371/journal.pone.0175469] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/27/2017] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spillover of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and peri-urban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species. 79 red foxes, 17 stone martens and 10 raccoon dogs were collected from traps or hunts. In order to detect morphological changes and potential infectious diseases, necropsy and pathohistological work-up was performed. Additionally, in selected animals immunohistochemistry (influenza A virus, parvovirus, feline leukemia virus, Borna disease virus, tick-borne encephalitis, canine adenovirus, Neospora caninum, Toxoplasma gondii and Listeria monocytogenes), next-generation sequencing, polymerase chain reaction (fox circovirus) and serum-neutralisation analysis (canine distemper virus) were performed. Furthermore, all animals were screened for fox rabies virus (immunofluorescence), canine distemper virus (immunohistochemistry) and Aujeszky's disease (virus cultivation). The most important findings included encephalitis (n = 16) and pneumonia (n = 20). None of the investigations revealed a specific cause for the observed morphological alterations except for one animal with an elevated serum titer of 1:160 for canine distemper. Animals displayed macroscopically and/or histopathologically detectable infections with parasites, including Taenia sp., Toxocara sp. and Alaria alata. In summary, wildlife predators carry zoonotic parasitic disease and suffer from inflammatory diseases of yet unknown etiology, possibly bearing infectious potential for other animal species and humans. This study highlights the value of monitoring terrestrial wildlife following the "One Health" notion, to estimate the incidence and the possible spread of zoonotic pathogens and to avoid animal to animal spillover as well as transmission to humans.
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Affiliation(s)
- Charlotte Lempp
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Nicole Jungwirth
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Miguel L. Grilo
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Anja Reckendorf
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Arlena Ulrich
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Abbo van Neer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Rogier Bodewes
- Department of Viroscience, The Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Christian Bauer
- Institute of Parasitology, Justus Liebig University Giessen, Giessen, Germany
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
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37
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Focosi D, Antonelli G, Pistello M, Maggi F. Torquetenovirus: the human virome from bench to bedside. Clin Microbiol Infect 2016; 22:589-93. [PMID: 27093875 DOI: 10.1016/j.cmi.2016.04.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/04/2016] [Accepted: 04/10/2016] [Indexed: 12/15/2022]
Abstract
Torquetenovirus (TTV) is the most abundant component of human virome. Virologists have long ignored this orphan and highly divergent virus, in part because TTV cannot be cultured and because it lacks serology reagents and animal models. Nevertheless, it is almost endemic worldwide and is insensitive to current antiviral drugs, so its monitoring is useful in various conditions. To date, TTV as a marker has proved useful in at least two circumstances: to identify anthropogenic pollution and to assess functional immune competence in immunosuppressed individuals. This review summarizes recent findings about TTV and discusses the main hurdles in translating them into clinical diagnostics.
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Affiliation(s)
- D Focosi
- North-Western Tuscany Blood Bank, Italy
| | - G Antonelli
- Laboratory of Virology, Department of Molecular Medicine, and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - M Pistello
- Virology Unit and Retrovirus Centre, Pisa University Hospital, Italy; Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - F Maggi
- Virology Unit and Retrovirus Centre, Pisa University Hospital, Italy.
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38
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Abstract
Why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. The viral envelope serves several functions, including protecting the RNA or DNA molecule(s), evading recognition by the immune system, and facilitating virus entry. Despite these commonalities, viral envelopes come in a wide variety of shapes and configurations. The evolution of the viral envelope is made more puzzling by the fact that nonenveloped viruses are able to infect a diverse range of hosts across the tree of life. We reviewed the entry, transmission, and exit pathways of all (101) viral families on the 2013 International Committee on Taxonomy of Viruses (ICTV) list. By doing this, we revealed a strong association between the lack of a viral envelope and the presence of a cell wall in the hosts these viruses infect. We were able to propose a new hypothesis for the existence of enveloped and nonenveloped viruses, in which the latter represent an adaptation to cells surrounded by a cell wall, while the former are an adaptation to animal cells where cell walls are absent. In particular, cell walls inhibit viral entry and exit, as well as viral transport within an organism, all of which are critical waypoints for successful infection and spread. Finally, we discuss how this new model for the origin of the viral envelope impacts our overall understanding of virus evolution.
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39
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Canuti M, van Beveren NJM, Jazaeri Farsani SM, de Vries M, Deijs M, Jebbink MF, Zaaijer HL, van Schaik BDC, van Kampen AHC, van der Kuyl AC, de Haan L, Storosum JG, van der Hoek L. Viral metagenomics in drug-naïve, first-onset schizophrenia patients with prominent negative symptoms. Psychiatry Res 2015; 229:678-84. [PMID: 26304023 DOI: 10.1016/j.psychres.2015.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 07/16/2015] [Accepted: 08/14/2015] [Indexed: 12/16/2022]
Abstract
Although several studies suggest a virus or (endogenous) retrovirus involvement at the time of onset of schizophrenia, the unequivocal identification of one or more infectious agents, by means of an undirected catch-all technique, has never been conducted. In this study VIDISCA, a virus discovery method, was used in combination with Roche-454 high-throughput sequencing as a tool to determine the possible presence of viruses (known or unknown) in blood of first-onset drugs-naïve schizophrenic patients with prominent negative symptoms. Two viruses (the Anellovirus Torque Teno virus and GB virus C) were detected. Both viruses are commonly found in healthy individuals and no clear link with disease was ever established. Viruses from the family Anelloviridae were also identified in the control population (4.8%). Besides, one patient sample was positive for human endogenous retroviruses type K (HML-2) RNA but no specific predominant strain was detected, instead 119 different variants were found. In conclusion, these findings indicate no evidence for viral or endogenous retroviral involvement in sera at the time of onset of schizophrenia.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Nico J M van Beveren
- Antes, Institute for Mental Health Care, Rotterdam, The Netherlands; Erasmus University Medical Center, Department of Neuroscience, Rotterdam, The Netherlands; Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands; Tehran University of Medical Sciences, Tehran, Iran
| | - Michel de Vries
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hans L Zaaijer
- Department of Blood-Borne Infections, Sanquin Blood Supply Foundation, Amsterdam, The Netherlands; Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Amsterdam, The Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Lieuwe de Haan
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Jitschak G Storosum
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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40
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Canuti M, Buka S, Jazaeri Farsani SM, Oude Munnink BB, Jebbink MF, van Beveren NJM, de Haan L, Goldstein J, Seidman LJ, Tsuang MT, Storosum JG, van der Hoek L. Reduced maternal levels of common viruses during pregnancy predict offspring psychosis: potential role of enhanced maternal immune activity? Schizophr Res 2015; 166:248-54. [PMID: 26004694 DOI: 10.1016/j.schres.2015.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 01/09/2023]
Abstract
Viral infections during the prenatal or early childhood periods are one of the environmental factors which might play an etiological role in psychoses. Several studies report higher antibody levels against viruses during pregnancy in blood of mothers of offspring with psychotic disorders, but the presence of such viruses has never been demonstrated. The goal of this study was to investigate the potential association between viral infections during pregnancy and progeny with psychotic disorders and, for this purpose, we performed a nested case-control study involving pregnant mothers of offspring with schizophrenia or bipolar disorder with psychotic features (cases, N=43) and pregnant women with healthy offspring (controls, N=95). Since several potential viral candidates have been suggested in prior work, a broad-spectrum virus detection system was necessary. A metagenomic analysis performed with the virus discovery method VIDISCA-454 revealed only common blood-associated viruses in all cohorts. However, a significantly lower viral prevalence was detected in the group of cases and in the sub-population of pregnant mothers of offspring with schizophrenia (p<0.05). Consistent with the existing inverse correlation between the level of these viruses and the immunocompetence of an individual, we hypothesized the presence of a higher immune activity during pregnancy in mothers whose offspring later develop a psychotic disorder as compared to controls. Combining our results with previously available literature data on antibody levels during the gestation period suggests that a more prominent maternal immune activity can be considered a risk factor for developing psychosis.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.
| | - Stephen Buka
- Department of Epidemiology, Brown University, Providence, RI, USA.
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Nico J M van Beveren
- Antes, Institute for Mental Health Care, Rotterdam, The Netherlands; Erasmus University Medical Center, Department of Neuroscience, Rotterdam, The Netherlands; Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieuwe de Haan
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Jill Goldstein
- Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Larry J Seidman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, USA
| | - Jitschak G Storosum
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Abstract
Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.
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Exploring the potential of next-generation sequencing in detection of respiratory viruses. J Clin Microbiol 2014; 52:3722-30. [PMID: 25100822 DOI: 10.1128/jcm.01641-14] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Efficient detection of human respiratory viral pathogens is crucial in the management of patients with acute respiratory tract infection. Sequence-independent amplification of nucleic acids combined with next-generation sequencing technology and bioinformatics analyses is a promising strategy for identifying pathogens in clinical and public health settings. It allows the characterization of hundreds of different known pathogens simultaneously and of novel pathogens that elude conventional testing. However, major hurdles for its routine use exist, including cost, turnaround time, and especially sensitivity of the assay, as the detection limit is dependent on viral load, host genetic material, and sequencing depth. To obtain insights into these aspects, we analyzed nasopharyngeal aspirates from a cohort of 81 Thai children with respiratory disease for the presence of respiratory viruses using a sequence-independent next-generation sequencing approach and routinely used diagnostic real-time reverse transcriptase PCR (real-time RT-PCR) assays. With respect to the detection of rhinovirus and human metapneumovirus, the next-generation sequencing approach was at least as sensitive as diagnostic real-time RT-PCR in this small cohort, whereas for bocavirus and enterovirus, next-generation sequencing was less sensitive than real-time RT-PCR. The advantage of the sequencing approach over real-time RT-PCR was the immediate availability of virus-typing information. Considering the development of platforms capable of generating more output data at declining costs, next-generation sequencing remains of interest for future virus diagnosis in clinical and public health settings and certainly as an additional tool when screening results from real-time RT-PCR are negative.
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43
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Leblanc D, Houde A, Gagné MJ, Plante D, Bellon-Gagnon P, Jones TH, Muehlhauser V, Wilhelm B, Avery B, Janecko N, Brassard J. Presence, viral load and characterization of Torque teno sus viruses in liver and pork chop samples at retail. Int J Food Microbiol 2014; 178:60-4. [DOI: 10.1016/j.ijfoodmicro.2014.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 02/24/2014] [Accepted: 03/03/2014] [Indexed: 11/15/2022]
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44
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Smits SL, Zijlstra EE, van Hellemond JJ, Schapendonk CME, Bodewes R, Schürch AC, Haagmans BL, Osterhaus ADME. Novel cyclovirus in human cerebrospinal fluid, Malawi, 2010-2011. Emerg Infect Dis 2014; 19. [PMID: 23968557 PMCID: PMC3810929 DOI: 10.3201/eid1909.130404] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
To identify unknown human viruses, we analyzed serum and cerebrospinal fluid samples from patients with unexplained paraplegia from Malawi by using viral metagenomics. A novel cyclovirus species was identified and subsequently found in 15% and 10% of serum and cerebrospinal fluid samples, respectively. These data expand our knowledge of cyclovirus diversity and tropism.
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45
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Bodewes R, Rubio García A, Wiersma LCM, Getu S, Beukers M, Schapendonk CME, van Run PRWA, van de Bildt MWG, Poen MJ, Osinga N, Sánchez Contreras GJ, Kuiken T, Smits SL, Osterhaus ADME. Novel B19-like parvovirus in the brain of a harbor seal. PLoS One 2013; 8:e79259. [PMID: 24223918 PMCID: PMC3818428 DOI: 10.1371/journal.pone.0079259] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/20/2013] [Indexed: 11/26/2022] Open
Abstract
Using random PCR in combination with next-generation sequencing, a novel parvovirus was detected in the brain of a young harbor seal (Phoca vitulina) with chronic non-suppurative meningo-encephalitis that was rehabilitated at the Seal Rehabilitation and Research Centre (SRRC) in the Netherlands. In addition, two novel viruses belonging to the family Anelloviridae were detected in the lungs of this animal. Phylogenetic analysis of the coding sequence of the novel parvovirus, tentatively called Seal parvovirus, indicated that this virus belonged to the genus Erythrovirus, to which human parvovirus B19 also belongs. Although no other seals with similar signs were rehabilitated in SRRC in recent years, a prevalence study of tissues of seals from the same area collected in the period 2008-2012 indicated that the Seal parvovirus has circulated in the harbor seal population at least since 2008. The presence of the Seal parvovirus in the brain was confirmed by real-time PCR and in vitro replication. Using in situ hybridization, we showed for the first time that a parvovirus of the genus Erythrovirus was present in the Virchow-Robin space and in cerebral parenchyma adjacent to the meninges. These findings showed that a parvovirus of the genus Erythrovirus can be involved in central nervous system infection and inflammation, as has also been suspected but not proven for human parvovirus B19 infection.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- * E-mail:
| | - Ana Rubio García
- Seal Rehabilitation and Research Centre, Pieterburen, the Netherlands
| | | | - Sarah Getu
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Martijn Beukers
- Division of Diagnostic Imaging, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | | | | | - Marjolein J. Poen
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Nynke Osinga
- Seal Rehabilitation and Research Centre, Pieterburen, the Netherlands
| | | | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Saskia L. Smits
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Viroclinics Biosciences B.V., Rotterdam, the Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
- Viroclinics Biosciences B.V., Rotterdam, the Netherlands
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46
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Smits SL, Raj VS, Oduber MD, Schapendonk CME, Bodewes R, Provacia L, Stittelaar KJ, Osterhaus ADME, Haagmans BL. Metagenomic analysis of the ferret fecal viral flora. PLoS One 2013; 8:e71595. [PMID: 23977082 PMCID: PMC3748082 DOI: 10.1371/journal.pone.0071595] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Ferrets are widely used as a small animal model for a number of viral infections, including influenza A virus and SARS coronavirus. To further analyze the microbiological status of ferrets, their fecal viral flora was studied using a metagenomics approach. Novel viruses from the families Picorna-, Papilloma-, and Anelloviridae as well as known viruses from the families Astro-, Corona-, Parvo-, and Hepeviridae were identified in different ferret cohorts. Ferret kobu- and hepatitis E virus were mainly present in human household ferrets, whereas coronaviruses were found both in household as well as farm ferrets. Our studies illuminate the viral diversity found in ferrets and provide tools to prescreen for newly identified viruses that potentially could influence disease outcome of experimental virus infections in ferrets.
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Affiliation(s)
- Saskia L. Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- Viroclinics Biosciences BV, Rotterdam, The Netherlands
- * E-mail:
| | - V. Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Minoushka D. Oduber
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisette Provacia
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- Viroclinics Biosciences BV, Rotterdam, The Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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47
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Brassard J, Gagné MJ, Leblanc D. Real-time PCR study of the infection dynamics of Torque teno sus viruses in naturally infected pigs from nursery to slaughterhouse. Vet J 2013; 197:506-8. [DOI: 10.1016/j.tvjl.2013.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/05/2012] [Accepted: 01/07/2013] [Indexed: 10/27/2022]
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48
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Increased prevalence of anellovirus in pediatric patients with fever. PLoS One 2012; 7:e50937. [PMID: 23226428 PMCID: PMC3511395 DOI: 10.1371/journal.pone.0050937] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/25/2012] [Indexed: 01/03/2023] Open
Abstract
The Anelloviridae family consists of non-enveloped, circular, single-stranded DNA viruses. Three genera of anellovirus are known to infect humans, named TTV, TTMDV, and TTMV. Although anelloviruses were initially thought to cause non-A-G viral hepatitis, continued research has shown no definitive associations between anellovirus and human disease to date. Using high-throughput sequencing, we investigated the association between anelloviruses and fever in pediatric patients 2–36 months of age. We determined that although anelloviruses were present in a large number of specimens from both febrile and afebrile patients, they were more prevalent in the plasma and nasopharyngeal (NP) specimens of febrile patients compared to afebrile controls. Using PCR to detect each of the three species of anellovirus that infect humans, we found that anellovirus species TTV and TTMDV were more prevalent in the plasma and NP specimens of febrile patients compared to afebrile controls. This was not the case for species TTMV which was found in similar percentages of febrile and afebrile patient specimens. Analysis of patient age showed that the percentage of plasma and NP specimens containing anellovirus increased with age until patients were 19–24 months of age, after which the percentage of anellovirus positive patient specimens dropped. This trend was striking for TTV and TTMDV and very modest for TTMV in both plasma and NP specimens. Finally, as the temperature of febrile patients increased, so too did the frequency of TTV and TTMDV detection. Again, TTMV was equally present in both febrile and afebrile patient specimens. Taken together these data indicate that the human anellovirus species TTV and TTMDV are associated with fever in children, while the highly related human anellovirus TTMV has no association with fever.
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49
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Galmès J, Li Y, Rajoharison A, Ren L, Dollet S, Richard N, Vernet G, Javouhey E, Wang J, Telles JN, Paranhos-Baccalà G. Potential implication of new torque teno mini viruses in parapneumonic empyema in children. Eur Respir J 2012; 42:470-9. [PMID: 23060626 PMCID: PMC3729974 DOI: 10.1183/09031936.00107212] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An unexplained increase in the incidence of parapneumonic empyema (PPE) in pneumonia cases has been reported in recent years. The present study investigated the genetic and biological specifications of new isolates of torque teno mini virus (TTMV) detected in pleural effusion samples from children hospitalised for severe pneumonia with PPE. A pathogen discovery protocol was applied in undiagnosed pleural effusion samples and led to the identification of three new isolates of TTMV (TTMV-LY). Isolated TTMV-LY genomes were transfected into A549 and human embryonic kidney 293T cells and viral replication was assessed by quantitative real-time PCR and full-length genome amplification. A549 cells were further infected with released TTMV-LY virions and the induced-innate immune response was measured by multiplex immunoassays. Genetic analyses of the three TTMV-LY genomes revealed a classic genomic organisation but a weak identity (<64%) with known sequences. We demonstrated the in vitro replication of TTMV-LY in alveolar epithelial cells and the effective release of infectious viral particles. We also showed a selective production of inflammatory mediators in response to TTMV infection. This study reports the description of replicative TTMV-LY isolated from parapneumonic effusions of children hospitalised with PPE, suggesting a potential role of the virus in the pathogenesis of pneumonia.
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Affiliation(s)
- Johanna Galmès
- Laboratoire des Pathoge`nes Emergents, Fondation Me´rieux, Lyon, France
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50
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Smits SL, Manandhar A, van Loenen FB, van Leeuwen M, Baarsma GS, Dorrestijn N, Osterhaus ADME, Margolis TP, Verjans GMGM. High prevalence of anelloviruses in vitreous fluid of children with seasonal hyperacute panuveitis. J Infect Dis 2012; 205:1877-84. [PMID: 22492851 PMCID: PMC7107317 DOI: 10.1093/infdis/jis284] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Seasonal hyperacute panuveitis (SHAPU) is a potentially blinding ocular disease occurring in Nepal that principally affects young children. Random amplification of partially purified vitreous fluid (VF)–derived nucleic acid revealed the presence of human anelloviruses in VF of SHAPU patients. In a comparative study of patients with different ocular pathologies, SHAPU patients were at highest risk of harboring anelloviruses in their eyes. The majority of SHAPU patients had multiple anelloviruses in their VF. The ocular anellovirus load in SHAPU and non-SHAPU patients did not differ and no SHAPU-specific anellovirus variant was detected. Analysis of paired serum and VF samples from SHAPU and non-SHAPU patients showed that the anellovirus detected in VF samples most likely originated from the systemic viral pool during viremia, potentially through breakdown of the blood-ocular barrier. The detection of anelloviruses in VF samples of uveitis patients, profoundly so in SHAPU patients, is imperative and warrants elucidation of its clinical significance.
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Affiliation(s)
- Saskia L Smits
- Department of Virology, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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