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Carmona RDCC, Cilli A, da Costa AC, Reis FC, Leal É, dos Santos FCP, Machado BC, Lopes CS, Afonso AMS, Timenetsky MDCST. Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics. Microorganisms 2023; 12:19. [PMID: 38257846 PMCID: PMC10818654 DOI: 10.3390/microorganisms12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.
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Affiliation(s)
| | - Audrey Cilli
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | | | - Fabricio Caldeira Reis
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belem 66075-000, Brazil;
| | | | - Bráulio Caetano Machado
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Cristina Santiago Lopes
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
| | - Ana Maria Sardinha Afonso
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
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da Silva AS, de Campos GM, Villanova MG, Bezerra RDS, Santiago LMM, Haddad R, Covas DT, Giovanetti M, Alcantara LCJ, Elias MC, Sampaio SC, Kashima S, Slavov SN. Human Pegivirus-1 Detection and Genotyping in Brazilian Patients with Fulminant Hepatitis. Pathogens 2023; 12:1122. [PMID: 37764930 PMCID: PMC10536510 DOI: 10.3390/pathogens12091122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/20/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Fulminant hepatitis is a severe clinical disease characterized by a marked decline in liver function and encephalopathy. In a previous survey, using metagenomics in a group of 27 patients with this clinical condition, we observed an expressive quantity of reads of the Human pegivirus-1 (HPgV-1). Therefore, the objective of this study was to evaluate the frequency, molecular features, and HPgV-1 circulating genotypes in patients with fulminant hepatitis. After testing the collected plasma samples, we discovered twelve samples (44.4%) that were positive for HPgV-1 RNA (using both real-time and nested PCR). The positive samples presented a mean cycle threshold (Ct) of 28.5 (±7.3). Genotyping assignments revealed that all HPgV-1 positive samples belonged to the HPgV-1 genotype 2 (both subgenotypes 2A and 2B were identified). Although HPgV-1 is considered a commensal virus, little is known regarding its prevalence and genotypes in cases of fulminant hepatitis. More research is needed to understand whether HPgV-1 can be implicated in clinical disorders and infectious diseases.
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Affiliation(s)
- Anielly Sarana da Silva
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Marcia Guimarães Villanova
- Department of Gastroenterology, University Hospital, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil;
| | - Rafael dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Luciana Maria Mendes Santiago
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Rodrigo Haddad
- Faculty of Ceilândia, University of Brasília, Brasília 72220-275, DF, Brazil;
| | - Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, MG, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
| | - Luiz Carlos Junior Alcantara
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
| | - Maria Carolina Elias
- Center for Scientific Development, Butantan Institute, São Paulo 05503-900, SP, Brazil; (M.C.E.); (S.C.S.)
| | - Sandra Coccuzzo Sampaio
- Center for Scientific Development, Butantan Institute, São Paulo 05503-900, SP, Brazil; (M.C.E.); (S.C.S.)
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil; (A.S.d.S.); (G.M.d.C.); (R.d.S.B.); (L.M.M.S.); (D.T.C.); (S.K.)
- Center for Scientific Development, Butantan Institute, São Paulo 05503-900, SP, Brazil; (M.C.E.); (S.C.S.)
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Luciola Zanette D, Andrade Coelho KBC, de Carvalho E, Aoki MN, Nardin JM, Araújo Lalli L, dos Santos Bezerra R, Giovanetti M, Simionatto Zucherato V, Montenegro de Campos G, de Souza Todão Bernardino J, Louis Viala V, Ciccozzi M, Junior Alcantara LC, Coccuzzo Sampaio S, Elias MC, Kashima S, Tadeu Covas D, Nanev Slavov S. Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer. Mol Cell Oncol 2023; 10:2188858. [PMID: 36950183 PMCID: PMC10026895 DOI: 10.1080/23723556.2023.2188858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Growing evidence suggests that metavirome changes could be associated increased risk for malignant cell transformation. Considering Viruses have been proposed as factors for prostate cancer induction. The objective of this study was to examine the composition of the plasma metavirome of patients with prostate cancer. Blood samples were obtained from 49 male patients with primary prostate adenocarcinoma. Thirty blood donors were included as a control group. The obtained next-generation sequencing data were analyzed using a bioinformatic pipeline for virus metagenomics. Viral reads with higher abundance were assembled in contigs and analyzed taxonomically. Viral agents of interest were also confirmed by qPCR. Anelloviruses and the Human Pegivirus-1 (HPgV-1) were the most abundant component of plasma metavirome. Clinically important viruses like hepatitis C virus (HCV), cytomegalovirus and human adenovirus type C were also identified. In comparison, the blood donor virome was exclusively composed of torque teno virus types (TTV) types. The performed HPgV-1 and HCV phylogeny revealed that these viruses belong to commonly detected in Brazil genotypes. Our study sheds light on the plasma viral abundance in patients with prostatic cancer. The obtained viral diversity allowed us to separate the patients and controls, probably suggesting that malignant processes may influence virome composition. More complex and multiple approach investigations are necessary to examine the likely causal relationship between metavirome and its nvolvement in prostate cancer.
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Affiliation(s)
- Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | | | - Mateus Nobrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | - Larissa Araújo Lalli
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | - Rafael dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victória Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | | | - Massimo Ciccozzi
- Epidemiology and Statistic Unit, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | | | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- CONTACT Svetoslav Nanev Slavov Laboratory of Bioinformatics, Department of Biotechnology (NuCeL), Butantan Institute in Ribeirao Preto, 2501 Tenente Catao Roxo Street, Ribeirao Preto, Sao Paulo14051-140, Brazil
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Valyraki N, Maillart E, Pourcher V, Shor N, Tran S, Boudot de la Motte M, Houiller C, Domont F, Morvan E, Touat M, Del Mar Amador M, Aboab J, Mathon B, Hesters A, Vignal-Clermont C, Dehais C, Bonnin S, Lafitte F, Villain N, Varnous S, Gout O, Eloit M, Rodriguez C, Deschamps R. Human pegivirus identified in severe myelitis and optic neuritis in immunocompromised patients: A pathogenic role for a forgotten virus? Rev Neurol (Paris) 2022; 179:361-367. [PMID: 36302709 DOI: 10.1016/j.neurol.2022.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 11/05/2022]
Abstract
The role of Human pegivirus (HPgV) in patients with encephalitis has been recently questioned. We present cases of 4 patients with similar clinical, biological, and radiological characteristics, including a past history of transplantation with long-term immunosuppression and a progressive course of severe and predominantly myelitis, associated in 3 cases with optic neuropathy causing blindness. Extensive workup was negative but analysis of the CSF by use of pan-microorganism DNA- and RNA-based shotgun metagenomics was positive for HPgV. This case series further supports the hypothesis of HPgV CNS infection and highlights the utility of metagenomic next-generation sequencing of CSF in immunocompromised patients.
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Stapleton JT. Human Pegivirus Type 1: A Common Human Virus That Is Beneficial in Immune-Mediated Disease? Front Immunol 2022; 13:887760. [PMID: 35707535 PMCID: PMC9190258 DOI: 10.3389/fimmu.2022.887760] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022] Open
Abstract
Two groups identified a novel human flavivirus in the mid-1990s. One group named the virus hepatitis G virus (HGV) and the other named it GB Virus type C (GBV-C). Sequence analyses found these two isolates to be the same virus, and subsequent studies found that the virus does not cause hepatitis despite sharing genome organization with hepatitis C virus. Although HGV/GBV-C infection is common and may cause persistent infection in humans, the virus does not appear to directly cause any other known disease state. Thus, the virus was renamed “human pegivirus 1” (HPgV-1) for “persistent G” virus. HPgV-1 is found primarily in lymphocytes and not hepatocytes, and several studies found HPgV-1 infection associated with prolonged survival in people living with HIV. Co-infection of human lymphocytes with HPgV-1 and HIV inhibits HIV replication. Although three viral proteins directly inhibit HIV replication in vitro, the major effects of HPgV-1 leading to reduced HIV-related mortality appear to result from a global reduction in immune activation. HPgV-1 specifically interferes with T cell receptor signaling (TCR) by reducing proximal activation of the lymphocyte specific Src kinase LCK. Although TCR signaling is reduced, T cell activation is not abolished and with sufficient stimulus, T cell functions are enabled. Consequently, HPgV-1 is not associated with immune suppression. The HPgV-1 immunomodulatory effects are associated with beneficial outcomes in other diseases including Ebola virus infection and possibly graft-versus-host-disease following stem cell transplantation. Better understanding of HPgV-1 immune escape and mechanisms of inflammation may identify novel therapies for immune-based diseases.
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Affiliation(s)
- Jack T. Stapleton
- Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, United States
- Departments of Internal Medicine, Microbiology & Immunology, University of Iowa, Iowa City, IA, United States
- *Correspondence: Jack T. Stapleton,
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Infection of Glia by Human Pegivirus Suppresses Peroxisomal and Antiviral Signaling Pathways. J Virol 2021; 95:e0107421. [PMID: 34524914 DOI: 10.1128/jvi.01074-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human pegivirus (HPgV) infects peripheral leukocytes but was recently shown to be a neurotropic virus associated with leukoencephalitis in humans. In the present study, we investigated the neural cell tropism of HPgV as well as its effects on host immune responses. HPgV wild type (WT) and a mutant virus with a deletion in the HPgV NS2 gene (ΔNS2) were able to productively infect human astrocytes and microglia but not neurons or an oligodendrocyte-derived cell line. Of note, the ΔNS2 virus replicated better than WT pegivirus in astrocytes, with both viruses being able to subsequently infect and spread in fresh human astrocyte cultures. Infection of human glia by HPgV WT and ΔNS2 viruses resulted in suppression of peroxisome-associated genes, including PEX11B, ABCD1, PEX7, ABCD3, PEX3, and PEX5L, during peak viral production, which was accompanied by reduced expression of IFNB, IRF3, IRF1, and MAVS, particularly in ΔNS2-infected cells. These data were consistent with analyses of brain tissue from patients infected with HPgV in which we observed suppression of peroxisome and type I interferon gene transcripts, including PEX11B, ABCD3, IRF1, and IRF3, with concurrent loss of PMP70 immunoreactivity in glia. Our data indicate that human astrocytes and microglia are permissive to HPgV infection, resulting in peroxisome injury and suppressed antiviral signaling that is influenced by viral diversity. IMPORTANCE Human pegiviruses are detected in 1 to 5% of the general population, principally infecting leukocytes, although their effects on human health remain uncertain. Here, we show that human pegivirus infects specific neural cell types in culture and human brain and, like other neurotropic flaviviruses, causes suppression of peroxisome and antiviral signaling pathways, which could favor ongoing viral infection and perhaps confer susceptibility to the development of neurological disease.
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Filipiak A, Barć K, Caraballo Cortés K, Pawełczyk A, Radkowski M, Laskus T. Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics. PLoS One 2020; 15:e0240601. [PMID: 33112911 PMCID: PMC7592794 DOI: 10.1371/journal.pone.0240601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Agata Filipiak
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Barć
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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Soliman HK, Abouelhoda M, El Rouby MN, Ahmed OS, Esmat G, Hassan ZK, Hafez MM, Mehaney DA, Selvaraju M, Darwish RK, Osman YA, Zekri ARN. Whole-genome sequencing of human Pegivirus variant from an Egyptian patient co-infected with hepatitis C virus: a case report. Virol J 2019; 16:132. [PMID: 31711510 PMCID: PMC6849219 DOI: 10.1186/s12985-019-1242-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/14/2019] [Indexed: 01/02/2023] Open
Abstract
Background Human pegivirus (HPgV) is structurally similar to hepatitis C virus (HCV) and was discovered 20 years ago. Its distribution, natural history and exact rule of this viral group in human hosts remain unclear. Our aim was to determine, by deep next-generation sequencing (NGS), the entire genome sequence of HPgV that was discovered in an Egyptian patient while analyzing HCV sequence from the same patient. We also inspected whether the co-infection of HCV and HPgV will affect the patient response to HCV viral treatment. To the best of our knowledge, this is the first report for a newly isolated HPgV in an Egyptian patient who is co-infected with HCV. Case presentation The deep Next Generation Sequencing (NGS) technique was used to detect HCV sequence in hepatitis C patient’s plasma. The results revealed the presence of HPgV with HCV. This co-infection was confirmed using conventional PCR of the HPgV 5′ untranslated region. The patient was then subjected to direct-acting-antiviral treatment (DAA). At the end of the treatment, the patient showed a good response to the HCV treatment (i.e., no HCV-RNA was detected in the plasma), while the HPgV-RNA was still detected. Sequence alignment and phylogenetic analyses demonstrated that the detected HPgV was a novel isolate and was not previously published. Conclusion We report a new variant of HPgV in a patient suffering from hepatitis C viral infection.
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Affiliation(s)
- Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, 12613, Egypt
| | - Mahmoud N El Rouby
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - G Esmat
- Endemic Medicine and Hepatology Department, Faculty of Medicine, Cairo University, Cairo, 11562, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Dina Ahmed Mehaney
- Clinical and chemical pathology Department, Faculty of Medicine, Cairo University, Cairo, 11562, Egypt
| | | | - Rania Kamal Darwish
- Clinical and chemical pathology Department, Faculty of Medicine, Cairo University, Cairo, 11562, Egypt
| | - Yehia A Osman
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 33516, Egypt
| | - Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
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Kelishadi M, Hashemi P, Ashrafi G, Behnampour N, Tabarraei A. Presence of GB Virus C in Whole-Blood Derivatives: A Pilot Study. MEDICAL LABORATORY JOURNAL 2019. [DOI: 10.29252/mlj.13.5.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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10
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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: 7] [Impact Index Per Article: 1.4] [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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11
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Molecular and Clinical Profiles of Human Pegivirus Type 1 Infection in Individuals Living with HIV-1 in the Extreme South of Brazil. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8048670. [PMID: 31309117 PMCID: PMC6594344 DOI: 10.1155/2019/8048670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 01/25/2023]
Abstract
Human pegivirus type 1 (HPgV-1) infection has been associated with a beneficial effect on the prognosis of human immunodeficiency virus type 1 (HIV-1)-coinfected individuals. However, the mechanisms involved in this protection are not yet fully elucidated. To date, circulating HPgV-1 genotypes in HIV-1-infected individuals have not yet been identified in the extreme south of Brazil. The present study aimed to determine the genotypic circulation of HPgV-1 and the influence of HPgV-1 status and persistence time on the evolution of HIV-1 infection. A retrospective cohort of 110 coinfected individuals was analyzed. Samples were subjected to viral RNA extraction, cDNA synthesis, nested PCR, and genotyping. Genotypes 1 (2.8%), 2 (47.9% of subtype 2a and 42.3% of subtype 2b), and 3 (7%) were identified. In antiretroviral treatment-naïve subjects HPgV-1 subtype 2b was associated with lower HIV-1 viral load (VL) rates (p = 0.04) and higher CD4+ T-cell counts (p = 0.03) than was subtype 2a, and the positivity for HPgV-1 was associated with higher CD4+ T-cell counts (p = 0.02). However, there was no significant difference in HIV-1 VL between HPgV-1-positive and HPgV-1-negative subjects (p = 0.08). There was no significant association between the different groups in HPgV-1 persistence and median HIV-1 VL (p = 0.66) or CD4+ T-cell counts (p = 0.15). HPgV-1 subtype 2b is associated with better prognosis of HIV-1 infection. Although HPgV-1 infection is persistent, our data suggest that the time of infection does not influence HIV-1 VL or CD4+ T-cell counts in coinfected subjects.
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Bukowska-Ośko I, Perlejewski K, Pawełczyk A, Rydzanicz M, Pollak A, Popiel M, Cortés KC, Paciorek M, Horban A, Dzieciątkowski T, Radkowski M, Laskus T. Human Pegivirus in Patients with Encephalitis of Unclear Etiology, Poland. Emerg Infect Dis 2019; 24:1785-1794. [PMID: 30226156 PMCID: PMC6154136 DOI: 10.3201/eid2410.180161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of human pegivirus from 3 patients indicates that the central nervous system constitutes a separate viral compartment from serum. Human pegivirus (HPgV), previously called hepatitis G virus or GB virus C, is a lymphotropic virus with undefined pathology. Because many viruses from the family Flaviviridae, to which HPgV belongs, are neurotropic, we studied whether HPgV could infect the central nervous system. We tested serum and cerebrospinal fluid samples from 96 patients with a diagnosis of encephalitis for a variety of pathogens by molecular methods and serology; we also tested for autoantibodies against neuronal antigens. We found HPgV in serum and cerebrospinal fluid from 3 patients who had encephalitis of unclear origin; that is, all the markers that had been tested were negative. Single-strand confirmation polymorphism and next-generation sequencing analysis revealed differences between the serum and cerebrospinal fluid–derived viral sequences, which is compatible with the presence of a separate HPgV compartment in the central nervous system. It is unclear whether HPgV was directly responsible for encephalitis in these patients.
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13
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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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14
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Balcom EF, Doan MAL, Branton WG, Jovel J, Blevins G, Edguer B, Hobman TC, Yacyshyn E, Emery D, Box A, van Landeghem FKH, Power C. Human pegivirus-1 associated leukoencephalitis: Clinical and molecular features. Ann Neurol 2018; 84:781-787. [PMID: 30246885 DOI: 10.1002/ana.25343] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/14/2018] [Accepted: 09/10/2018] [Indexed: 01/23/2023]
Abstract
Etiologic diagnosis is uncertain in 35% to 50% of patients with encephalitis, despite its substantial global prevalence and disease burden. We report on 2 adult female patients with fatal leukoencephalitis associated with human pegivirus-1 (HPgV-1) brain infection. Neuroimaging showed inflammatory changes in cerebral white matter. Brain-derived HPgV-1 RNA sequences clustered phylogenetically with other pegiviruses despite an 87-nucleotide deletion in the viral nonstructural (NS)2 gene. Neuropathology disclosed lymphocyte infiltration and gliosis predominantly in brain white matter. HPgV-1 NS5A antigen was detected in lymphocytes as well as in astrocytes and oligodendrocytes. HPgV-1 neuroadaptation should be considered in the differential diagnosis of progressive leukoencephalitis in humans. Ann Neurol 2018;84:789-795.
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Affiliation(s)
- Erin F Balcom
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Matthew A L Doan
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | | - Juan Jovel
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Gregg Blevins
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Beste Edguer
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Tom C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Elaine Yacyshyn
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Derek Emery
- Department of Radiology & Diagnostic Imaging, University of Alberta, Edmonton, AB, Canada
| | - Adrian Box
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada
| | - Frank K H van Landeghem
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada.,Department of Neuroscience & Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Christopher Power
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Department of Neuroscience & Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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15
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Kriesel JD, Bhetariya PJ, Chan BK, Wilson T, Fischer KF. Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases. ACTA ACUST UNITED AC 2017; 3. [PMID: 29202119 PMCID: PMC5707126 DOI: 10.16966/2473-1846.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Our group has used deep sequencing to identify viral RNA signatures in human brain specimens. We have previously used this method to detect HSV1, GBV-C, and measles virus sequence in brain tissue from deceased donors. Deep sequencing was performed on brain specimens from a cohort of patients who died with progressive forms of MS, revealing evidence of increased expression of some human endogenous retrovirus (HERV) domains. Objectives Identify RNA sequences and new antigens involved in the pathogenesis of MS Methods Deep sequencing was performed on RNA extracted from 12 progressive MS, 2 neuromyelitis optica (MS/NMO = demyelination group), 14 normal control, and 7 other neurologic disease (OND) control frozen brain specimens. The resulting single-ended 50 bp sequences (reads) were compared to a non redundant viral database representing (NRVDB) all 1.2 M viral records in GenBank. A retroviral gene catalog (RVGC) was prepared by identifying human genetic loci (GRCh37.p13) homologous to domains contained in the Gypsy 2.0 retro element database. Reads were aligned to the RVGC and human transcriptome with Bowtie2. The resulting viral hit rates (VHRs) were normalized by the number of high quality reads. The expression of human genes, including HERVs, was determined using Cufflinks. Comparisons between the groups were performed using the false discovery rate. Results Fifty to 131 million high quality reads per specimen were obtained. Comparison of the reads to the NRVDB suggested that the demyelination and OND specimens had higher VHRs against some retroviral sequences compared with the controls. This was confirmed by retroviral domain averaging. Gene expression analysis showed differential expression among some HERV sequences. Single read mapping revealed one envelope and one reverse transcriptase sequence record that were significantly enriched among the demyelination samples compared to the normal controls. Less restrictive (comprehensive) read mapping showed that 2 integrase, 2 core, 2 envelope, and 3 KRAB sequences that were overexpressed in the demyelination group. Conclusions These data demonstrate that some endogenous retroviral sequences are significantly overexpressed in these demyelination brain tissue specimens, but the magnitude of this overexpression is small. This is consistent with the concept of HERV activation as a part of the innate immune response.
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Affiliation(s)
- J D Kriesel
- Department of Internal Medicine, Division of Infectious Diseases, USA
| | - P J Bhetariya
- Department of Internal Medicine, Division of Infectious Diseases, USA
| | - B K Chan
- Yale University, Department of Ecology and Evolutionary Biology, New Haven, Connecticut, USA
| | - T Wilson
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - K F Fischer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
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16
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Mentis AFA, Dardiotis E, Grigoriadis N, Petinaki E, Hadjigeorgiou GM. Viruses and Multiple Sclerosis: From Mechanisms and Pathways to Translational Research Opportunities. Mol Neurobiol 2017; 54:3911-3923. [PMID: 28455696 DOI: 10.1007/s12035-017-0530-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/06/2017] [Indexed: 12/26/2022]
Abstract
Viruses are directly or indirectly implicated in multiple sclerosis (MS). Here, we review the evidence on the virus-related pathophysiology of MS, introduce common experimental models, and explore the ways in which viruses cause demyelination. By emphasizing knowledge gaps, we highlight future research directions for effective MS diagnostics and therapies: (i) identifying biomarkers for at-risk individuals, (ii) searching for direct evidence of specific causative viruses, (iii) establishing the contribution of host genetic factors and viruses, and (iv) investigating the contribution of immune regulation at extra-CNS sites. Research in these areas is likely to be facilitated by the application of high-throughput technologies, the development of systems-based bioinformatic approaches, careful selection of experimental models, and the acquisition of high-quality clinical material for tissue-based research.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Department of Microbiology, University Hospital of Larissa, University of Thessaly, Larissa, Greece. .,The Johns Hopkins University, AAP, Baltimore, MD, USA.
| | - Efthimios Dardiotis
- Department of Neurology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Nikolaos Grigoriadis
- B' Department of Neurology, Laboratory of Experimental Neurology and Neuroimmunology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Petinaki
- Department of Microbiology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Georgios M Hadjigeorgiou
- Department of Neurology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
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Human pegivirus-1 in the CSF of patients with HIV-associated neurocognitive disorder (HAND) may be derived from blood in highly viraemic patients. J Clin Virol 2017; 91:58-61. [PMID: 28499138 DOI: 10.1016/j.jcv.2017.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 04/05/2017] [Indexed: 11/20/2022]
Abstract
BACKGROUND Human pegivirus-1 (HPgV-1) infection in the brain has not been extensively examined and its association with disease remains unconfirmed. In a high throughput sequencing study to look for infectious agents that could play a role in HIV-associated neurocognitive disorder (HAND), this virus was detected in 3 of 8 CSF samples. OBJECTIVES To determine the significance of this finding, additional patients were screened and the viral load and viral diversity in blood and CSF were examined. STUDY DESIGN Nested PCR of the viral 5'NCR region was performed on blood and CSF pairs from 16 HAND patients. PCR products were cloned, sequenced and analysed to determine viral diversity in blood and CSF. HPgV-1 viral loads were determined in paired blood and CSF of 2 patients by digital droplet PCR. Nested PCR was also performed on CSF samples from patients with other brain disorders. RESULTS Virus was detected in both blood and CSF in 3 of 16 HAND patients. Viral loads were very high in blood (8.81 and 10.56 log copies/ml) and 4-5 logs lower in CSF (4.68 and 5.84 log copies/ml). Sequence analysis of 5'NCR clones in blood and CSF showed limited variation. The dominant viral variant (based on clonal sequence identity) in blood and CSF was usually identical. HPgV-1 was detected in CSF from patients with other brain disorders at a similar frequency (15% versus 18.75% in HAND patients). CONCLUSION While several studies have reported HPgV-1 detection in CSF of patients with brain disease, this is the only study that has examined both blood and CSF compartments simultaneously. Our findings show that virus in CSF always coincided with viraemia and levels were 4-5 logs higher in blood. While a rare, but specific brain tropism cannot be excluded, blood is the more probable source of virus in HAND patients.
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18
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Parker J, Chen J. Application of next generation sequencing for the detection of human viral pathogens in clinical specimens. J Clin Virol 2016; 86:20-26. [PMID: 27902961 DOI: 10.1016/j.jcv.2016.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/02/2016] [Accepted: 11/21/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis. OBJECTIVES To investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods. STUDY DESIGN Illumina MiSeq system was used to detect viral pathogens alongside other conventional virology methods using typical clinical specimen matrices. Sixteen clinical specimens and two CDC proficiency panels containing seventeen specimens were analyzed. RESULTS Known pathogenic viral nucleic acid was positively identified in all clinical specimens, correlating and building upon results obtained by more conventional laboratory methods. Sequencing depths ranged from 0.008X to 319 and genome coverage ranged from 0.6% to 99.9%. To substantiate the described methods used to analyze data derived from clinical specimens, the results of a clinical proficiency panel are also presented. DISCUSSION Our results reveal true scarcity of known pathogenic viral nucleic acids in clinical specimens. NGS outperforms more conventional detection methods in this study by turnaround time as well as the improved depth of knowledge in regards to serotyping and drug resistance.
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Affiliation(s)
- Jayme Parker
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA
| | - Jack Chen
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA.
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19
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Human pegivirus detected in a patient with severe encephalitis using a metagenomic pan-virus array. J Clin Virol 2016; 77:5-8. [PMID: 26872326 PMCID: PMC7106502 DOI: 10.1016/j.jcv.2016.01.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/04/2015] [Accepted: 01/27/2016] [Indexed: 01/20/2023]
Abstract
Metagenomic microarray for unbiased detection of virus in patient samples. Discovery of an occult viral infection, HPgV, in the spinal fluid of a patient with severe encephalitis. HPgV can on rare occasions enter the CSF at high viral load, but uncertain if its presence in the CNS has any clinical implications.
We have used a metagenomic microarray to detect genomic RNA from human pegivirus in serum and cerebrospinal fluid from a patient suffering from severe encephalitis. No other pathogen was detected. HPgV in cerebrospinal fluid during encephalitis has never been reported before and its prevalence in cerebrospinal fluid needs further investigation.
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20
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Application of “Omics” Technologies for Diagnosis and Pathogenesis of Neurological Infections. Curr Neurol Neurosci Rep 2015. [DOI: 10.1007/s11910-015-0580-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Detection of GB virus C genomic sequence in the cerebrospinal fluid of a HIV-infected patient in China: a case report and literature review. Epidemiol Infect 2015; 144:106-12. [PMID: 26081197 DOI: 10.1017/s0950268815001326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Hepatitis G virus or GB virus C (GBV-C) is a human virus of the Flaviviridae family that is structurally and epidemiologically closest to hepatitis C virus, but replicates primarily in lymphocytes. Co-infection with GBV-C has been reported to confer beneficial outcomes in some HIV-positive patients. Up to now, however, studies on GBV-C infection in the central nervous system (CNS) of HIV-infected patient have rarely been reported. Herein, we report on a 32-year-old HIV-1-infected patient with cerebral toxoplasmosis and fungal encephalitis. GBV-C viral loads were detected in CSF by quantitative real-time reverse transcription polymerase chain reaction (RT-PCR), and the results showed that GBV-C viral load was 6·5 log copies/ml. We amplified and sequenced the E2 and 5'-untranslated regions from the purified viral RNA from CSF by RT-PCR. Both sequences belong to genotype 3 and there were some minor nucleotide divergence among the E2 sequences from the CSF of the patient. These data suggest that GBV-C may be able to penetrate the blood-brain barrier and colonize the CNS of HIV-infected patients. However, the exact mechanisms and potential effect of the infected GBV-C in CNS on HIV-associated neuropathy needs to be further explored.
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Ganova-Raeva L, Punkova L, Campo DS, Dimitrova Z, Skums P, Vu NH, Dat DT, Dalton HR, Khudyakov Y. Cryptic Hepatitis B and E in Patients With Acute Hepatitis of Unknown Etiology. J Infect Dis 2015; 212:1962-9. [PMID: 26155829 DOI: 10.1093/infdis/jiv315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/25/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Up to 30% of acute viral hepatitis has no known etiology. To determine the disease etiology in patients with acute hepatitis of unknown etiology (HUE), serum specimens were obtained from 38 patients residing in the United Kingdom and Vietnam and from 26 healthy US blood donors. All specimens tested negative for known viral infections causing hepatitis, using commercially available serological and nucleic acid assays. METHODS Specimens were processed by sequence-independent complementary DNA amplification and next-generation sequencing (NGS). Sufficient material for individual NGS libraries was obtained from 12 HUE cases and 26 blood donors; the remaining HUE cases were sequenced as a pool. Read mapping was done by targeted and de novo assembly. RESULTS Sequences from hepatitis B virus (HBV) were detected in 7 individuals with HUE (58.3%) and the pooled library, and hepatitis E virus (HEV) was detected in 2 individuals with HUE (16.7%) and the pooled library. Both HEV-positive cases were coinfected with HBV. HBV sequences belonged to genotypes A, D, or G, and HEV sequences belonged to genotype 3. No known hepatotropic viruses were detected in the tested normal human sera. CONCLUSIONS NGS-based detection of HBV and HEV infections is more sensitive than using commercially available assays. HBV and HEV may be cryptically associated with HUE.
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Affiliation(s)
- Lilia Ganova-Raeva
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lili Punkova
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David S Campo
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Zoya Dimitrova
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pavel Skums
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Harry R Dalton
- Cornwall Gastrointestinal Unit, Royal Cornwall Hospital Trust and European Centre for the Environment and Human Health, University of Exeter Medical School, Truro, United Kingdom
| | - Yury Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
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Chan BK, Wilson T, Fischer KF, Kriesel JD. Deep sequencing to identify the causes of viral encephalitis. PLoS One 2014; 9:e93993. [PMID: 24699691 PMCID: PMC3974838 DOI: 10.1371/journal.pone.0093993] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/10/2014] [Indexed: 01/19/2023] Open
Abstract
Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue.
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Affiliation(s)
- Benjamin K. Chan
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Theodore Wilson
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Kael F. Fischer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - John D. Kriesel
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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McElroy K, Thomas T, Luciani F. Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. MICROBIAL INFORMATICS AND EXPERIMENTATION 2014; 4:1. [PMID: 24428920 PMCID: PMC3902414 DOI: 10.1186/2042-5783-4-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/07/2014] [Indexed: 12/15/2022]
Abstract
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies. While it is clear that deep sequencing has unprecedented potential for assessing the genetic structure and evolutionary history of pathogen populations, bioinformatic challenges remain. We summarise current approaches to overcoming these challenges, in particular methods for detecting low frequency variants in the context of sequencing error and reconstructing individual haplotypes from short reads.
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Affiliation(s)
- Kerensa McElroy
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia.
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25
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Calabrese C, Mangiulli M, Manzari C, Paluscio AM, Caratozzolo MF, Marzano F, Kurelac I, D'Erchia AM, D'Elia D, Licciulli F, Liuni S, Picardi E, Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, Tullo A. A platform independent RNA-Seq protocol for the detection of transcriptome complexity. BMC Genomics 2013; 14:855. [PMID: 24308330 PMCID: PMC4046740 DOI: 10.1186/1471-2164-14-855] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein coding genes and their splice variants. Indeed, most transcripts are the result of antisense, overlapping and non-coding RNA expression. In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the choice of the strategy for cDNA library construction. The protocols developed so far provide the utilization of the entire library for a single sequencing run with a specific platform. RESULTS We set up a unique protocol to generate and amplify a strand-specific cDNA library representative of all RNA species that may be implemented with all major platforms currently available on the market (Roche 454, Illumina, ABI/SOLiD). Our method is reproducible, fast, easy-to-perform and even allows to start from low input total RNA. Furthermore, we provide a suitable bioinformatics tool for the analysis of the sequences produced following this protocol. CONCLUSION We tested the efficiency of our strategy, showing that our method is platform-independent, thus allowing the simultaneous analysis of the same sample with different NGS technologies, and providing an accurate quantitative and qualitative portrait of complex whole transcriptomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Apollonia Tullo
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy.
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Handel AE, Disanto G, Ramagopalan SV. Next-generation sequencing in understanding complex neurological disease. Expert Rev Neurother 2013; 13:215-27. [PMID: 23368808 DOI: 10.1586/ern.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.
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Affiliation(s)
- Adam E Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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Poojari S, Alabi OJ, Fofanov VY, Naidu RA. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 2013; 8:e64194. [PMID: 23755117 PMCID: PMC3673993 DOI: 10.1371/journal.pone.0064194] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/10/2013] [Indexed: 01/25/2023] Open
Abstract
A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.
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Affiliation(s)
- Sudarsana Poojari
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
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Wood HM, Bolt R, Hunter KD. Is next-generation sequencing an important tool in HPV subtype diagnosis? Expert Rev Mol Diagn 2013; 12:663-5. [PMID: 23153231 DOI: 10.1586/erm.12.67] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Harris MG, Fabry Z. Initiation and Regulation of CNS Autoimmunity: Balancing Immune Surveillance and Inflammation in the CNS. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/nm.2012.33026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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