151
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Kufner V, Plate A, Schmutz S, Braun DL, Günthard HF, Capaul R, Zbinden A, Mueller NJ, Trkola A, Huber M. Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases. Genes (Basel) 2019; 10:genes10090661. [PMID: 31470675 PMCID: PMC6770117 DOI: 10.3390/genes10090661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 01/28/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plate
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Dominique L Braun
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
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152
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Abstract
Neuroinfectious diseases continue to cause morbidity and mortality worldwide, with many emerging or reemerging infections resulting in neurologic sequelae. Careful clinical evaluation coupled with appropriate laboratory investigations still forms the bedrock for making the correct etiologic diagnosis and implementing appropriate management. The treating physician needs to understand the individual test characteristics of each of the many conventional candidate-based diagnostics: culture, pathogen-specific polymerase chain reaction, antigen, antibody tests, used to diagnose the whole array of neuroinvasive infections. In addition, there is a growing need for more comprehensive, agnostic testing modalities that can identify a diversity of infections with a single assay.
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Affiliation(s)
- Prashanth S Ramachandran
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, 675 Nelson Rising Lane, NS212A, Campus Box 3206, San Francisco, CA 94158, USA
| | - Michael R Wilson
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, 675 Nelson Rising Lane, NS212A, Campus Box 3206, San Francisco, CA 94158, USA.
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153
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Lim XF, Lee CB, Pascoe SM, How CB, Chan S, Tan JH, Yang X, Zhou P, Shi Z, Sessions OM, Wang LF, Ng LC, Anderson DE, Yap G. Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches. J Gen Virol 2019; 100:1363-1374. [PMID: 31418677 PMCID: PMC7079695 DOI: 10.1099/jgv.0.001307] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bats are important reservoirs and vectors in the transmission of emerging infectious diseases. Many highly pathogenic viruses such as SARS-CoV and rabies-related lyssaviruses have crossed species barriers to infect humans and other animals. In this study we monitored the major roost sites of bats in Singapore, and performed surveillance for zoonotic pathogens in these bats. Screening of guano samples collected during the survey uncovered a bat coronavirus (Betacoronavirus) in Cynopterus brachyotis, commonly known as the lesser dog-faced fruit bat. Using a capture-enrichment sequencing platform, the full-length genome of the bat CoV was sequenced and found to be closely related to the bat coronavirus HKU9 species found in Leschenault’s rousette discovered in the Guangdong and Yunnan provinces.
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Affiliation(s)
- Xiao Fang Lim
- Environmental Health Institute, National Environment Agency, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | | | | | - Choon Beng How
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Sharon Chan
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Jun Hao Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Xinglou Yang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peng Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Zhengli Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - October M Sessions
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Grace Yap
- Environmental Health Institute, National Environment Agency, Singapore
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154
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Mishra N, Ng TFF, Marine RL, Jain K, Ng J, Thakkar R, Caciula A, Price A, Garcia JA, Burns JC, Thakur KT, Hetzler KL, Routh JA, Konopka-Anstadt JL, Nix WA, Tokarz R, Briese T, Oberste MS, Lipkin WI. Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis. mBio 2019; 10:e01903-19. [PMID: 31409689 PMCID: PMC6692520 DOI: 10.1128/mbio.01903-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023] Open
Abstract
Acute flaccid myelitis (AFM) has caused motor paralysis in >560 children in the United States since 2014. The temporal association of enterovirus (EV) outbreaks with increases in AFM cases and reports of fever, respiratory, or gastrointestinal illness prior to AFM in >90% of cases suggest a role for infectious agents. Cerebrospinal fluid (CSF) from 14 AFM and 5 non-AFM patients with central nervous system (CNS) diseases in 2018 were investigated by viral-capture high-throughput sequencing (VirCapSeq-VERT system). These CSF and serum samples, as well as multiple controls, were tested for antibodies to human EVs using peptide microarrays. EV RNA was confirmed in CSF from only 1 adult AFM case and 1 non-AFM case. In contrast, antibodies to EV peptides were present in CSF of 11 of 14 AFM patients (79%), significantly higher than controls, including non-AFM patients (1/5 [20%]), children with Kawasaki disease (0/10), and adults with non-AFM CNS diseases (2/11 [18%]) (P = 0.023, 0.0001, and 0.0028, respectively). Six of 14 CSF samples (43%) and 8 of 11 sera (73%) from AFM patients were immunoreactive to an EV-D68-specific peptide, whereas the three control groups were not immunoreactive in either CSF (0/5, 0/10, and 0/11; P = 0.008, 0.0003, and 0.035, respectively) or sera (0/2, 0/8, and 0/5; P = 0.139, 0.002, and 0.009, respectively).IMPORTANCE The presence in cerebrospinal fluid of antibodies to EV peptides at higher levels than non-AFM controls supports the plausibility of a link between EV infection and AFM that warrants further investigation and has the potential to lead to strategies for diagnosis and prevention of disease.
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MESH Headings
- Adolescent
- Adult
- Antibodies, Viral/blood
- Antibodies, Viral/cerebrospinal fluid
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Central Nervous System Viral Diseases/blood
- Central Nervous System Viral Diseases/cerebrospinal fluid
- Child
- Enterovirus D, Human/genetics
- Enterovirus D, Human/immunology
- Enterovirus D, Human/isolation & purification
- Enterovirus Infections/blood
- Enterovirus Infections/cerebrospinal fluid
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Middle Aged
- Myelitis/blood
- Myelitis/cerebrospinal fluid
- Neuromuscular Diseases/blood
- Neuromuscular Diseases/cerebrospinal fluid
- Protein Array Analysis
- RNA, Viral/blood
- RNA, Viral/cerebrospinal fluid
- RNA, Viral/genetics
- Young Adult
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Affiliation(s)
- Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Adrian Caciula
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Joel A Garcia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Jane C Burns
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Kiran T Thakur
- Division of Critical Care and Hospitalist Neurology, Department of Neurology, Columbia Irving University Medical Center, New York, New York, USA
| | - Kimbell L Hetzler
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janell A Routh
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
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155
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Novel insights and therapeutic approaches in idiopathic multicentric Castleman disease. Blood 2019; 132:2323-2330. [PMID: 30487129 DOI: 10.1182/blood-2018-05-848671] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/05/2018] [Indexed: 12/12/2022] Open
Abstract
Castleman disease (CD) describes a heterogeneous group of hematologic disorders that share characteristic lymph node histopathology. Patients of all ages present with either a solitary enlarged lymph node (unicentric CD) or multicentric lymphadenopathy (MCD) with systemic inflammation, cytopenias, and life-threatening multiple organ dysfunction resulting from a cytokine storm often driven by interleukin 6 (IL-6). Uncontrolled human herpesvirus-8 (HHV-8) infection causes approximately 50% of MCD cases, whereas the etiology is unknown in the remaining HHV-8-negative/idiopathic MCD cases (iMCD). The limited understanding of etiology, cell types, and signaling pathways involved in iMCD has slowed development of treatments and contributed to historically poor patient outcomes. Here, recent progress for diagnosing iMCD, characterizing etio-pathogenesis, and advancing treatments are reviewed. Several clinicopathological analyses provided the evidence base for the first-ever diagnostic criteria and revealed distinct clinical subtypes: thrombocytopenia, anasarca, fever, reticulin fibrosis/renal dysfunction, organomegaly (iMCD-TAFRO) or iMCD-not otherwise specified (iMCD-NOS), which are both observed all over the world. In 2014, the anti-IL-6 therapy siltuximab became the first iMCD treatment approved by the US Food and Drug Administration, on the basis of a 34% durable response rate; consensus guidelines recommend it as front-line therapy. Recent cytokine and proteomic profiling has revealed normal IL-6 levels in many patients with iMCD and potential alternative driver cytokines. Candidate novel genomic alterations, dysregulated cell types, and signaling pathways have also been identified as candidate therapeutic targets. RNA sequencing for viral transcripts did not reveal novel viruses, HHV-8, or other viruses pathologically associated with iMCD. Despite progress, iMCD remains poorly understood. Further efforts to elucidate etiology, pathogenesis, and treatment approaches, particularly for siltuximab-refractory patients, are needed.
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156
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Sichtig H, Minogue T, Yan Y, Stefan C, Hall A, Tallon L, Sadzewicz L, Nadendla S, Klimke W, Hatcher E, Shumway M, Aldea DL, Allen J, Koehler J, Slezak T, Lovell S, Schoepp R, Scherf U. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun 2019; 10:3313. [PMID: 31346170 PMCID: PMC6658474 DOI: 10.1038/s41467-019-11306-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes as a public database for diagnostic purposes and demonstrate its utility on the example of two use cases. We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests. The use of FDA-ARGOS as an in silico target sequence comparator tool combined with representative clinical testing could reduce the burden for completing ID-NGS clinical trials. To be able to use infectious disease next generation sequencing as a diagnostic tool, appropriate reference datasets are required. Here, Sichtig et al. describe FDA-ARGOS, a reference database for high-quality microbial reference genomes, and demonstrate its utility on the example of two use cases.
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Affiliation(s)
- Heike Sichtig
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
| | - Timothy Minogue
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA.
| | - Yi Yan
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Christopher Stefan
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Adrienne Hall
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Luke Tallon
- Institute for Genome Sciences at the University of Maryland, 670 W. Baltimore Street, Baltimore, MD, 21201, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences at the University of Maryland, 670 W. Baltimore Street, Baltimore, MD, 21201, USA
| | - Suvarna Nadendla
- Institute for Genome Sciences at the University of Maryland, 670 W. Baltimore Street, Baltimore, MD, 21201, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Eneida Hatcher
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Martin Shumway
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | | | - Jonathan Allen
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA, 94551, USA
| | - Jeffrey Koehler
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Tom Slezak
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA, 94551, USA
| | - Stephen Lovell
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Randal Schoepp
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Uwe Scherf
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
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157
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Hor KN, Johnston P, Kinnett K, Mah ML, Stiver C, Markham L, Cripe L. Progression of Duchenne Cardiomyopathy Presenting with Chest Pain and Troponin Elevation. J Neuromuscul Dis 2019; 4:307-314. [PMID: 28984614 DOI: 10.3233/jnd-170253] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Improved neuromuscular and respiratory therapies have altered the natural history of Duchenne muscular dystrophy (DMD) such that the most common cause of mortality is progressive cardiomyopathy. Despite imaging evidence of progressive cardiomyopathy, troponin I (cTn) is not significantly elevated in asymptomatic DMD patients. RESULTS We describe eight boys with DMD evaluated for acute chest pain (ACP) and found to have acute cTn elevation with depressed left ventricular ejection fraction (LVEF). Of our eight patients, five presented with a primary complaint of ACP, while three presented with secondary myocardial injury in the context of systemic illness requiring hospitalization. Electrocardiograms showed diffuse ST changes and mean peak cTn level was 44±15.4 ng/mL (reference range <0.03 ng/mL). cTn levels normalized with only supportive care. Cardiac magnetic resonance imaging (CMR) was performed during the event on all but one patient, demonstrating increased late gadolinium enhancement (LGE) from 12.4±11.4% to 36.5±10.3% with associated deterioration of LVEF from 61±4.4% to 47.6±6.6% which remained depressed on follow-up CMR study (49.1±7.8%). All viral studies were negative. Additional investigations varied among patients, but no causative findings were demonstrated. CONCLUSIONS ACP with cTn elevation occurs in DMD boys and may be indicative of cardiomyopathy progression as evidenced by acute left ventricular dysfunction and development or progression of myocardial fibrosis. This clinical presentation is under recognized. These events may represent an important pathophysiological mechanism in cardiomyopathy progression.
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Affiliation(s)
- Kan N Hor
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Kathi Kinnett
- Parent Project Muscular Dystrophy, Hackensack, NJ, USA
| | - May Ling Mah
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Corey Stiver
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Larry Markham
- Department of Pediatrics, Division of Pediatric Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Cripe
- Nationwide Children's Hospital, Columbus, OH, USA
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158
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Neil JA, Cadwell K. The Intestinal Virome and Immunity. THE JOURNAL OF IMMUNOLOGY 2019; 201:1615-1624. [PMID: 30181300 DOI: 10.4049/jimmunol.1800631] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
The composition of the human microbiome is considered a major source of interindividual variation in immunity and, by extension, susceptibility to diseases. Intestinal bacteria have been the major focus of research. However, diverse communities of viruses that infect microbes and the animal host cohabitate the gastrointestinal tract and collectively constitute the gut virome. Although viruses are typically investigated as pathogens, recent studies highlight a relationship between the host and animal viruses in the gut that is more akin to host-microbiome interactions and includes both beneficial and detrimental outcomes for the host. These viruses are likely sources of immune variation, both locally and extraintestinally. In this review, we describe the components of the gut virome, in particular mammalian viruses, and their ability to modulate host responses during homeostasis and disease.
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Affiliation(s)
- Jessica A Neil
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016; and Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Ken Cadwell
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016; and Department of Microbiology, New York University School of Medicine, New York, NY 10016
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159
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Nabel CS, Sameroff S, Shilling D, Alapat D, Ruth JR, Kawano M, Sato Y, Stone K, Spetalen S, Valdivieso F, Feldman MD, Chadburn A, Fosså A, van Rhee F, Lipkin WI, Fajgenbaum DC. Virome capture sequencing does not identify active viral infection in unicentric and idiopathic multicentric Castleman disease. PLoS One 2019; 14:e0218660. [PMID: 31242229 PMCID: PMC6594611 DOI: 10.1371/journal.pone.0218660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/06/2019] [Indexed: 01/09/2023] Open
Abstract
Castleman disease (CD) describes a spectrum of heterogeneous disorders defined by characteristic lymph node histopathology. Enlarged lymph nodes demonstrating CD histopathology can occur in isolation (unicentric CD; UCD) sometimes accompanied by mild symptoms, or at multiple sites (multicentric CD, MCD) with systemic inflammation and cytokine-driven multi-organ dysfunction. The discovery that Kaposi sarcoma herpesvirus/human herpesvirus (HHV)-8 drives MCD in a subset of patients has led to the hypotheses that UCD and MCD patients with negative HHV-8 testing by conventional methods may represent false negatives, or that these cases are driven by another virus, known or unknown. To investigate these hypotheses, the virome capture sequencing for vertebrate viruses (VirCapSeq-VERT) platform was employed to detect RNA transcripts from known and novel viruses in fresh frozen lymph node tissue from CD patients (12 UCD, 11 HHV-8-negative MCD [idiopathic MCD; iMCD], and two HHV-8-positive MCD) and related diseases (three T cell lymphoma and three Hodgkin lymphoma). This assay detected HHV-8 in both HHV-8-positive cases; however, HHV-8 was not found in clinically HHV-8-negative iMCD or UCD cases. Additionally, no novel viruses were discovered, and no single known virus was detected with apparent association to HHV-8-negative CD cases. Herpesviridae family members, notably including Epstein-Barr virus (EBV), were detected in 7 out of 12 UCD and 5 of 11 iMCD cases with apparent correlations with markers of disease severity in iMCD. Analysis of a separate cohort of archival formalin-fixed, paraffin-embedded lymph node tissue by In situ hybridization revealed significantly fewer EBV-positive cells in UCD and iMCD compared to tissue from HHV-8-positive MCD and EBV-associated lymphoproliferative disorder. In an additional cohort, quantitative testing for EBV by PCR in peripheral blood during disease flare did not detect systemic EBV viremia, suggesting detection lymph node tissue is due to occult, local reactivation in UCD and iMCD. This study confirms that HHV-8 is not present in UCD and iMCD patients. Further, it fails to establish a clear association between any single virus, novel or known, and CD in HHV-8-negative cases. Given that distinct forms of CD exist with viral and non-viral etiological drivers, CD should be considered a group of distinct and separate diseases with heterogeneous causes worthy of further study.
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Affiliation(s)
- Christopher S. Nabel
- Dana-Farber Cancer Institute, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, United States of America
| | - Stephen Sameroff
- Columbia University, New York, New York, United States of America
| | - Dustin Shilling
- Castleman Disease Collaborative Network, Philadelphia, Pennsylvania, United States of America
| | - Daisy Alapat
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Jason R. Ruth
- Castleman Disease Collaborative Network, Philadelphia, Pennsylvania, United States of America
| | | | - Yasuharu Sato
- Division of Pathophysiology, Okayama University Graduate School of Health Sciences, Okayama, Japan
| | - Katie Stone
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | | | - Federico Valdivieso
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael D. Feldman
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | | | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - W. Ian Lipkin
- Columbia University, New York, New York, United States of America
| | - David C. Fajgenbaum
- Castleman Disease Collaborative Network, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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160
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Carleton HA, Besser J, Williams-Newkirk AJ, Huang A, Trees E, Gerner-Smidt P. Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges. Foodborne Pathog Dis 2019; 16:474-479. [PMID: 31170005 PMCID: PMC6653786 DOI: 10.1089/fpd.2019.2636] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.
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Affiliation(s)
- Heather A Carleton
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Besser
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda J Williams-Newkirk
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Andrew Huang
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eija Trees
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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161
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Abstract
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.
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Affiliation(s)
- Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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162
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Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol 2019; 51:39-45. [PMID: 31077935 DOI: 10.1016/j.mib.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 03/08/2019] [Indexed: 10/26/2022]
Abstract
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Alp Aydin
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Michael J Strinden
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Justin O'Grady
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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163
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Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples. PLoS Negl Trop Dis 2019; 13:e0007184. [PMID: 31022183 PMCID: PMC6504110 DOI: 10.1371/journal.pntd.0007184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 05/07/2019] [Accepted: 01/23/2019] [Indexed: 11/19/2022] Open
Abstract
The frequency of epidemics caused by Dengue viruses 1-4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009-2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% ± 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses.
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164
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A Novel Orthohepadnavirus Identified in a Dead Maxwell's Duiker ( Philantomba maxwellii) in Taï National Park, Côte d'Ivoire. Viruses 2019; 11:v11030279. [PMID: 30893858 PMCID: PMC6466360 DOI: 10.3390/v11030279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/11/2019] [Accepted: 03/16/2019] [Indexed: 12/16/2022] Open
Abstract
New technologies enable viral discovery in a diversity of hosts, providing insights into viral evolution. We used one such approach, the virome capture sequencing for vertebrate viruses (VirCapSeq-VERT) platform, on 21 samples originating from six dead Maxwell’s duikers (Philantomba maxwellii) from Taï National Park, Côte d’Ivoire. We detected the presence of an orthohepadnavirus in one animal and characterized its 3128 bp genome. The highest viral copy numbers were detected in the spleen, followed by the lung, blood, and liver, with the lowest copy numbers in the kidney and heart; the virus was not detected in the jejunum. Viral copy numbers in the blood were in the range known from humans with active chronic infections leading to liver histolytic damage, suggesting this virus could be pathogenic in duikers, though many orthohepadnaviruses appear to be apathogenic in other hosts, precluding a formal test of this hypothesis. The virus was not detected in 29 other dead duiker samples from the Côte d’Ivoire and Central African Republic, suggesting either a spillover event or a low prevalence in these populations. Phylogenetic analysis placed the virus as a divergent member of the mammalian clade of orthohepadnaviruses, though its relationship to other orthohepadnaviruses remains uncertain. This represents the first orthohepadnavirus described in an artiodactyl. We have tentatively named this new member of the genus Orthohepadnavirus (family Hepadnaviridae), Taï Forest hepadnavirus. Further studies are needed to determine whether it, or some close relatives, are present in a broader range of artiodactyls, including livestock.
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165
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Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection. Sci Rep 2019; 9:2760. [PMID: 30809003 PMCID: PMC6391440 DOI: 10.1038/s41598-019-39406-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/18/2019] [Indexed: 01/17/2023] Open
Abstract
Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980’s. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.
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166
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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167
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Kim KW, Horton JL, Pang CNI, Jain K, Leung P, Isaacs SR, Bull RA, Luciani F, Wilkins MR, Catteau J, Lipkin WI, Rawlinson WD, Briese T, Craig ME. Higher abundance of enterovirus A species in the gut of children with islet autoimmunity. Sci Rep 2019; 9:1749. [PMID: 30741981 PMCID: PMC6370883 DOI: 10.1038/s41598-018-38368-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Enteroviruses (EVs) are prime candidate environmental triggers of islet autoimmunity (IA), with potential as vaccine targets for type 1 diabetes prevention. However, the use of targeted virus detection methods and the selective focus on EVs by most studies increases the risk for substantial investigation bias and an overestimated association between EV and type 1 diabetes. Here we performed comprehensive virome-capture sequencing to examine all known vertebrate-infecting viruses without bias in 182 specimens (faeces and plasma) collected before or at seroconversion from 45 case children with IA and 48 matched controls. From >2.6 billion reads, 28 genera of viruses were detected and 62% of children (58/93) were positive for ≥1 vertebrate-infecting virus. We identified 129 viruses as differentially abundant between the gut of cases and controls, including 5 EV-A types significantly more abundant in the cases. Our findings further support EV’s hypothesised contribution to IA and corroborate the proposal that viral load may be an important parameter in disease pathogenesis. Furthermore, our data indicate a previously unrecognised association of IA with higher EV-A abundance in the gut of children and provide a catalog of viruses to be interrogated further to determine a causal link between virus infection and type 1 diabetes.
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Affiliation(s)
- Ki Wook Kim
- School of Women's and Children's Health, University of New South Wales Faculty of Medicine, Sydney, Australia.,Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
| | - Jessica L Horton
- School of Women's and Children's Health, University of New South Wales Faculty of Medicine, Sydney, Australia.,Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
| | - Chi Nam Ignatius Pang
- School of Biotechnology and Biomedical Sciences, University of New South Wales Faculty of Science, Sydney, Australia
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA
| | - Preston Leung
- Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales Faculty of Medicine, Sydney, Australia
| | - Sonia R Isaacs
- School of Women's and Children's Health, University of New South Wales Faculty of Medicine, Sydney, Australia.,Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
| | - Rowena A Bull
- Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales Faculty of Medicine, Sydney, Australia
| | - Fabio Luciani
- Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales Faculty of Medicine, Sydney, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomedical Sciences, University of New South Wales Faculty of Science, Sydney, Australia
| | - Jacki Catteau
- Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Sydney, Australia
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA.,Department of Pathology and Neurology, College of Physicians & Surgeons, Columbia University, New York, USA
| | - William D Rawlinson
- School of Women's and Children's Health, University of New South Wales Faculty of Medicine, Sydney, Australia.,Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia.,Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, Prince of Wales Hospital, Sydney, Australia
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Maria E Craig
- School of Women's and Children's Health, University of New South Wales Faculty of Medicine, Sydney, Australia. .,Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia. .,Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Sydney, Australia. .,Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia.
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168
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Jouet A, Saunders DGO, McMullan M, Ward B, Furzer O, Jupe F, Cevik V, Hein I, Thilliez GJA, Holub E, van Oosterhout C, Jones JDG. Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. THE NEW PHYTOLOGIST 2019; 221:1529-1543. [PMID: 30288750 DOI: 10.1111/nph.15417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversity and the consequences of host immunosuppression are poorly understood in the field. We report a method that enables sequencing of DNA of plant pathogens and plant-associated microbes directly from field samples (Pathogen Enrichment Sequencing: PenSeq). We apply this method to explore race diversity in A. candida and to detect A. candida-associated microbes in the field (91 A. candida-infected plants). We show with unprecedented resolution that each host plant species supports colonization by one of 17 distinct phylogenetic lineages, each with an unique repertoire of effector candidate alleles. These data reveal the crucial role of sexual and asexual reproduction, polyploidy and host domestication in A. candida specialization on distinct plant species. Our bait design also enabled phylogenetic assignment of DNA sequences from bacteria and fungi from plants in the field. This paper shows that targeted sequencing has a great potential for the study of pathogen populations while they are colonizing their hosts. This method could be applied to other microbes, especially to those that cannot be cultured.
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Affiliation(s)
- Agathe Jouet
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Ben Ward
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Oliver Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- University of North Carolina, Chapel Hill, NC, 27599-2200, USA
| | - Florian Jupe
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA, 92037, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Ingo Hein
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Division of Plant Sciences at the James Hutton Institute, the University of Dundee, Dundee, DD2 5DA, UK
| | - Gaetan J A Thilliez
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Quadram Institute Bioscience, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
| | - Eric Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Warwick, CV35 9EF, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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169
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Wook Kim K, Allen DW, Briese T, Couper JJ, Barry SC, Colman PG, Cotterill AM, Davis EA, Giles LC, Harrison LC, Harris M, Haynes A, Horton JL, Isaacs SR, Jain K, Lipkin WI, Morahan G, Morbey C, Pang ICN, Papenfuss AT, Penno MAS, Sinnott RO, Soldatos G, Thomson RL, Vuillermin PJ, Wentworth JM, Wilkins MR, Rawlinson WD, Craig ME. Distinct Gut Virome Profile of Pregnant Women With Type 1 Diabetes in the ENDIA Study. Open Forum Infect Dis 2019; 6:ofz025. [PMID: 30815502 PMCID: PMC6386807 DOI: 10.1093/ofid/ofz025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/05/2019] [Accepted: 01/15/2019] [Indexed: 12/11/2022] Open
Abstract
Background The importance of gut bacteria in human physiology, immune regulation, and disease pathogenesis is well established. In contrast, the composition and dynamics of the gut virome are largely unknown; particularly lacking are studies in pregnancy. We used comprehensive virome capture sequencing to characterize the gut virome of pregnant women with and without type 1 diabetes (T1D), longitudinally followed in the Environmental Determinants of Islet Autoimmunity study. Methods In total, 61 pregnant women (35 with T1D and 26 without) from Australia were examined. Nucleic acid was extracted from serial fecal specimens obtained at prenatal visits, and viral genomes were sequenced by virome capture enrichment. The frequency, richness, and abundance of viruses were compared between women with and without T1D. Results Two viruses were more prevalent in pregnant women with T1D: picobirnaviruses (odds ratio [OR], 4.2; 95% confidence interval [CI], 1.0–17.1; P = .046) and tobamoviruses (OR, 3.2; 95% CI, 1.1–9.3; P = .037). The abundance of 77 viruses significantly differed between the 2 maternal groups (≥2-fold difference; P < .02), including 8 Enterovirus B types present at a higher abundance in women with T1D. Conclusions These findings provide novel insight into the composition of the gut virome during pregnancy and demonstrate a distinct profile of viruses in women with T1D.
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Affiliation(s)
- Ki Wook Kim
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Digby W Allen
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York
| | - Jennifer J Couper
- Adelaide Medical School, Faculty and Health and Medical Sciences, University of Adelaide Robinson Research Institute, Australia
| | - Simon C Barry
- Adelaide Medical School, Faculty and Health and Medical Sciences, University of Adelaide Robinson Research Institute, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, The Royal Melbourne Hospital Victoria, Australia
| | | | | | - Lynne C Giles
- School of Public Health, University of Adelaide, Australia
| | - Leonard C Harrison
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Mark Harris
- Children's Health Queensland Hospital and Health Service, Australia
| | - Aveni Haynes
- Telethon Kids Institute, The University of Western Australia, Perth
| | - Jessica L Horton
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Sonia R Isaacs
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York
| | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York
| | - Grant Morahan
- Centre for Diabetes Research, The Harry Perkins Institute for Medical Research, Perth, Australia
| | | | - Ignatius C N Pang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Megan A S Penno
- Adelaide Medical School, Faculty and Health and Medical Sciences, University of Adelaide Robinson Research Institute, Australia
| | - Richard O Sinnott
- Department of Computing and Information Systems, University of Melbourne, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Rebecca L Thomson
- Adelaide Medical School, Faculty and Health and Medical Sciences, University of Adelaide Robinson Research Institute, Australia
| | | | - John M Wentworth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - William D Rawlinson
- Serology and Virology Division, SEALS Microbiology, Prince of Wales Hospital, Sydney, Australia
| | - Maria E Craig
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, Australia
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170
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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171
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2019; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2019] [Indexed: 12/02/2022] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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172
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Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 2019; 37:160-168. [PMID: 30718881 PMCID: PMC6587591 DOI: 10.1038/s41587-018-0006-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
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Affiliation(s)
- Hayden C. Metsky
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Katherine J. Siddle
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | | | - James Qu
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - David K. Yang
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Patrick Brehio
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andrew Goldfarb
- 000000041936754Xgrid.38142.3cFaculty of Arts and Sciences, Harvard University, Cambridge, MA USA
| | - Anne Piantadosi
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Shirlee Wohl
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Amber Carter
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Aaron E. Lin
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kayla G. Barnes
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA
| | - Damien C. Tully
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Bjӧrn Corleis
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Scott Hennigan
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Giselle Barbosa-Lima
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R. Vieira
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M. Paul
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Amanda L. Tan
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Kimberly F. Garcia
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A. Parham
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Philomena Eromon
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria
| | - Onikepe A. Folarin
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Etienne Simon-Lorière
- 0000 0001 2353 6535grid.428999.7Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Lisa Hensley
- 0000 0001 2164 9667grid.419681.3Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD USA
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- 0000 0001 2181 7878grid.47840.3fDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Douglas S. Kwon
- 0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Todd M. Allen
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Jonathan A. Runstadler
- 0000 0004 1936 7531grid.429997.8Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA USA
| | - Sandra Smole
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Fernando A. Bozza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago M. L. Souza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sharon Isern
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Scott F. Michael
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Ivette Lorenzana
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Lee Gehrke
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA USA
| | - Irene Bosch
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Gregory Ebel
- 0000 0004 1936 8083grid.47894.36Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Donald S. Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone ,0000 0001 2290 9707grid.442296.fCollege of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Christian T. Happi
- 000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Daniel J. Park
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andreas Gnirke
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Pardis C. Sabeti
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Chevy Chase, MD USA
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173
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Cinek O, Kramna L, Mazankova K, Kunteová K, Chudá K, C J Claas E, Stene LC, Tapia G. Virus genotyping by massive parallel amplicon sequencing: adenovirus and enterovirus in the Norwegian MIDIA study. J Med Virol 2018; 91:606-614. [PMID: 30537228 DOI: 10.1002/jmv.25361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
OBJECTIVES Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types in a sample, or due to varying efficacy of PCR amplifying the capsid gene on the background of foreign nucleic acids. Here we present a simple protocol for virus genotyping using massive parallel amplicon sequencing. METHODS The protocol utilized a set of 16 tailed degenerate primers flanking the seventh hypervariable region of the adenovirus hexon gene and 9 tailed degenerate primers targeted to the proximal portion of the enterovirus VP1 gene. Subsequent addition of dual indices enabled simultaneous sequencing of 384 different samples on an Illumina MiSeq instrument. Downstream bioinformatic analysis was based on remapping to a set of references representative of the presently known repertoire of virus types. RESULTS After validation with known virus types, the sequencing method was applied on 301 adenovirus-positive samples and 350 enterovirus-positive samples from a longitudinally collected series of stools from 83 children aged 3 to 36 months. We detected 7 different adenovirus types and 27 different enterovirus types. There were 37 (6.2%) samples containing more than one genotype of the same viral genus. At least one dual infection was experienced by 23 of 83 (28%) of the children observed over the 3 years' observation period. CONCLUSIONS Amplicon sequencing with a multiplex set of degenerate primers seems to be a rapid and reliable technical solution for genotyping of large collections of samples where simultaneous infections with multiple strains can be expected.
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Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Kramna
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Kunteová
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Chudá
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lars C Stene
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - German Tapia
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
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174
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Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol 2018; 26:1035-1048. [PMID: 30193960 PMCID: PMC6249990 DOI: 10.1016/j.tim.2018.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions.
| | - Ola Brønstad Brynildsrud
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway; These authors made equal contributions
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Hongbin Chen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Kathryn A Harris
- Great Ormond Street Hospital NHS Foundation Trust, Department of Microbiology, Virology & Infection Prevention & Control, London WC1N 3JH, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Vegard Eldholm
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
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175
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Fajgenbaum DC. Novel insights and therapeutic approaches in idiopathic multicentric Castleman disease. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2018; 2018:318-325. [PMID: 30504327 PMCID: PMC6245974 DOI: 10.1182/asheducation-2018.1.318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Castleman disease (CD) describes a heterogeneous group of hematologic disorders that share characteristic lymph node histopathology. Patients of all ages present with either a solitary enlarged lymph node (unicentric CD) or multicentric lymphadenopathy (MCD) with systemic inflammation, cytopenias, and life-threatening multiple organ dysfunction resulting from a cytokine storm often driven by interleukin 6 (IL-6). Uncontrolled human herpesvirus-8 (HHV-8) infection causes approximately 50% of MCD cases, whereas the etiology is unknown in the remaining HHV-8-negative/idiopathic MCD cases (iMCD). The limited understanding of etiology, cell types, and signaling pathways involved in iMCD has slowed development of treatments and contributed to historically poor patient outcomes. Here, recent progress for diagnosing iMCD, characterizing etio-pathogenesis, and advancing treatments are reviewed. Several clinicopathological analyses provided the evidence base for the first-ever diagnostic criteria and revealed distinct clinical subtypes: thrombocytopenia, anasarca, fever, reticulin fibrosis/renal dysfunction, organomegaly (iMCD-TAFRO) or iMCD-not otherwise specified (iMCD-NOS), which are both observed all over the world. In 2014, the anti-IL-6 therapy siltuximab became the first iMCD treatment approved by the US Food and Drug Administration, on the basis of a 34% durable response rate; consensus guidelines recommend it as front-line therapy. Recent cytokine and proteomic profiling has revealed normal IL-6 levels in many patients with iMCD and potential alternative driver cytokines. Candidate novel genomic alterations, dysregulated cell types, and signaling pathways have also been identified as candidate therapeutic targets. RNA sequencing for viral transcripts did not reveal novel viruses, HHV-8, or other viruses pathologically associated with iMCD. Despite progress, iMCD remains poorly understood. Further efforts to elucidate etiology, pathogenesis, and treatment approaches, particularly for siltuximab-refractory patients, are needed.
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Affiliation(s)
- David C Fajgenbaum
- Division of Translational Medicine & Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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176
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Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture. J Clin Microbiol 2018; 56:JCM.01123-18. [PMID: 30232133 DOI: 10.1128/jcm.01123-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022] Open
Abstract
Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.
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177
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Gaudin M, Desnues C. Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases. Front Microbiol 2018; 9:2924. [PMID: 30542340 PMCID: PMC6277869 DOI: 10.3389/fmicb.2018.02924] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 01/12/2023] Open
Abstract
This review describes target-enrichment approaches followed by next generation sequencing and their recent application to the research and diagnostic field of modern and past infectious human diseases caused by viruses, bacteria, parasites and fungi.
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Affiliation(s)
- Maxime Gaudin
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Christelle Desnues
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
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178
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Mukherjee S, Joardar N, Sengupta S, Sinha Babu SP. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. J Nutr Biochem 2018; 61:111-128. [PMID: 30196243 PMCID: PMC7126101 DOI: 10.1016/j.jnutbio.2018.07.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
Abstract
The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.
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Affiliation(s)
- Suprabhat Mukherjee
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Nikhilesh Joardar
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Subhasree Sengupta
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Santi P Sinha Babu
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India.
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179
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Optimizing a Metatranscriptomic Next-Generation Sequencing Protocol for Bronchoalveolar Lavage Diagnostics. J Mol Diagn 2018; 21:251-261. [PMID: 30389465 DOI: 10.1016/j.jmoldx.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/16/2022] Open
Abstract
Compared with conventional serologic, culture-based, and molecular-based diagnostic tests, next-generation sequencing (NGS) provides sequence-evidenced detection of various microbes, without prior knowledge, and thus is becoming a novel diagnostic approach. Herein we describe an RNA-based metatranscriptomic NGS (mtNGS) protocol for culture-independent detection of potential infectious pathogens, using clinical bronchoalveolar lavage specimens as an example. We present both an optimized workflow for experimental sequence data collection and a simplified pipeline for bioinformatics sequence data processing. As shown, the whole protocol takes approximately 24 to 36 hours to detect a wide range of Gram-positive and -negative bacteria and possibly other viral and/or fungal pathogens. In particular, we introduce a spike-in RNA mix as an internal control, which plays a critical role in mitigating false-positive and false-negative results of clinical diagnostic tests. Moreover, our mtNGS method can detect antibiotic resistance genes and virulence factors; although it may not be comprehensive, such information is imperative and helpful for the clinician to make better treatment decisions. Results from our preliminary testing suggest that the mtNGS approach is a useful alterative in diagnostic detection of emerging infectious pathogens in clinical laboratories. However, further improvements are needed to achieve better sensitivity and accuracy.
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180
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Franke N, Bette M, Marquardt A, Briese T, Lipkin WI, Kurz C, Ehrenreich J, Mack E, Baying B, Beneš V, Rodepeter FR, Neff A, Teymoortash A, Eivazi B, Geisthoff U, Stuck BA, Bakowsky U, Mandic R. Virome Analysis Reveals No Association of Head and Neck Vascular Anomalies with an Active Viral Infection. In Vivo 2018; 32:1323-1331. [PMID: 30348684 DOI: 10.21873/invivo.11382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/28/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Vascular anomalies encompass different vascular malformations [arteriovenous (AVM), lymphatic (LM), venous lymphatic (VLM), venous (VM)] and vascular tumors such as hemangiomas (HA). The pathogenesis of vascular anomalies is still poorly understood. Viral infection was speculated as a possible underlying cause. MATERIALS AND METHODS A total of 13 human vascular anomalies and three human skin control tissues were used for viral analysis. RNA derived from AVM (n=4) and normal skin control (n=3) tissues was evaluated by RNA sequencing. The Virome Capture Sequencing Platform for Vertebrate Viruses (VirCapSeq-VERT) was deployed on 10 tissues with vascular anomalies (2×AVM, 1×HA, 1×LM, 2×VLM, 4×VM). RESULTS RNA sequencing did not show any correlation of AVM with viral infection. By deploying VirCapSeq-VERT, no consistent viral association was seen in the tested tissues. CONCLUSION The analysis does not point to the presence of an active viral infection in vascular anomalies. However, transient earlier viral infections, e.g. during pregnancy, cannot be excluded with this approach.
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Affiliation(s)
- Nora Franke
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Michael Bette
- Institute of Anatomy and Cell Biology, Philipps University, Marburg, Germany
| | - André Marquardt
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York City, NY, U.S.A
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York City, NY, U.S.A
| | - Christopher Kurz
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Jovine Ehrenreich
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Elisabeth Mack
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Beneš
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Andreas Neff
- Department of Oral and Maxillofacial Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Afshin Teymoortash
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Behfar Eivazi
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Urban Geisthoff
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Boris A Stuck
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Udo Bakowsky
- Department of Pharmaceutical Technology and Biopharmacy, Philipps University, Marburg, Germany
| | - Robert Mandic
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
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181
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Abstract
BacCapSeq is a method for differential diagnosis of bacterial infections and defining antimicrobial sensitivity profiles that has the potential to reduce morbidity and mortality, health care costs, and the inappropriate use of antibiotics that contributes to the development of antimicrobial resistance. We report a platform that increases the sensitivity of high-throughput sequencing for detection and characterization of bacteria, virulence determinants, and antimicrobial resistance (AMR) genes. The system uses a probe set comprised of 4.2 million oligonucleotides based on the Pathosystems Resource Integration Center (PATRIC) database, the Comprehensive Antibiotic Resistance Database (CARD), and the Virulence Factor Database (VFDB), representing 307 bacterial species that include all known human-pathogenic species, known antimicrobial resistance genes, and known virulence factors, respectively. The use of bacterial capture sequencing (BacCapSeq) resulted in an up to 1,000-fold increase in bacterial reads from blood samples and lowered the limit of detection by 1 to 2 orders of magnitude compared to conventional unbiased high-throughput sequencing, down to a level comparable to that of agent-specific real-time PCR with as few as 5 million total reads generated per sample. It detected not only the presence of AMR genes but also biomarkers for AMR that included both constitutive and differentially expressed transcripts.
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182
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Goldstein T, Anthony SJ, Gbakima A, Bird BH, Bangura J, Tremeau-Bravard A, Belaganahalli MN, Wells HL, Dhanota JK, Liang E, Grodus M, Jangra RK, DeJesus VA, Lasso G, Smith BR, Jambai A, Kamara BO, Kamara S, Bangura W, Monagin C, Shapira S, Johnson CK, Saylors K, Rubin EM, Chandran K, Lipkin WI, Mazet JAK. The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses. Nat Microbiol 2018; 3:1084-1089. [PMID: 30150734 PMCID: PMC6557442 DOI: 10.1038/s41564-018-0227-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/25/2018] [Indexed: 11/08/2022]
Abstract
Here we describe the complete genome of a new ebolavirus, Bombali virus (BOMV) detected in free-tailed bats in Sierra Leone (little free-tailed (Chaerephon pumilus) and Angolan free-tailed (Mops condylurus)). The bats were found roosting inside houses, indicating the potential for human transmission. We show that the viral glycoprotein can mediate entry into human cells. However, further studies are required to investigate whether exposure has actually occurred or if BOMV is pathogenic in humans.
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Affiliation(s)
- Tracey Goldstein
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Simon J Anthony
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- EcoHealth Alliance, New York, NY, USA.
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Brian H Bird
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - James Bangura
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Alexandre Tremeau-Bravard
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Manjunatha N Belaganahalli
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Heather L Wells
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jasjeet K Dhanota
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eliza Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | - Michael Grodus
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Veronica A DeJesus
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Gorka Lasso
- Department of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY, USA
| | - Brett R Smith
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sorie Kamara
- Livestock and Veterinary Services Division, Ministry of Agriculture, Forestry and Food Security, Freetown, Sierra Leone
| | - William Bangura
- Forestry and Wildlife Division, Ministry of Agriculture, Forestry and Food Security, Freetown, Sierra Leone
| | - Corina Monagin
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
- Metabiota, Inc., San Francisco, CA, USA
| | - Sagi Shapira
- Department of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY, USA
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Christine K Johnson
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jonna A K Mazet
- One Health Institute & Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
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183
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Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality. mSystems 2018; 3:mSystems00081-18. [PMID: 30271878 PMCID: PMC6156273 DOI: 10.1128/msystems.00081-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022] Open
Abstract
Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status. Epstein-Barr virus (EBV) is convincingly associated with gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. To test the hypothesis that there are additional cancer types with high prevalence of EBV, we determined EBV viral expression in all the Cancer Genome Atlas Project (TCGA) mRNA sequencing (mRNA-seq) samples (n = 10,396) from 32 different tumor types. We found that EBV was present in gastric adenocarcinoma and lymphoma, as expected, and was also present in >5% of samples in 10 additional tumor types. For most samples, EBV transcript levels were low, which suggests that EBV was likely present due to infected infiltrating B cells. In order to determine if there was a difference in the B-cell populations, we assembled B-cell receptors for each sample and found B-cell receptor abundance (P ≤ 1.4 × 10−20) and diversity (P ≤ 8.3 × 10−27) were significantly higher in EBV-positive samples. Moreover, diversity was independent of B-cell abundance, suggesting that the presence of EBV was associated with an increased and altered B-cell population. IMPORTANCE Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status.
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184
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Xiao YL, Ren L, Zhang X, Qi L, Kash JC, Xiao Y, Wu F, Wang J, Taubenberger JK. Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift. mSphere 2018; 3:e00462-18. [PMID: 30232169 PMCID: PMC6147129 DOI: 10.1128/mspheredirect.00462-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus (IAV) infections are a major public health concern, including annual epidemics, epizootic outbreaks, and pandemics. A significant IAV epizootic outbreak was the H7N9 avian influenza A outbreak in China, which was first detected in 2013 and which has spread over 5 waves from 2013 to 2017, causing human infections in many different Chinese provinces. Here, RNA from primary clinical throat swab samples from 20 H7N9-infected local patients with different clinical outcomes, who were admitted and treated at one hospital in Shanghai, China, from April 2013 to April 2015, was analyzed. Whole-transcriptome amplification, with positive enrichment of IAV RNA, was performed, all 20 samples were subjected to deep sequencing, and data from 16 samples were analyzed in detail. Many single-nucleotide polymorphisms, including ones not previously reported, and many nonsynonymous changes that could affect hemagglutinin head and stalk antibody binding epitopes were observed. Minor populations representing viral quasispecies, including nonsynonymous hemagglutinin changes shared by antigenically variant H7N9 clades identified in the most recent wave of H7N9 infections in 2016 to 2017, were also identified.IMPORTANCE H7N9 subtype avian influenza viruses caused infections in over 1,400 humans from 2013 to 2017 and resulted in almost 600 deaths. It is important to understand how avian influenza viruses infect and cause disease in humans and to assess their potential for efficient person-to-person transmission. In this study, we used deep sequencing of primary clinical material to assess the evolution and potential for human adaptation of H7N9 influenza viruses.
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Affiliation(s)
- Yong-Li Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Li Qi
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John C Kash
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yan Xiao
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Fan Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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185
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Yamaguchi J, Olivo A, Laeyendecker O, Forberg K, Ndembi N, Mbanya D, Kaptue L, Quinn TC, Cloherty GA, Rodgers MA, Berg MG. Universal Target Capture of HIV Sequences From NGS Libraries. Front Microbiol 2018; 9:2150. [PMID: 30271393 PMCID: PMC6146096 DOI: 10.3389/fmicb.2018.02150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/22/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains. Illumina Nextera barcoded libraries of either gene-specific or randomly primed cDNA derived from infected plasma were hybridized to probes in a single pool and unbound sequences were washed away. Captured viral cDNA was amplified by Illumina adaptor primers, sequenced on a MiSeq, and NGS reads were demultiplexed for alignment with CLC Bio software. Results: HIV-xGen probes selectively captured and amplified reads spanning the entirety of the HIV phylogenetic tree. HIV sequences clearly present in unenriched libraries of specimens but previously not observed due to high host background levels, insufficient sequencing depth or the extent of multiplexing, were now enriched by >1,000-fold. Thus, xGen selection not only substantially increased the depth of existing sequence, but also extended overall genome coverage by an average of 40%. We characterized 50 new, diverse HIV strains from clinical specimens and demonstrated a viral load cutoff of approximately log 3.5 copies/ml for full length coverage. Genome coverage was <20% for 5/10 samples with viral loads <log 3.5 copies/ml and >90% for 35/40 samples with higher viral loads. Conclusions: Characterization of >20 complete genomes at a time is now possible from a single probe hybridization and MiSeq run. With the versatility to capture all HIV strains and the sensitivity to detect low titer specimens, HIV-xGen will serve as an important tool for monitoring HIV sequence diversity.
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Affiliation(s)
- Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | | | - Dora Mbanya
- Université de Yaoundé 1, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | - Thomas C Quinn
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Gavin A Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Mary A Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Michael G Berg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
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186
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Xiao Y, Nolting JM, Sheng ZM, Bristol T, Qi L, Bowman AS, Taubenberger JK. Design and validation of a universal influenza virus enrichment probe set and its utility in deep sequence analysis of primary cloacal swab surveillance samples of wild birds. Virology 2018; 524:182-191. [PMID: 30212665 DOI: 10.1016/j.virol.2018.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/25/2022]
Abstract
Influenza virus infections in humans and animals are major public health concerns. In the current study, a set of universal influenza enrichment probes was developed to increase the sensitivity of sequence-based virus detection and characterization for all influenza viruses. This universal influenza enrichment probe set contains 46,953 120nt RNA biotin-labeled probes designed based on all available influenza viral sequences and it can be used to enrich for influenza sequences without prior knowledge of type or subtype. Marked enrichment was demonstrated in influenza A/H1N1, influenza B, and H1-to-H16 hemagglutinin plasmids spiked into human DNA and in cultured influenza A/H2N1 virus. Furthermore, enrichment effects and mixed influenza A virus infections were revealed in wild bird cloacal swab samples. Therefore, this universal influenza virus enrichment probe system can capture and enrich influenza viral sequences selectively and effectively in different samples, especially ones with degraded RNA or containing low amount of influenza RNA.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, NIH/NIAID, 33 North Drive MSC 3203, Bethesda, MD 20892-3203, USA.
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, NIH/NIAID, 33 North Drive MSC 3203, Bethesda, MD 20892-3203, USA
| | - Tyler Bristol
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, NIH/NIAID, 33 North Drive MSC 3203, Bethesda, MD 20892-3203, USA
| | - Li Qi
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, NIH/NIAID, 33 North Drive MSC 3203, Bethesda, MD 20892-3203, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, NIH/NIAID, 33 North Drive MSC 3203, Bethesda, MD 20892-3203, USA
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187
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Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality. J Clin Microbiol 2018; 56:JCM.00850-18. [PMID: 29976592 DOI: 10.1128/jcm.00850-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Metagenomics approaches based on shotgun next-generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these approaches to transform how clinical pathogen identification and analysis are performed. In an article in this issue of the Journal of Clinical Microbiology, M. I. Ivy et al. (J Clin Microbiol 56:e00402-18, 2018, https://doi.org/10.1128/JCM.00402-18) have applied a shotgun metagenomics approach to the diagnosis of prosthetic joint infections directly from synovial fluid. The results from this work demonstrate both the potentials and challenges of this approach applied in the clinical microbiology laboratory.
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188
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Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches. mSphere 2018; 3:3/4/e00311-18. [PMID: 30135221 PMCID: PMC6106054 DOI: 10.1128/msphere.00311-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Characterization of the viruses found in the blood of febrile patients provides information pertinent to public health and diagnostic medicine. PCR and culture have historically played an important role in clinical microbiology; however, these methods require a targeted approach and may lack the capacity to identify novel or mixed viral infections. High-throughput sequencing can overcome these constraints. As the cost of running multiple samples continues to decrease, the implementation of high-throughput sequencing for diagnostic purposes is becoming more feasible. Here we present a comparative analysis of findings from an investigation of unexplained febrile illness using two strategies: unbiased high-throughput sequencing and VirCapSeq-VERT, a positive selection high-throughput sequencing system. High-throughput sequencing can provide insights into epidemiology and medicine through comprehensive surveys of viral genetic sequences in environmental and clinical samples. Here, we characterize the plasma virome of Tanzanian patients with unexplained febrile illness by using two high-throughput sequencing methods: unbiased sequencing and VirCapSeq-VERT (a positive selection system). Sequences from dengue virus 2, West Nile virus, human immunodeficiency virus type 1, human pegivirus, and Epstein-Barr virus were identified in plasma. Both sequencing strategies recovered nearly complete genomes in samples containing multiple viruses. Whereas VirCapSeq-VERT had better sensitivity, unbiased sequencing provided better coverage of genome termini. Together, these data demonstrate the utility of high-throughput sequencing strategies in outbreak investigations. IMPORTANCE Characterization of the viruses found in the blood of febrile patients provides information pertinent to public health and diagnostic medicine. PCR and culture have historically played an important role in clinical microbiology; however, these methods require a targeted approach and may lack the capacity to identify novel or mixed viral infections. High-throughput sequencing can overcome these constraints. As the cost of running multiple samples continues to decrease, the implementation of high-throughput sequencing for diagnostic purposes is becoming more feasible. Here we present a comparative analysis of findings from an investigation of unexplained febrile illness using two strategies: unbiased high-throughput sequencing and VirCapSeq-VERT, a positive selection high-throughput sequencing system.
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189
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The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels. Adv Virol 2018; 2018:3248285. [PMID: 30158979 PMCID: PMC6109506 DOI: 10.1155/2018/3248285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/04/2018] [Accepted: 07/24/2018] [Indexed: 12/04/2022] Open
Abstract
Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.
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190
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Greninger AL, Roychoudhury P, Xie H, Casto A, Cent A, Pepper G, Koelle DM, Huang ML, Wald A, Johnston C, Jerome KR. Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture. mSphere 2018; 3:e00283-18. [PMID: 29898986 PMCID: PMC6001610 DOI: 10.1128/mspheredirect.00283-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 11/20/2022] Open
Abstract
Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100× coverage in 72 h at viral loads that allow whole-genome recovery from latently infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low-passage-number clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.IMPORTANCE Herpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding the global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda Casto
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anne Cent
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Gregory Pepper
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - David M Koelle
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Anna Wald
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Christine Johnston
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
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191
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Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG. Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico. Cell Host Microbe 2018; 23:855-864.e7. [PMID: 29805095 PMCID: PMC6006413 DOI: 10.1016/j.chom.2018.04.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tony Li
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mariateresa de Cesare
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Angel Balmaseda
- Laboratory Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rory Bowden
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | - Trevor Brooks
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medcine, Baltimore, MD, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - José E Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cesar R González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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192
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Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis. Methods Mol Biol 2018; 1838:125-140. [PMID: 30128994 PMCID: PMC7121196 DOI: 10.1007/978-1-4939-8682-8_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A large number of viruses can individually and concurrently cause various respiratory illnesses. Metagenomic sequencing using next-generation sequencing (NGS) technology is capable of identifying a variety of pathogens. Here, we describe a method using a large panel of oligo probes to enrich sequence targets of 34 respiratory DNA and RNA viruses that reduces non-viral reads in NGS data and achieves high performance of sequencing-based pathogen identification. The approach can be applied to total nucleic acids purified from respiratory swabs stored in viral transport medium. Illumina TruSeq RNA Access Library procedure is used in targeted sequencing of respiratory viruses. The samples are subjected to RNA fragmentation, random reverse transcription, random PCR amplification, and ligation with barcoded library adaptors. The libraries are pooled and subjected to two rounds of enrichments by using a large panel of oligos designed to capture whole genomes of 34 respiratory viruses. The enriched libraries are amplified and sequenced using Illumina MiSeq sequencing system and reagents. This method can achieve viral detection sensitivity comparable with molecular assay and obtain partial to complete genome sequences for each virus to allow accurate genotyping and variant analysis.
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193
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O'Flaherty BM, Li Y, Tao Y, Paden CR, Queen K, Zhang J, Dinwiddie DL, Gross SM, Schroth GP, Tong S. Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing. Genome Res 2018; 28:869-877. [PMID: 29703817 PMCID: PMC5991510 DOI: 10.1101/gr.226316.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 04/10/2018] [Indexed: 01/01/2023]
Abstract
Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%–99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.
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Affiliation(s)
- Brigid M O'Flaherty
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Yan Li
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Ying Tao
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Clinton R Paden
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Krista Queen
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Jing Zhang
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,IHRC Incorporated, Atlanta, Georgia 30346, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, Clinical Translational Science Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - Gary P Schroth
- Illumina, Incorporated, San Diego, California 92122, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
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194
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2018; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 08/17/2023] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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195
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Allen DW, Kim KW, Rawlinson WD, Craig ME. Maternal virus infections in pregnancy and type 1 diabetes in their offspring: Systematic review and meta-analysis of observational studies. Rev Med Virol 2018; 28:e1974. [DOI: 10.1002/rmv.1974] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/30/2018] [Accepted: 02/05/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Digby W. Allen
- School of Women's and Children's Health; University of New South Wales Medicine; Sydney Australia
- POWH and UNSW Virology Research Laboratory; Prince of Wales Hospital; Sydney Australia
- School of Medical Sciences, Faculty of Medicine; University of New South Wales; Sydney Australia
| | - Ki Wook Kim
- School of Women's and Children's Health; University of New South Wales Medicine; Sydney Australia
- POWH and UNSW Virology Research Laboratory; Prince of Wales Hospital; Sydney Australia
| | - William D. Rawlinson
- School of Women's and Children's Health; University of New South Wales Medicine; Sydney Australia
- POWH and UNSW Virology Research Laboratory; Prince of Wales Hospital; Sydney Australia
- School of Medical Sciences, Faculty of Medicine; University of New South Wales; Sydney Australia
- School of Biotechnology and Biomolecular Science, Faculty of Science; University of New South Wales; Sydney Australia
| | - Maria E. Craig
- School of Women's and Children's Health; University of New South Wales Medicine; Sydney Australia
- POWH and UNSW Virology Research Laboratory; Prince of Wales Hospital; Sydney Australia
- School of Medical Sciences, Faculty of Medicine; University of New South Wales; Sydney Australia
- Institute of Endocrinology and Diabetes; The Children's Hospital at Westmead; Sydney Australia
- Discipline of Child and Adolescent Health, The Children's Hospital at Westmead Clinical School; The University of Sydney; Sydney Australia
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196
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Elimination of Viral Hepatitis and an Update on Blood Safety Technology. HEPATITIS MONTHLY 2018. [DOI: 10.5812/hepatmon.66577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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197
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Carroll D, Watson B, Togami E, Daszak P, Mazet JA, Chrisman CJ, Rubin EM, Wolfe N, Morel CM, Gao GF, Burci GL, Fukuda K, Auewarakul P, Tomori O. Building a global atlas of zoonotic viruses. Bull World Health Organ 2018; 96:292-294. [PMID: 29695886 PMCID: PMC5872013 DOI: 10.2471/blt.17.205005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/04/2017] [Accepted: 02/07/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Dennis Carroll
- Pandemic Influenza and other Emerging Threats Unit, Bureau for Global Health, United States Agency for International Development, Washington DC, United States of America (USA)
| | | | - Eri Togami
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, USA
| | | | - Jonna Ak Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cara J Chrisman
- Pandemic Influenza and other Emerging Threats Unit, Bureau for Global Health, United States Agency for International Development, Washington DC, United States of America (USA)
| | | | | | - Carlos M Morel
- Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - George F Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gian Luca Burci
- International Law Department, Graduate Institute of International and Development Studies, Geneva, Switzerland
| | - Keiji Fukuda
- School of Public Health, Hong Kong University, Hong Kong, China
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Oyewale Tomori
- Nigerian Academy of Science, University of Lagos, Lagos, Nigeria
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198
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Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV. Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions. Microbiol Mol Biol Rev 2018; 82:e00044-17. [PMID: 29237726 PMCID: PMC5813887 DOI: 10.1128/mmbr.00044-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission. These ERVs sometimes remain infectious and can themselves give rise to XRVs. This review integrates recent developments in the phylogenetic classification of retroviruses and the identification of retroviral receptors to elucidate the origins and evolution of XRVs and ERVs. We consider whether ERVs may recurrently pressure XRVs to shift receptor usage to sidestep ERV interference. We discuss how related retroviruses undergo alternative fates in different host lineages after endogenization, with koala retrovirus (KoRV) receiving notable interest as a recent invader of its host germ line. KoRV is heritable but also infectious, which provides insights into the early stages of germ line invasions as well as XRV generation from ERVs. The relationship of KoRV to primate and other retroviruses is placed in the context of host biogeography and the potential role of bats and rodents as vectors for interspecies viral transmission. Combining studies of extant XRVs and "fossil" endogenous retroviruses in koalas and other Australasian species has broadened our understanding of the evolution of retroviruses and host-retrovirus interactions.
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Affiliation(s)
- Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sean P O'Brien
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Maribeth V Eiden
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
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199
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Anderson ME, Nagy-Szakal D, Jain K, Patrone CC, Frattini MG, Lipkin WI, Geskin LJ. Highly Sensitive Virome Capture Sequencing Technique VirCapSeq-VERT Identifies Partial Noncoding Sequences but no Active Viral Infection in Cutaneous T-Cell Lymphoma. J Invest Dermatol 2018; 138:1671-1673. [PMID: 29427587 DOI: 10.1016/j.jid.2018.01.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022]
Affiliation(s)
- Mary E Anderson
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA
| | - Dorottya Nagy-Szakal
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Christina C Patrone
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA
| | - Mark G Frattini
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Larisa J Geskin
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA.
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200
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ViroFind: A novel target-enrichment deep-sequencing platform reveals a complex JC virus population in the brain of PML patients. PLoS One 2018; 13:e0186945. [PMID: 29360822 PMCID: PMC5779639 DOI: 10.1371/journal.pone.0186945] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Deep nucleotide sequencing enables the unbiased, broad-spectrum detection of viruses in clinical samples without requiring an a priori hypothesis for the source of infection. However, its use in clinical research applications is limited by low cost-effectiveness given that most of the sequencing information from clinical samples is related to the human genome, which renders the analysis of viral genomes challenging. To overcome this limitation we developed ViroFind, an in-solution target-enrichment platform for virus detection and discovery in clinical samples. ViroFind comprises 165,433 viral probes that cover the genomes of 535 selected DNA and RNA viruses that infect humans or could cause zoonosis. The ViroFind probes are used in a hybridization reaction to enrich viral sequences and therefore enhance the detection of viral genomes via deep sequencing. We used ViroFind to detect and analyze all viral populations in the brain of 5 patients with progressive multifocal leukoencephalopathy (PML) and of 18 control subjects with no known neurological disease. Compared to direct deep sequencing, by using ViroFind we enriched viral sequences present in the clinical samples up to 127-fold. We discovered highly complex polyoma virus JC populations in the PML brain samples with a remarkable degree of genetic divergence among the JC virus variants of each PML brain sample. Specifically for the viral capsid protein VP1 gene, we identified 24 single nucleotide substitutions, 12 of which were associated with amino acid changes. The most frequent (4 of 5 samples, 80%) amino acid change was D66H, which is associated with enhanced tissue tropism, and hence likely a viral fitness advantage, compared to other variants. Lastly, we also detected sparse JC virus sequences in 10 of 18 (55.5%) of control samples and sparse human herpes virus 6B (HHV6B) sequences in the brain of 11 of 18 (61.1%) control subjects. In sum, ViroFind enabled the in-depth analysis of all viral genomes in PML and control brain samples and allowed us to demonstrate a high degree of JC virus genetic divergence in vivo that has been previously underappreciated. ViroFind can be used to investigate the structure of the virome with unprecedented depth in health and disease state.
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