1
|
Quan PL, Alvarez-Amador M, Jiang Y, Sauzade M, Brouzes E. Robust and rapid partitioning in thermoplastic. Analyst 2023; 149:100-107. [PMID: 37982399 PMCID: PMC10777811 DOI: 10.1039/d3an01869e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Partitioning is the core technology supporting digital assays. It divides a sample into thousands of individual reactors prior to amplification and absolute quantification of target molecules. Thermoplastics are attractive materials for large scale manufacturing, however they have been seldomly used for fabricating partitioning arrays. Patitioning in thermoplastic devices has proven difficult due to the challenge of efficiently displacing the air trapped in the nanoliter structures during priming of thousands of chambers. Here, we report the design of an array of chambers made of thermoplastics where the progression of the liquid-air interface is controlled by capillary effects. Our device performs robust partitioning over a wide range of pressures and can be actuated at low pressure by a simple micropipette. Our thermoplastic device lays the foundation to cost-effective and instrument-free partitioning platforms, which could be deployed in low-resource settings.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Maria Alvarez-Amador
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Yuhe Jiang
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Cancer Center, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
- Institute for Engineering Driven Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
2
|
Briese T, Tokarz R, Bateman L, Che X, Guo C, Jain K, Kapoor V, Levine S, Hornig M, Oleynik A, Quan PL, Wong WH, Williams BL, Vernon SD, Klimas NG, Peterson DL, Montoya JG, Ian Lipkin W. A multicenter virome analysis of blood, feces, and saliva in myalgic encephalomyelitis/chronic fatigue syndrome. J Med Virol 2023; 95:e28993. [PMID: 37526404 DOI: 10.1002/jmv.28993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is estimated to affect 0.4%-2.5% of the global population. Most cases are unexplained; however, some patients describe an antecedent viral infection or response to antiviral medications. We report here a multicenter study for the presence of viral nucleic acid in blood, feces, and saliva of patients with ME/CFS using polymerase chain reaction and high-throughput sequencing. We found no consistent group-specific differences other than a lower prevalence of anelloviruses in cases compared to healthy controls. Our findings suggest that future investigations into viral infections in ME/CFS should focus on adaptive immune responses rather than surveillance for viral gene products.
Collapse
Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Wai H Wong
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Bruce W. Carter Miami Veterans Affairs Medical Center, Geriatric Research Education and Research Center, Miami, Florida, USA
| | | | - Jose G Montoya
- Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto Medical Foundation, Palo Alto, USA
| | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| |
Collapse
|
3
|
Yu J, Oh K, Moorthi S, Li L, Strey HH, Schuster M, Luberto C, Quan PL, Brouzes E. Enzymatic-based cytometry, a sensitive single-cell cytometric method to assess BCR-ABL1 activity in CML. Lab Chip 2020; 20:942-948. [PMID: 32031548 PMCID: PMC7439560 DOI: 10.1039/c9lc01213c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We developed a simple, rapid and cost-effective enzymatic-based cytometry platform to measure intracellular signaling pathway activity. Our single-cell microwell array platform quantifies protein phosphorylation using enzymatic signal amplification and exploiting Michaelis-Menten kinetics. Our method provides a two-fold increase in resolution compared to conventional flow cytometry.
Collapse
Affiliation(s)
- Jinzhu Yu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Ki Oh
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Sitapriya Moorthi
- Department of Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, NY 11794, USA
| | - Ling Li
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Helmut H Strey
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA. and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael Schuster
- Hematology Department, Stony Brook Cancer Center, Stony Brook, NY 11794, USA
| | - Chiara Luberto
- Department of Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, NY 11794, USA
| | - Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA. and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA and Cancer Center, Stony Brook School of Medicine, Stony Brook, NY 11794, USA and Institute for Engineering Driven Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
4
|
Liu SZ, Guo LW, Cao XQ, Chen Q, Zhang SK, Zhang M, Yu D, Quan PL, Sun XB, Chen WQ. [Estimation on the incidence and mortality of kidney cancer in China, in 2014]. Zhonghua Liu Xing Bing Xue Za Zhi 2019; 39:1346-1350. [PMID: 30453435 DOI: 10.3760/cma.j.issn.0254-6450.2018.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To estimate the incidence and mortality of kidney cancer in China in 2014, based on the cancer registration data. Data was collected through the National Central Cancer Registry (NCCR). Methods: All together, 449 cancer registries submitted required data on incidence and deaths of kidney cancer occurred in 2014, to the NCCR. After evaluation on the quality of data,339 registries were accepted for analysis and stratified by areas (urban/rural) and age groups. Combined with data from the National population in 2014, the nationwide incidence and mortality of kidney cancer were estimated. Data from the 2000 National census was used, and with Segi's population used for the rates of age-standardized incidence/mortality. Results: The qualified 339 cancer registries covered a total population of 288 243 347, with 144 061 915 in urban and 144 181 432 in rural areas. The percentage of morphologically verified cases and cases with only available death certificates were 72.70% and 1.27%, respectively. The mortality to incidence ratio was 0.37. The estimates of new cases were around 68 300 in whole China, in 2014, with a crude incidence rate as 4.99/100 000 (95%CI: 4.95/100 000-5.03/100 000). The age-standardized incidence rates of kidney cancer, estimated by China standard population (ASR China) and world standard population (ASR world) were 3.43/100 000 (95%CI: 3.40/100 000-3.46/100 000) and 3.40/100 000 (95%CI: 3.37/100 000- 3.43/100 000), respectively. The cumulative incidence rate of kidney cancer was 0.40% in China. The crude and ASR China incidence rates for males appeared as 6.09/100 000 (6.03/100 000-6.15/100 000) and 4.32/100 000 (4.28/100 000-4.36/100 000), respectively, whereas those were 3.84/100 000 (3.79/100 000-3.89/100 000) and 2.54/100 000 (2.50/100 000-2.58/100 000) for females. The crude and ASR China incidence rates in urban areas appeared as 6.60/100 000 (95%CI: 6.54/100 000-6.66/100 000) and 4.25/100 000 (95%CI: 4.21/100 000-4.29/100 000), respectively, whereas those were 3.05/100 000 (95%CI: 3.01/100 000-3.09/100 000) and 2.29/100 000 (95%CI: 2.25/100 000-2.33/100 000) in rural areas. The estimates of kidney cancer deaths were around 25 600 in the country, in 2014, with a crude mortality rate of 1.87/100 000 (95%CI: 1.85/100 000-1.89/100 000). The ASR China and ASR world mortality rates appeared as 1.16/100 000 (95%CI: 1.14/100 000-1.18/100 000) and 1.16/100 000(95%CI: 1.14/100 000-1.18/100 000), respectively, with a cumulative mortality rate (0-74 years old) of 0.12%. The crude and ASR China mortality rates were 2.31/100 000 (95%CI: 2.27/100 000- 2.35/100 000) and 1.52/100 000 (95%CI: 1.50/100 000-1.54/100 000) for males, respectively, whereas those were 1.41/100 000 (95%CI: 1.38/100 000-1.44/100 000) and 0.81/100 000 (95%CI: 0.79/100 000- 0.83/100 000) for females. The crude and ASR China mortality rates were 2.49/100 000 (95%CI: 2.45/100 000-2.53/100 000) and 1.42/100 000 (95%CI: 1.40/100 000-1.44/100 000) in urban areas, respectively, whereas those were 1.12/100 000 (95%CI: 1.09/100 000-1.15/100 000) and 0.78/100 000 (95%CI: 0.76/100 000-0.80/100 000) in the rural areas. Conclusions: Both the incidence and mortality of kidney cancer seemed low, in China. However, the incidence of kidney cancer had greatly increased. Our findings suggested that prevention and control strategies for kidney cancer should be focused on males in the urban areas.
Collapse
Affiliation(s)
- S Z Liu
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - L W Guo
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China; Office of Cancer Screening, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union College, Beijing 100021, China
| | - X Q Cao
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - Q Chen
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - S K Zhang
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - M Zhang
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - D Yu
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - P L Quan
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - X B Sun
- Affiliated Tumor Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, China
| | - W Q Chen
- Office of Cancer Screening, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union College, Beijing 100021, China
| |
Collapse
|
5
|
Scanga R, Chrastecka L, Mohammad R, Meadows A, Quan PL, Brouzes E. Correction: Click chemistry approaches to expand the repertoire of PEG-based fluorinated surfactants for droplet microfluidics. RSC Adv 2018; 9:255-256. [PMID: 35521578 PMCID: PMC9059278 DOI: 10.1039/c8ra90097c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/21/2022] Open
Abstract
[This corrects the article DOI: 10.1039/C8RA01254G.].
Collapse
Affiliation(s)
- Randall Scanga
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Lucie Chrastecka
- Department of Biomedical Engineering, Stony Brook UniversityStony BrookNew YorkUSA
| | - Ridhwan Mohammad
- Department of Biomedical Engineering, Stony Brook UniversityStony BrookNew YorkUSA
| | - Austin Meadows
- Department of Biomedical Engineering, Stony Brook UniversityStony BrookNew YorkUSA
| | - Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook UniversityStony BrookNew YorkUSA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook UniversityStony BrookNew YorkUSA,Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookNew YorkUSA
| |
Collapse
|
6
|
Abstract
Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
7
|
Scanga R, Chrastecka L, Mohammad R, Meadows A, Quan PL, Brouzes E. Click Chemistry Approaches to Expand the Repertoire of PEG-based Fluorinated Surfactants for Droplet Microfluidics. RSC Adv 2018; 8:12960-12974. [PMID: 31592185 PMCID: PMC6779154 DOI: 10.1039/c8ra01254g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report the novel and simplified synthesis of fluorinated surfactants for droplet microfluidics. The range of applications of droplet microfluidics has greatly expanded during the last decade thanks to its ability to manipulate and process tiny amount of sample and reagents at high throughput in independent reactors. A critical component of the technology is the formulation of the immiscible oil phase that contains surfactants to stabilize droplets. The success of droplet microfluidics relies mostly on a single fluorinated formulation that uses a PFPE–PEG triblock surfactant. The synthesis of this surfactant is laborious and requires skills in synthetic chemistry preventing the wider community to explore the synthesis of surfactants with alternate structures. We sought to provide a simplified synthesis for novel PFPE–PEG surfactants based on click chemistry approaches such as copper-catalyzed azide-alkyne cycloaddition (CuAAC) and UV-activated thiol–yne reactions. Our strategy is based on converting a moisture sensitive intermediate typically used in the synthesis of the triblock PFPE–PEG surfactant into a stable and click ready molecule. We successfully combined that fluorinated tail with differently functionalized PEG and glycerol ethoxylate molecules to generate surfactants with diverse structures via CuACC and thiol–yne reactions. We report the characterization, biocompatibility and ability to stabilize emulsions of those surfactants, as well as the unique advantages and challenges of the strategy. Click-synthesis of fluorinated surfactants for droplet microfluidics.![]()
Collapse
Affiliation(s)
- Randall Scanga
- Department of chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lucie Chrastecka
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Ridhwan Mohammad
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Austin Meadows
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| |
Collapse
|
8
|
Kennedy PGE, Quan PL, Lipkin WI. Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances. Viruses 2017; 9:v9060138. [PMID: 28587310 PMCID: PMC5490815 DOI: 10.3390/v9060138] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 12/26/2022] Open
Abstract
Viral encephalitis causes acute inflammation of the brain parenchyma and is a significant cause of human morbidity and mortality. Although Herpes Simplex encephalitis is the most frequent known cause of fatal sporadic encephalitis in humans, an increasingly wide range of viruses and other microbial pathogens are implicated. Up to 60% of cases of presumed viral encephalitis remain unexplained due to the failure of conventional laboratory techniques to detect an infectious agent. High-throughput DNA sequencing technologies have the potential to detect any microbial nucleic acid present in a biological specimen without any prior knowledge of the target sequence. While there remain challenges intrinsic to these technologies, they have great promise in virus discovery in unexplained encephalitis.
Collapse
Affiliation(s)
- Peter G E Kennedy
- Department of Neurology, Institute of Neurological Sciences, Glasgow University, Southern General Hospital, Glasgow G51 4TF, UK.
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th Street, New York, NY 10032, USA.
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th Street, New York, NY 10032, USA.
| |
Collapse
|
9
|
Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics 2015; 16:416. [PMID: 26714571 PMCID: PMC4696252 DOI: 10.1186/s12859-015-0840-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. RESULTS The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. CONCLUSIONS By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.
Collapse
Affiliation(s)
- Andy Kilianski
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | | | - Shijie Yao
- OptiMetrics, Inc, Abingdon, MD, USA. .,Joint Genome Institute, Department of Energy, LBNL, Berkley, CA, USA.
| | - Pierce Roth
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | | | | | | | - Jessica M Hill
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Alvin T Liem
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Oliver Elliot
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
| | - Alexandra Petrosov
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Dereje D Jima
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Tyghe G Vallard
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Melanie C Melendrez
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | | | - Phenix-Lan Quan
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - W Ian Lipkin
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Henry S Gibbons
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | - David L Hirschberg
- The Center for Infection and Immunity, Columbia University, New York, NY, USA. .,Department of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA.
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - C Nicole Rosenzweig
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| |
Collapse
|
10
|
Palacios T, Bartelt L, Scheld W, Lopes MB, Kelting SM, Holland S, Lipkin WI, Quan PL, Borish L, Lawrence M. Fatal Coxsackie meningoencephalitis in a patient with B-cell lymphopenia and hypogammaglobulinemia following rituximab therapy. Ann Allergy Asthma Immunol 2015; 115:148-50. [PMID: 26048250 DOI: 10.1016/j.anai.2015.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/21/2015] [Accepted: 05/04/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Thamiris Palacios
- Division of Asthma, Allergy and Immunology, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - Luther Bartelt
- Division of Infectious Disease, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - William Scheld
- Division of Infectious Disease, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - M Beatriz Lopes
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Sarah M Kelting
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Steven Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York
| | - Larry Borish
- Division of Asthma, Allergy and Immunology, University of Virginia School of Medicine, Charlottesville, Virginia; Department of Microbiology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Monica Lawrence
- Division of Asthma, Allergy and Immunology, University of Virginia School of Medicine, Charlottesville, Virginia
| |
Collapse
|
11
|
Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
Collapse
|
12
|
Quan PL, Williams DT, Johansen CA, Jain K, Petrosov A, Diviney SM, Tashmukhamedova A, Hutchison SK, Tesh RB, Mackenzie JS, Briese T, Lipkin WI. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res 2011; 160:206-13. [PMID: 21740935 DOI: 10.1016/j.virusres.2011.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Jabado OJ, Conlan S, Quan PL, Hui J, Palacios G, Hornig M, Briese T, Lipkin WI. Nonparametric methods for the analysis of single-color pathogen microarrays. BMC Bioinformatics 2010; 11:354. [PMID: 20584331 PMCID: PMC2909221 DOI: 10.1186/1471-2105-11-354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 06/28/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. RESULTS Positive predictive value and false positive rates were examined to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, the chi-square proved most useful. CONCLUSIONS The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.
Collapse
Affiliation(s)
- Omar J Jabado
- Center for Infection and Immunity Mailman School of Public Health Columbia University New York, NY, USA
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Quan PL, Junglen S, Tashmukhamedova A, Conlan S, Hutchison SK, Kurth A, Ellerbrok H, Egholm M, Briese T, Leendertz FH, Lipkin WI. Moussa virus: a new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d'Ivoire. Virus Res 2009; 147:17-24. [PMID: 19804801 DOI: 10.1016/j.virusres.2009.09.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/24/2009] [Accepted: 09/27/2009] [Indexed: 01/01/2023]
Abstract
Characterization of arboviruses at the interface of pristine habitats and anthropogenic landscapes is crucial to comprehensive emergent disease surveillance and forecasting efforts. In context of a surveillance campaign in and around a West African rainforest, particles morphologically consistent with rhabdoviruses were identified in cell cultures infected with homogenates of trapped mosquitoes. RNA recovered from these cultures was used to derive the first complete genome sequence of a rhabdovirus isolated from Culex decens mosquitoes in Côte d'Ivoire, tentatively named Moussa virus (MOUV). MOUV shows the classical genome organization of rhabdoviruses, with five open reading frames (ORF) in a linear order. However, sequences show only limited conservation (12-33% identity at amino acid level), and ORF2 and ORF3 have no significant similarity to sequences deposited in GenBank. Phylogenetic analysis indicates a potential new species with distant relationship to Tupaia and Tibrogargan virus.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Towner JS, Sealy TK, Khristova ML, Albariño CG, Conlan S, Reeder SA, Quan PL, Lipkin WI, Downing R, Tappero JW, Okware S, Lutwama J, Bakamutumaho B, Kayiwa J, Comer JA, Rollin PE, Ksiazek TG, Nichol ST. Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 2008; 4:e1000212. [PMID: 19023410 PMCID: PMC2581435 DOI: 10.1371/journal.ppat.1000212] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 10/20/2008] [Indexed: 02/04/2023] Open
Abstract
Over the past 30 years, Zaire and Sudan ebolaviruses have been responsible for large hemorrhagic fever (HF) outbreaks with case fatalities ranging from 53% to 90%, while a third species, Côte d'Ivoire ebolavirus, caused a single non-fatal HF case. In November 2007, HF cases were reported in Bundibugyo District, Western Uganda. Laboratory investigation of the initial 29 suspect-case blood specimens by classic methods (antigen capture, IgM and IgG ELISA) and a recently developed random-primed pyrosequencing approach quickly identified this to be an Ebola HF outbreak associated with a newly discovered ebolavirus species (Bundibugyo ebolavirus) distantly related to the Côte d'Ivoire ebolavirus found in western Africa. Due to the sequence divergence of this new virus relative to all previously recognized ebolaviruses, these findings have important implications for design of future diagnostic assays to monitor Ebola HF disease in humans and animals, and ongoing efforts to develop effective antivirals and vaccines. In this report we describe a newly discovered ebolavirus species which caused a large hemorrhagic fever outbreak in western Uganda. The virus is genetically distinct, differing by more than 30% at the genome level from all other known ebolavirus species. The unique nature of this virus created challenges for traditional filovirus molecular based diagnostic assays and genome sequencing approaches. Instead, we quickly determined over 70% of the virus genome using a recently developed random-primed pyrosequencing approach that allowed the rapid development of a molecular detection assay that was deployed in the disease outbreak response. This draft sequence allowed easy completion of the whole genome sequence using a traditional primer walking approach and prompt confirmation that this virus represented a new ebolavirus species. Current efforts to design effective diagnostics, antivirals and vaccines will need to take into account the distinct nature of this important new member of the filovirus family.
Collapse
Affiliation(s)
- Jonathan S. Towner
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Tara K. Sealy
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Marina L. Khristova
- Scientific Resources Program, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - César G. Albariño
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Serena A. Reeder
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Robert Downing
- Global AIDS Program, Centers for Disease Control and Prevention, Entebbe, Uganda
| | - Jordan W. Tappero
- Global AIDS Program, Centers for Disease Control and Prevention, Entebbe, Uganda
| | - Samuel Okware
- Ministry of Health, Republic of Uganda, Kampala, Uganda
| | | | | | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - James A. Comer
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Pierre E. Rollin
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thomas G. Ksiazek
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stuart T. Nichol
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|
16
|
Quan PL, Briese T, Palacios G, Ian Lipkin W. Rapid sequence-based diagnosis of viral infection. Antiviral Res 2008; 79:1-5. [PMID: 18367256 PMCID: PMC10071640 DOI: 10.1016/j.antiviral.2008.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 02/12/2008] [Accepted: 02/13/2008] [Indexed: 12/27/2022]
Abstract
With globalization of microbial threats and an increasing appreciation for the role of infection in chronic as well as acute diseases, there is burgeoning interest in the development of specific antiviral drugs. Less attention has been focused on the establishment and implementation of rapid viral diagnostic methods, without which it will not be possible to obtain the full benefit of new therapies. Here we review the current status of viral diagnostics and the utility of various sequence-based diagnostic platforms for applications in clinical microbiology, surveillance and pathogen discovery.
Collapse
|
17
|
Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, Conlan S, Quan PL, Hui J, Marshall J, Simons JF, Egholm M, Paddock CD, Shieh WJ, Goldsmith CS, Zaki SR, Catton M, Lipkin WI. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 2008; 358:991-8. [PMID: 18256387 DOI: 10.1056/nejmoa073785] [Citation(s) in RCA: 473] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. METHODS We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. RESULTS High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points. CONCLUSIONS Unbiased high-throughput sequencing is a powerful tool for the discovery of pathogens. The use of this method during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation.
Collapse
Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI. A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder. Science 2007; 318:283-7. [PMID: 17823314 DOI: 10.1126/science.1146498] [Citation(s) in RCA: 946] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In colony collapse disorder (CCD), honey bee colonies inexplicably lose their workers. CCD has resulted in a loss of 50 to 90% of colonies in beekeeping operations across the United States. The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD. We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by the examination of samples collected from several sites over a period of 3 years. One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD.
Collapse
Affiliation(s)
- Diana L Cox-Foster
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Quan PL, Palacios G, Jabado OJ, Conlan S, Hirschberg DL, Pozo F, Jack PJM, Cisterna D, Renwick N, Hui J, Drysdale A, Amos-Ritchie R, Baumeister E, Savy V, Lager KM, Richt JA, Boyle DB, García-Sastre A, Casas I, Perez-Breña P, Briese T, Lipkin WI. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol 2007; 45:2359-64. [PMID: 17553978 PMCID: PMC1951265 DOI: 10.1128/jcm.00737-07] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Jerome L. and Dawn Greene Infectious Disease Laboratory, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1801, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Palacios G, Quan PL, Jabado OJ, Conlan S, Hirschberg DL, Liu Y, Zhai J, Renwick N, Hui J, Hegyi H, Grolla A, Strong JE, Towner JS, Geisbert TW, Jahrling PB, Büchen-Osmond C, Ellerbrok H, Sanchez-Seco MP, Lussier Y, Formenty P, Nichol ST, Feldmann H, Briese T, Lipkin WI. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 2007; 13:73-81. [PMID: 17370518 PMCID: PMC2725825 DOI: 10.3201/eid1301.060837] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To facilitate rapid, unbiased, differential diagnosis of infectious diseases, we designed GreeneChipPm, a panmicrobial microarray comprising 29,455 sixty-mer oligonucleotide probes for vertebrate viruses, bacteria, fungi, and parasites. Methods for nucleic acid preparation, random primed PCR amplification, and labeling were optimized to allow the sensitivity required for application with nucleic acid extracted from clinical materials and cultured isolates. Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004-2005.
Collapse
Affiliation(s)
- Gustavo Palacios
- Columbia University, New York, New York, USA
- These authors contributed equally to this study
| | - Phenix-Lan Quan
- Columbia University, New York, New York, USA
- These authors contributed equally to this study
| | | | - Sean Conlan
- Columbia University, New York, New York, USA
| | | | - Yang Liu
- University of Chicago, Chicago, Illinois, USA
| | - Junhui Zhai
- Columbia University, New York, New York, USA
| | | | - Jeffrey Hui
- Columbia University, New York, New York, USA
| | - Hedi Hegyi
- Columbia University, New York, New York, USA
- Institute of Enzymology, Budapest, Hungary
| | - Allen Grolla
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | | | - Thomas W. Geisbert
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Peter B. Jahrling
- National Institutes of Health Integrated Research Facility, Fort Detrick, Frederick, Maryland, USA
| | | | | | | | | | | | - Stuart T. Nichol
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heinz Feldmann
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | |
Collapse
|
21
|
Delcroix-Genête D, Quan PL, Roger MG, Hazan U, Nisole S, Rousseau C. Antiviral properties of two trimeric recombinant gp41 proteins. Retrovirology 2006; 3:16. [PMID: 16515685 PMCID: PMC1435769 DOI: 10.1186/1742-4690-3-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Accepted: 03/03/2006] [Indexed: 01/30/2023] Open
Abstract
Background As it is the very first step of the HIV replication cycle, HIV entry represents an attractive target for the development of new antiviral drugs. In this context, fusion inhibitors are the third class of anti-HIV drugs to be used for treatment, in combination with nucleoside analogues and antiproteases. But the precise mechanism of HIV fusion mechanism is still unclear. Gp41 ectodomain-derived synthetic peptides represent ideal tools for clarifying this mechanism, in order to design more potent anti-HIV drugs. Results Two soluble trimeric recombinant gp41 proteins, termed Rgp41B and Rgp41A were designed. Both comprise the N- and C-terminal heptad repeat regions of the ectodomain of HIV-1 gp41, connected by a 7-residue hydrophilic linker, in order to mimic the trimeric fusogenic state of the transmembrane glycoprotein. Both recombinant proteins were found to inhibit HIV-1 entry into target cells in a dose-dependent manner. Rgp41A, the most potent inhibitor, was able to inhibit both X4 and R5 isolates into HeLa cells and primary T lymphocytes. X4 viruses were found to be more susceptible than R5 isolates to inhibition by Rgp41A. In order to elucidate how the trimeric recombinant gp41 protein can interfere with HIV-1 entry into target cells, we further investigated its mode of action. Rgp41A was able to bind gp120 but did not induce gp120-gp41 dissociation. Furthermore, this inhibitor could also interfere with a late step of the fusion process, following the mixing of lipids. Conclusion Taken together, our results suggest that Rgp41A can bind to gp120 and also interfere with a late event of the fusion process. Interestingly, Rgp41A can block membrane fusion without preventing lipid mixing. Although further work will be required to fully understand its mode of action, our results already suggest that Rgp41A can interfere with multiple steps of the HIV entry process.
Collapse
Affiliation(s)
- Delphine Delcroix-Genête
- Institut Cochin, Department of Infectious Diseases, 22 rue Méchain, 75014 Paris, France, INSERM, U 567, CNRS, UMR 8104, Faculté de Médecine René Descartes, UMR-S 8104, 75014 Paris, France
| | - Phenix-Lan Quan
- Institut Cochin, Department of Infectious Diseases, 22 rue Méchain, 75014 Paris, France, INSERM, U 567, CNRS, UMR 8104, Faculté de Médecine René Descartes, UMR-S 8104, 75014 Paris, France
- Mymetics Corporation, 14, rue de la Colombière, 1260 Nyon, Switzerland
| | | | - Uriel Hazan
- Institut Cochin, Department of Infectious Diseases, 22 rue Méchain, 75014 Paris, France, INSERM, U 567, CNRS, UMR 8104, Faculté de Médecine René Descartes, UMR-S 8104, 75014 Paris, France
- Université Paris 7-Denis Diderot, UFR de Biochimie, 2 Place Jussieu, 75251 Paris, France
| | - Sébastien Nisole
- Institut Cochin, Department of Infectious Diseases, 22 rue Méchain, 75014 Paris, France, INSERM, U 567, CNRS, UMR 8104, Faculté de Médecine René Descartes, UMR-S 8104, 75014 Paris, France
- Université Paris 7-Denis Diderot, UFR de Biochimie, 2 Place Jussieu, 75251 Paris, France
| | - Cécile Rousseau
- Institut Cochin, Department of Infectious Diseases, 22 rue Méchain, 75014 Paris, France, INSERM, U 567, CNRS, UMR 8104, Faculté de Médecine René Descartes, UMR-S 8104, 75014 Paris, France
| |
Collapse
|