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de Melo SA, Pinto SD, Ferreira EDS, Brotas R, Marinho EPM, da Silva VA, Monte RL, Feitoza PVS, Reis MF, Almeida TVR, Ferreira LCDL, Bastos MDS. Molecular diagnosis of opportunistic infections in the central nervous system of HIV-infected adults in Manaus, Amazonas. Front Med (Lausanne) 2024; 10:1298435. [PMID: 38264048 PMCID: PMC10803427 DOI: 10.3389/fmed.2023.1298435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Background Opportunistic infections in the central nervous system (CNS) of people with HIV/AIDS (PLWHA) remain significant contributors to morbidity and mortality, especially in resource-limited scenarios. Diagnosing these infections can be challenging, as brain imaging is non-specific and expensive. Therefore, molecular analysis of cerebrospinal fluid (CSF) may offer a more accurate and affordable method for diagnosing pathogens. Methods We conducted extensive real-time PCR testing (qPCR) on CSF to evaluate etiological agents in PLWHA with neurological manifestations. Primers targeting DNA from specific pathogens, including cytomegalovirus (CMV), herpes simplex virus (HSV), varicella-zoster virus (VZV), Epstein-Barr virus (EBV), John Cunningham virus (JCV), Toxoplasma gondii, and human T-lymphotropic virus types 1 and 2 (HTLV-1 and HTLV-2), were used. Results Cerebrospinal fluid samples revealed 90 pathogens (36.7%). Toxoplasma gondii was the most frequently detected pathogen, found in 22 samples (30.5%). Other pathogens included Cryptococcus sp. (7.7%), EBV (5.3%), CMV, VZV, and JCV (4.0% each). Conclusion Despite antiretroviral therapy and medical follow-up, opportunistic central nervous system infections remain frequent in PLWHA. Herpesviruses are commonly detected, but T. gondii is the most prevalent opportunistic pathogen in our study population. Therefore, molecular diagnosis is a crucial tool for identifying opportunistic infections, even in patients undergoing treatment.
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Affiliation(s)
| | | | | | - Reinan Brotas
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | | | | | - Rossiclea Lins Monte
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | | | | | - Taynná V. Rocha Almeida
- Departamento de Formação em Emergências em Saúde Pública, Ministério da Saúde, Brasília, Distrito Federal, Brazil
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Alves AD, Melgaço JG, Cássia Nc Garcia RD, Raposo JV, de Paula VS, Araújo CC, Pinto MA, Amado LA. Persistence of Parvovirus B19 in liver from transplanted patients with acute liver failure. Future Microbiol 2021; 15:307-317. [PMID: 32286103 DOI: 10.2217/fmb-2019-0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: In this study, we investigated the presence of B19V in liver tissues from patients with acute liver failure (ALF) and evaluated the viral activity in infected liver. Methods: Serum and liver samples from 30 patients who underwent liver transplantation for ALF were investigated for B19V infection by real-time PCR, serological tests and examination of B19V mRNA (transcript) expression in the liver. Results: The serum and liver samples from seven patients were B19V DNA positive (103-105 copies/ml). Most of them presented detectable anti-B19V IgG, indicating persistent infection. B19V mRNA was detected in all patients, demonstrating intra-hepatic replication. Conclusion: B19V infection of the liver during the course of non-A-E ALF suggested a role of B19V, which produced the worst outcome in co-infected patients and in patients with cryptogenic ALF, in liver damage.
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Affiliation(s)
- Arthur Dr Alves
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juliana G Melgaço
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Rita de Cássia Nc Garcia
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, RJ, Brasil
| | - Jessica V Raposo
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Vanessa S de Paula
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | - Marcelo A Pinto
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Luciane A Amado
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
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3
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Li Y, Wan Z, Zuo L, Li S, Liu H, Ma Y, Zhou L, Jin X, Li Y, Zhang C. A Novel 2-dimensional Multiplex qPCR Assay for Single-Tube Detection of Nine Human Herpesviruses. Virol Sin 2021; 36:746-754. [PMID: 33635517 DOI: 10.1007/s12250-021-00354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human herpesviruses are double-stranded DNA viruses that are classified into nine species. More than 90% of adults are ever infected with one or more herpesviruses. The symptoms of infection with different herpesviruses are diverse ranging from mild or asymptomatic infections to deadly diseases such as aggressive lymphomas and sarcomas. Timely and accurate detection of herpesvirus infection is critical for clinical management and treatment. In this study, we established a single-tube nonuple qPCR assay for detection of all nine herpesviruses using a 2-D multiplex qPCR method with a house-keeping gene as the internal control. The novel assay can detect and distinguish different herpesviruses with 30 to 300 copies per 25 µL single-tube reaction, and does not cross-react with 20 other human viruses, including DNA and RNA viruses. The robustness of the novel assay was evaluated using 170 clinical samples. The novel assay showed a high consistency (100%) with the single qPCR assay for HHVs detection. The features of simple, rapid, high sensitivity, specificity, and low cost make this assay a high potential to be widely used in clinical diagnosis and patient treatment.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Lulu Zuo
- Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, China
| | - Honglian Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lianqun Zhou
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Wang Z, Chen Y, Yang J, Han Y, Shi J, Zhan S, Peng R, Li R, Zhang R, Li J, Zhang R. External Quality Assessment for Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Clinical Laboratories. J Mol Diagn 2020; 23:19-28. [PMID: 33122140 PMCID: PMC7587075 DOI: 10.1016/j.jmoldx.2020.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a huge threat to public health. Viral nucleic acid testing is the diagnostic gold standard and can play an important role in the prevention and control of this infection. In this study, bacteriophage MS2 virus-like particles encapsulating specific RNA sequences of SARS-CoV-2 and other coronaviruses were prepared by genetic engineering. The assessment panel, consisting of four positive samples with concentrations of 2.8, 3.5, 4.2, and 4.9 log10 copies/mL and five negative samples with other human coronaviruses, was prepared and distributed to evaluate the accuracy of routine viral RNA detection. Results of 931 panels from 844 laboratories were collected. The overall percentage agreement, positive percentage agreement (PPA), and negative percentage agreement, defined as the percentage of agreement between the correct results and total results submitted for all, positive, and negative samples were 96.8% (8109/8379), 93.9% (3497/3724), and 99.1% (4612/4655), respectively. For samples with concentrations of 4.9 and 4.2 log10 copies/mL, the PPAs were >95%. However, for 3.5 and 2.8 log10 copies/mL, the PPAs were 94.6% (881/931) and 84.9% (790/931), respectively. For all negative samples, the negative percentage agreement values were >95%. Thus, most laboratories can reliably detect SARS-CoV-2. However, further improvement and optimization are required to ensure the accuracy of detection in panel members with lower concentrations of viral RNA.
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Affiliation(s)
- Zhe Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Yang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Shaohua Zhan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China.
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Lima LRP, Silva APD, Schmidt-Chanasit J, Paula VSD. Diagnosis of human herpes virus 1 and 2 (HHV-1 and HHV-2): use of a synthetic standard curve for absolute quantification by real time polymerase chain reaction. Mem Inst Oswaldo Cruz 2017; 112:220-223. [PMID: 28225902 PMCID: PMC5319368 DOI: 10.1590/0074-02760160354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/23/2016] [Indexed: 02/02/2023] Open
Abstract
The use of quantitative real time polymerase chain reaction (qPCR) for herpesvirus detection has improved the sensitivity and specificity of diagnosis, as it is able to detect shedding episodes in the absence of clinical lesions and diagnose clinical specimens that have low viral loads. With an aim to improve the detection and quantification of herpesvirus by qPCR, synthetic standard curves for human herpesvirus 1 and 2 (HHV-1 and HHV-2) targeting regions gD and gG, respectively, were designed and evaluated. The results show that synthetic curves can replace DNA standard curves in diagnostic herpes qPCR.
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Affiliation(s)
- Lyana Rodrigues Pinto Lima
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Desenvolvimento Tecnológico em Virologia, Rio de Janeiro, RJ, Brasil
| | - Amanda Perse da Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Desenvolvimento Tecnológico em Virologia, Rio de Janeiro, RJ, Brasil
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, Diagnostic Virology Laboratory, Hamburg, Germany
| | - Vanessa Salete de Paula
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Desenvolvimento Tecnológico em Virologia, Rio de Janeiro, RJ, Brasil
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6
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Melgaço JG, Soriani FM, Sucupira PHF, Pinheiro LA, Vieira YR, de Oliveira JM, Lewis-Ximenez LL, Araújo CCV, Pacheco-Moreira LF, Menezes GB, Cruz OG, Vitral CL, Pinto MA. Changes in cellular proliferation and plasma products are associated with liver failure. World J Hepatol 2016; 8:1370-1383. [PMID: 27917263 PMCID: PMC5114473 DOI: 10.4254/wjh.v8.i32.1370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/03/2016] [Accepted: 09/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To study the differences in immune response and cytokine profile between acute liver failure and self-limited acute hepatitis.
METHODS Forty-six patients with self-limited acute hepatitis (AH), sixteen patients with acute liver failure (ALF), and twenty-two healthy subjects were involved in this study. The inflammatory and anti-inflammatory products in plasma samples were quantified using commercial enzyme-linked immunoassays and quantitative real-time PCR. The cellular immune responses were measured by proliferation assay using flow cytometry. The groups were divided into viral- and non-viral-induced self-limited AH and ALF. Thus, we worked with five groups: Hepatitis A virus (HAV)-induced self-limited acute hepatitis (HAV-AH), HAV-induced ALF (HAV-ALF), non-viral-induced self-limited acute hepatitis (non-viral AH), non-viral-induced acute liver failure (non-viral ALF), and healthy subjects (HC). Comparisons among HAV and non-viral-induced AH and ALF were performed.
RESULTS The levels of mitochondrial DNA (mtDNA) and the cytokines investigated [interleukin (IL)-6, IL-8, IL-10, interferon gamma, and tumor necrosis factor] were significantly increased in ALF patients, independently of etiology (P < 0.05). High plasma mtDNA and IL-10 were the best markers associated with ALF [mtDNA: OR = 320.5 (95%CI: 14.42-7123.33), P < 0.0001; and IL-10: OR = 18.8 (95%CI: 1.38-257.94), P = 0.028] and death [mtDNA: OR = 12.1 (95%CI: 2.57-57.07), P = 0.002; and IL-10: OR = 8.01 (95%CI: 1.26-50.97), P = 0.027]. In the cellular proliferation assay, NKbright, NKT and regulatory T cells (TReg) predominated in virus-specific stimulation in HAV-induced ALF patients with an anergic behavior in the cellular response to mitotic stimulation. Therefore, in non-viral-induced ALF, anergic behavior of activated T cells was not observed after mitotic stimulation, as expected and as described by the literature.
CONCLUSION mtDNA and IL-10 may be predictors of ALF and death. TReg cells are involved in immunological disturbance in HAV-induced ALF.
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7
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Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
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Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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8
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Development and Validation of a Laboratory-Developed Multiplex Real-Time PCR Assay on the BD Max System for Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA in Various Clinical Specimens. J Clin Microbiol 2015; 53:1921-6. [PMID: 25878344 DOI: 10.1128/jcm.03692-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/07/2015] [Indexed: 01/06/2023] Open
Abstract
A multiplex real-time PCR (quantitative PCR [qPCR]) assay detecting herpes simplex virus (HSV) and varicella-zoster virus (VZV) DNA together with an internal control was developed on the BD Max platform combining automated DNA extraction and an open amplification procedure. Its performance was compared to those of PCR assays routinely used in the laboratory, namely, a laboratory-developed test for HSV DNA on the LightCycler instrument and a test using a commercial master mix for VZV DNA on the ABI7500fast system. Using a pool of negative cerebrospinal fluid (CSF) samples spiked with either calibrated controls for HSV-1 and VZV or dilutions of a clinical strain that was previously quantified for HSV-2, the empirical limit of detection of the BD Max assay was 195.65, 91.80, and 414.07 copies/ml for HSV-1, HSV-2, and VZV, respectively. All the samples from HSV and VZV DNA quality control panels (Quality Control for Molecular Diagnostics [QCMD], 2013, Glasgow, United Kingdom) were correctly identified by the BD Max assay. From 180 clinical specimens of various origins, 2 CSF samples were found invalid by the BD Max assay due to the absence of detection of the internal control; a concordance of 100% was observed between the BD Max assay and the corresponding routine tests. The BD Max assay detected the PCR signal 3 to 4 cycles earlier than did the routine methods. With results available within 2 h on a wide range of specimens, this sensitive and fully automated PCR assay exhibited the qualities required for detecting simultaneously HSV and VZV DNA on a routine basis.
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Rosenstierne MW, McLoughlin KS, Olesen ML, Papa A, Gardner SN, Engler O, Plumet S, Mirazimi A, Weidmann M, Niedrig M, Fomsgaard A, Erlandsson L. The microbial detection array for detection of emerging viruses in clinical samples--a useful panmicrobial diagnostic tool. PLoS One 2014; 9:e100813. [PMID: 24963710 PMCID: PMC4070998 DOI: 10.1371/journal.pone.0100813] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/29/2014] [Indexed: 11/30/2022] Open
Abstract
Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range of emerging viruses present in both non-clinical and clinical samples using two different microarray data analysis methods.
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Affiliation(s)
- Maiken W. Rosenstierne
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Kevin S. McLoughlin
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Majken Lindholm Olesen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Papa
- Department of Microbiology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Shea N. Gardner
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Olivier Engler
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Sebastien Plumet
- Virology department, French Army Forces Biomedical Institute (IRBA), Marseille, France
| | - Ali Mirazimi
- Swedish Institute for Communicable Disease Control, Solna, Sweden
- National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | | | - Anders Fomsgaard
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lena Erlandsson
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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10
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Silva APD, Lopes JF, Paula VSD. RNA interference inhibits herpes simplex virus type 1 isolated from saliva samples and mucocutaneous lesions. Braz J Infect Dis 2014; 18:441-4. [PMID: 24835621 PMCID: PMC9427528 DOI: 10.1016/j.bjid.2014.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/26/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to evaluate the use of RNA interference to inhibit herpes simplex virus type-1 replication in vitro. For herpes simplex virus type-1 gene silencing, three different small interfering RNAs (siRNAs) targeting the herpes simplex virus type-1 UL39 gene (sequence si-UL 39-1, si-UL 39-2, and si-UL 39-3) were used, which encode the large subunit of ribonucleotide reductase, an essential enzyme for DNA synthesis. Herpes simplex virus type-1 was isolated from saliva samples and mucocutaneous lesions from infected patients. All mucocutaneous lesions’ samples were positive for herpes simplex virus type-1 by real-time PCR and by virus isolation; all herpes simplex virus type-1 from saliva samples were positive by real-time PCR and 50% were positive by virus isolation. The levels of herpes simplex virus type-1 DNA remaining after siRNA treatment were assessed by real-time PCR, whose results demonstrated that the effect of siRNAs on gene expression depends on siRNA concentration. The three siRNA sequences used were able to inhibit viral replication, assessed by real-time PCR and plaque assays and among them, the sequence si-UL 39-1 was the most effective. This sequence inhibited 99% of herpes simplex virus type-1 replication. The results demonstrate that silencing herpes simplex virus type-1 UL39 expression by siRNAs effectively inhibits herpes simplex virus type-1 replication, suggesting that siRNA based antiviral strategy may be a potential therapeutic alternative.
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Affiliation(s)
- Amanda Perse da Silva
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Juliana Freitas Lopes
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Vanessa Salete de Paula
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
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McGilligan VE, Moore JE, Tallouzi M, Atkinson SD, O’Neill H, Feeney S, Novitskaya ES, Sharma A, Shah S, Jackson JA, Frazer DG, Moore TCB. A Comparison of the Clinical and Molecular Diagnosis of Herpes Simplex Keratitis. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ojoph.2014.43011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rodrigues D, de-Paris F, Paiva RM. Minimum detection limit of an in-house nested-PCR assay for herpes simplex virus and varicella zoster virus. Rev Soc Bras Med Trop 2013; 46:625-8. [DOI: 10.1590/0037-8682-1520-2013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/06/2012] [Indexed: 11/21/2022] Open
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Hasib L, Dilcher M, Hufert F, Meyer-König U, Weidmann M. Development of a flow-through [corrected] microarray based reverse transcriptase multiplex ligation-dependent probe amplification assay for the detection of European Bunyaviruses. [corrected]. Mol Biotechnol 2012; 49:176-86. [PMID: 21390485 PMCID: PMC3172416 DOI: 10.1007/s12033-011-9389-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is suspected that apart from tick-borne encephalitis virus several additional European Arboviruses such as the sandfly borne Toscana virus, sandfly fever Sicilian virus and sandfly fever Naples virus, mosquito-borne Tahyna virus, Inkoo virus, Batai virus and tick-borne Uukuniemi virus cause aseptic meningo-encephalitis or febrile disease in Europe. Currently, the microarray technology is developing rapidly and there are many efforts to apply it to infectious diseases diagnostics. In order to arrive at an assay system useful for high throughput analysis of samples from aseptic meningo-encephalitis cases the authors developed a combined multiplex ligation-dependent probe amplification and flow-through microarray assay for the detection of European Bunyaviruses. These results show that this combined assay indeed is highly sensitive, and specific for the accurate detection of multiple viruses.
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Affiliation(s)
- Lekbira Hasib
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57 37075, Göttingen, Germany.
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Affiliation(s)
- Ramon Kranaster
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
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Srinivasan BS, Evans EA, Flannick J, Patterson AS, Chang CC, Pham T, Young S, Kaushal A, Lee J, Jacobson JL, Patrizio P. A universal carrier test for the long tail of Mendelian disease. Reprod Biomed Online 2010; 21:537-51. [PMID: 20729146 DOI: 10.1016/j.rbmo.2010.05.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/22/2010] [Accepted: 05/24/2010] [Indexed: 01/03/2023]
Abstract
Mendelian disorders are individually rare but collectively common, forming a 'long tail' of genetic disease. A single highly accurate assay for this long tail would allow the scaling up of the Jewish community's successful campaign of population screening for Tay-Sachs disease to the general population, thereby improving millions of lives, greatly benefiting minority health and saving billions of dollars. This need has been addressed by designing a universal carrier test: a non-invasive, saliva-based assay for more than 100 Mendelian diseases across all major population groups. The test has been exhaustively validated with a median of 147 positive and 525 negative samples per variant, demonstrating a multiplex assay whose performance compares favourably with the previous standard of care, namely blood-based single-gene carrier tests. Because the test represents a dramatic reduction in the cost and complexity of large-scale population screening, an end to many preventable genetic diseases is now in sight. Moreover, given that the assay is inexpensive and requires only a saliva sample, it is now increasingly feasible to make carrier testing a routine part of preconception care.
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Seeb JE, Pascal CE, Ramakrishnan R, Seeb LW. SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms. Methods Mol Biol 2009; 578:277-92. [PMID: 19768601 DOI: 10.1007/978-1-60327-411-1_18] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Population genetics studies play an increasingly important role in the management and conservation of nonmodel organisms. Unlike studies with model organisms, a typical population genetics study of a nonmodel organism may be conducted by analyzing thousands or hundreds of thousands of individuals for several dozen single nucleotide polymorphisms (SNPs). The use of robust, robotically mediated TaqMan reactions provides substantial advantages in these types of studies. We describe the methods and laboratory setup for analyzing a sustained high throughput of SNP assays in routine university or natural resource agency laboratories with a handful of thermal cyclers. Agencies sustain rates of nearly 150,000 assays per week using uniplex reactions with the Applied Biosystems 7900HT Fast Real-Time PCR System (AB 7900HT). We further describe the medium-density array run on the BioMark from Fluidigm, which increases this rate to over 500,000 assays per week by multiplexing 96 samples for 96 SNPs.
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Affiliation(s)
- James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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