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Gill P, Hadian Amree A. AS-LAMP: A New and Alternative Method for Genotyping. Avicenna J Med Biotechnol 2020; 12:2-8. [PMID: 32153732 PMCID: PMC7035465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In recent decades, different methods have been introduced for the genotyping of Single Nucleotide Polymorphisms (SNPs) and mutations in nucleic acid sequences. These methods have several applications ranging from agriculture to medicine. The Loop-mediated isothermal amplification (LAMP) method was first introduced by Notomi et al. Since then, different methods derived from LAMP have been extensively applied in detecting pathogens. The LAMP method is an isothermal technique that amplifies the target DNA segment using four different primers that have been uniquely designed for recognizing six distinct zones on the objective gene; the process of reaction continues at a constant temperature via a strand displacement reaction. Amplifying and detecting the targeted zone can be accomplished in one stage. Although the LAMP method is mostly used for pathogen detection, several studies have used this method for genotyping. The present article reviewed various studies that used the LAMP method for SNP detection. The outcomes indicated that the LAMP technique could be a reliable and alternative technique for genotyping. Further studies are recommended to use this approach for genotyping.
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Affiliation(s)
- Pooria Gill
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Arash Hadian Amree
- Student Research Committee, Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran,Corresponding author: Arash Hadian Amree, M.D., Ph.D. Candidate, Student Research Committee, Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran, Tel: +98 9111548344, Fax: +98 11 33361626, E-mail:
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Gill P, Amree AH. Allele-Specific Loop-Mediated Isothermal Amplification for the Detection of IVSII-I G>A Mutation On β-Globin Gene. Open Access Maced J Med Sci 2019; 7:1582-1587. [PMID: 31210804 PMCID: PMC6560289 DOI: 10.3889/oamjms.2019.285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Thalassemia is one of the most common genetic health problems in the world. More than 200 different mutations have been identified in the beta-globin gene and among the 24 β-globin gene mutations in β-thalassemia carriers in the north of Iran IVSII-I G>A mutation has the highest frequency. Using fast, inexpensive, simple and reliable methods for the detection of the mutations in β-thal carriers is very important in prenatal diagnosis, and introduction of alternative methods to the existing ones can help to simplify the detection of mutations. Since its introduction, different methods derived from LAMP have been widely used for SNPs detection. AIM This study was aimed to design a new method for the detection of IVSII-I G>A mutation on β-globin gene based on AS - LAMP technique. METHODS Primer explorer V5 software was used for the design of LAMP primers. Three sets of primers were designed. In the first set, the BIP primers were exactly complementary to the normal and mutant alleles. In the second set, 1 nucleotide (T) was inserted at the 5' end of BIP primers, and in the last set, one nucleotide at the 5' end of BIP primer was changed. The other required primers for the LAMP reaction (FIP, B3, and F3) were the same for all 3 sets of primers. The LAMP reaction was applied on three DNA samples (Wild type, Heterozygote and Homozygote for IVSII-I G>A mutation) and synthetic DNA. RESULTS The results of the present study showed that LAMP reaction using three sets of primers could not successfully detect the IVSII-I G > A mutation among subjects DNA sample and synthetic DNA. CONCLUSION Although several studies have successfully used ARMS-LAMP method to detect the SNPs, and other studies use a variety of methods to identify IVSII-I G>A mutation, the present study was unable to differentiate between a normal allele and IVSII-I G>A mutation. Hence further studies are recommended to consider redesigning of primer set, DNA concentration and using commercial LAMP Master Mix to detect the mutation.
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Affiliation(s)
- Pooria Gill
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Sari, Iran.,Nano Medicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Arash Hadian Amree
- Hemoglobinopathy Institute, Thalassemia Research Center, Mazandaran University of Medical Science, Sari, Iran
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Neely M, Louie S, Xu J, Anthony P, Thuvamontolrat K, Mordwinkin N, Kovacs A. Simultaneous plasma and genital pharmacokinetics and pharmacodynamics of atazanavir and efavirenz in HIV-infected women starting therapy. J Clin Pharmacol 2015; 55:798-808. [PMID: 25683232 DOI: 10.1002/jcph.481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/09/2015] [Indexed: 11/10/2022]
Abstract
Few studies have characterized longitudinal female plasma and genital antiretroviral pharmacokinetics and pharmacodynamics. Among 20 regimen-naive HIV-infected adult women initiating atazanavir-based therapy (n = 9) or efavirenz-based therapy (n = 11), we measured blood CD4+ T lymphocytes, and paired plasma and genital HIV RNA and atazanavir or efavirenz 2 days before starting therapy and 2, 4, 7, 10, 21, 28, 60, 120, and 180 days after. The mean (range) log10 baseline plasma viral load was 4.89 copies/mL (2.64-6.09 copies/mL), and genital was3.30 (1.60-5.00). In the atazanavir and efavirenz groups, mean (SD) days to a 50% decrease in plasma viral load was 8.2 (4.9) versus 9.3 (7.4), P = .7, and in the genital tract it was 7.3 (3.5) versus 9.3 (7.7), P = .5. The median (interquartile range) plasma:genital concentration ratio for atazanavir was 0.11 (0.001-0.46) versus 0.34 (0.05-1.30) for efavirenz, P = .5. Average plasma efavirenz or atazanavir concentrations over time did not affect virologic response. Blood CD4+ percentages increased by +2.3 (P = .06) and +3.0 (P = .003) for every 1 mg/L increase in average plasma and genital drug concentration, respectively. Plasma and genital viral pharmacodynamics were similar between the groups and independent of average concentrations, but blood CD4+ response was related in particular to genital extravascular drug concentrations.
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Affiliation(s)
- Michael Neely
- Laboratory of Applied Pharmacokinetics, Children's Hospital Los Angeles and the Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Stan Louie
- Titus Family Department of Clinical Pharmacy and Pharmaceutical Economics & Policy Faculty, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jiaao Xu
- Maternal, Child and Adolescent Center for Virology and Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Patricia Anthony
- Maternal, Child and Adolescent Center for Virology and Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kasalyn Thuvamontolrat
- Maternal, Child and Adolescent Center for Virology and Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Andrea Kovacs
- Maternal, Child and Adolescent Center for Virology and Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Ghartey J, Kovacs A, Burk RD, Stewart Massad L, Minkoff H, Xie X, Dʼsouza G, Xue X, Heather Watts D, Levine AM, Einstein MH, Colie C, Anastos K, Eltoum IE, Herold BC, Palefsky JM, Strickler HD. Genital tract HIV RNA levels and their associations with human papillomavirus infection and risk of cervical precancer. J Acquir Immune Defic Syndr 2014; 66:316-23. [PMID: 24694931 PMCID: PMC4267467 DOI: 10.1097/qai.0000000000000157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Plasma HIV RNA levels have been associated with the risk of human papillomavirus (HPV) and cervical neoplasia in HIV-seropositive women. However, little is known regarding local genital tract HIV RNA levels and their relation with cervical HPV and neoplasia. DESIGN/METHODS In an HIV-seropositive women's cohort with semiannual follow-up, we conducted a nested case-control study of genital tract HIV RNA levels and their relation with incident high-grade squamous intraepithelial lesions (HSIL) subclassified as severe (severe HSIL), as provided for under the Bethesda 2001 classification system. Specifically, 66 incidents of severe HSIL were matched to 130 controls by age, CD4 count, highly active antiretroviral therapy use, and other factors. We also studied HPV prevalence, incident detection, and persistence in a random sample of 250 subjects. RESULTS Risk of severe HSIL was associated with genital tract HIV RNA levels (odds ratio comparing HIV RNA ≥ the median among women with detectable levels versus undetectable, 2.96; 95% confidence interval: 0.99 to 8.84; Ptrend = 0.03). However, this association became nonsignificant (Ptrend = 0.51) after adjustment for plasma HIV RNA levels. There was also no association between genital tract HIV RNA levels and the prevalence of any HPV or oncogenic HPV. However, the incident detection of any HPV (Ptrend = 0.02) and persistence of oncogenic HPV (Ptrend = 0.04) were associated with genital tract HIV RNA levels, after controlling plasma HIV RNA levels. CONCLUSIONS These prospective data suggest that genital tract HIV RNA levels are not a significant independent risk factor for cervical precancer in HIV-seropositive women, but they leave open the possibility that they may modestly influence HPV infection, an early stage of cervical tumorigenesis.
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Affiliation(s)
- Jeny Ghartey
- *Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY; †Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Bronx, NY; ‡Department of Pediatrics, University of Southern California, Los Angeles, CA; §Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY; ‖Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO; ¶Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, NY; #Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY; **Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD; ††Department of Health and Human Services, National Institute of Child Health and Human Development, Bethesda, MD; ‡‡Department of Hematology, City of Hope National Medical Center, Duarte, CA; §§Department of Obstetrics and Gynecology, Georgetown University Medical Center, Washington, DC; ‖‖Department of Pathology, University of Alabama, Birmingham, AL; and ¶¶Department of Medicine, University of California, San Francisco, CA
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Botes M, de Kwaadsteniet M, Cloete TE. Application of quantitative PCR for the detection of microorganisms in water. Anal Bioanal Chem 2013; 405:91-108. [PMID: 23001336 PMCID: PMC7079929 DOI: 10.1007/s00216-012-6399-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/13/2022]
Abstract
The occurrence of microorganisms in water due to contamination is a health risk and control thereof is a necessity. Conventional detection methods may be misleading and do not provide rapid results allowing for immediate action. The quantitative polymerase chain reaction (qPCR) method has proven to be an effective tool to detect and quantify microorganisms in water within a few hours. Quantitative PCR assays have recently been developed for the detection of specific adeno- and polyomaviruses, bacteria and protozoa in different water sources. The technique is highly sensitive and able to detect low numbers of microorganisms. Quantitative PCR can be applied for microbial source tracking in water sources, to determine the efficiency of water and wastewater treatment plants and act as a tool for risk assessment. Different qPCR assays exist depending on whether an internal control is used or whether measurements are taken at the end of the PCR reaction (end-point qPCR) or in the exponential phase (real-time qPCR). Fluorescent probes are used in the PCR reaction to hybridise within the target sequence to generate a signal and, together with specialised systems, quantify the amount of PCR product. Quantitative reverse transcription polymerase chain reaction (q-RT-PCR) is a more sensitive technique that detects low copy number RNA and can be applied to detect, e.g. enteric viruses and viable microorganisms in water, and measure specific gene expression. There is, however, a need to standardise qPCR protocols if this technique is to be used as an analytical diagnostic tool for routine monitoring. This review focuses on the application of qPCR in the detection of microorganisms in water.
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Affiliation(s)
- Marelize Botes
- Department of Microbiology, University of Stellenbosch, Private Bag XI, Matieland 7602, Stellenbosch, Western Cape 7602, South Africa.
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Gimeno A, Plazas J, Sánchez-Payá J, Llopis C, Boix V, Portilla J. [Reproducibility of a method to quantify vaginal human immunodeficiency virus viral load]. Enferm Infecc Microbiol Clin 2010; 28:439-41. [PMID: 20541846 DOI: 10.1016/j.eimc.2010.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 12/28/2009] [Accepted: 01/27/2010] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To assess the reproducibility of a method to collect and quantify HIV nucleic acids in vaginal secretions. METHODS We analysed two consecutive vaginal samples collected by direct aspiration from 52 HIV infected women. Nucleic acids were extracted by QIAamp RNA-viral and quantified with a modified Cobas Amplicor HIV-1 Monitor. RESULTS Intra-class correlation coefficient between matched samples: 0.99. Differences of pooled HIV DNA+RNa and RNA were <0.40 uLog for 95% of all samples (Bland-Altman plots). CONCLUSIONS This method is a standard and reproducible assay to detect and measure HIV vaginal viral load.
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Affiliation(s)
- Adelina Gimeno
- Laboratorio de Microbiología Molecular, Hospital General Universitario de Alicante, Alicante, España
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Gill P, Ghaemi A. Nucleic acid isothermal amplification technologies: a review. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:224-43. [PMID: 18260008 DOI: 10.1080/15257770701845204] [Citation(s) in RCA: 309] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nucleic acid amplification technologies are used in the field of molecular biology and recombinant DNA technologies. These techniques are used as leading methods in detecting and analyzing a small quantity of nucleic acids. The polymerase chain reaction (PCR) is the most widely used method for DNA amplification for detection and identification of infectious diseases, genetic disorders and other research purposes. However, it requires a thermocycling machine to separate two DNA strands and then amplify the required fragment. Novel developments in molecular biology of DNA synthesis in vivo demonstrate the possibility of amplifying DNA in isothermal conditions without the need of a thermocycling apparatus. DNA polymerase replicates DNA with the aid of various accessory proteins. Recent identification of these proteins has enabled development of new in vitro isothermal DNA amplification methods, mimicking these in vivo mechanisms. There are several types of isothermal nucleic acid amplification methods such as transcription mediated amplification, nucleic acid sequence-based amplification, signal mediated amplification of RNA technology, strand displacement amplification, rolling circle amplification, loop-mediated isothermal amplification of DNA, isothermal multiple displacement amplification, helicase-dependent amplification, single primer isothermal amplification, and circular helicase-dependent amplification. In this article, we review these isothermal nucleic acid amplification technologies and their applications in molecular biological studies.
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Affiliation(s)
- Pooria Gill
- Research Center for Molecular Biology, Baqiyatallah Medical Sciences University, Tehran, Iran.
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Neely MN, Benning L, Xu J, Strickler HD, Greenblatt RM, Minkoff H, Young M, Bremer J, Levine AM, Kovacs A. Cervical shedding of HIV-1 RNA among women with low levels of viremia while receiving highly active antiretroviral therapy. J Acquir Immune Defic Syndr 2007; 44:38-42. [PMID: 17106279 PMCID: PMC3126662 DOI: 10.1097/01.qai.0000248352.18007.1f] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Among women with low or undetectable quantities of HIV-1 RNA in plasma, factors associated with genital HIV-1 RNA shedding, including choice of treatment regimen, are poorly characterized. METHODS We measured HIV-1 RNA in cervical swab specimens obtained from participants in the Women's Interagency HIV Study who had concurrent plasma viral RNA levels <500 copies/mL, and we assessed factors associated with genital HIV shedding. The study was powered to determine the relative effects of antiretroviral protease inhibitors (PIs) versus nonnucleoside reverse transcriptase inhibitors (NNRTIs) on viral RNA shedding. RESULTS Overall, 44 (15%) of 290 women had detectable HIV-1 RNA in cervical specimens. In the final multivariate model, shedding was independently associated with NNRTI (vs. PI) use (odds ratio [OR], 95% confidence interval [CI]: 2.24, 1.13 to 4.45) and illicit drug use (OR, 95% CI: 2.41, 0.96 to 5.69). CONCLUSIONS This is the largest study to define risks for genital HIV-1 RNA shedding in women with low/undetectable plasma virus. Shedding in this population was common, and NNRTI-based highly active antiretroviral therapy (HAART) (vs. PI-based HAART) was associated with genital HIV shedding. Further study is required to determine the impact of these findings on transmission of HIV from mother to child or to sexual partners.
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Affiliation(s)
- Michael N Neely
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Sherlock CH, Lott PM, Money DM, Merrick L, Arikan Y, Remple VP, Craib K, Burdge DR. Use of Sno Strip filter-paper wicks for collection of genital-tract samples allows reproducible determination of human immunodeficiency virus type 1 (HIV-1) RNA viral load with a commercial HIV-1 viral load assay. J Clin Microbiol 2006; 44:1115-9. [PMID: 16517908 PMCID: PMC1393121 DOI: 10.1128/jcm.44.3.1115-1119.2006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To assess the reproducibility of measurements of cervical and vaginal human immunodeficiency virus (HIV) viral load, 92 duplicate cervical and 88 duplicate vaginal samples were collected from 13 HIV-infected women using Sno Strip filter-paper wicks. RNA was eluted from the strips, extracted, and assayed using a modified protocol for the Roche Cobas Amplicor HIV-1 Monitor assay. Pearson's correlation coefficient (R), coefficient of determination (D), and Bland-Altman plots (BA) were used to compare paired log10-transformed viral loads. Analysis of duplicate same-site samples showed good reproducibility (cervix: R = 0.72, D = 52%, BA = 89% within range; vagina: R = 0.72, D = 51%, BA = 87% within range); paired cervix/vagina measurements showed moderate correlation only (R = 0.56; D = 31.3%). Standardized sample collection and simple modification of the Roche Cobas Amplicor HIV-1 Monitor assay allows reproducible measurement of genital viral load.
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Affiliation(s)
- Christopher H Sherlock
- Diagnostic Virology and Reference Laboratory, Providence Health Care, University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada.
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Yao J, Liu Z, Ko LS, Pan G, Jiang Y. Quantitative detection of HIV-1 RNA using NucliSens EasyQ HIV-1 assay. J Virol Methods 2005; 129:40-6. [PMID: 15961170 DOI: 10.1016/j.jviromet.2005.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 03/30/2005] [Accepted: 04/05/2005] [Indexed: 10/25/2022]
Abstract
HIV-1 RNA viral load has become the major biological marker for disease prognosis and outcome of antiretroviral therapy in the treatment of HIV-infected individuals. The aim of this study was to compare the performance of the new CE marked NucliSens EasyQ HIV-1 assay with NucliSens HIV-1 QT assay (reference method). NucliSens EasyQ HIV-1 (EasyQ) couples nucleic acid sequence-based amplification (NASBA) with real-time detection using molecular beacons utilizing the NucliSens EasyQ analyzer. NASBA is a sensitive, isothermal, transcription-based amplification system designed specifically for the detection of RNA targets. There was significant correlation (r = 0.878, P < 0.0001) between the two different assays in the analysis of clinical samples and the frequency of concordant results (log difference <0.5) was 74%. The two assays detected HIV-1 RNA in 81 specimens, and neither detected (below the lower detection limit, 400 copies/ml for NucliSens HIV-1 QT and 500IU/ml for EasyQ) HIV-1 RNA in 12 specimens. Three clinical specimens had detectable HIV-1 RNA using the EasyQ only, and two specimens had detectable HIV-1 RNA using the NucliSens HIV-1 QT only. The EasyQ procedure can analyze 48 clinical samples within 6h. The coefficient of variation of EasyQ ranged from 3.0 to 9.5% (3% at 4.9 log; 5.7% at 3.7 log; 9.5% at 2.7 log). The new assay is shown to be a rapid, convenient, and reliable procedure for HIV-1 RNA viral load monitoring.
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Affiliation(s)
- Jun Yao
- National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Xuan Wu District, Beijing 100050, PR China
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Nowicki MJ, Laskus T, Nikolopoulou G, Radkowski M, Wilkinson J, Du WB, Rakela J, Kovacs A. Presence of hepatitis C virus (HCV) RNA in the genital tracts of HCV/HIV-1-coinfected women. J Infect Dis 2005; 192:1557-65. [PMID: 16206070 PMCID: PMC3164119 DOI: 10.1086/491742] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 05/27/2005] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV)-infected women--in particular, those coinfected with human immunodeficiency virus type 1 (HIV-1)--can transmit infection to their children and sex partners. METHODS The present study was conducted to analyze the presence of HCV RNA in cervicovaginal lavage (CVL) fluid from 71 women (58 HCV/HIV-1-coinfected women and 13 HCV-infected, HIV-1-uninfected women) enrolled in the Women's Interagency HIV Study. RESULTS HCV RNA was detected (by a commercial polymerase chain reaction assay) in CVL fluid from 18 (29%) of the HIV-1-infected women and from none of the HIV-1-uninfected women (P<.05). Multivariate analysis revealed that risk factors for the presence of HCV RNA in CVL fluid were HCV viremia (odds ratio [OR], 16.81; P=.02) and HIV-1 RNA in CVL fluid (OR, 19.87; P=.02). This observation suggests local interactions between HIV-1 and HCV in the genital tract compartment. There was no correlation between HCV RNA in CVL fluid and CD4, CD8, or CD3 cell counts, HIV-1 RNA viremia, the number of leukocytes in CVL fluid, or HIV-1 therapy. Furthermore, in 3 of 5 analyzed patients who had a detectable CVL HCV RNA load, we found viral variants differing in the 5' untranslated region that were present neither in plasma nor in peripheral-blood mononuclear cells. CONCLUSIONS Our observations point to the importance of the genital tract compartment, in which local HCV replication could be facilitated by local HIV-1 replication.
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Affiliation(s)
- Marek J Nowicki
- Maternal-Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles 90033, and Mayo Clinic, Scottsdale, USA.
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Cohn JA, Hashemi FB, Camarca M, Kong F, Xu J, Beckner SK, Kovacs AA, Reichelderfer PS, Spear GT. HIV-Inducing Factor in Cervicovaginal Secretions Is Associated With Bacterial Vaginosis in HIV-1-Infected Women. J Acquir Immune Defic Syndr 2005; 39:340-6. [PMID: 15980696 PMCID: PMC3118994 DOI: 10.1097/01.qai.0000146599.47925.e0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Certain cervicovaginal lavage (CVL) fluid samples obtained from HIV-1-infected and uninfected women stimulate in vitro HIV-1 replication. This activity, HIV-inducing factor (HIF), changes when CVL fluid is heated. We sought to confirm a previous observation that HIF was associated with bacterial vaginosis (BV). METHODS HIF was measured in unheated and heated CVL fluid obtained from HIV-1-infected women and compared with the presence of BV by Nugent scores, other genital tract conditions, and cervicovaginal HIV-1 shedding. RESULTS Among the 295 women studied, 54% of CVL samples had HIF activity and 21% showed heat-stable HIF activity. In adjusted logistic regression, heat-stable HIF was associated with BV (odds ratio [OR]=51.7, 95% confidence interval [CI]: 5.0, 530.7) and with intermediate flora (OR=43.3, 95% CI: 3.6, 521.1); heat-labile HIF was not associated with BV. Neither heat-stable nor heat-labile HIF was associated with other cervicovaginal conditions nor, after controlling for plasma viral load, with genital tract HIV-1 shedding. CONCLUSION We confirmed the association of HIF with BV and attribute it to the heat-stable component. Heat-stable activity is also associated, although less strongly, with intermediate vaginal flora. We propose that heat-stable HIF is a result of products of BV-associated bacteria.
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Affiliation(s)
- Jonathan A Cohn
- Division of Infectious Diseases, Department of Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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Nag P, Kim J, Sapiega V, Landay AL, Bremer JW, Mestecky J, Reichelderfer P, Kovacs A, Cohn J, Weiser B, Baum LL. Women with cervicovaginal antibody-dependent cell-mediated cytotoxicity have lower genital HIV-1 RNA loads. J Infect Dis 2004; 190:1970-8. [PMID: 15529262 PMCID: PMC3119045 DOI: 10.1086/425582] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 06/21/2004] [Indexed: 11/03/2022] Open
Abstract
Antibodies that mediate human immunodeficiency virus (HIV)-specific antibody-dependent cell-mediated cytotoxicity (ADCC) are present in the cervical fluid of many HIV-positive women; however, the role that these antibodies play in host defense against HIV is not known. To understand the contribution of ADCC in cervical secretions as a protective mechanism against HIV, we evaluated ADCC titers in paired serum and cervical-lavage (CVL) samples from >300 HIV-1-positive women who participated in the multicenter Division of AIDS Treatment Research Initiative Study 009. The present study demonstrates that women with CVL ADCC activity had lower genital viral loads than did women with serum ADCC activity only. Women with CVL ADCC activity were likely to have HIV-1 gp120-specific immunoglobulin (Ig) G, but not IgA, in their cervical fluid. This finding suggests that specific IgG in cervical fluid can mediate ADCC activity that inversely correlates with genital viral load.
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Affiliation(s)
- Pratip Nag
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois
| | - Jenney Kim
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois
| | - Vytautas Sapiega
- Pediatric Critical Care, Lutheran General Hospital, Park Ridge, Chicago, Illinois
| | - Alan L. Landay
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois
| | - James W. Bremer
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois
| | | | | | - Andrea Kovacs
- University of Southern California Medical Center, Los Angeles
| | - Jonathan Cohn
- Wayne State University School of Medicine, Detroit, Michigan
| | - Barbara Weiser
- Wadsworth Center, New York State Department of Health, Albany
| | - Linda L. Baum
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois
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Coombs RW, Reichelderfer PS, Landay AL. Recent observations on HIV type-1 infection in the genital tract of men and women. AIDS 2003; 17:455-80. [PMID: 12598766 DOI: 10.1097/00002030-200303070-00001] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Robert W Coombs
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, Washington, USA
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DeVange Panteleeff D, Emery S, Richardson BA, Rousseau C, Benki S, Bodrug S, Kreiss JK, Overbaugh J. Validation of performance of the gen-probe human immunodeficiency virus type 1 viral load assay with genital swabs and breast milk samples. J Clin Microbiol 2002; 40:3929-37. [PMID: 12409354 PMCID: PMC139629 DOI: 10.1128/jcm.40.11.3929-3937.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency type 1 (HIV-1) continues to spread at an alarming rate. The virus may be transmitted through blood, genital secretions, and breast milk, and higher levels of systemic virus in the index case, as measured by plasma RNA viral load, have been shown to correlate with increased risk of transmitting HIV-1 both vertically and sexually. Less is known about the correlation between transmission and HIV-1 levels in breast milk or genital secretions, in part because reliable quantitative assays to detect HIV-1 in these fluids are not available. Here we show that the Gen-Probe HIV-1 viral load assay can be used to accurately quantify viral load in expressed breast milk and in cervical and vaginal samples collected on swabs. Virus could be quantified from breast milk and swab samples spiked with known amounts of virus, including HIV-1 subtypes A, C, and D. As few as 10 copies of HIV-1 RNA could be detected above background threshold levels in > or =77% of assays performed with spiked breast milk supernatants and mock swabs. In genital swab samples from HIV-1-infected women, similar levels of HIV-1 RNA were consistently detected in duplicate swabs taken from the same woman on the same clinic visit, suggesting that the RNA values from a single swab sample can be used to measure genital viral load.
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Affiliation(s)
- Dana DeVange Panteleeff
- Divisions of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Burchill SA, Perebolte L, Johnston C, Top B, Selby P. Comparison of the RNA-amplification based methods RT-PCR and NASBA for the detection of circulating tumour cells. Br J Cancer 2002; 86:102-9. [PMID: 11857020 PMCID: PMC2746547 DOI: 10.1038/sj.bjc.6600014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2001] [Revised: 08/15/2001] [Accepted: 10/15/2001] [Indexed: 11/12/2022] Open
Abstract
Increasingly, reverse transcriptase polymerase chain reaction (RT-PCR) is used to detect clinically significant tumour cells in blood or bone marrow. This may result in a redefinition of disease-free and clinical relapse. However, its clinical utility may be limited by lack of automation or reproducibility. Recent studies have suggested nucleic acid sequence-based amplification of target RNA may be more robust. In this study, nucleic acid sequence-based amplification was established to detect melanoma, colorectal and prostate cancer cells. Nucleic acid sequence-based amplification and RT-PCR both successfully amplified target RNA in peripheral blood samples from patients with melanoma and colorectal cancer, but only RT-PCR detected PSA in blood samples from patients with prostate cancer. There was relatively good agreement between sample replicates analyzed by RT-PCR (Kappa values of one for tyrosinase, 0.67 for CK-20 and one for PSA), but less agreement when analyzed by nucleic acid sequence-based amplification. This may limit the routine use of NASBA for the detection of clinically significant disease. In summary, RT-PCR appears at present to be the most reliable and reproducible method for the detection of low-level disease in cancer patients, although prospective studies are warranted to assess the clinical utility of different molecular diagnostic methods.
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Affiliation(s)
- S A Burchill
- Children's Cancer Research Laboratory, St. James's University Hospital, Leeds LS9 7TF, UK.
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17
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Kovacs A, Wasserman SS, Burns D, Wright DJ, Cohn J, Landay A, Weber K, Cohen M, Levine A, Minkoff H, Miotti P, Palefsky J, Young M, Reichelderfer P. Determinants of HIV-1 shedding in the genital tract of women. Lancet 2001; 358:1593-601. [PMID: 11716886 DOI: 10.1016/s0140-6736(01)06653-3] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Plasma HIV-1 RNA concentration has been the best predictor for risk of heterosexual and perinatal transmission. However, direct contact with HIV-1 present locally in the genital tract might be necessary for transmission. We aimed to assess the relation between HIV-1 shedding (RNA or culturable virus) in female genital secretions and other factors that might affect HIV-1 shedding. METHODS This was a cross-sectional study within the Women's Interagency HIV Study (WIHS), a prospective longitudinal cohort study of HIV-infected women. We enrolled 311 HIV positive women from Jan 30, 1997 to July 1, 1998. We did clinical assessments, cultured HIV-1, and measured RNA in peripheral blood mononuclear cells (PBMC) and genital secretions. We compared the results with univariate and multivariate analyses. Presence of HIV-1 RNA or culturable virus in genital secretions was defined as HIV-1 shedding. FINDINGS HIV-1 RNA was present in genital secretions of 57% (152/268) of women whereas infectious virus was detected only in 6% (17/271). Genital tract HIV-1 shedding was found in 80% (130/163) of women with detectable plasma RNA and 78% (116/148) of women with positive PBMC cultures. 33% (27/83) of women with less than 500 copies/mL plasma RNA and 39% (35/90) of those with negative PBMC cultures also had genital tract shedding. INTERPRETATION Plasma RNA concentration, both qualitatively and quantitatively, was the most important factor in predicting genital HIV-1 shedding, even among women receiving potent antiretroviral therapy. However, HIV-1 shedding did occur in women with less than 500 copies/mL plasma HIV-1 RNA. This finding suggests that a separate reservoir of HIV-1 replication may exist in some women.
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Affiliation(s)
- A Kovacs
- Maternal-Child and Adolescent HIV Management and Research Center, University of Southern California School of Medicine, Los Angeles, CA 90033, USA.
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18
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Si-Mohamed A, Andreoletti L, Colombet I, Carreno MP, Lopez G, Chatelier G, Kazatchkine MD, Belec L. Quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in cell-free cervicovaginal secretions: comparison of reverse transcription-PCR amplification (AMPLICOR HIV-A MONITOR 1.5) with enhanced-sensitivity branched-DNA assay (Quantiplex 3.0). J Clin Microbiol 2001; 39:2055-9. [PMID: 11376034 PMCID: PMC88088 DOI: 10.1128/jcm.39.6.2055-2059.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two commercially available hypersensitive assays for human immunodeficiency virus type 1 (HIV-1) RNA quantitation, AMPLICOR HIV-1 Monitor Test 1.5 and Quantiplex HIV RNA 3.0, were compared to detect and quantify HIV-1 RNA in the cell-free fraction of cervicovaginal secretions collected by vaginal washing. Three panel specimens were used: pooled cervicovaginal secretions spiked with HIV-1 subtype A or HIV-1 subtype B and cervicovaginal lavages from HIV-positive and HIV-negative women. Compared to the AMPLICOR HIV-1 Monitor Test 1.5 assay, the Quantiplex HIV-1 3.0 assay yielded higher estimates of HIV-1 RNA concentrations in several tested samples spiked with HIV-1 RNA subtype A, as well as subtype B, particularly samples containing low amounts of HIV-1 RNA. The sensitivity and specificity of the AMPLICOR HIV-1 Monitor Test 1.5 assay were 93 and 100%, respectively; the sensitivity and specificity of the Quantiplex HIV RNA 3.0 assay were 97 and 50%, respectively. In conclusion, in quantifying HIV-1 RNA in cervicovaginal secretions, the Quantiplex HIV RNA 3.0 may lack specificity, and the AMPLICOR HIV-1 Monitor Test 1.5 assay, although highly specific, may lack sensitivity.
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Affiliation(s)
- A Si-Mohamed
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, 20, rue Leblanc, 75 908 Paris Cedex 15, France.
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Affiliation(s)
- Christine C. Ginocchio
- North Shore-Long Island Jewish Health System Laboratories, Lake Success, and Department of Microbiology and Genetics, School of Medicine, State University of New York at Stony Brook, Stony Brook, NY
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Reichelderfer PS, Coombs RW, Wright DJ, Cohn J, Burns DN, Cu-Uvin S, Baron PA, Coheng MH, Landay AL, Beckner SK, Lewis SR, Kovacs AA. Effect of menstrual cycle on HIV-1 levels in the peripheral blood and genital tract. WHS 001 Study Team. AIDS 2000; 14:2101-7. [PMID: 11061650 DOI: 10.1097/00002030-200009290-00005] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To assess the variation in HIV-1 over the menstrual cycle, including RNA levels in the female genital tract, plasma HIV-1-RNA levels, CD4 cell counts, and culturable virus. DESIGN A prospective analysis of 55 HIV-1-infected women. METHODS Blood and genital tract specimens were collected weekly over 8 weeks, spanning two complete menstrual cycles. Applying repeated-measures models that used menses as the reference level, the variation in viral RNA levels was compared in endocervical canal fluid and cells (collected by Sno-strips and cytobrush, respectively) and ectocervicovaginal lavage (CVL) fluid. Repeated-measures models were also used to assess the variation in plasma CD4 cell counts and viral load. RESULTS Shedding patterns differed among the three sampling methods, independent of genital tract co-infections. Genital tract HIV-1-RNA levels from CVL fluid and endocervical canal cytobrush specimens were highest during menses and lowest immediately thereafter (P = 0.001 and P = 0.04). The HIV-1-RNA level in endocervical canal fluid was highest in the week preceding menses (P = 0.003). The menstrual cycle had no effect on blood levels of RNA (P = 0.62), culturable virus (P = 0.34), or CD4 cell counts (P = 0.55). HIV-1-RNA levels were higher in endocervical canal fluid than in peripheral blood plasma during the late luteal phase (P = 0.03). CONCLUSION HIV-1-RNA levels vary with the menstrual cycle in the female genital tract but not the blood compartment. HIV-1-RNA levels are higher in endocervical canal fluid than in blood plasma. These findings may have important implications for sex-specific pathogenesis, heterosexual transmission, and contraceptive hormone interventions in HIV-1-infected women.
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Affiliation(s)
- P S Reichelderfer
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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