Molecular methods for virus detection d wiedbrauk, d farkas (AP, 1995)

MOLECULAR METHODS FOR VIRUS DETECTION MOLECULAR METHODS FOR VIRUS DETECTION This Page Intentionally Left Blank MOLECULAR METHODS FOR VIRUS DETECTION Edited by Danny L Wiedbrauk Daniel H Farkas William Beaumont Hospital Royal Oak, Michigan ACADEMIC PRESS San Diego New York Boston Sydney Tokyo Toronto London Front cover illustration represents an electron micrograph of vesicular stomatitis virus (family Rhabdoviridae) Illustration by Mary Haddad This book is printed on acid-flee paper ( ~ Copyright 1995 by ACADEMIC PRESS, INC All Rights Reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission inwriting from the publisher Academic Press, Inc A Division of Harcourt Brace & Company 525 B Street, Suite 1900, San Diego, California 92101-4495 United Kingdom Edition published by Academic Press Limited 24-28 Oval Road, London NW1 7DX Library of Congress Cataloging-in-Publication Data Molecular methods for virus detection / edited by Danny L Wiedbrauk, Daniel H Farkas p cm Includes index ISBN 0-12-748920-7 (case) Virus diseases Molecular diagnosis Polymerase chain reaction Nucleic acid probes I Wiedbrauk, Danny L II Farkas, Daniel H RC114.5.M656 1994 616.9' 250756-dc20 94-28603 CIP PRINTED IN THE UNITED STATES OF AMERICA 95 96 97 98 99 00 EB Contents Contributors Preface xi xv Nucleic Acid Detection Methods Danny L Wiedbrauk and Ann M Drevon I II III IV V VI VII VIII Introduction Specimen Processing Target Amplification Probe Amplification Detection Systems 11 Potential Applications 19 Difficulties and Disadvantages Conclusions 22 References 22 20 Quality Assurance in the Molecular Virology Laboratory 25 Danny [ Wiedbrauk and Jay Stoerker I Introduction 25 II Specimen Quality 26 III Facilities and Equipment 27 vi Contents IV Pipettes and Pipetting 29 V Biochemical Methods of Preventing Amplicon Carryover 30 VI Protective Clothing 32 VII Reagents and Glassware 32 VIII Procedural Controls 34 IX Proficiency Testing 34 X Conclusions 35 References 35 Nucleic Acid Blotting Techniques for Virus Detection Daniel L Stolerand Nelson I Michael I Introduction 4t) II Sample Preparation III IV V VI VII VIII IX X XI XII 40 Nucleic Acid Quantification 44 Southern Blotting 45 Northern Blotting 51 Dot/Slot Blotting DNA and RNA 53 Hybridization Theory 55 Hybridization Probes 57 Filter Hybridization 62 Methods of Detection and Quantification 64 Examples of Blotting Technology 66 Southern Blotting and the Polymerase Chain Reaction References 71 In Situ Hybridization 75 Jeanne Cart I Introduction 75 II General Procedures 76 III Instrumentation 85 IV Detection of Human Papillomavirus by in Situ Hybridization 85 V Selected Studies 94 VI In Situ Hybridization in Conjunction with Other Techniques 39 94 71 Contents vii VII Vendors 96 VIII Conclusion 97 References 97' Antiviral Susceptibility Testing Using D N A - D N A Hybridization 103 Richard L Hodinka I Introduction 103 II Principle of the Test 110 III Collection and Preparation of Herpes Simplex Virus Isolates 110 IV Preliminary Considerations 111 V Antiviral Susceptibility Assay VI Conclusions References 117 125 126 Quantification of Viral Nucleic Acids Using Branched DNA Signal Amplification 131 Judith C Wilbur and Mickey S Ordea I Introduction 131 II Description of the Procedure 132 III Components of the bDNA Assay IV Uses of bDNA Assays 140 V Sample Collection and Stability VI Conclusion References 134 142 143 143 Detection Methods Using Chemiluminescence 147 Irena Bronstein and Corinne E M Olesen I General Introduction 147 II Chemiluminescence Methods 148 III Instrumentation for Chemiluminescence Assays IV Chemiluminescence Assays for Virus Detection V Chemiluminescence Detection Protocols VI Conclusion References 166 167 159 153 154 viii Contents Detection of Viral Pathogens Using PCR Amplification Bruce J McCreedy I Overview of PCR Amplification 175 175 II Considerations for Diagnostic Assay Design i 81 III PCR Amplification for the Qualitative Detection of HIV-1 Proviral DNA References 183 189 Quantitation of RNA Targets Using the Polymerase Chain Reaction 193 Francois Ferre, Patrick Pezzoli, Eric Buxton, Chris Duffy, Annie Marchese, and Anne Daigle I Introduction 193 II PCR Methods for Viral RNA Quantification 194 III Development and Validation of an RT-PCR Assay for the Precise Quantification of HIV-1 RNA in the Peripheral Blood Mononuclear Cells of Infected Individuals 214 IV General Conclusion References 205 215 10 Multiplex Polymerase Chain Reaction 219 James B Mahony and Max A Chernesky 219 I Introduction II Methodology 220 III Developing a Multiplex PCR Assay 231 IV Quality Assurance References 234 1 PCR in Situ Hybridization Gerard J Nuovo 237 I Introduction II Methods III Applications References 240 249 258 237 224 ix Contents 12 Nucleic Acid Sequence-BasedAmplification 261 Roy Sooknanan, Bob van Gemen, and Lawrence T Malek I Background 261 II Application for the Detection of HIV-1 RNA in Plasma or Serum 271 III Required Materials and Solutions References 278 284 13 The Self-Sustained Sequence Replication Reaction and Its Application in Clinical Diagnostics and Molecular B i o l o g y 287 Soumitra S Ghosh, Eoin Fahy, and Thomas R Gingeras I Introduction 287 289 II Characteristics of the 3SR Reaction III Hybridization and Detection of 3SR Products IV Sterilization of 3SR Reactions 297 V Applications of the 3SR Reaction 295 298 301 VI Experimental Procedures for Detection of HIV-1 VII Conclusions References 311 312 14 Ligase Chain Reaction for the Detection of Infectious Agents 315 John D Burczak, Shanfon Ching, Hsiang-Yun Hu, and Helen H Lee I Introduction 315 II Principle of the Ligase Chain Reaction 316 III Application for Detection of Infectious Agents IV Methodology 321 V Conclusions References 318 327 327 15 A Chemiluminescent DNA Probe Test Based on Strand Displacement Amplification 329 G T Walker, C A Spargo, C M Nycz, J A Down, M S Dey, A H Waiters, D R Howard, W E Keating, M C Little, J G Nadeau, S R Jurgensen, V R Neece, and P 7wadyk, Jr I Introduction 330 372 David M Schuster et al The LAT amplification and immunocapture solution hybridization methodologies were combined for rapid amplification and detection of nucleic acid analytes The results are quantitative for both amplification and nonradioactive detection Application of LAT amplification to detection of HPV was demonstrated in a model system and in clinical specimens The results have a strong correlation to those obtained by RT-PCR and demonstrate the validity of LAT amplification for the detection of biologically relevant nucleic acid sequences in clinical specimens ACKNOWLEDGMENTS We wish to recognize and thank George Buchman and Charles Thornton for their many contributions to the development of the LAT method, Atilla Lorincz and Mindy Goldsborough for providing the clinical biopsy material and sharing their RT-PCR data on detection of E6* mRNA, and Gary Temple for his support and thoughtful discussions throughout this project REFERENCES Barany, F (1991a) Genetic disease detection and DNA amplification using cloned thermostable ligase Proc Natl Acad Sci USA 88, 189-193 Barany, F (1991b) The ligase chain reaction in a PCR world PCR Meth Appl 1, 5-16 Barringer, K J., Orgel, L., Wahl, G., and Gingeras, T R (1990) Blunt end and single-strand ligations by Escherchia coli ligase: Influence on an in vitro amplification scheme Gene 89, 117-122 Boguslawski, S J., Smith, D E., Michalak, M A., Mickelson, K E., Yehle, C O., Patterson, W L., and Carrico, R J (1986) Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids J Immunol Meth 89, 123-130 Doorbar, J., Patton, A., Hartley, K., Banks, L., Crook, T., Stanley, M., and Crawford, L (1990) Detection of novel splicing patterns in a HPV16-containing keratinocyte cell line Virology 178, 254-262 Falcinelli, C., Van Belkum, A., Schrauen, L., Seldenrijk, K., and Quint, W G V (1993) Absence of human papillomavirus type 16 E6 transcripts in HPV 16-infected, cytologically normal cervical scrapings J Med Virol 40, 261-265 Griep, A E., Herber, R., Jeon, S., Lohse, J K., Dubielzig, R R., and Lambert, P F (1993) Tumorigenicity by human papillomavirus type 16 E6 and E7 in transgenic mice correlates with alterations in epithelial cell growth and differentiation J Virol 67, 1373-1384 Guatelli, J C., Whitfield, K M., Kwoh, D Y., Barringer, K J., Richman, D D., and Gingeras, T R (1990) Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication Proc Natl Acad Sci USA 87, 1874-1878 Johnson, M A., Blomfield, P I., Bevan, I S., Woodman, C B., and Young, L S (1990) Analysis of human papillomavirus type 16 E6-E7 transcription in cervical carcinomas and normal cervical epithelium using the polymerase chain reaction J Gen Virol 71, 1473-1479 16 Ligation-Activated Transcription 373 Kawasaki, E S (1990) Amplification of RNA In "PCR Protocols: A Guide to Methods and Applications" (M A Innis, D H Gelfand, J J Sninsky, and T J White, eds.) Academic Press, San Diego Kwoh, D Y., Davis, G R., Whitfield, K M., Chappell, H L., DiMichele, L J., and Gingeras, T R (1989) Transcription-based amplification system and detection of amplified human immunodeficiency virus type with a bead-based sandwich hybridization format Proc Natl Acad Sci USA 86, 1173-1177 Lambert, P F., Pan, H., Pitot, H.C., Liem, A., Jackson, M., and Griep, A E (1993) Epidermal cancer associated with expression of human papillomavirus type 16 E6 and E7 oncogenes in the skin of transgenic mice Proc Natl Acad Sci USA 90, 5583-5587 Lizardi, P M., Guerra, C E., Lomeli, H., Tussie-Luna, I., and Kramer, F R (1988) Exponential amplification of recombinant RNA hybridization probes Biotechnology 6, 1197-1202 Mackey, J., Guan, N., and Rashtchian, A (1992) Direct coupling of alkaline phosphatase to oligonucleotide probes for increased sensitivity and simplified non-radioactive detection Focus 14, 112-116 Mulis, K B., and Faloona, F A (1987) Specific synthesis of DNA in vitro via polymerasecatalyzed chain reaction Meth Enzymol 155, 335-350 Nasseri, M., Gage, J R., Lorincz, A., and Wettstein, F O (1991) Human papillomavirus type 16 immortalized cervical keratinocytes contain transcripts encoding E6, E7, and E2 initiated at the P97 promoter and express high levels of E7 Virology 184, 131-140 Rashtchian A., Eldrege, J., Ottaviani, M., Abbott, M., Mock, G., Lovem, D., Klinger, J., and Parsons, G (1987) Immunological capture of nucleic acid hybrids and application to nonradioactive DNA probe assays Clin Chem 33, 1526-1530 Rashtchian, A., Schuster, D., Buchman, G., Berninger, M., and Temple, G F (1990) A nonradioactive sandwich hybridization assay using paramagnetic microbeads and unlabeled RNA probes Sixth International Congress on Rapid Methods and Automation in Microbiology and Immunology Helsinki, Finland Sambrook, J., Fritsch, E F., and Maniatis, T (1989) "Molecular Cloning: A Laboratory Manual," 2d Ed Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY Saiki, R K., Scharf, S., Faloona, F A., Mullis, K B., Horn, G T., Erlich, H A., and Arnheim, N (1985) Enzymatic amplification of beta- globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Science 230, 1350-1354 Schaap, A P., and Akhaven-Tafti, H (1990) New chemiluminescent 1,2-dioxetane derivatives WO Patent 9007511 Schaap, A P., Akhaven, H., and Romano, L J (1989) Chemiluminescent substrates for alkaline phosphatase: Applications to ultra-sensitive enzyme-linked immunoassays and DNA probes Clin Chem 35, 1863-1864 Seedorf, K., Kraemmer, G., Duerst, M., Suhai, S., and Roewekamp, W G (1985) Human papillomavirus type 16 DNA sequence Virology 65, 181-185 Smotkin, D., and Wettstein, F O (1986) Transcription of human papiUomavirus type 16 early genes in a cervical cancer and a cancer-derived cell line and identification of the E7 protein Proc Natl Acad Sci USA 83, 4680-4684 Smotkin, D., Prokoph, H., and Wettstein, F O (1989) Oncogenic and nononcogenic human genital papillomaviruses generate the E7 mRNA by different mechanisms J Virol 63, 1441-1447 Stollar, B D., and Rashtchian, A (1987) Immunochemical approaches to gene probe assays Anal Biochem 161, 387-394 Thomas, P (1983) Hybridization of denatured RNA transferred or dotted to nitrocellulose paper Meth Enzymol 100, 255-266 Urdea, M S., Running, J A., Horn, T., Clyne, J., Ku, L., and Warner, B D (1987) A novel method for the rapid detection of specific nucleotide sequences in crude biologic samples 374 David M Schuster et al without blotting or radioactivity: Application to the analysis of hepatitis B virus in human serum Gene 61, 253-264 Urdea, M S., Warner, B., Running, J A., Kolberg, J A., Clyne, J M., Sanchez-Pescador, R., and Horn, T (1990) Nucleic acid multimer for hybridization assays WO Patent 8903891 Index A260/A280, 27 N-Acetyl cysteine, 340 Acridinium esters, 151-152, 158-159 Acyclovir, 107, 114-115, 121, 122, 124-125 AE, s e e Acridinium esters Agarose, 282-283, 311 for delivery of IP-10, 296-297 Alkaline phosphatase, 83, 148-150, 368 in chemiluminescence detection methods, 148-150 advantages, 150 conjugation, 343-345 labeled probe, 137, 149-150, 159-162, 296 4'-Aminomethyl-4,5-dimethylpsoralen, 30-31,296-297, 310-311 Amplicon carryover in bDNA signal amplification, 143, 178-179 control, 31-32, 179-181 prevention, 30-32, 32 quality assurance, 34 Amplification, s e e a l s o NASBA advantages, 351-352 coamplification, 220, 225 comparison of systems, 351-352 conditions, 291 DNA, 304 ligation-activated transcription, 360, 365-366 ligation chain reaction, 322-324 NASBA, 262-263 non-specific, 226 nucleic acid sequence-based, s e e NASBA optimization, 265 protocol, 207 rate, 293-294 ribonucleic acid, 303-305 RNA, 303-305 selective, 293-295 signal, 16-18 strand-displacement, 330-333 AMV transcriptase, 288 Antibodies, monoclonal, 299-301 Antibody-capture solution, 353-354 Antiviral susceptibility testing, s e e a l s o DNA-DNA hybridization applications, 103-107, 124-125 assay dye uptake, 107-109 plaque reduction, 107-109 cytotoxicity, 121 drug resistance, 104-105 equipment, 113 laboratory technique, 116-117 protocol, 111-122 safety precautions, 116-117 Antiviral therapy, 103-104, 131-132, 215 drug resistance to, 132-133 Argon, 306 Assay capture/detection, 341-347 oligonucleotide probe gel retardation, 276 Autoradiography, 64-66 Avian myeloblastosis virus transcriptase, 288 Avidin, 83 375 376 Index Azidothymidine, s e e Zidovudine AZT, s e e Zidovudine Balances, quality assurance, 29 BBSH, s e e Hybridization, bead-based sandwich B cell development studies, 301 bDNA signal amplification advantages, 132, 143 amplifiers, 137 application, 132-134, 139-142, 204 description, 132-139 probe, 134-137, 137 quantification, 139 reproducibility, 141, 143 sensitivity, 139-140 specificity, 140, 141 standards, 139 Bead glass, 206, 209-210 magnetic, 368 polystyrene, 306-307 preparation, 362-364 Bead-based sandwich hybridization, s e e Hybridization, bead-based sandwich Biogel P-60, 283 Bioluminescence, 153, 159 Biotin, 83, 84, 149 Bleach, 31 Blood collection, 143, 185-186 enzyme immunoassay, 318 nucleic acid preparation, 272 plasma samples, 199-200 sample, 26, 201,234, 322 shipping, storage effects, 3-4 Blot, s e e s p e c i f i c t y p e Branched chain DNA signal amplification, s e e bDNA signal amplification Bromphenol blue, 48 Cell B cell development studies, 301 CD4, 141-142, 214-215,238 fixation, 243-244 mixed cell experiment, 249 mononuclear, 195 Cell culture, ll0-112 assay, 154-155 in cytotoxicity study, 121 for herpes simplex virus antiviral study, 116, 123 Centrifuge, quality assurance, 28 Chemiluminescence detection methods acridinium esters, 151-152, 158-159 advantage, 18, 148, 150, 166 application, 154-159, 158, 165-166, 346-347 bDNA signal amplification, 134 bioluminescence, 153, 159 description, 18, 147-148, 162-163 detection, 160-161 detection threshold, 166 dioxetane, 148-150, 155, 158, 159-162 electrochemiluminescence, 152-153, 159 enhanced, 151 equipment, 153-154 hybridization, 151, 155, 166 immunoassay, 155 for ligation-activated transcription, 367-369 luminol, 150-151, 158 method type, 148-153 microwell assay, 346-347 plates, 347 protocol, 159-166,_163-166 quantification, 137, 153-154, 161-162, 165 retrovirus detection, 158 sandwich assay advantages, 335 bead-based, 296 for strand-displacement amplification detection, 335,341-347 sensitivity, 152, 161-162, 163, 165-166 in situ hybridization, 163-166 x-ray film, 347 Chlamydia trachomatis Camera, photon-counting, 154 Capture/detection assay, 341-347 Carryover contamination, s e e Amplicon carryover; Contamination CD4 cell, 141-142, 214-215, 238 cDNA synthesis, by RT-PCR, 196 detection chemiluminescence detection methods, 158-159 ligase chain reaction, 320-321 multiplex polymerase chain reaction, 226-228, 233 Index 377 urethral swab, 320-321,322 urine specimen, 320-321 Christmas tree method, 16-18 Chromatography, oligo-dT cellulose, 44 Chronic myelocytic leukemia, detection NASBA, 271 RT-PCR, 271 Chronic myelogenous leukemia, s e e Chronic myelocytic leukemia Clothing, protective, 32, 116, 186, 231,340 Complementary DNA, synthesis by RTPCR, 196 Condyloma, 249-250 Contamination carryover, 229-230, 231,296 RNase, 42-43 source, 29-30, 32, 276 surface, 31 CPE, 107, 120 CPT, s e e Cycling probe technology cRNA, 60-61 Cross-contamination, s e e Contamination Cross-linking, 78, 79 CRT-PCR, 197-198 Cycling probe technology, 10-11, 11 Cytomegalovirus, detection sensitivity, 149 Cytometry, flow, 228 Cytotoxicity, 107, 121 Densitometer, 66 Deoxy:dideoxy NTP, 284 Deoxyribonucleic acid, s e e DNA Deoxyribonucleotide triphosphates, s e e dNTP DEPC, s e e Diethylpyrocarbonate Dextran sulfate, 57 Diagnostics, molecular advantages, 19, 315-316 application, 19-20 centralized, 21 development, 25-26 disadvantage, 20-21 Diethylpyrocarbonate, 43,271,355 glassware treatment, 33 Digoxigenin, 84, 244, 247 Dimethyl sulfoxide, 225,265, 270, 292, 323 Dioxetane, 148-150, 155, 158, 159-162 Dithiothreitol, 282 DMSO, s e e Dimethyl sulfoxide DM5 solution, 309 DNA, s e e a l s o Amplification complementary, synthesis, 207 contaminants, 27 detection by immunocapture assay, 325 by NASBA, 273 sensitivity, 151 slot blot, 53-55 threshold, 239, 240 extraction, 41-42, 45-51, 160 from mycobacteria, 339 migration in gels, 46 quality, 27 quantification, 44-45, 66, 266-267 restriction, 45-46 sequencing, 269 structure, 55 transfer to membranes capillary, 48-51 pressure, 51 vacuum, 51 DNA chips, 16 DNA-DNA hybridization, s e e a l s o Antiviral susceptibility testing advantages, 109-110, 125 application, 124-125 calculations, 121 control, 118-120, 122 description, 110 false positive, 120 laboratory technique, 120 probe, non-radioactive, 125 quality control, 122 results, 124 standardization, 124 troubleshooting, 120, 123-125 DNA hybridization in chemiluminescence detection methods, 155 ECL, 158 virus detection, 158-159 DNA hybridization assay advantages, 154-155 and chemiluminescence detection methods, 154-159 description, 152-153 DNA ligase, 324, 352-353 DNA polymerase, 233 DNA probe assay, 53-55, 76-77, 81-83, 163-166, 327 DNase, 59, 241 378 Index dNTP, 317 dUTP, 179-181 solution, 336 Dot blot, 53-55, 70-71, 163-166 detection methods, 64-66 glyoxal, 361-362 hybridization, 62-64 for ligation-activated transcription detection, 360-362 protocol, 360-362 for self-sustained sequence replication, 309-310 Drug resistance, 107, 132-133,298-299 DTT, s e e Dithiothreitol Electrochemiluminescence, 152-153, 159 advantages, 152 Electrophoresis, 227 agarose gel, 46-48, 52-53,227, 275-276, 334 loading buffer, 283 molecular weight standards, 52 polyacrylamide gel, 266 loading buffer, 48 voltage, 46 Embedding, 78-79 Endocervical swab, for C h l a m y d i a t r a c h o m a t i s , 322 Endonuclease, restriction, 45 Enzyme immunoassay, 12-13 advantages, 12-13 blood screening, 318 microparticle immunoassay, 325 modifications, 13 Enzymes, 303-304 preparation, 282 stability, 355 storage, 45 Equipment, 85, 88, 113, 153-154 quality assurance, 28-29 Facility design, 27-28, 65,271,340 for M-PCR, 231 space requirements, 27-28 Fixation, specimen, 78 Flow cytometry, 228 Fluorescence, 228, 295, 296 Formalin, 244 Formamide, 284 Foscarnet, 107, 114-115, 122 Gamma counter, 121, 122 Gel, see Agarose; Electrophoresis Glassware, 33 Gloves, 32 Glycerol, 323 Glyoxal, 52 Gold, in immunochromatography, 14 Guanidinium salts, 43 Hantavirus, 19 Hapten, 324 Hemoglobin, 230 Hepatitis B virus, detection bDNA signal amplification, 132-134, 140-141 chemiluminescence detection methods, 159-163 ligase chain reaction, 318 Hepatitis C virus clinical characterization, 140 copy number, 255 detection bDNA signal amplification, 132-134, 139-140 ligase chain reaction, 318 PCR in situ hybridization, 253,255-257 RT-PCR in situ hybridization, 255 histology, 253,255-257, 257 sample preparation, 142-143 Herpes simplex virus antiviral susceptibility testing, 107-110, 111-122 cell culture, 110-111, 122, 123 detection chemiluminescence, 163-166 ligase chain reaction, 320-321 drug resistant, 107, 122-123, 124-125 heterogeneity, 123 sample preparation, 110-111 storage, 122 High-performance liquid chromatography, see HPLC High-pressure liquid chromatography, s e e HPLC H i n c II, 330-333 HIV, see Human immunodeficiency virus Hood, laminar flow, 231 379 Index Horseradish peroxidase, 150-151 HPA, see Hybridization protection assay HPLC, 228, 343,344 HPV, see Human papillomavirus Human immunodeficiency virus assessment, 214-215 CD4 counts, 204 clinical aspects, 141-142, 183, 185 detection bDNA signal amplification, 132-134, 141-142, 204 ligase chain reaction, 318 NASBA, 270-271 PCR, 19, 183-189 PCR in situ hybridization, 238, 239-240, 251,253 RT-PCR, 66-71, 194-195, 198, 203-205, 205,211-212, 214-215 RT-PCR in situ hybridization, 251,253 self-sustained sequence replication, 293-294, 295-296, 298-299, 301-311 sensitivity, 152 threshold, 153 drug resistant, 298-299 histology, 253 infection status, 251,253 pathogenesis, 238 prognostic indicator, 213-215,214-215 quantification, 213-214 sample preparation, 142-143 Human papillomavirus detection methods, 92 in situ hybridization, 85-91 ligation-activated transcription, 362, 365-367, 369-371 multiplex PCR, 221 PCR in situ hybridization, 249-250 E7, 369 histology, 253 lesions, 250 multiple infection, 92 viral typing, 165-166, 318-310 Human T-lymphotropic virus type I detection by ligase chain reaction, 318 viral typing, 319 Human T-lymphotropic virus type II, 319 Hybridization, see also specific detection methods antibody-capture solution, 353-354 in bDNA signal amplification, 135-137 bead-based sandwich, 295-296, 298-299, 307-309 application, 312 in chemiluminescence detection methods, 151,155, 166 cross-hybridization, 92 deoxyribonucleic acid, 153 filter, 56, 62-64, 239 kinetics, 56-57 melting temperature, 56-57 M-PCR, 228 in multiplex PCR, 233 Northern blot, 62-64 nucleic acid, 351 protocol, 160, 164-165 for self-sustained sequence replication, 295-296 sensitivity, 63 solid-phase, 228 solution method, 163 Southern blot, 227-228 stringency, 63, 64, 310 theory, 55-57 Hybridization, bead-based sandwich, 295-296 Hybridization, in situ, 75-97, 239, 243,251, 253 advantages, 76, 97 applications, 85-91, 94-95, 97 chemiluminescence detection methods, 163-166 controls, 84-85, 91 denaturation, 93 description, 76 diffusion, 243 digestion, 92-93, 93 equipment, 85, 88 immunohistochemistry, 94 kinetics, 80-81 limitations, 94 nonspecific signal, 84, 91, 93-94 PCR, 96 prehybridization, 79-80 probe labeling, 81-83 nonisotopic, 76-77 product detection, 83-84, 90-91 protocol, 86-91, 90, 243 results, 92 RT-PCR, 96 380 Index Hybridization ( c o n t i n u e d ) sample preparation, 78-79, 89, 92-93 sensitivity, 85 slide preparation, 88, 93 mounting, 79 stringency, 81 troubleshooting, 92-94 vendors, 96 Hybridization protection assay, 18, 151-152 Hydroxylamine, 31 IDs0, s e e Inhibitory dose, 50% Immunoassay, s e e a l s o Enzyme immunoassay chemiluminescence detection method, 155 \ microparticle, 325 Immunocapture assay, 325 for ligation-activated transcription, 362-365, 371 Immunochromatography, 13-14 Immunohistochemistry, 94 Infection, dual, 20-21 Inhibitory dose, 50% acyclovir, 121-122, 125 antiviral susceptibility assay, 123 determination, 107, 108-109, 110 foscarnet, 121-122 for herpes simplex virus, 125 Intensifying screen, 64-65 Interleukin, quantification, 198 IP-10, s e e 4'-Aminomethyl-4,5dimethylpsoralen Irradiation, ultraviolet, 231 ISH, s e e Hybridization, in s i t u Isopsoralen, s e e 4'-Aminomethyl-4,5dimethylpsoralen Klenow fragment, s e e a l s o DNA polymerase exo- fragment, 330-331 in random priming, 58 Laboratory, s e e Facility design Laminar flow hood, 28, 231 LAT, s e e Ligation-activated transcription LCR advantages, 318-321,320, 327 amplification, 322-324 application, 318-321 contamination control, 326 description, 8-9, 316-317 detection of product, 324-325 gap, 317, 324 probe considerations, 323 protocol, 321-325 quality control, 326 reagents, 324 sensitivity, 320, 324 specificity, 8, 319, 320 specimen preparation, 321-322 target sequence considerations, 322-323 thermal cycling, 323-324 Leukemia, chronic myelogeneous, s e e Chronic myelocytic leukemia Ligase, 324 Ligase chain reaction, s e e LCR Ligation-activated transcription advantages, 371 amplification, 359-360 application, 365-371,369 chemiluminescence detection methods, 367-369 description, 7, 352-353,365-367, 371-372 detection of product, 353-353,360-365, 367-369 detection threshold, 368-369 efficiency, 367 enzymes, 355 immunocapture assay, 362-365, 371 kinetics, 366 oligonucleotide preparation, 356-358 probe, 369, 371 detection, 367-369 synthesis, 363-364 protocol, 354-365 proto-promotor ligation, 358-359 synthesis, 357-358 quality assurance, 359 validity, 371,372 yield, 7, 366, 371 Liver, 255 D-Luciferin, 153 Luminol, 150-151, 158 Luminometer, 153-154 Macrophage, 253 Magnesium chloride, 230, 243,281,336 Manifold, dot/slot filtration, 54 MEIA, s e e Microparticle immunoassay Membrane nitrocellulose, 48, 51 381 Index nylon, 48, 49, 51, 63-64 transfer methods, 48-51; 53 transfer technique, 48-51 Microparticle immunoassay, 325 Microwell plate assay description, 341-342 plate coating procedure, 341-342 protocol, 346-347 Molecular diagnostic methods, s e e Diagnostics, molecular Molecular weight standards, 46 Monoclonal antibodies, 299-301 M-PCR advantages, 34, 221,224 application, 220, 221 control, 231-232 description, 220 electrophoresis, 227 facility design, 231 false negative, 232-234, 233-234 and flow cytometry, 228 fluorescence, 228 hot start, 225,230 HPLC, 228 hybridization, 228 nonspecific product, 230, 232-234 optimizing, 225 primer, 224-225 protocol, 226-227 quality control, 231-234, 232 results, 227-228, 233-234 sensitivity, 225,228-229, 232 specificity, 228-229, 230, 232 specimen preparation, 226, 233 temperature, 225,230 troubleshooting, 229-230 Multiplex polymerase chain reaction, s e e PCR Mycobacteria, DNA preparation, 339 Mycobacterium tuberculosis detection by strand-displacement amplification, 335-339 sample processing, 339-340 sterilization, 339-340 NALC, 340 NASBA advantages, 269-270 amplification, 267, 269, 273-274 application, 270-271 contamination, 271,272 M- description, 5-6, 261-263 detection method, 274-278 enzymes, 261-263,266 facility design, 271 kinetics, 266-269, 269, 270 primer, 264, 274 nested, 263 P1,266 P2, 267 protocol, 271-284 quantification, 266-267 reagents, 265 sequencing, 269 solutions, 273-274, 280-284 temperature, 265 troubleshooting, 266 yield, N e i s s e r i a g o n o r r h o e a e , detection LCR, 320-321 M-PCR, 226-228 Nevirapine, 299 Nick translation, 59-60, 81 protocol, 59-60 Nitrocellulose, s e e Membrane, nitrocellulose Nonisotopic detection methods, s e e Chemiluminescence detection methods Northern blot description, 40 detection methods, 64-66 hybridization, 62-64 protocol, 52-53, 68-69 transfer to membrane, 53 Nucleation, 55 Nucleic acid, s e e a l s o DNA; RNA cartier, 79 degradation, 26 detection threshold, 316 extraction, extraction protocol, 271-272 quantification, 44-45 sequence analysis, 276-278 yield, 26 Nucleic acid sequence based amplification, s e e NASBA Oligonucleotide, 151,205-206 attachment to support, 305-307 branched, 132, 137 HIR1, 205-208 382 Index Oligonucleotide (continued) labeling chemiluminescence, 149-150 5' end-labeling, 60-61 for ligation-activated transcription, 356 proto-promotor, 357-358 solution for, 284 Oligonucleotide probe gel retardation assay, 276 Optical density, 206 32p, 64 PAGE, see Electrophoresis, polyacrylamide gel PARV7A/2, 304-305 Parvovirus, 149 PBMC, 209 PCR, see also Amplicon carryover; bDNA signal amplification; CRT-PCR; M-PCR; PCR in situ hybridization; RT-PCR advantages, 5, 239, 270 amplicon carryover, 179-180, 240 amplification, 181-182, 186-187 application, 183-185, 219-220 control, 33, 34, 185, 187-188 description, 4-5, 175-176 false negative, 34, 188 false positive, 29, 30-32, 178-179 hot start, 29-30, 96, 239 nested, 182-183 primer selection, 182 product detection, 182-183 protocol, 185-189, 242 quality control, 179, 181, 188-189 quantification, 152 reproducibility, 188 results, 188-189 sensitivity, 180-181 specificity, 178-179, 187-188 PCR in situ hybridization advantages, 239-240, 250 amplification, 242 application, 237-238, 240, 249-257 background signal, 240 control, 244-249 histology, 244, 247 hot start, 238, 240-242, 243 limitations, 239 mixed cell experiment, 249 nonspecific signal, 247 primer, 238 protease digestion, 244-247 sample preparation, 241 sensitivity, 239 specificity, 249, 253 troubleshooting, 243-249 Peripheral blood mononuclear cell, 209 Peroxidase, horseradish, 84, 150-151 PFU, see Plaque forming unit pH meter, quality assurance, 28-29 Phosphorus-32, 64 Pipette, 91, 271 mechanical, 30 positive displacement, 29 technique, 120, 187 tips, aerosol-resistant, 29 Plaque forming unit, 115-116 Polymerase DNA, 233 reverse transcriptase, 201 T7, 266, 267 Taq, 177, 195-196, 201,233 inhibitors, 230 Tth, 195,201 Polymerase chain reaction, see PCR Potassium chloride, 281 Power supply, quality assurance, 28 Primer, 182, 195, 210, 224-225, 230 GC composition, 264, 301-302 in M-PCR, 220 multiple, 224-225, 238 in NASBA, 264, 266, 267, 274, 281-282 nested, 263 for PCR, 182 for self-sustained sequence replication, 289 sequencing, 277-278 SK39, 210 for strand-displacement amplification, 335-336 testing, 230 T7 promoter, 301-302 Probe, 57-62, 162-163,228, 371 alkaline phosphatase, 310, 335 in antibody-capture solution hybridization, 354 for bDNA signal amplification, 134-137 capture, 335, 337, 343-344 characteristics, 57, 302 control, 91 denaturation, 63 383 Index detector, 337, 343-345 DNA, 149-150 GC composition, 302 labeling technique, 81-83, 151 5' end-labeling, 60-61 horseradish peroxidase, 151 nick translation, 59-60, 81 nonisotopic, 82-83 oligonucleotide, synthetic, 82 32p, 64-65, 307-308, 360-361 radioactive, disadvantage, 155 random primer extension, 81 universal linkage system, 82-83 for LCR, 316-317, 323 for ligation-activated transcription, 367-369 multi-probe systems, 16-18 nonisotopic, detection systems, 83-84 in PCR, 183 preparation, 58-62 RNA, complementary, 60-61 ruthenium (II) tris(bipyridyl), 152-153 self-sustained sequence replication, 298-299, 302, 307 sensitivity, 149-150 specificity, 84 storage, 344 for strand-displacement amplification, 342 synthesis, 343-344, 363-364 random priming, 58 in vitro transcription, 60-61 Proficiency testing, s e e Testing, proficiency Protease digestion, 244-247, 244-249 treatment, 241 Protective clothing, s e e Clothing, protective Proteinase K, 42, 322 Psoralen, s e e 4'-Aminomethyl-4,5dimethylpsoralen Q-Beta replicase system, 9-10 QBR, s e e Q-Beta replicase system Quality assurance cost, 26 for equipment, 28-29 Quality control, 122-123 Radioisotopic detection methods, disadvantages, 18, 20, 155 Reagent expiration date, 33 preparation, 32-33 storage, 33, 113 testing, 232 Replication, sequence, self-sustained, s e e Self-sustained sequence replication Resin preparation, 305 Restriction endonuclease, 45 Reverse transcriptase, 195-196, 201,233, 352-353 from avian myeloblastosis virus, 288, 292 Reverse transcriptase polymerase chain reaction, s e e RT-PCR Reverse transcriptase in situ PCR, s e e RTPCR in situ hybridization Reverse transcription, 241-242 Ribonuclease, 276 H, 352-353 inhibitor, 359-360 Ribonucleic acid, s e e RNA Ribonucleic acid, complementary, in vitro transcription, 60-61 RNA, s e e a l s o bDNA signal amplification; Northern blot; RT-PCR amplification, 289, 311 by ligation-activated transcription, 365 control, 196-197 characterization, 203 construction of, 205-206 cRNA, 57 denaturation, 52-53, 55 detection antibody-capture solution hybridization, 353-354 ligation-activated transcription, 360 NASBA, 262-263,270 RT-PCR in situ hybridization, 240-243 self-sustained sequence replication, 295 slot blot, 55 extraction protocol, 42-43,209-210, 302 polyadenylated messenger RNA, 44 g a g sequence, 211 nucleic acid sequence based amplification, 273 purification, 206 quantification, 44-45,209-211,295,302, 368 application, 197-198 cRT-PCR, 197-198 size markers, 52 384 Index RNA ( c o n t i n u e d ) synthesis, kinetics, 266-267, 269 transcription detection, 311 RNA polymerase, 352-353 RNase, 143,355 activity, 266 contamination, 33 E coli, 292 H, 288, 292, 352-353 RNase A mismatch scanning technique, 312 RNase contamination, see Contamination, RNase RNasin, 359-360 Rotor, centrifuge, 28 RT buffer, 283 RT-PCR, 66-68, 269 advantages, 214-215 amplification step, 207-208 application, 193-194, 197-198, 200, 213-214, 214-215, 369-371 artifact, 197 background, 210 cDNA synthesis, 196 coamplification, 196-198, 201, 210 control, 198-200, 203-205,207, 208 cRNA, 214-215 exogenous, 196 external, 200-203,204-205 internal, 200-203 ribonucleic acid, 196-198 development, 194-195 enzymes, 201 human immunodeficiency virus detection, 203-205 and ligation-activated transcription, 369-371 optimization, 210 primer, 195 protocol, 205-214 quantification, 195-198, 198, 200, 203-205,207-208, 210-211 real-time analysis, 202 reproducibility, 196, 200, 212-213 results, 207-208 sample preparation, 201 sensitivity, 195,210, 212 specificity, 201, 212 validation, 212-213 RT-PCR in situ hybridization, see also PCR in situ hybridization controls, 247, 255,257 description, 96, 239 hot start, 240 mixed cell experiment, 249 protocol, 240-243 sensitivity, 255 specificity, 249, 253,255 troubleshooting, 243-249 Ruthenium(II) tris(bipyridyl), 152-153 Safety, 116-117, 186, 339-340, 340-341 Sample contamination, 29, 30-32 preparation, 241 for branched oligodeoxyribonucleotide signal amplification, 142-143 for DNA, 40-42 for ligase chain reaction, 321-322 for PCR, 185-186 for RT-PCR, 201 for self-sustained sequence replication, 302 problems in, processing, 2-5, 27 quality, 26-27 shipping, stability, storage conditions, 26-27 storage effects, for strand-displacement amplification, 333-334, 339-340 SBD, see Sequence-based detection Screen, intensifying, 64-65 SDA, see Strand-displacement amplification Self-sustained sequence replication, 5-6 advantages, 295,299-301 amplification, 292 DNA, 304 RNA, 303-305 selective, 293-295 amplification product detection, 307-310 quantification, 308 application, 298-301, 311-312 with bead-based sandwich hybridization, 298-299 conditions, 291-292 control, 304-305 description, 288-289 detection method, 295 by bead-based sandwich hybridization, 307-309 Index 385 enzymes, 303-304 false positive, 296 gene expression, 293 hybridization, 295-296 kinetics, 293-295 monoclonal antibody production, 299-301 nonspecific product, 294 primer, 289, 301-302 protocol, 301-311 purification, 305-307 quality control, 296-297, 310-311 sample preparation, 302 selectivity, 292-293 sterilization, 310-311 target, 292 yield, 6, 305 Semen, 231,234 Sequence-based detection applications, 16 description, 14-16 Sequence replication, self-sustained, s e e Self-sustained sequence replication Signal amplification, s e e Amplification, signal SIL, 249 Silica, suspension protocol, 278,280 I n situ hybridization, s e e Hybridization, in situ Slides mounting, 79 preparation, 88, 93 Slot blot, s e e Dot blot Sodium hydroxide, 231 Southern blot, 71,228 controls, 45-46 description, 40 detection methods, 64-66 hybridization, 62-64 protocol, 45-51 restriction, 45-46 for self-sustained sequence replication, 299 transfer, 48-51 Specimen, s e e Sample Spectrophotometry nucleic acid evaluation, 27 nucleic acid quantification, 45 Spleen fragment culture, 299-301 Sputum, processing, 340-341 Squamous intraepithelial lesions, 237 SSC solution, 307 SSPE solution, 307 SSSR, s e e Self-sustained sequence replication Sterilization, s e e Contamination Strand-displacement amplification advantages, 330 application, 335-339 contamination, 345 control, 333-334, 336, 337, 345-346 description, 7-8, 330-333 detection of product, 334-335,345-347 by chemiluminescence, 341-347 disadvantages, 330 false negative, 333-334 genomic DNA, 332 inhibitor, 339 kinetics, 331 nonspecific signal, 334 primer, 335-336 probes, 337, 342-345 capture, 346 detection, 346 product yield, 330 protocol, 335-340 quality control, 345, 346 safety, 340-341 sample preparation, 332-333 samples, 341 specimen preparation, 339-340 stringency, 334 target, synthetic, 345 yield, 7-8 Streptavidin, s e e Avidin Swab endocervical, 226 for C h l a m y d i a t r a c h o m a t i s , 322 urethral, 226 polymerase, 195-196, 201,233 inhibitors, 230 TAS, 288 Temperature, melting, 80-81,224-225,343 TE solution, 307, 364 Testing, proficiency, 34-35 Thermocycler, 227 decontamination, 28 quality assurance, 28 Thermocycling, 176-177, 187 LCR, 8-9, 323-324 M-PCR, 227 PCR, 4-5, 176-177, 242 RT-PCR, 207 Taq 386 Index Thermus thermophilus, 233 3SR, see Self-sustained sequence replication Tissue culture, see Cell culture T m, see Temperature, melting TNT buffer, 364 T7 polymerase, 266, 267 T7 promoter, 356-357 in primers, 289 Transcription ligation-activated, see Ligation-activated transcription reverse, 210 in oitro, 60-61 Transcription-based amplification system, 288 Tris, 281 Trisacryl support, 305 T7 RNA polymerase, 264, 288, 292 promoter sequence, 264, 352-353 Tth polymerase, 195,201 Tubes, microcentrifuge, 29 for pipettes, 30 quality assurance, 28 UNG, see Uracil-N-glycosylase Universal linkage system, 82-83 Uracil-N-glycosylase, 31, 179-181,230 advantages, 180-181 Urethral swab, for Chlamydia trachomatis, 322 Urine specimen, 231,322 for Chlamydia trachomatis, 320-321,322 for multiplex PCR, 226 UV lights, see Ultraviolet light Virus, see specific types Water, quality assurance, 33 Wax, paraffin, 230 X-ray film, 65, 347 Xylene cyanol, 48 ULS, 82-83 Ultraviolet light, 231,361 cross-linking DNA, 49-50 Zidovudine, 298-299 .. .MOLECULAR METHODS FOR VIRUS DETECTION This Page Intentionally Left Blank MOLECULAR METHODS FOR VIRUS DETECTION Edited by Danny L Wiedbrauk Daniel H Farkas William Beaumont... laboratories that employ molecular methods for virus detection Danny L Wiedbrauk Daniel H Farkas Nucleic Acid Detection Methods Ann M Drevon Molecular Probe Laboratory Department of Clinical Pathology... cloned DNA probes to detect viral nucleic acids Proponents of the new molecular diagnostic methods predicted that nucleic acid tests would rapidly replace traditional virus detection methods (Kulski