Human Retroviru s Protocol s

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1 Human Retroviru s Protocol s Virology and Molecular Biolog y Tuofu Zhu

2 Methods in Molecular Biology'

3 Preface Contributors v x i PART I. METHODS FOR VIRUS ISOLATION AND DETECTIO N 1 Enhanced Culture Assay for Detection and Quantitatio n of Latently Infected, Resting CD4 + T-Cells Carryin g Replication-Competent Virus in HIV-1-Infected Individual s Janet D. Siliciano and Robert F. Siliciano 3 2 Isolation, Propagation, and Titration of Human Immunodeficienc y Virus Type 1 From Peripheral Blood of Infected Individual s Hanneke Schuitemaker and Neeltje A. Kootstra Isolation of Human Immunodeficiency Virus Type 1 From Periphera l Blood Monocyte s Paul R. Corry, Secondo Sonza, Katherine Kedzierska, and Suzanne M. Crowe 25 4 Isolation, Propagation, and HIV-1 Infection of Monocyte-Derive d Macrophages and Recovery of Virus From Brai n and Cerebrospinal Flui d Santhi Gorantla, Myhanh Che, and Howard E. Gendelman 35 5 Isolation and HIV-1 Infection of Primary Human Microgli a From Fetal and Adult Tissu e Kathleen Borgmann, Howard E. Gendelman, and Anuja Ghorpade Isolation of Human Immunodeficiency Virus Type 1 From Seme n and Vaginal Fluid s Ann A. Kiessling 71 7 Isolation and Quantification of HIV From Lymph Node s Catherine Tamalet 87 8 Isolation of Human Immunodeficiency Virus Type 2 Biologica l Clones From Peripheral Blood Lymphocyte s Hetty Blaak 95 9 Isolation and Confirmation of Human T-Cell Leukemia Viru s Type 2 From Peripheral Blood Mononuclear Cell s Michael D. Lairmore and Andy Montgomery 113

4 10 Isolation of Foamy Viruses From Peripheral Blood Lymphocytes Joelle Tobaly-Tapiero, Patricia Bittoun, and Ali Saito A/u-LTR Real-Time Nested PCR Assay for Quantifyin g Integrated HIV-1 DN A Audrey Brussel, Olivier Delelis, and Pierre Sonigo Quantification of HFV-Integrated DNA in Human Cell s by Alu-LTR Real-Time PC R Olivier Delelis, Audrey Brussel, and Pierre Sonigo Detection of HIV-1 Provirus and RNA by In Situ Amplificatio n Alcina Nicol and Gerard J. Nuovo Detection of HTLV-1 Gene on Cytologic Smear Slide s Kenji Kashima, Tsutomu Daa, and Shigeo Yokoyama Detection of HIV-2 by PC R Feng Gao Quantitation of HIV-1 Viral RNA in Blood Plasm a and Genital Secretion s Susan A. Fiscus Quantification of Proviral DNA Load of Human Immunodeficienc y Virus Type 2 Subtypes A and B Using Real-Time PC R Marie Gueudin, Florence Damond, and Francois Simon Plasma RNA Viral Load in HIV-1 Group 0 Infectio n by Real-Time PC R Marie Gueudin and Francois Simon A New Combined HIV p24 Antigen and Anti-HIV-1/2/ 0 Screening Assa y Susanne Polywka, Hedwig Duttmann, Frank Lübben, Rainer Laufs, and Jürgen Feldner A New Automated Fourth-Generation HIV Screening Assay With Sensitive Antigen Detection Module and High Specificit y Bernard Weber Detection of Antiviral Antibodies Using Enzyme-Linke d Immunosorbent Assa y Ingrid G. Winkler Plaque-Reduction Assays for Human and Simia n Immunodeficiency Virus Neutralizatio n Anna Nordqvist and Eva Maria Fenyö Detection of Drug-Resistant HIV-1 Strain s Ann A. Kiessling, S. J. Eyre, and B. D. Desmarais 287

5 PART H. MOLECULAR BIOLOGY METHOD S 24 Determination of Cell Tropism of HIV- 1 Neeltje A. Kootstra and Hanneke Schuitemaker Determination of Co-Receptor Usage of HIV- 1 Hanneke Schuitemaker and Neeltje A. Kootstra Quantitative Evaluation of HIV and SIV Co-Receptor Us e With GHOST(3) Cell Assa y Dalma Vödrös and Eva Maria Fenyö Phenotypic Characterization of Blood Monocytes From HIV-Infected Individual s Philip J. Ellery and Suzanne M. Crowe Methods to Determine HIV-1 Ex Vivo Fitnes s Awet Abraha, Ryan M. Troyer, Miguel E. Quinones-Mateu, and Eric J. Arts A Yeast Recombination-Based Cloning Syste m to Produce Chimeric HIV-1 Viruses and Express HIV-1 Gene s Dawn M. Moore, Eric J. Arts, Yong Gao, and Andre J. Marozsan PCR Amplification, Cloning, and Construction of HIV-1 Infectiou s Molecular Clones From Virtually Full-Length HIV-1 Genome s Philip K. Ehrenberg and Nelson L. Michael Amplification and Cloning of Near Full-Length HIV-2 Genome s Feng Gao Growth and Manipulation of a Human T-Cell Leukemia Viru s Type 2 Full-Length Molecular Clon e Matthew Anderson and Patrick L. Green Construction and Analysis of Genomic, Full-Lengt h Infectious Foamy Virus DNA Clone s Roman Wirtz and Martin Löchelt Molecular Characterization of Proteolytic Processin g of the Gag Proteins of Human Spumaretroviru s Klaus-ingmar Pfrepper and Rolf M. Flügel Assessing the Relative Efficacy of Antiretroviral Activit y of Different Drugs on Macrophage s Stefano Aquaro and Carlo-Federico Perno Gene Expression Profiling of HIV-1 Infectio n Using cdna Microarray s Angelique B. van 't Wout 455

6 37 Determination of DC-SIGN and DC-SIGNR Repeat Regio n Variation s Huanliang Liu and Tuofu Zhu 47 1 Index 483

A PROJECT ON HIV INTRODUCED BY. Abdul Wahab Ali Gabeen Mahmoud Kamal Singer

A PROJECT ON HIV INTRODUCED BY Abdul Wahab Ali Gabeen Mahmoud Kamal Singer Introduction: Three groups of nations have been identified in which the epidemiology of HIV(Human Immunodeficiency Virus) varies: