Human Retrovirus Protocols

Abstract

This book is a cutting-edge collection of basic and state-of-the-art methods optimized for investigating the molecular biology of this class of retrovirus. These readily reproducible techniques range from methods for the isolation and detection of human retroviruses to cutting-edge methods for exploring the interplay between the viruses and the host. Here, the researcher will find up-to-date techniques for the isolation and propagation of HIV, HTLV, and foamy virus from a variety of sources.; There are also assays for determining the cell tropism of HIV-1, the coreceptor usage of HIV-1, and human gene expression with HIV-1 infection by microarrays, as well as for phenotyping HIV-1 infected monocytes and examining their fitness. Highlights include the detection and quantification of HIV-1 in resting CD4+, a new cloning system for making recombinent virus, cDNA microarrays, and the determination of genetic polymorphisms in two recently identified HIV-1 co-factors that are critical for HIV-1 infection. Enhanced culture assay for detection and quantitation of latently infected, resting cd4+ t-cells carrying replication-competent virus in HIV-1-infected individuals / J.D. Siliciano and R.F. Siliciano -- Isolation, propagation, and titration of human immunodeficiency virus type 1 from peripheral blood of infected individuals / H. Schuitemaker and N.A. Kootstra -- Isolation of human immunodeficiency virus type 1 from peripheral blood monocytes / P.R. Gorry [and others] -- Isolation, propagation, and HIV-1 infection of monocyte-derived macrophages and recovery of virus from brain and cerebrospinal fluid / S. Gorantla, M. Che and H.E. Gendelman -- Isolation and HIV-1 infection of primary human microglia from fetal and adult tissue / K. Borgmann, H.E. Gendelman and A. Ghorpade -- Isolation of human immunodeficiency virus type 1 from semen and vaginal fluids / A.A. Kiessling -- Isolation and quantification of HIV from lymph nodes / C. Tamalet -- Isolation of human immunodeficiency virus type 2 biological clones from peripheral blood lymphocytes / H. Blaak -- Isolation and confirmation of human t-cell leukemia virus type 2 from peripheral blood mononuclear cells / M.D. Lairmore and A. Montgomery -- Isolation of foamy viruses from peripheral blood lymphocytes / J. Tobaly-Tapiero, P. Bittoun and A. Saib -- Alu-ltr real-time nested PCR assay for quantifying integrated HIV-1 DNA / A. Brussel, O. Delelis and P. Sonigo -- Quantification of hfv-integrated DNA in human cells by alu-ltr real-time PCR / O. Delelis, A. Brussel and P. Sonigo -- Detection of HIV-1 provirus and rna by in situ amplification / A. Nicol and G.J. Nuovo -- Detection of htlv-1 gene on cytologic smear slides / K. Kashima, T. Daa and S. Yokoyama -- Detection of HIV-2 by PCR / F. Gao -- Quantitation of HIV-1 viral rna in blood plasma and genital secretions / S.A. Fiscus -- Quantification of proviral DNA load of human immunodeficiency virus type 2 subtypes a and b using real-time PCR / M. Gueudin, F. Damond and F. Simon -- Plasma rna viral load in HIV-1 group o infection by real-time PCR / M. Gueudin and F. Simon -- A new combined HIV p24 antigen and anti-HIV-1/2/o screening assay / S. Polywka [and others] -- A new automated fourth-generation HIV screening assay with sensitive antigen detection module and high specificity / B. Weber -- Detection of antiviral antibodies using enzyme-linked immunosorbent assay / I.G. Winkler -- Plaque-reduction assays for human and simian immunodeficiency virus neutralization / A. Nordqvist and E.M. Fenyo -- Detection of drug-resistant HIV-1 strains / A.A. Kiessling, S.J. Eyre and B.D. Desmarais -- Determination of cell tropism of HIV-1 / N.A. Kootstra and H. Schuitemaker -- Determination of co-receptor usage of HIV-1 / H. Schuitemaker and N.A. Kootstra -- Quantitative evaluation of HIV and SIV co-receptor use with ghost(3) cell assay / D. Vodros and E.M. Fenyo -- Phenotypic characterization of blood monocytes from HIV-infected individuals / P.J. Ellery and S.M. Crowe -- Methods to determine HIV-1 ex vivo fitness / A. Abraha [and others] -- A yeast recombination-based cloning system to produce chimeric HIV-1 viruses and express HIV-1 genes / D.M. Moore [and others] -- PCRs amplification, cloning, and construction of HIV-1 infectious molecular clones from virtually full-length HIV-1 genomes / P.K. Ehrenberg and N.L. Michael -- Amplification and cloning of near full-length HIV-2 genomes / F. Gao -- Growth and manipulation of a human t-cell leukemia virus type 2 full-length molecular clone / M. Anderson and P.L. Green -- Construction and analysis of genomic, full-length infectious foamy virus DNA clones / R. Wirtz and M. Lochelt -- Molecular characterization of proteolytic processing of the gag proteins of human spumaretrovirus / K.I. Pfrepper and R.M. Flugel -- Assessing the relative efficacy of antiretroviral activity of different drugs on macrophages / S. Aquaro and C.F. Perno -- Gene expression profiling of HIV-1 infection using cdna microarrays / A.B. van 't Wout -- Determination of DC-sign and DC-signr repeat region variations / H. Liu and T. Zhu.