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Douglas Richman

Publications and source records attributed to Douglas Richman.

12 recordsLinked to original sources
PubMed2006

Clinical utility of HIV standard genotyping among antiretroviral-naive individuals with unknown duration of infection.

In clinical settings, we have found a high rate of human immunodeficiency virus (HIV) drug resistance among antiretroviral-naive patients for whom the duration of infection was unknown. These high rates were most likely the result of both transmitted resistance and informal antiretroviral use, and they suggest that routine resistance testing among antiretroviral-naive patients would be a cost-effective clinical practice.

Anti-HIV Agents↗
PubMed2006

The XIVth International HIV Drug Resistance Workshop, Quebec City, Canada, June 2005.

This report summarizes research advances that further our understanding of the evolution, mechanisms and clinical impact of HIV drug resistance presented at the XIVth International HIV Drug Resistance Workshop held in Quebec City, Canada from June 7-11, 2005. The topics that were discussed included the clinical implications of resistance in mother-to-child transmission, breakthroughs in technologies for studying resistance, resistance to new antiretroviral agents, mechanisms of HIV drug resistance, epidemiological trends, and HIV fitness and pathogenesis.

Animals↗
PubMed2005

Characterizing anti-HIV monoclonal antibodies and immune sera by defining the mechanism of neutralization.

Understanding the nature of neutralization may provide information for crafting improvements in HIV vaccines. Using JR-FL as a prototype primary pseudovirus, we first investigated anti-HIV monoclonal antibodies (mAbs) in several neutralization formats designed to elucidate the timing of neutralization. MAb b12 was most effective before receptor binding, 2G12 neutralized effectively even after CD4 binding, and X5 and a V3 loop mAb (LE311) were inactive in a standard format but were induced by sCD4. Consistent with this latter finding, native PAGE indicated that X5 and V3 mAb binding to Envelope trimers was dependent on sCD4 binding. In contrast, 2F5 and 4E10 were active even post-CD4/CCR5 engagement. We next analyzed the neutralization mechanism of a panel of HIV+ donor plasmas of various potencies. All mediated high levels of post-CD4 neutralization that was not associated with activity in the standard format. None, however, neutralized effectively in the post-CD4/CCR5 format, suggesting that 2F5/4E10-like Abs were absent or at low concentrations. Finally, we analyzed a non-neutralizing plasma spiked with mAbs b12, 2G12 or 2F5, which resulted in increases in neutralization titers consistent with the activities of the mAbs. We conclude that these methods, together with other mapping approaches, may provide a better understanding of neutralization that could be useful in vaccine research.

AIDS Vaccines↗
PubMed2004

Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome.

HIV-1 deleted for the vif accessory gene encapsidates the cellular cytidine deaminase APOBEC3G. Upon infection, the encapsidated APOBEC3G induces G-->A mutations in the viral reverse transcripts. The G-->A mutations result either from C-->U deamination of the minus strand or deamination of both strands followed by repair of the plus strand. We report here that minus-strand deamination occurred over the length of the virus genome, preferentially at CCCA sequences, with a graded frequency in the 5'-->3' direction. APOBEC3G induced previously undetected C-->T mutations in the 5' U3 and the primer-binding site, both of which become transiently single-stranded during reverse transcription. In vitro, APOBEC3G bound and deaminated single-stranded DNA (ssDNA) but not double-stranded DNA (dsDNA) or DNA-RNA hybrids. We propose that the requirement for ssDNA accounts for the minus-strand mutations, the 5'-->3' graded frequency of deamination and the rare C-->T mutations.

APOBEC-3G Deaminase↗
PubMed2003

Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection.

Human immunodeficiency virus type 1 (HIV-1) alters gene expression in infected cells, leading to cellular dysfunction. We uncovered a number of host cell genes that are modulated in both CD4(+) T cell lines and primary CD4(+) T lymphocytes infected with HIV-1, using high-density oligonucleotide probe microarray technology. We focused on one gene in particular, nuclear factor I-B2 (NFI-B2), because of its high level of expression. NFI-B2 is a member of the nuclear factor I family of nuclear proteins, which are known to be involved in viral and cellular transcription. To better understand the role of NFI-B2 during HIV-1 infection, we generated a Jurkat T cell line that constitutively expressed NFI-B2. After infection with HIV-1, these cells produced fewer viruses because of a downregulation of surface CD4 expression. The surface expression of the coreceptor, CXCR4, remained unchanged. Furthermore, levels of CD4 mRNA were reduced in NFI-B2-producing cells, suggesting that expression of NFI-B2 impairs CD4 transcription. Modulation of NFI-B2 by HIV-1 may represent yet another mechanism by which HIV infection reduces cell surface expression of CD4.

CCAAT-Enhancer-Binding Proteins↗
PubMed2003

A new perspective on V3 phenotype prediction.

The particular coreceptor used by a strain of HIV-1 to enter a host cell is highly indicative of its pathology. HIV-1 coreceptor usage is primarily determined by the amino add sequences of the V3 loop region of the viral envelope glycoprotein. The canonical approach to sequence-based prediction of coreceptor usage was derived via statistical analysis of a less reliable and significantly smaller data set than is presently available. We aimed to produce a superior phenotypic classifier by applying modern machine learning (ML) techniques to the current database of V3 loop sequences with known phenotype. The trained classifiers along with the sequence data are available for public use at the supplementary website: http://genomiac2.ucsd.edu:8080/wetcat/v3.html and http://www.cs.waikato.ac.nz/ml/weka[corrected].

Amino Acid Sequence↗
PubMed2002

The clinical relevance of non-nucleoside reverse transcriptase inhibitor hypersusceptibility: a prospective cohort analysis.

OBJECTIVE: To evaluate the clinical significance of hypersusceptibility to non-nucleoside reverse transcriptase inhibitors (NNRTI). DESIGN: Analysis of a prospective clinical trial cohort. PATIENTS: NNRTI-naive patients failing a stable antiretroviral regimen. MEASUREMENTS: HIV phenotype, HIV RNA, and CD4 cell counts were prospectively collected after patients changed to a new regimen. Hypersusceptibility to NNRTI was defined as a fold-change (FC) in IC50 (inhibitory concentration of 50%) of < 0.4. RESULTS: The 177 patients had a mean HIV RNA of 4.1 log10 copies/ml, CD4 cell count of 322 x 10(6) cells/l and 41 months of prior antiretroviral treatment. Hypersusceptibility to one or more NNRTI was present in 29%. Both longer duration and reduced susceptibility to nucleoside reverse transcriptase inhibitors were associated with efavirenz hypersusceptibility (P < 0.05). NNRTI-containing regimens were initiated in 106 patients at baseline. The mean change in log HIV RNA after 6 months was greater for patients with hypersusceptibility (-1.2 log10 copies/ml; n = 21) than in patients without (-0.8 log10 copies/ml; n = 77) (P = 0.016). Differences persisted to month 12 (P = 0.023). Multiple linear regression models confirmed that hypersusceptibility to NNRTI was a significant independent predictor of the magnitude of early (months 1-4) HIV RNA reduction, after accounting for the baseline HIV RNA and the number of drugs to which the patient's virus was susceptible (P < 0.02). CD4 cell increases (months 4-10) were 28- 60 x 10(6) cells/l greater in patients with hypersusceptible virus (P < or = 0.1). CONCLUSION: NNRTI hypersusceptibility occurred in more than 20% of nucleoside-experienced patients and was associated with greater reduction of HIV RNA and increase in CD4 cells.

Adult↗
PubMed2002

A phase II randomized study of the virologic and immunologic effect of zidovudine + stavudine versus stavudine alone and zidovudine + lamivudine in patients with >300 CD4 cells who were antiretroviral naive (ACTG 298).

Before the development of multidrug regimens for treatment of patients with HIV infection single or dual nucleoside therapy was the standard of care. The present study was designed to examine the relative short (12-week) and long-term (48-week) activity of zidovudine (ZDV) vs stavudine (d4T) vs the combination in antiretroviral naive patients. The study was modified so that lamivudine (3TC) was added to ZDV after 12 weeks of monotherapy. A total of 129 subjects entered the study; however, not all were followed for 48 weeks as the study was terminated early due to changing standards of care. The median baseline viral load and CD4 cell count were 10,008 copies/ml and 407 cells/mm(3), respectively. There were no significant differences in the initial (12-week) change in viral load across the three arms. The viral load reduction at 48 weeks was greater in the ZDV/ZDV plus 3TC arm, with an average change of -0.91 log(10) copies/ml than in the d4T alone (-0.47 log(10) copies/ml) or d4T plus ZDV (-0.33 log(10) copies/ml), p = 0.03 and 0.02, respectively. There was a marginally significant increase in the CD4 cell count at Week 12 in the d4T arm as compared to the ZDV/ZDV plus 3TC arm. In general the treatments were well tolerated. The combination of d4T plus ZDV did not result in additional antiviral suppression as compared to either drug alone at 12 weeks and appeared to have less antiviral activity after Week 12. Based on this study and other data, combining d4T and ZDV is not recommended.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Stampidine is a potent inhibitor of Zidovudine- and nucleoside analog reverse transcriptase inhibitor-resistant primary clinical human immunodeficiency virus type 1 isolates with thymidine analog mutations.

We report the antiretroviral activity of stavudine-5'-(p-bromophenyl methoxyalaninyl phosphate) (stampidine [STAMP]), a novel aryl phosphate derivative of stavudine, against primary clinical human immunodeficiency virus type 1 (HIV-1) isolates. STAMP inhibited each one of nine clinical HIV-1 isolates of non-B envelope subtype and 20 genotypically and phenotypically nucleoside analog reverse transcriptase inhibitor-resistant HIV-1 isolates at subnanomolar to low-nanomolar concentrations.

Anti-HIV Agents↗
PubMed2002

Vaccine-induced immune responses in rodents and nonhuman primates by use of a humanized human immunodeficiency virus type 1 pol gene.

A synthetic gene consisting of the reverse transcriptase (RT) and integrase (IN) domains of human immunodeficiency virus type 1 (HIV-1) pol was constructed using codons most frequently used in humans. The humanized pol gave dramatically improved levels of Rev-independent, in vitro protein production in mammalian cells and elicited much stronger cellular immunity in rodents than did virus-derived gene. Specifically, BALB/c mice were immunized with plasmids and/or recombinant vaccinia virus constructs expressing the synthetic gene. High frequencies of Pol-specific T lymphocytes were detected in these animals by the gamma interferon enzyme-linked immunospot assay against pools of short overlapping peptides. Characterization of the stimulatory peptides from these pools indicates that the optimized gene constructs are able to effectively activate both CD4+ and CD8+ T cells. Immunization of rhesus macaques with DNA vaccines expressing the humanized pol coupled to a human tissue plasminogen activator leader sequence led to pronounced in vitro cytotoxic T-lymphocyte killing activities and enhanced levels of circulating Pol-specific T cells, comparable to those observed in HIV-1-infected human subjects. Thus, optimizing the immunogenic properties of HIV-1 Pol at the level of the gene sequence validates it as an antigen and provides an important step toward the construction of a potent pol-based HIV-1 vaccine component.

AIDS Vaccines↗
PubMedDate not supplied

Update of the Drug Resistance Mutations in HIV-1: 2005.

Since 2000, the International AIDS Society-USA (IAS-USA) Drug Resistance Mutations Group has worked as an independent entity and forged a collaborative process to identify key HIV-1 drug resistance mutations. The goal of the group is to quickly deliver accurate and unbiased information to clinical practitioners on HIV-1 resistance. This April 2005 version of the IAS-USA Drug Resistance Mutations Figures replaces the version published in this journal in October 2004. The IAS-USA Drug Resistance Mutations Figures are designed for use in identifying mutations associated with viral resistance to antiretroviral drugs and in making therapeutic decisions. Care should be taken when using this list of mutations for surveillance or epidemilogic studies of transmission of drug-resistant virus. A number of amino acid substitutions, particularly minor mutations, represent polymorphisms that, in isolation, may not reflect prior drug selective pressure or reduced drug susceptibility.

Anti-HIV Agents↗