Dr. Kozal was appointed Senior Associate Dean for Veteran Affairs at Stanford School of Medicine and Chief of Staff at VA Palo Alto Health Care System in 2021. Prior to coming to Stanford, he served as Associate Dean for Veteran Affairs at Yale University School of Medicine and the Chief of Staff at VA Connecticut Healthcare System.

Dr. Kozal is a translational researcher who has focused his research career on three areas: 1) investigating the genetic determinants of HIV and HCV drug resistance, 2) the development of new molecular methods to detect viral mutations, and 3) HIV and HCV clinical trials involving new drugs and diagnostic technology. Dr. Kozal is an expert in microarray and deep sequencing technology receiving patents for his work in genotyping. Dr. Kozal previously directed the Yale HIV Clinical Trials Group and has more than 20 years of experience in running clinical trials, serving as the principal investigator or site investigator on >40 HIV and Hepatitis C trials. He has served on multiple VA and NIH/NCI review panels and is a current a member of the DHHS/NIH Panel on Antiretroviral Guidelines for Adults and Adolescents.

Academic Appointments

Administrative Appointments

  • Senior Associate Dean for Veteran Affairs, Stanford School of Medicine (2021 - Present)
  • Chief of Staff, VA Palo Alto Healthcare System (2021 - Present)
  • Associate Dean for Veteran Affairs, Yale University School of Medicine (2020 - 2021)
  • Chief of Staff, VA Connecticut Healthcare System (2019 - 2021)
  • Professor of Medicine, Yale University School of Medicine (2010 - 2021)
  • Medicine Service line Director, VISN 1 (2017 - 2019)
  • Vice Chair for Veteran Affairs, Dept. of Medicine, Yale University School of Medicine (2013 - 2020)
  • Chief of Medicine, VA Connecticut Healthcare System (2013 - 2020)
  • Director, Yale HIV Clinical Trials Program, Yale University School of Medicine (2009 - 2017)
  • Associate Professor, Yale University School of Medicine (2005 - 2010)
  • Chief, Section of Infectious Diseases, VA Connecticut Healthcare System (2006 - 2013)
  • Assistant Professor, Yale University School of Medicine (2000 - 2005)

Honors & Awards

  • VISN 1 Network Director’s ICARE Award (Integrity, Commitment, Advocacy, Respect & Excellence), VHA (2019)
  • Honorary Master of Arts (MAH), Yale University (2011)

Boards, Advisory Committees, Professional Organizations

  • Member, DHHS/NIH Panel on Antiretroviral Guidelines for Adults and Adolescents (2015 - Present)
  • Reviewer, NIH/NIAID SBIR -Topic areas 33, 34 and 35 Phase I (2016 - 2016)
  • Member, NCI intramural site visit review team of the AIDS and Cancer Virus Program (2015 - 2015)
  • Chair, Special Emphasis Panel, NIAID Review Panel: RFA AI-12-018 Clinical Trial Units for NIAID Networks (UM1) (2013 - 2013)
  • Member, NCI intramural site visit review team of the AIDS and Cancer Virus Program (2011 - 2011)
  • Member, VA Career Development Award Study Section (2008 - 2008)
  • Member, Review Panel, NIH Adult AIDS Clinical Trials Support Laboratories (2003 - 2003)

Professional Education

  • Fellowship, Stanford University, Infectious Diseases (1994)
  • Residency, University of Nebraska Medical Center, Internal Medicine (1991)
  • MD, University of Nebraska College of Medicine, Medicine (1988)


  • Michael J Kozal. "United States Patent US20100173795A1 HIV and HCV microarray to detect drug resistance", Yale University and the United States Government VHA, Mar 18, 2010
  • Michael J. Kozal, Thomas C Merigan. "United States Patent US RE38,352E1 Polymerase chain reaction assays for monitoring antiretroviral therapy and making therapeutic decisions in the treatment of acquired immunodeficiency syndrome.", Stanford University, Dec 16, 2003
  • Michael J. Kozal, Thomas C. Merigan. "United States Patent 5,856,086 Polymerase chain reaction assays for monitoring antiretroviral therapy and making therapeutic decisions in the treatment of acquired immunodeficiency syndrome.", Stanford University, Jan 5, 1999
  • Michael J. Kozal, Thomas C. Merigan. "United States Patent 5,650,268 Polymerase chain reaction assays for monitoring antiretroviral therapy and making therapeutic decisions in the treatment of acquired immunodeficiency syndrome.", Stanford University, Jul 22, 1997
  • Michael Kozal, Thomas Merigan. "United States Patent 5,631,128 Polymerase chain reaction assays for monitoring antiretroviral therapy and making therapeutic decisions in the treatment of acquired immunodeficiency syndrome.", Stanford University, May 20, 1997

All Publications

  • Academic Medical Centers and the U.S. Department of Veterans Affairs: A 75-Year Partnership Influences Medical Education, Scientific Discovery, and Clinical Care. Academic medicine : journal of the Association of American Medical Colleges Petrakis, I. L., Kozal, M. 2022


    The historic academic affiliation program between the U.S. Department of Veterans Affairs and academic medical centers recently marked its 75th anniversary. The partnership has dramatically influenced medical education, research, and clinical care in the United States. In commemorating the anniversary, this article highlights areas in medicine that the partnership has influenced. The authors provide examples from their own experiences of particularly effective collaborations and describe some of the limitations they have encountered. Looking toward the future, they highlight other areas in which collaboration may be particularly effective.

    View details for DOI 10.1097/ACM.0000000000004734

    View details for PubMedID 35507451

  • Fostemsavir in Adults with Multidrug-Resistant HIV-1 Infection. The New England journal of medicine Kozal, M., Aberg, J., Pialoux, G., Cahn, P., Thompson, M., Molina, J. M., Grinsztejn, B., Diaz, R., Castagna, A., Kumar, P., Latiff, G., DeJesus, E., Gummel, M., Gartland, M., Pierce, A., Ackerman, P., Llamoso, C., Lataillade, M. 2020; 382 (13): 1232-1243


    Among some patients with human immunodeficiency virus type 1 (HIV-1) infection who have undergone multiple antiretroviral therapies and have limited options for treatment, new classes of antiretroviral drugs with novel mechanisms of action are needed. Fostemsavir is the prodrug of temsavir, a first-in-class investigational HIV-1 attachment inhibitor.In this ongoing phase 3 trial in 23 countries, we enrolled patients with multidrug-resistant HIV-1 infection in two cohorts, according to their remaining treatment options. In the first cohort, we assigned (in a 3:1 ratio) patients who had the option of using at least one fully active, approved antiretroviral drug in at least one but no more than two antiretroviral classes to add either fostemsavir (at a dose of 600 mg twice daily) or placebo to their failing regimen for 8 days, followed by open-label fostemsavir plus optimized background therapy (randomized cohort). In the second cohort, patients who had no remaining antiretroviral options were started on open-label fostemsavir plus optimized background therapy on day 1 (nonrandomized cohort). The primary end point was the mean change in the HIV-1 RNA level from day 1 through day 8 in the randomized cohort.A total of 371 patients were treated, including 272 in the randomized cohort and 99 in the nonrandomized cohort. At day 8, the mean decrease in the HIV-1 RNA level was 0.79 log10 copies per milliliter in the fostemsavir group and 0.17 log10 copies in the placebo group (P<0.001). At week 48, a virologic response (HIV-1 RNA level, <40 copies per milliliter) had occurred in 54% of the patients in the randomized cohort and in 38% of those in the nonrandomized cohort; the mean increase in the CD4+ T-cell count was 139 cells per cubic millimeter and 64 cells per cubic millimeter, respectively. Adverse events led to the discontinuation of fostemsavir in 7% of the patients. In the randomized cohort, glycoprotein 120 (gp120) substitutions were found in 20 of 47 patients (43%) with virologic failure.In patients with multidrug-resistant HIV-1 infection with limited therapy options, those who received fostemsavir had a significantly greater decrease in the HIV-1 RNA level than those who received placebo during the first 8 days. Efficacy was sustained through 48 weeks. (Funded by Bristol-Myers Squibb and GSK/ViiV Healthcare; BRIGHTE number, NCT02362503.).

    View details for DOI 10.1056/NEJMoa1902493

    View details for PubMedID 32212519

  • Safety and efficacy of the HIV-1 attachment inhibitor prodrug fostemsavir in heavily treatment-experienced individuals: week 96 results of the phase 3 BRIGHTE study. The lancet. HIV Lataillade, M., Lalezari, J. P., Kozal, M., Aberg, J. A., Pialoux, G., Cahn, P., Thompson, M., Molina, J. M., Moreno, S., Grinsztejn, B., Diaz, R. S., Castagna, A., Kumar, P. N., Latiff, G. H., De Jesus, E., Wang, M., Chabria, S., Gartland, M., Pierce, A., Ackerman, P., Llamoso, C. 2020; 7 (11): e740-e751


    Fostemsavir, a prodrug of the first-in-class attachment inhibitor, temsavir, is indicated for heavily treatment-experienced individuals with multidrug-resistant HIV-1. We previously reported superior efficacy of fostemsavir versus placebo in the randomised cohort of the BRIGHTE study after 8-day functional monotherapy (primary endpoint); here we report planned interim analyses through week 96.BRIGHTE (NCT02362503) is an ongoing multicentre, two-cohort, phase 3 trial, done at 108 centres in 22 countries. We enrolled heavily treatment-experienced adults (≥18 years) failing antiretroviral therapy (HIV-1 RNA ≥400 copies per mL) into two cohorts: the randomised cohort, in which patients with one or two fully active antiretrovirals remaining received oral fostemsavir (600 mg twice a day) or placebo in combination with their failing regimen for 8 days, followed by fostemsavir plus optimised background therapy; or the non-randomised cohort, in which patients with no remaining antiretroviral options received oral fostemsavir (600 mg twice a day) plus optimised background therapy from day 1. Endpoints for the week 96 interim analyses included the proportions of participants with plasma HIV-1 RNA of less than 40 copies per mL, changes from baseline in CD4 cell counts, and the frequency of adverse events, adverse events leading to discontinuation, and deaths. The intention-to-treat exposed population and the safety population both included all participants who received at least one dose of study treatment. The response rates (proportion of participants with HIV-1 RNA <40 copies per mL) in the intention-to-treat exposed population were calculated via snapshot analysis at weeks 24, 48, and 96.Between Feb 23, 2015, and Aug 11, 2016, 371 participants were enrolled and treated, of which 272 participants were in the randomised cohort and 99 in the non-randomised cohort. 320 (86%) of 371 reported a history of AIDS. In the randomised cohort, rates of virological suppression (HIV-1 RNA <40 copies per mL) increased from 53% (144 of 272) at week 24 to 60% (163 of 272) at week 96. Response rates in the non-randomised cohort were 37% (37 of 99) at week 24 and week 96. Mean increases in CD4 counts from baseline at week 96 were 205 cells per μL (SD 191) in the randomised cohort and 119 cells per μL (202) in the non-randomised cohort. Mean CD4/CD8 ratio increased from 0·20 at baseline to 0·44 at week 96 in the randomised cohort. Few adverse events led to discontinuation (26 [7%] of 371). 12 (4%) of 272 people in the randomised cohort and 17 (17%) of 99 in the non-randomised cohort died; the median baseline CD4 count for participants who died was 11 cells per μL.In heavily treatment-experienced individuals with advanced HIV-1 disease and limited treatment options, fostemsavir-based antiretroviral regimens were generally well tolerated and showed a distinctive trend of increasing virological and immunological response rates through 96 weeks; these findings support fostemsavir as a treatment option for this vulnerable population.ViiV Healthcare.

    View details for DOI 10.1016/S2352-3018(20)30240-X

    View details for PubMedID 33128903

  • Deep sequencing of HIV: clinical and research applications. Annual review of genomics and human genetics Chabria, S. B., Gupta, S., Kozal, M. J. 2014; 15: 295-325


    Human immunodeficiency virus (HIV) exhibits remarkable diversity in its genomic makeup and exists in any given individual as a complex distribution of closely related but nonidentical genomes called a viral quasispecies, which is subject to genetic variation, competition, and selection. This viral diversity clinically manifests as a selection of mutant variants based on viral fitness in treatment-naive individuals and based on drug-selective pressure in those on antiretroviral therapy (ART). The current standard-of-care ART consists of a combination of antiretroviral agents, which ensures maximal viral suppression while preventing the emergence of drug-resistant HIV variants. Unfortunately, transmission of drug-resistant HIV does occur, affecting 5% to >20% of newly infected individuals. To optimize therapy, clinicians rely on viral genotypic information obtained from conventional population sequencing-based assays, which cannot reliably detect viral variants that constitute <20% of the circulating viral quasispecies. These low-frequency variants can be detected by highly sensitive genotyping methods collectively grouped under the moniker of deep sequencing. Low-frequency variants have been correlated to treatment failures and HIV transmission, and detection of these variants is helping to inform strategies for vaccine development. Here, we discuss the molecular virology of HIV, viral heterogeneity, drug-resistance mutations, and the application of deep sequencing technologies in research and the clinical care of HIV-infected individuals.

    View details for DOI 10.1146/annurev-genom-091212-153406

    View details for PubMedID 24821496

  • Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA Li, J. Z., Paredes, R., Ribaudo, H. J., Svarovskaia, E. S., Metzner, K. J., Kozal, M. J., Hullsiek, K. H., Balduin, M., Jakobsen, M. R., Geretti, A. M., Thiebaut, R., Ostergaard, L., Masquelier, B., Johnson, J. A., Miller, M. D., Kuritzkes, D. R. 2011; 305 (13): 1327-35


    Presence of low-frequency, or minority, human immunodeficiency virus type 1 (HIV-1) drug resistance mutations may adversely affect response to antiretroviral treatment (ART), but evidence regarding the effects of such mutations on the effectiveness of first-line ART is conflicting.To evaluate the association of preexisting drug-resistant HIV-1 minority variants with risk of first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based antiretroviral virologic failure.Systematic review of published and unpublished studies in PubMed (1966 through December 2010), EMBASE (1974 through December 2010), conference abstracts, and article references. Authors of all studies were contacted for detailed laboratory, ART, and adherence data.Studies involving ART-naive participants initiating NNRTI-based regimens were included. Participants were included if all drugs in their ART regimen were fully active by standard HIV drug resistance testing. Cox proportional hazard models using pooled patient-level data were used to estimate the risk of virologic failure based on a Prentice weighted case-cohort analysis stratified by study.Individual data from 10 studies and 985 participants were available for the primary analysis. Low-frequency drug resistance mutations were detected in 187 participants, including 117 of 808 patients in the cohort studies. Low-frequency HIV-1 drug resistance mutations were associated with an increased risk of virologic failure (hazard ratio (HR], 2.3 [95% confidence interval {CI}, 1.7-3.3]; P < .001) after controlling for medication adherence, race/ethnicity, baseline CD4 cell count, and plasma HIV-1 RNA levels. Increased risk of virologic failure was most strongly associated with minority variants resistant to NNRTIs (HR, 2.6 [95% CI, 1.9-3.5]; P < .001). Among participants from the cohort studies, 35% of those with detectable minority variants experienced virologic failure compared with 15% of those without minority variants. The presence of minority variants was associated with 2.5 to 3 times the risk of virologic failure at either 95% or greater or less than 95% overall medication adherence. A dose-dependent increased risk of virologic failure was found in participants with a higher proportion or quantity of drug-resistant variants.In a pooled analysis, low-frequency HIV-1 drug resistance mutations, particularly involving NNRTI resistance, were significantly associated with a dose-dependent increased risk of virologic failure with first-line ART.

    View details for DOI 10.1001/jama.2011.375

    View details for PubMedID 21467286

    View details for PubMedCentralID PMC3325645

  • Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use PLOS ONE Le, T., Chiarella, J., Simen, B. B., Hanczaruk, B., Egholm, M., Landry, M. L., Dieckhaus, K., Rosen, M. I., Kozal, M. J. 2009; 4 (6)


    It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown.Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004-2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85-5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5-74.3, p = 0.0016).Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.

    View details for DOI 10.1371/journal.pone.0006079

    View details for Web of Science ID 000267465900013

    View details for PubMedID 19562031

    View details for PubMedCentralID PMC2698118

  • Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. The Journal of infectious diseases Simen, B. B., Simons, J. F., Hullsiek, K. H., Novak, R. M., Macarthur, R. D., Baxter, J. D., Huang, C., Lubeski, C., Turenchalk, G. S., Braverman, M. S., Desany, B., Rothberg, J. M., Egholm, M., Kozal, M. J. 2009; 199 (5): 693-701


    Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important.To compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF).The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified.Mutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P < .001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]).Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants.

    View details for DOI 10.1086/596736

    View details for PubMedID 19210162

  • A comparison of three highly active antiretroviral treatment strategies consisting of non-nucleoside reverse transcriptase inhibitors, protease inhibitors, or both in the presence of nucleoside reverse transcriptase inhibitors as initial therapy (CPCRA 058 FIRST Study): a long-term randomised trial. Lancet (London, England) MacArthur, R. D., Novak, R. M., Peng, G., Chen, L., Xiang, Y., Hullsiek, K. H., Kozal, M. J., van den Berg-Wolf, M., Henely, C., Schmetter, B., Dehlinger, M. 2006; 368 (9553): 2125-35


    Long-term data from randomised trials on the consequences of treatment with a protease inhibitor (PI), non-nucleoside reverse transcriptase inhibitor (NNRTI), or both are lacking. Here, we report results from the FIRST trial, which compared initial treatment strategies for clinical, immunological, and virological outcomes.Between 1999 and 2002, 1397 antiretroviral-treatment-naive patients, presenting at 18 clinical trial units with 80 research sites in the USA, were randomly assigned in a ratio of 1:1:1 to a protease inhibitor (PI) strategy (PI plus nucleoside reverse transcriptase inhibitor [NRTI]; n=470), a non-nucleoside reverse transcriptase inhibitor (NNRTI) strategy (NNRTI plus NRTI; n=463), or a three-class strategy (PI plus NNRTI plus NRTI; n=464). Primary endpoints were a composite of an AIDS-defining event, death, or CD4 cell count decline to less than 200 cells per mm3 for the PI versus NNRTI comparison, and average change in CD4 cell count at or after 32 months for the three-class versus combined two-class comparison. Analyses were by intention-to-treat. This study is registered, number NCT00000922.1397 patients were assessed for the composite endpoint. A total of 388 participants developed the composite endpoint, 302 developed AIDS or died, and 188 died. NNRTI versus PI hazard ratios (HRs) for the composite endpoint, for AIDS or death, for death, and for virological failure were 1.02 (95% CI 0.79-1.31), 1.07 (0.80-1.41), 0.95 (0.66-1.37), and 0.66 (0.56-0.78), respectively. 1196 patients were assessed for the three-class versus combined two-class primary endpoint. Mean change in CD4 cell count at or after 32 months was +234 cells per mm3 and +227 cells per mm3 for the three-class and the combined two-class strategies (p=0.62), respectively. HRs (three-class vs combined two-class) for AIDS or death and virological failure were 1.15 (0.91-1.45) and 0.87 (0.75-1.00), respectively. HRs (three-class vs combined two-class) for AIDS or death were similar for participants with baseline CD4 cell counts of 200 cells per mm3 or less and of more than 200 cells per mm3 (p=0.38 for interaction), and for participants with baseline HIV RNA concentrations less than 100 000 copies per mL and 100,000 copies per mL or more (p=0.26 for interaction). Participants assigned the three-class strategy were significantly more likely to discontinue treatment because of toxic effects than were those assigned to the two-class strategies (HR 1.58; p<0.0001).Initial treatment with either an NNRTI-based regimen or a PI-based regimen, but not both together, is a good strategy for long-term antiretroviral management in treatment-naive patients with HIV.

    View details for DOI 10.1016/S0140-6736(06)69861-9

    View details for PubMedID 17174704

  • Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays NATURE MEDICINE Kozal, M. J., Shah, N., Shen, N. P., Yang, R., FUCINI, R., Merigan, T. C., Richman, D. D., Morris, D., Hubbell, E. R., Chee, M., Gingeras, T. R. 1996; 2 (7): 753-759


    Naturally occurring mutations in HIV-1-infected patients have important implications for therapy and the outcome of clinical studies. However, little is known about the prevalence of mutations that confer resistance to HIV-1 protease inhibitors in isolates derived from patients naive for such inhibitors. In the first clinical application of high-density oligonucleotide array sequencing, the sequences of 167 viral isolates from 102 patients have been determined. The DNA sequence of USA HIV-1 clade B proteases was found to be extremely variable and 47.5% of the 99 amino acid positions varied. This level of amino acid diversity is greater than that previously known for all worldwide HIV-1 clades combined (40%). Many of the amino acid changes that are known to contribute to drug resistance occurred as natural polymorphisms in isolates from patients who had never received protease inhibitors.

    View details for Web of Science ID A1996UU68000030

    View details for PubMedID 8673920

  • Rate of response to initial antiretroviral therapy according to level of pre-existing HIV-1 drug resistance detected by next-generation sequencing in the strategic timing of antiretroviral treatment (START) study. HIV medicine Cozzi-Lepri, A., Dunn, D., Tostevin, A., Marvig, R. L., Bennedbaek, M., Sharma, S., Kozal, M. J., Gompels, M., Pinto, A. N., Lundgren, J., Baxter, J. D. 2023


    The main objective of this analysis was to evaluate the impact of pre-existing drug resistance by next-generation sequencing (NGS) on the risk of treatment failure (TF) of first-line regimens in participants enrolled in the START study.Stored plasma from participants with entry HIV RNA >1000 copies/mL were analysed using NGS (llumina MiSeq). Pre-existing drug resistance was defined using the mutations considered by the Stanford HIV Drug Resistance Database (HIVDB v8.6) to calculate the genotypic susceptibility score (GSS, estimating the number of active drugs) for the first-line regimen at the detection threshold windows of >20%, >5%, and >2% of the viral population. Survival analysis was conducted to evaluate the association between the GSS and risk of TF (viral load >200 copies/mL plus treatment change).Baseline NGS data were available for 1380 antiretroviral therapy (ART)-naïve participants enrolled over 2009-2013. First-line ART included a non-nucleoside reverse transcriptase inhibitor (NNRTI) in 976 (71%), a boosted protease inhibitor in 297 (22%), or an integrase strand transfer inhibitor in 107 (8%). The proportions of participants with GSS <3 were 7% for >20%, 10% for >5%, and 17% for the >2% thresholds, respectively. The adjusted hazard ratio of TF associated with a GSS of 0-2.75 versus 3 in the subset of participants with mutations detected at the >2% threshold was 1.66 (95% confidence interval 1.01-2.74; p = 0.05) and 2.32 (95% confidence interval 1.32-4.09; p = 0.003) after restricting the analysis to participants who started an NNRTI-based regimen.Up to 17% of participants initiated ART with a GSS <3 on the basis of NGS data. Minority variants were predictive of TF, especially for participants starting NNRTI-based regimens.

    View details for DOI 10.1111/hiv.13556

    View details for PubMedID 37775947

  • Week 96 Genotypic and Phenotypic Results of the Fostemsavir Phase 3 BRIGHTE Study in Heavily Treatment-Experienced Adults Living with Multidrug-Resistant HIV-1. Antimicrobial agents and chemotherapy Gartland, M., Cahn, P., DeJesus, E., Diaz, R. S., Grossberg, R., Kozal, M., Kumar, P., Molina, J., Mendo Urbina, F., Wang, M., Du, F., Chabria, S., Clark, A., Garside, L., Krystal, M., Mannino, F., Pierce, A., Ackerman, P., Lataillade, M. 2022: e0175121


    In the phase 3 BRIGHTE study in heavily treatment-experienced adults with multidrug-resistant HIV-1, fostemsavir plus optimized background therapy (OBT) resulted in sustained rates of virologic suppression through 96weeks. HIV-1 RNA <40 copies/mL was achieved in 163/272 (60%) Randomized Cohort (RC) participants (with 1 or 2 remaining approved fully active antiretrovirals) and 37/99 (37%) Non-randomized Cohort (NRC) participants (with 0 fully active antiretrovirals). Here we report genotypic and phenotypic analyses of HIV-1 samples from 63/272 (23%) RC participants and 49/99 (49%) NRC participants who met protocol-defined virologic failure (PDVF) criteria through Week 96. The incidence of PDVF was as expected in this difficult-to-treat patient population and, among RC participants, was comparable regardless of the presence of predefined gp120 amino acid substitutions that potentially influence phenotypic susceptibility to temsavir (S375H/I/M/N/T, M426L, M434I, M475I) or baseline temsavir 50% inhibitory concentration fold change (IC50 FC). The incidence of PDVF was lower among participants with higher overall susceptibility score to newly used antiretrovirals (OSS-new), indicating that OSS-new may be a preferred predictor of virologic outcome in heavily treatment-experienced individuals. Predefined gp120 substitutions, most commonly M426L or S375N, were emergent on treatment in 24/50 (48%) RC and 33/44 (75%) NRC participants with PDVF, with related increases in temsavir IC50 FC. In BRIGHTE, PDVF was not consistently associated with treatment-emergent genotypic or phenotypic changes in susceptibility to temsavir or to antiretrovirals in the initial OBT. Further research will be needed to identify which factors are most likely to contribute to virologic failure in this heavily treatment-experienced population (, NCT02362503).

    View details for DOI 10.1128/aac.01751-21

    View details for PubMedID 35502922

  • Fostemsavir: a first-in-class HIV-1 attachment inhibitor. Current opinion in HIV and AIDS Grant, P. M., Kozal, M. J. 2022; 17 (1): 32-35


    PURPOSE OF REVIEW: Fostemsavir is a recently Food and Drug Administration-approved HIV-1 attachment inhibitor that binds to HIV-1 gp120 and prevents viral attachment to the cellular CD4 receptor. Here, we review the pharmacology, efficacy, tolerability, and resistance profile of fostemsavir.RECENT FINDINGS: Fostemsavir is well tolerated and maintains virologic activity in individuals harboring multidrug-resistant HIV-1. In conjunction with optimal background therapy, a majority of heavily treatment-experienced clinical trial participants treated with fostemsavir achieved virologic suppression.SUMMARY: The approval of fostemsavir represents an important advance for individuals harboring multidrug resistant HIV-1 due to its novel mechanism of action and lack of cross-resistance to other antiretrovirals. Further study will better define the role of resistance testing for fostemsavir and fostemsavir's potential role outside of salvage therapy in heavily treatment-experienced individuals.

    View details for DOI 10.1097/COH.0000000000000712

    View details for PubMedID 34871189

  • Evaluation of HIV-1 reservoir size and broadly neutralizing antibodies (bNAb) susceptibility in acute ART treated individuals. AIDS (London, England) Moldt, B., Gunthard, H. F., Workowski, K. A., Little, S. J., Eron, J. J., Overton, E. T., Lehmann, C., Rokx, C., Kozal, M. J., Gandhi, R. T., Braun, D. L., Parvangada, A., Li, J., Martin, R., Selzer, L., Cox, S., Margot, N., Liu, H., Slamowitz, D., Makadzange, T., Collins, S. E., Geleziunas, R., Callebaut, C. 2021


    OBJECTIVE: Persistence of the viral reservoir is the main barrier to curing HIV. Initiation of ART during acute HIV infection can limit the size and diversity of the reservoir. In depth characterization of the reservoir in individuals who initiate ART during acute infection will be critical for clinical trial design and cure strategies.METHODS: Four cohorts with participants who initiated ART during acute infection or during chronic infection were enrolled in a cross-sectional, non-interventional study. Viral reservoir was evaluated by the Intact Proviral DNA Assay (IPDA), the Total HIV DNA assay (THDA) and the Quantitative Viral Outgrowth Assay (QVOA). Viral diversity and susceptibility to V3-glycan bNAbs were determined by genotyping of the viral envelope gene.RESULTS: Participants who initiated ART during the acute Fiebig I-IV stages had lower level of total HIV DNA than participants who initiated ART during chronic infection whereas no difference was observed in intact HIV DNA or outgrowth virus. Participants who initiated ART during Fiebig I-IV also had lower viral diversity and appeared to have higher susceptibility to bNAbs than participants initiating ART during chronic infection.CONCLUSIONS: Individuals initiating ART during Fiebig I-IV had small viral reservoirs, low viral diversity and high susceptibility to bNAbs, and would be an optimal target population for proof of concept HIV cure trials.

    View details for DOI 10.1097/QAD.0000000000003088

    View details for PubMedID 34586088

  • Transmitted HIV-1 drug resistance in a large international cohort using next-generation sequencing: results from the Strategic Timing of Antiretroviral Treatment (START) study. HIV medicine Baxter, J. D., Dunn, D., Tostevin, A., Marvig, R. L., Bennedbaek, M., Cozzi-Lepri, A., Sharma, S., Kozal, M. J., Gompels, M., Pinto, A. N., Lundgren, J. 2021; 22 (5): 360-371


    The aim of this analysis was to characterize transmitted drug resistance (TDR) in Strategic Timing of Antiretroviral Treatment (START) study participants by next-generation sequencing (NGS), a sensitive assay capable of detecting low-frequency variants.Stored plasma from participants with entry HIV RNA > 1000 copies/mL were analysed by NGS (Illumina MiSeq). TDR was based on the WHO 2009 surveillance definition with the addition of reverse transcriptase (RT) mutations T215N and E138K, and integrase strand transfer inhibitor (INSTI) surveillance mutations (Stanford HIVdb). Drug resistance mutations (DRMs) detected at three thresholds are reported: > 2%, 5% and 20% of the viral population.Between 2009 and 2013, START enrolled 4684 antiretroviral therapy (ART)-naïve individuals in 35 countries. Baseline NGS data at study entry were available for 2902 participants. Overall prevalence rates of TDR using a detection threshold of 2%/5%/20% were 9.2%/5.6%/3.2% for nucleoside reverse transcriptase inhibitors (NRTIs), 9.2%/6.6%/4.9% for non-NRTIs, 11.4%/5.5%/2.4% for protease inhibitors (PIs) and 3.5%/1.6%/0.1% for INSTI DRMs and varied by geographic region. Using the 2% detection threshold, individual DRMs with the highest prevalence were: PI M46IL (5.5%), RT K103NS (3.5%), RT G190ASE (3.1%), T215ISCDVEN (2.5%), RT M41L (2.2%), RT K219QENR (1.7%) and PI D30N (1.6%). INSTI DRMs were detected almost exclusively below the 20% detection threshold, most commonly Y143H (0.4%), Q148R (0.4%) and T66I (0.4%).Use of NGS in this study population resulted in the detection of a large proportion of low-level variants which would not have been detected by traditional Sanger sequencing. Global surveillance studies utilizing NGS should provide a more comprehensive assessment of TDR prevalence in different regions of the world.

    View details for DOI 10.1111/hiv.13038

    View details for PubMedID 33369017

    View details for PubMedCentralID PMC8049964

  • Fostemsavir for the treatment of HIV. Expert review of anti-infective therapy Seval, N., Frank, C., Kozal, M. 2021; 19 (8): 961-966


    Introduction: For those with heavily treatment experienced (HTE) HIV-1 and virologic failure, therapeutic options are limited. A variety of barriers such as drug resistance, side effects, past intolerance, and administration inability contribute to the need for novel drug classes in this population.Areas Covered: Herein, we review the pharmacology, clinical efficacy, and safety profile of fostemsavir, a first in its class attachment inhibitor recently FDA approved for use.Expert Opinion: Fostemsavir is a well-tolerated oral medication with relatively few drug-drug interactions. Clinical trial data demonstrates virologic and notable immunologic response in conjunction with optimal background therapy in HTE persons living with HIV. Fostemsavir exhibits no cross-resistance with other ARV classes and thus is an important advancement for patients harboring drug-resistant HIV. Further study will be needed to determine outstanding clinical questions such as the role of drug resistance testing and fostemsavir use outside of the HTE population.

    View details for DOI 10.1080/14787210.2021.1865801

    View details for PubMedID 33331202

  • Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents with HIV. Department of Health and Human Services. Panel-Member, Kozal, M. U.S. Department of Health and Human Services . 2021


  • Long-term efficacy and safety of fostemsavir among subgroups of heavily treatment-experienced adults with HIV-1. AIDS (London, England) Ackerman, P., Thompson, M., Molina, J. M., Aberg, J., Cassetti, I., Kozal, M., Castagna, A., Martins, M., Ramgopal, M., Sprinz, E., Treviño-Pérez, S., Streinu-Cercel, A., Latiff, G. H., Pialoux, G., Kumar, P. N., Wang, M., Chabria, S., Pierce, A., Llamoso, C., Lataillade, M. 2021; 35 (7): 1061-1072


    The aim of this study was to understand how demographic and treatment-related factors impact responses to fostemsavir-based regimens.BRIGHTE is an ongoing phase 3 study evaluating twice-daily fostemsavir 600 mg and optimized background therapy (OBT) in heavily treatment-experienced individuals failing antiretroviral therapy with limited treatment options (Randomized Cohort 1-2 and Nonrandomized Cohort 0 fully active antiretroviral classes).Virologic response rates (HIV-1 RNA <40 copies/ml, Snapshot analysis) and CD4+ T-cell count increases in the Randomized Cohort were analysed by prespecified baseline characteristics (age, race, sex, region, HIV-1 RNA, CD4+ T-cell count) and viral susceptibility to OBT. Safety results were analysed by baseline characteristics for combined cohorts (post hoc).In the Randomized Cohort, virologic response rates increased between Weeks 24 and 96 across most subgroups. Virologic response rates over time were most clearly associated with overall susceptibility scores for new OBT agents (OSS-new). CD4+ T-cell count increases were comparable across subgroups. Participants with baseline CD4+ T-cell counts less than 20 cells/μl had a mean increase of 240 cells/μl. In the safety population, more participants with baseline CD4+ T-cell counts less than 20 vs. at least 200 cells/μl had grade 3/4 adverse events [53/107 (50%) vs. 24/96 (25%)], serious adverse events [58/107 (54%) vs. 25/96 (26%)] and deaths [16/107 (15%) vs. 2/96 (2%)]. There were no safety differences by other subgroups.Week 96 results for BRIGHTE demonstrate comparable rates of virologic and immunologic response (Randomized Cohort) and safety (combined cohorts) across subgroups. OSS-new is an important consideration when constructing optimized antiretroviral regimens for heavily treatment-experienced individuals with limited remaining treatment options.

    View details for DOI 10.1097/QAD.0000000000002851

    View details for PubMedID 33946085

    View details for PubMedCentralID PMC8183480

  • SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent? PloS one Federman, D. G., Gupta, S., Stack, G., Campbell, S. M., Peaper, D. R., Dembry, L. M., Fisher, A., Tarabar, A. F., Kozal, M., Ruser, C. B. 2020; 15 (8): e0237127


    The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown.We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay.Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%).We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.

    View details for DOI 10.1371/journal.pone.0237127

    View details for PubMedID 32756602

    View details for PubMedCentralID PMC7406068

  • Ombitasvir/paritaprevir/ritonavir and dasabuvir±ribavirin for chronic HCV infection in US veterans with psychiatric disorders. Journal of medical virology Fuchs, M., Monto, A., Bräu, N., Charafeddine, M., Schmidt, W., Kozal, M., Naggie, S., Cheung, R., Schnell, G., Yu, Y., Richards, K., Mullally, V., Cohen, D. E., Toro, D. 2019


    Hepatitis C virus (HCV) infections are more common among US veterans receiving care through Veterans Affairs (VA) Medical Centers than among the general population. Historically, HCV therapies had lower efficacy rates in VA patients, possibly due to common comorbidities such as psychiatric disorders and substance abuse. The direct-acting antivirals ombitasvir/paritaprevir/ritonavir and dasabuvir (OBV/PTV/r+DSV)±ribavirin (RBV) are approved in the US for HCV genotype 1 (GT1)-infected adults with or without cirrhosis. This study prospectively evaluated the safety and efficacy of OBV/PTV/r+DSV±RBV in VA patients with HCV GT1 infection. TOPAZ-VA was a phase 3b, open-label trial. Adult US veterans with HCV GT1 infection, without cirrhosis or with compensated cirrhosis, were eligible for enrollment. Patients with GT1a infection received OBV/PTV/r +DSV+RBV for 12 weeks or 24 weeks (for those with cirrhosis); GT1b-infected patients without cirrhosis received OBV/PTV/r +DSV for 12 weeks; those with cirrhosis received OBV/PTV/r +DSV with RBV. The primary endpoint was sustained virologic response at posttreatment week 12 (SVR12); safety was also assessed. Ninety-nine patients were enrolled at 10 sites from May through November 2015. The majority were male (96%), white (60%), and with GT1a infection (68%); 49% reported ongoing psychiatric disorders. Overall, 94% (93/99) achieved SVR12; three patients had a virologic failure. The most common AEs were fatigue (28%), headache (20%), and nausea (15%); six patients discontinued treatment due to AEs. In US veterans with HCV GT1 infection, OBV/PTV/r +DSV±RBV yielded a 94% overall SVR12 rate and was well tolerated. The presence of psychiatric disorders and/or injection drug use did not impact efficacy.

    View details for DOI 10.1002/jmv.25655

    View details for PubMedID 31829433

    View details for PubMedCentralID PMC7687116

  • Interpretation of HIV drug resistance testing Uptodate Kozal, M. Uptodate, Waltham, MA. 2019
  • Overview of HIV drug resistance testing assays UptoDate Kozal, M. UptoDate, Waltham, MA. 2019
  • Guidance for Non-HIV-Specialized Providers Caring for Persons with HIV Who Have Been Displaced by Disasters (such as a Hurricane) Panel-Member, Kozal, M. US Department of Health and Human Services. 2018
  • Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents Living with HIV. Panel-Member, Kozal, M. Department of Health and Human Services. 2018
  • An Open-Label, Multicenter Study of Ombitasvir/Paritaprevir/Ritonavir and Dasabuvir with or without Ribavirin in US Veterans with Genotype 1 Chronic Hepatitis C Infection: Efficacy and Safety Results of TOPAZ-VA Fuchs, M., Morgan, T. R., Charafeddine, M., Brau, N., Schmidt, W. N., Kozal, M., Naggie, S., Cheung, R., Pilot-Matias, T., Yu, Y., Richards, K., Mullally, V., Cohen, D. E., Monto, A., Toro, D. H. WILEY. 2016: 488A
  • HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China PLOS ONE Chen, X., Zou, X., He, J., Zheng, J., Chiarella, J., Kozal, M. J. 2016; 11 (2)


    Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF).29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels.DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×10(4) c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1-4% and 24 (60%) at levels of 5-19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS.DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.

    View details for DOI 10.1371/journal.pone.0149215

    View details for Web of Science ID 000371223400038

    View details for PubMedID 26895182

  • Characterizing Patients with Very-Low-Level HIV Viremia: A Community-Based Study. Journal of the International Association of Providers of AIDS Care Helou, E., Shenoi, S., Kyriakides, T., Landry, M. L., Kozal, M., Barakat, L. A. 2016; 16 (3): 261-266


    Very-low-level viremia (VLLV) is a relatively new concept in the realm of human immunodeficiency virus (HIV) care. Newer generation assays are now able to detect plasma HIV RNA Viral Load (VL) levels as low as 20 copies/mL. The authors characterized patients with VLLV (VL between 20 and 50 copies/mL) in order to identify possible risk factors associated with virologic failure and poor clinical outcomes.The authors reviewed 119 consecutive charts of patients with VLLV. Sociodemographic data were extracted and viral load and CD4 counts were trended over a 12 month period (February 2013-February 2014). Regression analysis was used to assess the role of different factors on virologic failure at 1 year.Of the study participants with evaluable data (n = 100), the median age was 53 years (interquartile range: 43-57.5), 67% were nonwhite, 34% were women, 58% were smokers, 47% were alcoholics, 58% had a history of intravenous drug use, and 40% were coinfected with hepatitis C virus. More than half of the participants had 3 or more comorbidities and their HIV pill burden was high (more than 2 pills daily). After 12 months, 65 participants achieved undetectable viral load levels, whereas 15 experienced virologic failure (2 consecutive viral loads > 50 copies/mL) and the remaining 20 had persistent VLLV. In the virologic failure group, there was a predominance of white males (66%) with a significant number of comorbidities and pill burden. Univariate logistic regression suggested that there was a difference between the failure versus nonfailure groups in terms of race, ethnicity, and alcohol use. Multivariate regression with virological failure as the outcome suggested a trend only in terms of participant's alcohol use.Most patients with initial VLLV (70%) achieved virologic suppression at 1 year with no antiretroviral therapy changes. Thus, VLLV does not necessarily predict virologic failure and should not prompt more frequent clinic visits or antiretroviral regimen changes. Further research is needed in order to determine the predictors of virologic failure in this subset of patients and the clinicians' attitude toward VLLV.

    View details for DOI 10.1177/2325957416680028

    View details for PubMedID 27903948

    View details for PubMedCentralID PMC5423832

  • Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents Living with HIV. Panel-Member, Kozal, M. US Department of Health and Human Services. 2016
  • Global HIV-1 transmitted drug resistance in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial. HIV medicine Baxter, J. D., Dunn, D., White, E., Sharma, S., Geretti, A. M., Kozal, M. J., Johnson, M. A., Jacoby, S., Llibre, J. M., Lundgren, J. 2015; 16 Suppl 1: 77-87


    HIV-1 transmitted drug resistance (TDR) in treatment-naïve individuals is a well-described phenomenon. Baseline genotypic resistance testing is considered standard of care in most developed areas of the world. The aim of this analysis was to characterize HIV-1 TDR and the use of resistance testing in START trial participants.In the Strategic Timing of AntiRetroviral Treatment (START) trial, baseline genotypic resistance testing results were collected at study entry and analysed centrally to determine the prevalence of TDR in the study population. Resistance was based on a modified 2009 World Health Organization definition to reflect newer resistance mutations.Baseline resistance testing was available in 1946 study participants. Higher rates of testing occurred in Europe (86.7%), the USA (81.3%) and Australia (89.9%) as compared with Asia (22.2%), South America (1.8%) and Africa (0.1%). The overall prevalence of TDR was 10.1%, more commonly to nonnucleoside reverse transcriptase inhibitors (4.5%) and nucleoside reverse transcriptase inhibitors (4%) compared with protease inhibitors (2.8%). The most frequent TDR mutations observed were M41L, D67N/G/E, T215F/Y/I/S/C/D/E/V/N, 219Q/E/N/R, K103N/S, and G190A/S/E in reverse transcriptase, and M46I/L and L90M in protease. By country, the prevalence of TDR was highest in Australia (17.5%), France (16.7%), the USA (12.6%) and Spain (12.6%). No participant characteristics were identified as predictors of the presence of TDR.START participants enrolled in resource-rich areas of the world were more likely to have baseline resistance testing. In Europe, the USA and Australia, TDR prevalence rates varied by country.

    View details for DOI 10.1111/hiv.12236

    View details for PubMedID 25711326

    View details for PubMedCentralID PMC4341921

  • Transmission of HIV drug resistance: lessons from sensitive screening assays. Current opinion in infectious diseases Geretti, A. M., Paredes, R., Kozal, M. J. 2015; 28 (1): 23-30


    The review discusses new technologies for the sensitive detection of HIV drug resistance, with a focus on applications in antiretroviral treatment (ART)-naïve populations.Conventional sequencing is well established for detecting HIV drug resistance in routine care and guides optimal treatment selection in patients starting ART. Access to conventional sequencing is nearly universal in Western countries, but remains limited in Asia, Latin America, and Africa. Technological advances now allow detection of resistance with greatly improved sensitivity compared with conventional sequencing, variably increasing the yield of resistance testing in ART-naïve populations. There is strong cumulative evidence from retrospective studies that sensitive detection of resistant mutants in baseline plasma samples lacking resistance by conventional sequencing more than doubles the risk of virological failure after starting efavirenz-based or nevirapine-based ART.Sensitive resistance testing methods are mainly confined to research applications and in this context have provided great insight into the dynamics of drug resistance development, persistence, and transmission. Adoption in care settings is becoming increasingly possible, although important challenges remain. Platforms for diagnostic use must undergo technical improvements to ensure good performance and ease of use, and clinical validation is required to ensure utility.

    View details for DOI 10.1097/QCO.0000000000000136

    View details for PubMedID 25501541

  • Increased Levels of Macrophage Inflammatory Proteins Result in Resistance to R5-Tropic HIV-1 in a Subset of Elite Controllers. Journal of virology Walker, W. E., Kurscheid, S., Joshi, S., Lopez, C. A., Goh, G., Choi, M., Barakat, L., Francis, J., Fisher, A., Kozal, M., Zapata, H., Shaw, A., Lifton, R., Sutton, R. E., Fikrig, E. 2015; 89 (10): 5502-14


    Elite controllers (ECs) are a rare group of HIV seropositive individuals who are able to control viral replication without antiretroviral therapy. The mechanisms responsible for this phenotype, however, have not been fully elucidated. In this study, we examined CD4(+) T cell resistance to HIV in a cohort of elite controllers and explored transcriptional signatures associated with cellular resistance. We demonstrate that a subgroup of elite controllers possess CD4(+) T cells that are specifically resistant to R5-tropic HIV while remaining fully susceptible to X4-tropic and vesicular stomatitis virus G (VSV-G)-pseudotyped viruses. Transcriptome analysis revealed 17 genes that were differentially regulated in resistant elite controllers relative to healthy controls. Notably, the genes encoding macrophage inflammatory protein 1α (MIP-1α), CCL3 and CCL3L1, were found to be upregulated. The MIP-1α, MIP-1β, and RANTES chemokines are natural ligands of CCR5 and are known to interfere with HIV replication. For three elite controllers, we observed increased production of MIP-1α and/or MIP-1β at the protein level. The supernatant from resistant EC cells contained MIP-1α and MIP-1β and was sufficient to confer R5-tropic resistance to susceptible CD4(+) T cells. Additionally, this effect was reversed by using inhibitory anti-MIP antibodies. These results suggest that the T cells of these particular elite controllers may be naturally resistant to HIV infection by blocking R5-tropic viral entry.HIV is a pandemic health problem, and the majority of seropositive individuals will eventually progress to AIDS unless antiretroviral therapy (ART) is administered. However, rare patients, termed elite controllers, have a natural ability to control HIV infection in the absence of ART, but the mechanisms by which they achieve this phenotype have not been fully explored. This paper identifies one mechanism that may contribute to this natural resistance: some elite controllers have CD4(+) T cells that produce high levels of MIP chemokines, which block R5-tropic HIV entry. This mechanism could potentially be exploited to achieve a therapeutic effect in other HIV-seropositive individuals.

    View details for DOI 10.1128/JVI.00118-15

    View details for PubMedID 25740989

    View details for PubMedCentralID PMC4442529

  • Low-frequency NNRTI-resistant HIV-1 variants and relationship to mutational load in antiretroviral-naïve subjects. Viruses Gupta, S., Lataillade, M., Kyriakides, T. C., Chiarella, J., St John, E. P., Webb, S., Moreno, E. A., Simen, B. B., Kozal, M. J. 2014; 6 (9): 3428-37


    Low-frequency HIV variants possessing resistance mutations against non‑nucleoside reverse transcriptase inhibitors (NNRTI), especially at HIV reverse transcriptase (RT) amino acid (aa) positions K103 and Y181, have been shown to adversely affect treatment response. Therapeutic failure correlates with both the mutant viral variant frequency and the mutational load. We determined the prevalence of NNRTI resistance mutations at several RT aa positions in viruses from 204 antiretroviral (ARV)-naïve HIV-infected individuals using deep sequencing, and examined the relationship between mutant variant frequency and mutational load for those variants. Deep sequencing to ≥0.4% levels found variants with major NNRTI-resistance mutations having a Stanford-HIVdb algorithm value ≥30 for efavirenz and/or nevirapine in 52/204 (25.5%) ARV-naïve HIV-infected persons. Eighteen different major NNRTI mutations were identified at 11 different positions, with the majority of variants being at frequency >1%. The frequency of these variants correlated strongly with the mutational load, but this correlation weakened at low frequencies. Deep sequencing detected additional major NNRTI-resistant viral variants in treatment-naïve HIV-infected individuals. Our study suggests the significance of screening for mutations at all RT aa positions (in addition to K103 and Y181) to estimate the true burden of pre-treatment NNRTI-resistance. An important finding was that variants at low frequency had a wide range of mutational loads (>100-fold) suggesting that frequency alone may underestimate the impact of specific NNRTI-resistant variants. We recommend further evaluation of all low-frequency NNRTI-drug resistant variants with special attention given to the impact of mutational loads of these variants on treatment outcomes.

    View details for DOI 10.3390/v6093428

    View details for PubMedID 25256391

    View details for PubMedCentralID PMC4189030

  • Low-Frequency NNRTI-Resistant HIV-1 Variants and Relationship to Mutational Load in Antiretroviral-Naive Subjects VIRUSES-BASEL Gupta, S., Lataillade, M., Kyriakides, T. C., Chiarella, J., St John, E. P., Webb, S., Moreno, E. A., Simen, B. B., Kozal, M. J. 2014; 6 (9): 3428-3437


    Low-frequency HIV variants possessing resistance mutations against non‑nucleoside reverse transcriptase inhibitors (NNRTI), especially at HIV reverse transcriptase (RT) amino acid (aa) positions K103 and Y181, have been shown to adversely affect treatment response. Therapeutic failure correlates with both the mutant viral variant frequency and the mutational load. We determined the prevalence of NNRTI resistance mutations at several RT aa positions in viruses from 204 antiretroviral (ARV)-naïve HIV-infected individuals using deep sequencing, and examined the relationship between mutant variant frequency and mutational load for those variants. Deep sequencing to ≥0.4% levels found variants with major NNRTI-resistance mutations having a Stanford-HIVdb algorithm value ≥30 for efavirenz and/or nevirapine in 52/204 (25.5%) ARV-naïve HIV-infected persons. Eighteen different major NNRTI mutations were identified at 11 different positions, with the majority of variants being at frequency >1%. The frequency of these variants correlated strongly with the mutational load, but this correlation weakened at low frequencies. Deep sequencing detected additional major NNRTI-resistant viral variants in treatment-naïve HIV-infected individuals. Our study suggests the significance of screening for mutations at all RT aa positions (in addition to K103 and Y181) to estimate the true burden of pre-treatment NNRTI-resistance. An important finding was that variants at low frequency had a wide range of mutational loads (>100-fold) suggesting that frequency alone may underestimate the impact of specific NNRTI-resistant variants. We recommend further evaluation of all low-frequency NNRTI-drug resistant variants with special attention given to the impact of mutational loads of these variants on treatment outcomes.

    View details for DOI 10.3390/v6093428

    View details for Web of Science ID 000343107100006

    View details for PubMedCentralID PMC4189030

  • Prevalence of WHO Transmitted Drug Resistance Mutations by Deep Sequencing in Antiretroviral-Naive Subjects in Hunan Province, China PLOS ONE Zou Xiaobai, X. B., Xi, C., Tian, H., Williams, A. B., Wang, H., He, J., Zhen, J., Chiarella, J., Blake, L. A., Turenchalk, G., Kozal, M. J. 2014; 9 (6)


    There are few data on the prevalence of WHO transmitted drug resistance mutations (TDRs) that could affect treatment responses to first line antiretroviral therapy (ART) in Hunan Province, China.Determine the prevalence of WHO NRTI/NNRTI/PI TDRs in ART-naïve subjects in Hunan Province by deep sequencing.ART-naïve subjects diagnosed in Hunan between 2010-2011 were evaluated by deep sequencing for low-frequency HIV variants possessing WHO TDRs to 1% levels. Mutations were scored using the algorithm to infer drug susceptibility.Deep sequencing was performed on samples from 90 ART-naïve subjects; 83.3% were AE subtype. All subjects had advanced disease (average CD4 count 134 cells/mm3). Overall 25.6%(23/90) of subjects had HIV with major WHO NRTI/NNRTI TDRs by deep sequencing at a variant frequency level ≥ 1%; 16.7%(15/90) had NRTI TDR and 12.2%(11/90) had a major NNRTI TDR. The majority of NRTI/NNRTI mutations were identified at variant levels <5%. Mutations were analyzed by and 7.8% of subjects had variants with high-level nevirapine resistance; 4.4% had high-level NRTI resistance. Deep sequencing identified 24(27.6%) subjects with variants possessing either a PI TDR or PI mutation (algorithm value ≥ 15). 17(19.5%) had PI TDRs at levels >1%.ART-naïve subjects from Hunan Province China infected predominantly with subtype AE frequently possessed HIV variants with WHO NRTI/NNRTI TDRs by deep sequencing that would affect the first line ART used in the region. Specific mutations conferring nevirapine high-level resistance were identified in 7.8% of subjects. The majority of TDRs detected were at variant levels <5% likely due to subjects having advanced chronic disease at the time of testing. PI TDRs were identified frequently, but were found in isolation and at low variant frequency. As PI/r use is infrequent in Hunan, the existence of PI mutations likely represent AE subtype natural polymorphism at low variant level frequency.

    View details for DOI 10.1371/journal.pone.0098740

    View details for Web of Science ID 000338430700070

    View details for PubMedID 24896087

  • The VACS Index Accurately Predicts Mortality and Treatment Response among Multi-Drug Resistant HIV Infected Patients Participating in the Options in Management with Antiretrovirals (OPTIMA) Study PLOS ONE Brown, S. T., Tate, J. P., Kyriakides, T. C., Kirkwood, K. A., Holodniy, M., Goulet, J. L., Angus, B. J., Cameron, D. W., Justice, A. C. 2014; 9 (3)


    The VACS Index is highly predictive of all-cause mortality among HIV infected individuals within the first few years of combination antiretroviral therapy (cART). However, its accuracy among highly treatment experienced individuals and its responsiveness to treatment interventions have yet to be evaluated. We compared the accuracy and responsiveness of the VACS Index with a Restricted Index of age and traditional HIV biomarkers among patients enrolled in the OPTIMA study.Using data from 324/339 (96%) patients in OPTIMA, we evaluated associations between indices and mortality using Kaplan-Meier estimates, proportional hazards models, Harrel's C-statistic and net reclassification improvement (NRI). We also determined the association between study interventions and risk scores over time, and change in score and mortality.Both the Restricted Index (c = 0.70) and VACS Index (c = 0.74) predicted mortality from baseline, but discrimination was improved with the VACS Index (NRI = 23%). Change in score from baseline to 48 weeks was more strongly associated with survival for the VACS Index than the Restricted Index with respective hazard ratios of 0.26 (95% CI 0.14-0.49) and 0.39(95% CI 0.22-0.70) among the 25% most improved scores, and 2.08 (95% CI 1.27-3.38) and 1.51 (95%CI 0.90-2.53) for the 25% least improved scores.The VACS Index predicts all-cause mortality more accurately among multi-drug resistant, treatment experienced individuals and is more responsive to changes in risk associated with treatment intervention than an index restricted to age and HIV biomarkers. The VACS Index holds promise as an intermediate outcome for intervention research.

    View details for DOI 10.1371/journal.pone.0092606

    View details for Web of Science ID 000333675600053

    View details for PubMedID 24667813

    View details for PubMedCentralID PMC3965438

  • A Study of Financial Incentives to Reduce Plasma HIV RNA Among Patients in Care AIDS AND BEHAVIOR Farber, S., Tate, J., Frank, C., Ardito, D., Kozal, M., Justice, A. C., Braithwaite, R. 2013; 17 (7): 2293-2300


    The role of financial incentives in HIV care is not well studied. We conducted a single-site study of monetary incentives for viral load suppression, using each patient as his own control. The incentive size ($100/quarter) was designed to be cost-neutral, offsetting estimated downstream costs averted through reduced HIV transmission. Feasibility outcomes were clinic workflow, patient acceptability, and patient comprehension. Although the study was not powered for effectiveness, we also analyzed viral load suppression. Of 80 eligible patients, 77 consented, and 69 had 12 month follow-up. Feasibility outcomes showed minimal impact on patient workflow, near-unanimous patient acceptability, and satisfactory patient comprehension. Among individuals with detectable viral loads pre-intervention, the proportion of undetectable viral load tests increased from 57 to 69 % before versus after the intervention. It is feasible to use financial incentives to reward ART adherence, and to specify the incentive by requiring cost-neutrality and targeting biological outcomes.

    View details for DOI 10.1007/s10461-013-0416-1

    View details for Web of Science ID 000323246500002

    View details for PubMedID 23404097

    View details for PubMedCentralID PMC3742414

  • Impact of minority nonnucleoside reverse transcriptase inhibitor resistance mutations on resistance genotype after virologic failure. The Journal of infectious diseases Li, J. Z., Paredes, R., Ribaudo, H. J., Kozal, M. J., Svarovskaia, E. S., Johnson, J. A., Geretti, A. M., Metzner, K. J., Jakobsen, M. R., Hullsiek, K. H., Ostergaard, L., Miller, M. D., Kuritzkes, D. R. 2013; 207 (6): 893-7


    Drug-resistant human immunodeficiency virus type 1 (HIV-1) minority variants increase the risk of virologic failure for first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based regimens. We performed a pooled analysis to evaluate the relationship between NNRTI-resistant minority variants and the likelihood and types of resistance mutations detected at virologic failure. In multivariable logistic regression analysis, higher NNRTI minority variant copy numbers, non-white race, and nevirapine use were associated with a higher risk of NNRTI resistance at virologic failure. Among participants on efavirenz, K103N was the most frequently observed resistance mutation at virologic failure regardless of the baseline minority variant. However, the presence of baseline Y181C minority variant was associated with a higher probability of Y181C detection after virologic failure. NNRTI regimen choice and preexisting NNRTI-resistant minority variants were both associated with the probability and type of resistance mutations detected after virologic failure.

    View details for DOI 10.1093/infdis/jis925

    View details for PubMedID 23264671

    View details for PubMedCentralID PMC3571444

  • Overview of HIV drug resistance testing Uptodate Kozal, M. Uptodate, Waltham, MA. 2013; Version 13.0
  • Drug resistance testing in the management of HIV disease Uptodate Kozal, M. Uptodate, Waltham, MA. 2013; Version 13.0
  • Association between risk behaviors and antiretroviral resistance in HIV-infected patients receiving opioid agonist treatment. Journal of addiction medicine Tetrault, J. M., Kozal, M. J., Chiarella, J., Sullivan, L. E., Dinh, A. T., Fiellin, D. A. 2013; 7 (2): 102-7


    Antiretroviral (ARV) resistance is of concern. Opioid agonist treatment (ie, methadone or buprenorphine) is effective and decreases HIV transmission risk behaviors and HIV seroconversion. Despite prevention efforts, injection drug use (IDU) and risky sexual behaviors remain prevalent in patients receiving opioid agonist treatment. The purpose of this study is to determine in HIV-infected patients receiving opioid agonist treatment, the prevalence of HIV transmission risk behaviors, the prevalence of ARV resistance, and the prevalence of ARV resistance among those with risk behaviors.The design was a cross-sectional study of patients recruited from opioid treatment programs and outpatient practices. We measured demographic, drug treatment, and HIV clinical information (including ARV adherence), self-reported HIV risk behaviors and drug use, urine toxicologies, and genotype testing for ARV resistance (with both standard assays and ultradeep sequencing). Data analysis included descriptive statistics.Fifty-nine subjects were enrolled, 64% were male, 24% were white, and mean age was 46 years. Fifty-three percent were receiving methadone, 47% were receiving buprenorphine, and 80% were receiving opioid agonist treatment for 12 weeks or more. Fourteen percent reported unprotected sex, 7% reported sharing needles or works, and 60% had positive urine toxicology for illicit drug use. Fifteen percent had evidence of HIV resistance by standard genotyping; 7% with single class resistance, 3% with double class resistance, and 5% with triple class resistance. Ultradeep sequencing found additional class resistance in 5 subjects. Twenty-two percent of subjects with evidence of transmission risk behaviors versus 14% of subjects without risk behaviors had evidence of ARV resistance.Improved prevention and treatment efforts may be needed for HIV-infected, opioid dependent individuals receiving opioid agonist treatment to decrease transmission of ARV resistant virus, especially in resource limited settings.

    View details for DOI 10.1097/ADM.0b013e31827f9bdf

    View details for PubMedID 23388678

    View details for PubMedCentralID PMC3618545

  • Development of Elvitegravir Resistance and Linkage of Integrase Inhibitor Mutations with Protease and Reverse Transcriptase Resistance Mutations PLOS ONE Winters, M. A., Lloyd, R. M., Shafer, R. W., Kozal, M. J., Miller, M. D., Holodniy, M. 2012; 7 (7)


    Failure of antiretroviral regimens containing elvitegravir (EVG) and raltegravir (RAL) can result in the appearance of integrase inhibitor (INI) drug-resistance mutations (DRMs). While several INI DRMs have been identified, the evolution of EVG DRMs and the linkage of these DRMs with protease inhibitor (PI) and reverse transcriptase inhibitor (RTI) DRMs have not been studied at the clonal level. We examined the development of INI DRMs in 10 patients failing EVG-containing regimens over time, and the linkage of INI DRMs with PI and RTI DRMs in these patients plus 6 RAL-treated patients. A one-step RT-nested PCR protocol was used to generate a 2.7 kB amplicon that included the PR, RT, and IN coding region, and standard cloning and sequencing techniques were used to determine DRMs in 1,277 clones (mean 21 clones per time point). Results showed all patients had multiple PI, NRTI, and/or NNRTI DRMs at baseline, but no primary INI DRM. EVG-treated patients developed from 2 to 6 strains with different primary INI DRMs as early as 2 weeks after initiation of treatment, predominantly as single mutations. The prevalence of these strains fluctuated and new strains, and/or strains with new combinations of INI DRMs, developed over time. Final failure samples (weeks 14 to 48) typically showed a dominant strain with multiple mutations or N155H alone. Single N155H or multiple mutations were also observed in RAL-treated patients at virologic failure. All patient strains showed evidence of INI DRM co-located with single or multiple PI and/or RTI DRMs on the same viral strand. Our study shows that EVG treatment can select for a number of distinct INI-resistant strains whose prevalence fluctuates over time. Continued appearance of new INI DRMs after initial INI failure suggests a potent, highly dynamic selection of INI resistant strains that is unaffected by co-location with PI and RTI DRMs.

    View details for DOI 10.1371/journal.pone.0040514

    View details for Web of Science ID 000306548900028

    View details for PubMedID 22815755

  • Virologic Failures on Initial Boosted-PI Regimen Infrequently Possess Low-Level Variants with Major PI Resistance Mutations by Ultra-Deep Sequencing PLOS ONE Lataillade, M., Chiarella, J., Yang, R., Degrosky, M., Uy, J., Seekins, D., Simen, B., St John, E., Moreno, E., Kozal, M. 2012; 7 (2)


    It is unknown whether HIV-positive patients experiencing virologic failure (VF) on boosted-PI (PI/r) regimens without drug resistant mutations (DRM) by standard genotyping harbor low-level PI resistant variants. CASTLE compared the efficacy of atazanavir/ritonavir (ATV/r) with lopinavir/ritonavir (LPV/r), each in combination with TVD in ARV-naïve subjects.To determine if VF on an initial PI/r-based regimen possess low-level resistant variants that may affect a subsequent PI-containing regimen.Patients experiencing VF on a Tenofovir/Emtricitabine+PI/r regimen were evaluated by ultra deep sequencing (UDS) for mutations classified/weighted by Stanford HIVdb. Samples were evaluated for variants to 0.4% levels. 36 VF subjects were evaluated by UDS; 24 had UDS for PI and RT DRMs. Of these 24, 19 (79.2%) had any DRM by UDS. The most common UDS-detected DRM were NRTI in 18 subjects: M184V/I (11), TAMs(7) & K65R(4); PI DRMs were detected in 9 subjects: M46I/V(5), F53L(2), I50V(1), D30N(1), and N88S(1). The remaining 12 subjects, all with VLs<10,000, had protease gene UDS, and 4 had low-level PI DRMs: F53L(2), L76V(1), I54S(1), G73S(1). Overall, 3/36(8.3%) subjects had DRMs identified with Stanford-HIVdb weights >12 for ATV or LPV: N88S (at 0.43% level-mutational load 1,828) in 1 subject on ATV; I50V (0.44%-mutational load 110) and L76V (0.52%-mutational load 20) in 1 subject each, both on LPV. All VF samples remained phenotypically susceptible to the treatment PI/r.Among persons experiencing VF without PI DRMs with standard genotyping on an initial PI/r regimen, low-level variants possessing major PI DRMs were present in a minority of cases, occurred in isolation, and did not result in phenotypic resistance. NRTI DRMs were detected in a high proportion of subjects. These data suggest that PIs may remain effective in subjects experiencing VF on a PI/r-based regimen when PI DRMs are not detected by standard or UDS genotyping.

    View details for DOI 10.1371/journal.pone.0030118

    View details for Web of Science ID 000302741300007

    View details for PubMedID 22355307

    View details for PubMedCentralID PMC3280244

  • Relationship between minority nonnucleoside reverse transcriptase inhibitor resistance mutations, adherence, and the risk of virologic failure. AIDS (London, England) Li, J. Z., Paredes, R., Ribaudo, H. J., Svarovskaia, E. S., Kozal, M. J., Hullsiek, K. H., Miller, M. D., Bangsberg, D. R., Kuritzkes, D. R. 2012; 26 (2): 185-92


    To evaluate the risk of virologic failure conferred by suboptimal adherence to nonnucleoside reverse transcriptase inhibitors (NNRTIs) and minority NNRTI resistance mutations.Pooled analysis of the risk of virologic failure conferred by minority NNRTI resistance mutations and NNRTI adherence from three studies of treatment-naïve individuals initiating an NNRTI-based regimen.Participants from each study were categorized into both adherence quartiles (Q1-Q4) and four strata: at least 95%, 80-94%, 60-79%, and below 60%. Weighted Cox proportional hazard models were used to estimate the risk of virologic failure.The majority of participants (N = 768) had high measured adherence, but those in the lowest adherence quartile had the highest proportion of participants with virologic failure and the risk of virologic failure increased step-wise with adherence below 95%. Detection of minority NNRTI drug resistance mutations increased the proportion of participants with virologic failure across adherence quartiles (Cochran-Mantel-Haenszel P < 0.001) and adherence strata [Cochran-Mantel-Haenszel P < 0.001; <60% adherence, hazard ratio 1.7 (1.1-2.7), P = 0.02; 60-79% adherence, hazard ratio 1.2 (0.5-3.2), P = 0.67; 80-94% adherence, hazard ratio 2.5 (0.98-6.3), P = 0.06; ≥95% adherence, hazard ratio 3.6 (2.3-5.6), P < 0.001]. On multivariate analysis, the effect of minority variants was also most prominent at higher levels of medication adherence.The presence of minority NNRTI resistance mutations and NNRTI adherence were found to be independent predictors of virologic failure, but also modify each other's effects on virologic failure. In addition to the focus on medication adherence counseling, ultrasensitive HIV-1 drug resistance assays could play a role in optimizing the success rates of first-line antiretroviral therapy.

    View details for DOI 10.1097/QAD.0b013e32834e9d7d

    View details for PubMedID 22179227

    View details for PubMedCentralID PMC3437231

  • A nucleoside- and ritonavir-sparing regimen containing atazanavir plus raltegravir in antiretroviral treatment-naïve HIV-infected patients: SPARTAN study results. HIV clinical trials Kozal, M. J., Lupo, S., DeJesus, E., Molina, J. M., McDonald, C., Raffi, F., Benetucci, J., Mancini, M., Yang, R., Wirtz, V., Percival, L., Zhang, J., Zhu, L., Arikan, D., Farajallah, A., Nguyen, B. Y., Leavitt, R., McGrath, D., Lataillade, M. 2012; 13 (3): 119-30


    Nucleoside and ritonavir (RTV) toxicities have led to increased interest in nucleoside reverse transcriptase inhibitors (NRTIs) and RTV-sparing antiretroviral regimens. SPARTAN was a multicenter, randomized, open-label, noncomparative pilot study evaluating the efficacy, safety, and resistance profile of an investigational NRTI- and RTV-sparing regimen (experimental atazanavir [ATV] dose 300 mg bid + raltegravir [RAL] 400 mg bid [ATV+RAL]). The reference regimen consisted of ATV 300 mg/RTV 100 mg qd + tenofovir (TDF) 300 mg/emtricitabine (FTC) 200 mg qd (ATV/r+TDF/FTC).Treatment-naïve HIV-infected patients with HIV-RNA ≥5,000 copies/mL were randomized 2:1 to receive twice-daily ATV+RAL (n=63) or once-daily ATV/r+TDF/FTC (n=31). Efficacy at 24 weeks was determined by confirmed virologic response (CVR; HIV-RNA <50 copies/mL) with noncom-pleters counted as failures based on all treated subjects.The proportion of patients with CVR HIV RNA <50 copies/mL at week 24 was 74.6% (47/63) in the ATV+RAL arm and 63.3% (19/30) in the ATV/r+TDF/FTC arm. Systemic exposure to ATV in the ATV+RAL regimen was higher than historically observed with ATV/r+TDF/ FTC. Incidence of Grade 4 hyperbilirubinemia was higher on ATV+RAL (20.6%; 13/63) than on ATV/r+TDF/FTC (0%). The criteria for resistance testing (virologic failure [VF]: HIV-RNA ≥400 copies/mL) was met in 6/63 patients on ATV+RAL, and 1/30 on ATV/r+TDF/FTC; 4 VFs on ATV+RAL developed RAL resistance.ATV+RAL, an experimental NRTI- and RTV-sparing regimen, achieved virologic suppression rates comparable to current standards of care for treatment-naïve patients. The overall profile did not appear optimal for further clinical development given its development of resistance to RAL and higher rates of hyperbilirubinemia with twice-daily ATV compared with ATV/RTV.

    View details for DOI 10.1310/hct1303-119

    View details for PubMedID 22592092

  • Epidemiology, Seasonality, and Predictors of Outcome of AIDS-Associated Penicillium marneffei Infection in Ho Chi Minh City, Viet Nam CLINICAL INFECTIOUS DISEASES Thuy Le, L., Wolbers, M., Nguyen Huu Chi, H. C., Vo Minh Quang, M. Q., Nguyen Tran Chinh, T. C., Nguyen Phu Huong Lan, P. H., Pham Si Lam, S. L., Kozal, M. J., Shikuma, C. M., Day, J. N., Farrar, J. 2011; 52 (7): 945-952


    Penicillium marneffei is an important human immunodeficiency virus (HIV)-associated opportunistic pathogen in Southeast Asia. The epidemiology and the predictors of penicilliosis outcome are poorly understood.We performed a retrospective study of culture-confirmed incident penicilliosis admissions during 1996-2009 at the Hospital for Tropical Diseases in Ho Chi Minh City, Viet Nam. Seasonality of penicilliosis was assessed using cosinor models. Logistic regression was used to assess predictors of death or worsening disease based on 10 predefined covariates, and Cox regression was performed to model time-to-antifungal initiation.A total of 795 patients were identified; hospital charts were obtainable for 513 patients (65%). Cases increased exponentially and peaked in 2007 (156 cases), mirroring the trends in AIDS admissions during the study period. A highly significant seasonality for penicilliosis (P<.001) but not for cryptococcosis (P=.63) or AIDS admissions (P=.83) was observed, with a 27% (95% confidence interval, 14%-41%) increase in incidence during rainy months. All patients were HIV infected; the median CD4 cell count (62 patients) was 7 cells/μL (interquartile range, 4-24 cells/μL). Hospital outcome was an improvement in 347 (68%), death in 101 (20%), worsening in 42 (8%), and nonassessable in 23 (5%) cases. Injection drug use, shorter history, absence of fever or skin lesions, elevated respiratory rates, higher lymphocyte count, and lower platelet count independently predicted poor outcome in both complete-case and multiple-imputation analyses. Time-to-treatment initiation was shorter for patients with skin lesions (hazard ratio, 3.78; 95% confidence interval, 2.96-4.84; P<.001).Penicilliosis incidence correlates with the HIV/AIDS epidemic in Viet nam. The number of cases increases during rainy months. Injection drug use, shorter history, absence of fever or skin lesions, respiratory difficulty, higher lymphocyte count, and lower platelet count predict poor in-hospital outcome.

    View details for DOI 10.1093/cid/cir028

    View details for Web of Science ID 000288802600021

    View details for PubMedID 21427403

    View details for PubMedCentralID PMC3106230

  • Results of Antiretroviral Treatment Interruption and Intensification in Advanced Multi-Drug Resistant HIV Infection from the OPTIMA Trial PLOS ONE Holodniy, M., Brown, S. T., Cameron, D. W., Kyriakides, T. C., Angus, B., Babiker, A., Singer, J., Owens, D. K., Anis, A., Goodall, R., Hudson, F., Piaseczny, M., Russo, J., Schechter, M., Deyton, L., Darbyshire, J. 2011; 6 (3)


    Guidance is needed on best medical management for advanced HIV disease with multidrug resistance (MDR) and limited retreatment options. We assessed two novel antiretroviral (ARV) treatment approaches in this setting.We conducted a 2×2 factorial randomized open label controlled trial in patients with a CD4 count≤300 cells/µl who had ARV treatment (ART) failure requiring retreatment, to two options (a) re-treatment with either standard (≤4 ARVs) or intensive (≥5 ARVs) ART and b) either treatment starting immediately or after a 12-week monitored ART interruption. Primary outcome was time to developing a first AIDS-defining event (ADE) or death from any cause. Analysis was by intention to treat. From 2001 to 2006, 368 patients were randomized. At baseline, mean age was 48 years, 2% were women, median CD4 count was 106/µl, mean viral load was 4.74 log(10) copies/ml, and 59% had a prior AIDS diagnosis. Median follow-up was 4.0 years in 1249 person-years of observation. There were no statistically significant differences in the primary composite outcome of ADE or death between re-treatment options of standard versus intensive ART (hazard ratio 1.17; CI 0.86-1.59), or between immediate retreatment initiation versus interruption before re-treatment (hazard ratio 0.93; CI 0.68-1.30), or in the rate of non-HIV associated serious adverse events between re-treatment options.We did not observe clinical benefit or harm assessed by the primary outcome in this largest and longest trial exploring both ART interruption and intensification in advanced MDR HIV infection with poor retreatment NCT00050089.

    View details for DOI 10.1371/journal.pone.0014764

    View details for PubMedID 21483491

  • New technology to detect low-level drug-resistant HIV variants FUTURE VIROLOGY Gega, A., Kozal, M. J. 2011; 6 (1): 17-26

    View details for DOI 10.2217/FVL.10.77

    View details for Web of Science ID 000288058600008

  • Drug resistance testing in the management of HIV disease Uptodate Kozal, M. Uptodate, Waltham, MA. 2011; version 19.2
  • Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels. Antiviral therapy Kozal, M. J., Chiarella, J., St John, E. P., Moreno, E. A., Simen, B. B., Arnold, T. E., Lataillade, M. 2011; 16 (6): 925-9


    It has been reported that treatment-naive individuals infected with HIV-1 subtype C may be more likely to harbour viral variants possessing a K65R reverse transcriptase gene mutation. The objectives of this study were to determine the prevalence of low-level K65R variants within different HIV-1 subtypes and to assess the effects of antiretroviral exposure on K65R variant levels.Treatment-naive individuals infected with different HIV-1 subtypes were genotyped by ultra-deep sequencing. Samples were evaluated for low-level variants to 0.4% or 1% levels depending upon viral load. Estimated mutational load was calculated by multiplying the percentage of the variant by the plasma viral load.A total of 411 treatment-naive individuals were evaluated by ultra-deep sequencing to 1% levels; 4 subjects (0.97%) had K65R variants at ≥1% or had a very high mutation load. All four subjects had variants with linked drug resistance mutations suggesting transmitted resistant variants. 147 ARV-naive subjects were sequenced to 0.4% levels; 8.8% (13/147) had K65R low-level variants identified: 2.2% (2/92) in subtype B, 35.7% (10/28) in subtype C (P<0.001 for B versus C) and 3.7% (1/27) in non-B/C subtypes. The 13 ARV-naive subjects with K65R variants at <1% received tenofovir plus emtricitabine plus a ritonavir-boosted protease inhibitor (TDF+FTC+PI/r) and 5 subsequently experienced virological failure. There was no enhancement in K65R levels by percentage or mutational load compared to pre-therapy levels.Low-level K65R variants were more frequently identified in subtype C. K65R variants at >1% levels likely represent transmitted resistant variants. The clinical implication of low-level K65R variants below 1% in treatment-naive subjects who receive TDF+FTC+PI/r remains to be determined as the majority are very low-level and did not increase after antiretroviral exposure.

    View details for DOI 10.3851/IMP1851

    View details for PubMedID 21900725

  • Use of new technologies to detect and understand HIV drug resistance Kozal, M. J. BIOMED CENTRAL LTD. 2010: 6
  • Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PloS one Lataillade, M., Chiarella, J., Yang, R., Schnittman, S., Wirtz, V., Uy, J., Seekins, D., Krystal, M., Mancini, M., McGrath, D., Simen, B., Egholm, M., Kozal, M. 2010; 5 (6): e10952


    CASTLE compared the efficacy of atazanavir/ritonavir with lopinavir/ritonavir, each in combination with tenofovir-emtricitabine in ARV-naïve subjects from 5 continents.Determine the baseline rate and clinical significance of TDR mutations using ultra-deep sequencing (UDS) in ARV-naïve subjects in CASTLE.A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load. UDS was performed using 454 Life Sciences/Roche technology.Of 148 samples, 141 had successful UDS (86 subtype B, 55 non-B subtypes). Overall, 30.5% of subjects had a TDR mutation at baseline; 15.6% only had TDR(s) at <20% of the viral population. There was no difference in the rate of TDRs by B (30.2%) or non-B subtypes (30.9%). VF (51) and VS (90) had similar rates of any TDRs (25.5% vs. 33.3%), NNRTI TDRs (11.1% vs.11.8%) and NRTI TDRs (24.4% vs. 25.5%). Of 9 (6.4%) subjects with M184V/I (7 at <20% levels), 6 experienced VF. 16 (11.3%) subjects had multiple TAMs, and 7 experienced VF. 3 (2.1%) subjects had both multiple TAMs+M184V, and all experienced VF. Of 14 (9.9%) subjects with PI TDRs (11 at <20% levels): only 1 experienced virologic failure. The majority of PI TDRs were found in isolation (e.g. 46I) at <20% levels, and had low resistance algorithm scores.Among a representative sample of ARV-naïve subjects in CASTLE, TDR mutations were common (30.5%); B and non-B subtypes had similar rates of TDRs. Subjects with multiple PI TDRs were infrequent. Overall, TDRs did not affect virologic response for subjects on a boosted PI by week 48; however, a small subset of subjects with extensive NRTI backbone TDR patterns experienced virologic failure.

    View details for DOI 10.1371/journal.pone.0010952

    View details for PubMedID 20532178

    View details for PubMedCentralID PMC2880604

  • Overview of HIV drug resistance testing Uptodate Kozal, M. 2010; version 18.1
  • Drug-resistant human immunodefiency virus. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases Kozal, M. J. 2009; 15 Suppl 1: 69-73


    The development of antiretroviral therapy has led to a major reduction in human immunodeficiency virus (HIV)-related mortality. There are now six antiretroviral drug classes, with more than 20 unique antiretroviral drugs. However, HIV drug resistance occurs with all antiretroviral agents. Drug resistance can affect the response to antiretroviral therapy and is associated with increased mortality. The emergence of resistance in persons on antiretroviral therapy and the transmission of drug-resistant HIV strains to newly infected persons are now major public health concerns. Resistant variants that make up as little as 1% of the viral population in an HIV-infected person are clinically important, as they can rapidly grow under drug selection pressure and lead to therapy failure. However, current resistance assays used in the clinic reliably detect resistant variants only if they make up at least 20% of the circulating viral population. Recently, antiretroviral drugs have been developed that can inhibit HIV replication at new sites within the viral life cycle. These new drugs may improve clinical outcomes in persons infected with multidrug-resistant HIV. This review addresses the epidemiology and biological mechanisms of HIV drug resistance and the new approaches to detect and combat HIV drug resistance.

    View details for DOI 10.1111/j.1469-0691.2008.02687.x

    View details for PubMedID 19220361

  • Raltegravir with unboosted atazanavir 300 mg twice daily in antiretroviral treatment-experienced participants. Journal of the International Association of Physicians in AIDS Care (Chicago, Ill. : 2002) Gupta, S., Lataillade, M., Farber, S., Kozal, M. J. 2009; 8 (2): 87-92


    Raltegravir (RAL) is an HIV integrase inhibitor characterized by potent antiretroviral activity, few adverse effects, and lack of cross-resistance to other antiretroviral (ARV) agents. RAL is emerging as a component of effective alternative ARV therapy for those who experience therapeutic failure or intolerance to reverse transcriptase inhibitors (NRTI and NNRTI) and ritonavir (RTV)-boosted protease inhibitor (PI) containing regimens. The combination of RAL with atazanavir (ATV) without a concomitant NRTI-based backbone or the inclusion of RTV may provide an alternative strategy for those unable to tolerate these latter ARV agents. In this report the authors present a case series of treatment-experienced patients managed with RAL + ATV given without a boosting dose of RTV. All patients tolerated this regimen over a course of 25 to 82 weeks, and had good virologic and immunologic outcome with a decrease in HIV RNA levels to <50 copies/mL and a mean CD4 count increase of 234 cells/mm(3).

    View details for DOI 10.1177/1545109709332471

    View details for PubMedID 19270153

  • Development of an electronic medical record-based clinical decision support tool to improve HIV symptom management. AIDS patient care and STDs Nader, C. M., Tsevat, J., Justice, A. C., Mrus, J. M., Levin, F., Kozal, M. J., Mattocks, K., Farber, S., Rogers, M., Erdos, J., Brandt, C., Kudel, I., Braithwaite, R. 2009; 23 (7): 521-9


    Common symptoms associated with HIV disease and its management are often underrecognized and undertreated. A clinical decision support tool for symptom management was developed within the Veterans Health Administration electronic medical record (EMR), aiming at increasing provider awareness of and response to common HIV symptoms. Its feasibility was studied in March to May 2007 by implementing it within a weekly HIV clinic, comparing a 4-week intervention period with a 4-week control period. Fifty-six patients and their providers participated in the study. Patients' perceptions of providers' awareness of their symptoms, proportion of progress notes mentioning any symptom(s) and proportion of care plans mentioning any symptom(s) were measured. The clinical decision support tool used portable electronic "tablets" to elicit symptom information at the time of check-in, filtered, and organized that information into a concise and clinically relevant EMR note available at the point of care, and facilitated clinical responses to that information. It appeared to be well accepted by patients and providers and did not substantially impact workflow. Although this pilot study was not powered to detect effectiveness, 25 (93%) patients in the intervention group reported that their providers were very aware of their symptoms versus 27 (75%) control patients (p = 0.07). The proportion of providers' notes listing symptoms was similar in both periods; however, there was a trend toward including a greater number of symptoms in intervention period progress notes. The symptom support tool seemed to be useful in clinical HIV care. The Veterans Health Administration EMR may be an effective "laboratory" for developing and testing decision supports.

    View details for DOI 10.1089/apc.2008.0209

    View details for PubMedID 19538046

    View details for PubMedCentralID PMC3048777

  • Hepatitis C protease and polymerase inhibitors in development. AIDS patient care and STDs Liu-Young, G., Kozal, M. J. 2008; 22 (6): 449-57


    Hepatitis C infection (HCV) remains a global problem and the current anti-HCV therapies available in the clinic have sustained virologic response rates (SVR) of only about 50%, especially in HCV genotype 1-infected subjects. The SVR is even lower in HIV-HCV co-infected patients, estimated at only about 30-40%. However, exciting new research is under way to find new anti-HCV therapies. Presently, efforts to develop new anti-HCV agents for HCV-infected persons who fail pegylated interferon and ribavirin-based therapies have focused on inhibitors of key HCV enzymes such as the HCV NS3 protease and the NS5B polymerase. There are two protease inhibitors, telaprevir (VX-950, Vertex) and boceprevir (SCH 503034, Schering-Plough); and three polymerase inhibitors, valopicitabine (NM283, Idenix), R1626 (Roche), and HCV-796 (Viropharma) that have advanced to late-stage clinical trials. Of these aforementioned agents, telaprevir is the most advanced in clinical development. Early trial results on efficacy, safety, and HCV drug-resistance profiles of these novel agents will be discussed in this review paper.

    View details for DOI 10.1089/apc.2007.0199

    View details for PubMedID 18479202

    View details for PubMedCentralID PMC2928549

  • Virologic, immunologic, clinical, safety, and resistance outcomes from a long-term comparison of efavirenz-based versus nevirapine-based antiretroviral regimens as initial therapy in HIV-1-infected persons. HIV clinical trials van den Berg-Wolf, M., Hullsiek, K. H., Peng, G., Kozal, M. J., Novak, R. M., Chen, L., Crane, L. R., Macarthur, R. D. 2008; 9 (5): 324-36


    To compare long-term virologic, immunologic, and clinical outcomes in antiretroviral-naïve persons starting efavirenz (EFV)- versus nevirapine (NVP)-based regimens.The FIRST study randomized patients into three strategy arms: PI+NRTI, NNRTI+NRTI, and PI+NNRTI+NRTI. NNRTI was determined by optional randomization (NVP or EFV) or by choice. For this randomized substudy, the primary endpoint was HIV RNA >50 copies/mL after 8 months or death. Genotypic resistance testing was done at virologic failure (VF; HIV RNA >1,000 copies/mL at or after 4 months).228 persons (111 randomized to EFV, 117 to NVP) were followed for median 5 years. Rates per 100 person years for the primary endpoint were 41.2 (EFV) and 42.8 (NVP; p = .59). The percent of persons with HIV RNA <50 copies/mL was similar throughout follow-up (p = .24), as were average increases in CD4+ cells (p = .30). 423 persons declining the substudy chose EFV; 264 chose NVP. There were 915 persons in the combined cohort (randomized and choice). In the combined cohort, the risk of VF and VF with any NNRTI or NRTI resistance or resistance of any class was significantly less for EFV compared to NVP.EFV-based regimens as initial therapy resulted in a lower risk of VF and VF with resistance than did NVP-based regimens, although immunologic and clinical outcomes were similar.

    View details for DOI 10.1310/hct0905-324

    View details for PubMedID 18977721

  • Attitudes toward needle-sharing and HIV transmission risk behavior among HIV+ injection drug users in clinical care. AIDS care Norton, W. E., Amico, K. R., Fisher, W. A., Copenhaver, M. M., Kozal, M. J., Cornman, D. H., Friedland, G., Fisher, J. D. 2008; 20 (4): 462-9


    Risky behavior related to injection drug use accounts for a considerable proportion of incident HIV infection in the United States. Large numbers of injection drug users (IDUs) currently receive antiretroviral therapy in clinical settings and are accessible for risk-reduction interventions to reduce transmission of drug-resistant HIV and spread of HIV to uninfected others. The current study examined attitudes toward needle- or equipment-sharing among 123 HIV-positive IDUs in clinical care in an effort to understand the dynamics of such behavior and to create a basis for clinic-based risk-reduction interventions. Results indicate that at baseline, participants who reported extremely negative attitudes toward needle-sharing were less likely to have shared during the past month than those with less-extreme negative attitudes. Demographic, behavioral, and attitudinal variables were entered into a logistic regression model to examine needle-sharing group membership among HIV-positive IDUs. Being female and having less-extreme negative attitudes toward sharing were independent and significant correlates of sharing behavior. Interventions targeting needle-sharing attitudes deployed within the clinical care setting may be well-positioned to reduce HIV transmission among HIV-positive IDUs.

    View details for DOI 10.1080/09540120701867081

    View details for PubMedID 18449824

  • Evolution of genotypic resistance algorithms and their impact on the interpretation of clinical trials: An OPTIMA trial substudy HIV CLINICAL TRIALS Desai, S., Kyriakides, T., Holodniy, M., Al-Salman, J., Griffith, B., Kozal, M. 2007; 8 (5): 293-302


    The outdated rules of older HIV genotypic resistance algorithms can affect virologic responses. This study was designed to determine how often these incorrect resistance interpretations affect analyses of long-term clinical trials, antiretroviral (ARV) choices, and HIV disease progression rates.Baseline VIRCO virtual phenotypes (VVP) from patients screened in 2001-2002 for OPTIMA were compared to 2005 Stanford HIV resistance database algorithm (HIVDB-10/05, version 4.1.4) interpretations of the HIV-1 pol sequences. Drugs were called discordant if resistant by one algorithm and sensitive by the other.Of 2,341 drug comparisons, 501 (21.4%) were discordant, affecting 140 (86.4%) of 162 screened patients. NRTI/NtRTIs were more discordant than NNRTIs and PIs (38.6% vs. 4.3% vs. 12.8%; p < .0001). Sixty-nine (53%) patients were placed on 2 drugs reported as sensitive by VVP but resistant by HIVDB-10/05; they had higher than expected rates of disease progression and a similar time to first event or death as patients on ARVs classified as resistant by both algorithms (p = .61).Underestimation of drug resistance by older genotypic algorithms resulted in using ARVs incorrectly thought to be sensitive and in higher than expected rates of HIV disease progression. The use of older genotypes to interpret long-term clinical trials should account for this underestimation, because results may be different if viral sequences are interpreted with newer algorithms.

    View details for DOI 10.1310/hct0805-293

    View details for Web of Science ID 000250560300004

    View details for PubMedID 17956830

  • Adherence, virological and immunological outcomes for HIV-infected veterans starting combination antiretroviral therapies. AIDS (London, England) Braithwaite, R. S., Kozal, M. J., Chang, C. C., Roberts, M. S., Fultz, S. L., Goetz, M. B., Gibert, C., Rodriguez-Barradas, M., Mole, L., Justice, A. C. 2007; 21 (12): 1579-89


    We aimed to determine adherence, virological, and immunological outcomes one year after starting a first combination antiretroviral therapy (ART) regimen.Observational; synthesis of administrative, laboratory, and pharmacy data. Antiretroviral regimens were divided into efavirenz, nevirapine, boosted protease inhibitor (PI), and single PI categories. Propensity scores were used to control for confounding by treatment assignment. Adherence was estimated from pharmacy refill records.Veterans Affairs Healthcare System, all sites.HIV-infected individuals starting combination ART with a low likelihood of previous antiretroviral exposure.None.The proportion of antiretroviral prescriptions filled as prescribed, a change in log HIV-RNA, the proportion with log HIV-RNA viral suppression, a change in CD4 cell count.A total of 6394 individuals unlikely to have previous antiretroviral exposure started combination ART between 1996 and 2004, and were eligible for analysis. Adherence overall was low (63% of prescriptions filled as prescribed), and adherence with efavirenz (67%) and nevirapine (65%) regimens was significantly greater than adherence with boosted PI (59%) or single PI (61%) regimens (P < 0.001). Efavirenz regimens were more likely to suppress HIV-RNA at one year (74%) compared with nevirapine (62%), boosted PI (63%), or single PI (53%) regimens (all P < 0.001), and this superiority was maintained when analyses were adjusted for baseline clinical characteristics and propensity for treatment assignment. Efavirenz also yielded more favorable immunological outcomes.HIV-infected individuals initiating their first combination ART using an efavirenz-based regimen had improved virological and immunological outcomes and greater adherence levels.

    View details for DOI 10.1097/QAD.0b013e3281532b31

    View details for PubMedID 17630553

    View details for PubMedCentralID PMC3460378

  • Directly administered antiretroviral therapy for HIV-infected drug users does not have an impact on antiretroviral resistance: results from a randomized controlled trial. Journal of acquired immune deficiency syndromes (1999) Maru, D. S., Kozal, M. J., Bruce, R. D., Springer, S. A., Altice, F. L. 2007; 46 (5): 555-63


    Directly administered antiretroviral therapy (DAART) is an effective intervention that improves clinical outcomes among HIV-infected drug users. Its effects on antiretroviral drug resistance, however, are unknown.We conducted a community-based, prospective, randomized controlled trial of DAART compared with self-administered therapy (SAT). We performed a modified intention-to-treat analysis among 115 subjects who provided serum samples for HIV genotypic resistance testing at baseline and at follow-up. The main outcomes measures included total genotypic sensitivity score, future drug options, number of new drug resistance mutations (DRMs), and number of new major International AIDS Society (IAS) mutations.The adjusted probability of developing at least 1 new DRM did not differ between the 2 arms (SAT: 0.41 per person-year [PPY], DAART: 0.49 PPY; adjusted relative risk [RR] = 1.04; P = 0.90), nor did the number of new mutations (SAT: 0.76 PPY, DAART: 0.83 PPY; adjusted RR = 0.99; P = 0.99) or the probability of developing new major IAS new drug mutations (SAT: 0.30 PPY, DAART: 0.33 PPY; adjusted RR = 1.12; P = 0.78). On measures of GSS and FDO, the 2 arms also did not differ.In this trial, DAART provided on-treatment virologic benefit for HIV-infected drug users without affecting the rate of development of antiretroviral medication resistance.

    View details for DOI 10.1097/qai.0b013e318158c0bd

    View details for PubMedID 18193497

    View details for PubMedCentralID PMC2684061

  • Natural polymorphism of the HIV-1 integrase gene and mutations associated with integrase inhibitor resistance. Antiviral therapy Lataillade, M., Chiarella, J., Kozal, M. J. 2007; 12 (4): 563-70


    Two inhibitors of the HIV-1 integrase enzyme (INIs) are in late stage clinical development. To date, approximately 42 mutations within the HIV-1 integrase (IN) gene have been associated with INI drug resistance. Naturally occurring IN gene polymorphisms may have important implications for INI development. In this study, we evaluated clinical HIV-1 strains from INI-naive patients to determine the prevalence of IN gene polymorphisms, and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance and at sites crucial for LEDGF/p75 binding and HIV-1 integration.The IN gene from 67 INI-naive, HIV-1 clade B-infected patients were sequenced using standard population-based DNA sequencing methods. In addition, 176 unique full-length HIV-1 clade B IN gene sequences from INI-naive patients obtained from the HIV Los Alamos database were analysed.Analysis of 243 IN genes from HIV-1 clade B, INI-naive clinical strains revealed that 64% of the aa positions were polymorphic. Of the 42 aa substitutions currently associated with INI resistance, 21 occurred as natural polymorphisms: V72I, L74I, T97A, T112I, A128T, E138K, Q148H, V151I, S153Y/A, M154I, N155H, K156N, E157Q, G163R, V165I, V201I, I203M, T206S, S230N and R263K. IN aa positions crucial to LEDGF/P75 binding and HIV-1 integration were well conserved.Major INI mutations within the catalytic domain and extended active sites associated with high level resistance to the compounds in late stage development, especially strand transfer inhibitors (STIs), were infrequent in our study, which may help explain the excellent virological responses demonstrated in clinical trials.

    View details for PubMedID 17668566

  • The Incidence of HIV drug resistance and its impact on progression of HIV disease among antiretroviral-naïve participants started on three different antiretroviral therapy strategies. HIV clinical trials Kozal, M. J., Hullsiek, K. H., Macarthur, R. D., Berg-Wolf, M. v., Peng, G., Xiang, Y., Baxter, J. D., Uy, J., Telzak, E. E., Novak, R. M. 2007; 8 (6): 357-70


    Treatment-naïve participants were randomized to three antiretroviral strategies (all with nucleoside reverse transcriptase inhibitor [NRTI] background): protease inhibitor (PI), non-nucleoside reverse transcriptase inhibitor (NNRTI), or PI+NNRTI. The strategies were compared for drug resistance at first virologic failure (VF; HIV RNA >1000 copies/mL). The impact of resistance on AIDS or death was determined.Drug resistance was determined by genotype. Cox models were used to compare the strategies for VF with resistance and to determine the impact of resistance on AIDS or death.Of 1,360 participants, 866 experienced VF; 226 experienced AIDS or death (median follow-up 5 years). Rates (per 100 personyears) for VF with resistance were 14.9 (PI), 10.8 (NNRTI), and 11.5 (PI+NNRTI); hazard ratio (HR) was 0.78 (95% CI 0.61-0.99) for NNRTI versus PI. Compared to those with no VF, there was a significantly increased risk of AIDS or death for participants with solitary NNRTI resistance (HR 2.31, 95% CI 1.46-3.66) and for those failing with no known resistance (HR 1.78, 95% CI 1.18-2.68). Participants failing with solitary NNRTI resistance and with no resistance had the lowest percent of time on antiretroviral treatment (ART) and the lowest cumulative mean adherence scores.For treatment-naïve participants, the risk of AIDS or death is increased for those who failed virologically with solitary NNRTI resistance and those who failed with no known drug resistance compared to those with no virologic failure. Both the lack of ART exposure in nonadherent participants and the development of NNRTI resistance among those who take and fail their ART regimen predict poor clinical outcomes.

    View details for DOI 10.1310/hct0806-357

    View details for PubMedID 18042501

  • The hunt for HIV-1 integrase inhibitors. AIDS patient care and STDs Lataillade, M., Kozal, M. J. 2006; 20 (7): 489-501


    Currently, there are three distinct mechanistic classes of antiretrovirals: inhibitors of the HIV- 1 reverse transcriptase and protease enzymes and inhibitors of HIV entry, including receptor and coreceptor binding and cell fusion. A new drug class that inhibits the HIV-1 integrase enzyme (IN) is in development and may soon be available in the clinic. IN is an attractive drug target because it is essential for a stable and productive HIV-1 infection and there is no mammalian homologue of IN. Inhibitors of integrase enzyme (INI) block the integration of viral double-stranded DNA into the host cell's chromosomal DNA. HIV-1 integration has many potential steps that can be inhibited and several new compounds that target specific integration steps have been identified by drug developers. Recently, two INIs, GS-9137 and MK-0518, demonstrated promising early clinical trial results and have been advanced into later stage trials. In this review, we describe how IN facilitates HIV-1 integration, the needed enzyme cofactors, and the resultant byproducts created during integration. Furthermore, we review the different INIs under development, their mechanism of actions, site of IN inhibition, potency, resistance patterns, and discuss the early clinical trial results.

    View details for DOI 10.1089/apc.2006.20.489

    View details for PubMedID 16839248

  • Prevalence and impact of HIV-1 protease codon 33 mutations and polymorphisms in treatment-naive and treatment-experienced patients. Antiviral therapy Kozal, M. J., Hullsiek, K. H., Leduc, R., Novak, R. M., MacArthur, R. D., Lawrence, J., Baxter, J. D. 2006; 11 (4): 457-63


    HIV-1 protease gene mutations at codon 33 have been associated with resistance to some but not all protease inhibitors (PIs). Little is known about the difference in prevalence of codon 33 mutations and polymorphisms between treatment-naive and treatment-experienced patients, and the effect of codon 33F on PI phenotypic resistance patterns.Baseline genotypes (TRUGENE) from 772 patients participating in two different randomized clinical trials [504 antiretroviral treatment-naive patients and 268 antiretroviral treatment-experienced patients] were evaluated for the presence of protease codon 33 mutations and polymorphisms. Baseline phenotypes (Antivirogram), including fold-change in resistance for 16 antiretroviral drugs, were available for the 268 treatment-experienced patients. Multivariate linear regression models were used to determine factors associated with phenotypic fold-change for PIs.The prevalence of codon 33 mutations and polymorphisms was 5.2% in the naive cohort (0.2% 33F, 2.5% 33V, 2.5% 331) and 34.7% in the experienced cohort (30.2% 33F, 1.5% 33V, 3.0% 331). In the antiretroviral-experienced cohort (mean = 4.2 prior PIs, 10.6 prior antiretroviral drugs overall), a model adjusting for the presence of specific major protease and multi-PI resistance conferring mutations, the number of other minor PI mutations, prior PI drug exposure (current, prior only, never), and HIV transmission risk factor was used to estimate the phenotypic fold-change in resistance for those with and without mutation 33F. Those with 33F had a significantly higher fold-change for amprenavir (33 vs 19, P<0.0001), ritonavir (162 vs 82, P<0.0001), lopinavir (49 vs 38, P=0.04), and saquinavir (47 vs 41, P=0.02). The presence of the 33F was not a significant predictor of fold change in susceptibility for indinavir or nelfinavir.At protease codon 33, the prevalences of polymorphisms 33V and 331 were similar for PI-naive and PI-experienced patients (<3.0%), but the prevalence of 33F was significantly different (0.2% versus 30.2%). In the treatment-experienced cohort, the differences in phenotypic fold-change for amprenavir, lopinavir, saquinavir, and ritonavir between those with and without 33F persist after adjustment for the presence of other major PI mutations and PI drug exposure history. Given the availability of newer PIs that may select for 33F, monitoring for the presence of this mutation should be ongoing for both treatment-naive and treatment-experienced patients.

    View details for PubMedID 16856619

  • A population-based and longitudinal study of sexual behavior and multidrug-resistant HIV among patients in clinical care. MedGenMed : Medscape general medicine Kozal, M. J., Amico, K. R., Chiarella, J., Cornman, D., Fisher, W., Fisher, J., Friedland, G. 2006; 8 (2): 72


    Population-based and longitudinal information regarding sexual risk behavior among patients with multidrug resistant (MDR) HIV and their sexual partners is of great public health and clinical importance.To characterize the HIV sexual risk behaviors of patients with and without drug-resistant HIV in the clinical care setting over time.393 HIV-positive patients completed questionnaires of self-reported sexual risk behaviors at approximate 6-month intervals extending over 24 months. HIV viral load and genotypic drug resistance obtained during the same time points were matched to the behavioral data. Multidrug resistance was defined as having resistance to 2 or 3 antiretroviral (ARV) drug classes.In serial cross-sectional analyses, 393 patients (44% female and 79% heterosexual) contributed 919 matched behavioral and virologic results over the 24 months of data collection. Of these, 250 patients (64%) reported having sex during at least 1 survey period resulting in greater than 10,000 sexual events with more than 1000 partners. Unprotected sexual behavior was reported by 45% of sexually active patients, resulting in 34% of all sex events that exposed 29% of all partners. Of these patients with unprotected sexual events, 31% had HIV drug resistance--11.6% with resistance to 2 classes of ARVs (2-class), and 1.8% with 3-class ARV resistance at the time of a sexual risk event. Close to 1000 or 28% of all unprotected sexual events involved resistant strains (11% of these with resistance to 2 classes and 0.2% with 3-class resistance, exposing 20% of unprotected sexual partners to resistant HIV (8% to 2-class and 0.6% to 3-class resistance). In longitudinal analysis among the 78 patients who reported a cumulative total of 12 months of sexual history and had resistance testing, 38% reported engaging in unprotected sexual behavior. There was substantial and complex variation in the distribution of unprotected sexual events and in the detection of resistance over time.In this study of HIV sexual risk and resistance over time among HIV-infected patients in clinical care, a substantial proportion engaged in unprotected sex and had drug-resistant HIV, frequently exposing partners to 1- or 2-class resistant HIV strains. However, relatively few exposures involved 3-class resistance. The dynamics of sexual risk behavior and HIV drug resistance are complex and vary over time and urgently require both general and targeted interventions to reduce transmission of resistant HIV.

    View details for DOI 10.1186/1758-2652-8-2-72

    View details for PubMedID 16926811

    View details for PubMedCentralID PMC1785162

  • Efficacy and safety of abacavir plus lamivudine versus didanosine plus stavudine when combined with a protease inhibitor, a nonnucleoside reverse transcriptase inhibitor, or both in HIV-1 positive antiretroviral-naive persons. HIV clinical trials MacArthur, R. D., Chen, L., Peng, G., Novak, R. M., van den Berg-Wolf, M., Kozal, M., Besch, L., Yurik, T., Schmetter, B., Henley, C., Dehlinger, M. 2005; 5 (6): 361-70


    The combination of abacavir + lamivudine (ABC+3TC) versus didanosine + stavudine (ddI+d4T), each combined with other classes of antiretrovirals (ARVs) in ARV-naive patients, was compared for the combined endpoint of time to plasma HIV RNA >50 copies/mL (at or after the 8-month visit) or death (primary endpoint) in a nested substudy of an ongoing multicenter randomized trial.The substudy enrolled 182 patients; mean HIV RNA and CD4+ cell counts at baseline were 5.1 log10 copies/mL and 212 cells/mm3, respectively.After a median follow-up of 28 months, rates of primary endpoint were 57.2 and 67.8 per 100 person-years for the ABC+3TC and ddI+d4T groups (hazard ratio [HR]=0.81, 95% confidence interval [CI] 0.58-1.14, p=.23).There was a trend for treatments containing ABC+3TC to be better than treatments containing ddI+d4T with respect to HIV RNA decreases, CD4+ cell count increases, and tolerability.

    View details for DOI 10.1310/WEQG-QTHL-DL3X-FTXC

    View details for PubMedID 15682349

  • Prevalence of antiretroviral drug resistance mutations in chronically HIV-infected, treatment-naive patients: implications for routine resistance screening before initiation of antiretroviral therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Novak, R. M., Chen, L., MacArthur, R. D., Baxter, J. D., Huppler Hullsiek, K., Peng, G., Xiang, Y., Henely, C., Schmetter, B., Uy, J., van den Berg-Wolf, M., Kozal, M. 2005; 40 (3): 468-74


    The prevalence of drug resistance among persons with newly acquired human immunodeficiency virus (HIV) infection is well documented. However, it is unclear to what extent these mutations persist in chronically infected, treatment-naive patients.Prevalence of and factors associated with genotypic drug resistance were analyzed retrospectively in a subset of 491 chronically HIV-infected, antiretroviral-naive patients enrolled at 25 cities in the Terry Beirn Community Programs for Clinical Research on Acquired Immune Deficiency Syndrome (AIDS) Flexible Initial Retrovirus Suppressive Therapies trial during 1999-2001. Resistance was defined on the basis of the International AIDS Society 2003 definition, as well as the presence of additional mutations at codons 215 (C/D/E/S) and 69 (A/N/S) in the pol gene. Prevalence of mutations was estimated by use of techniques for stratified random samples. Logistic regression models were used to determine factors associated with resistance.Among the 491 chronically HIV-infected patients (mean CD4 cell count, 269 cells/mm(3); 31% of patients had a prior AIDS diagnosis), 57 (11.6%) had >or=1 resistance mutation, resulting in an estimated prevalence for the cohort of 10.8% (95% confidence interval [CI], 9.5%-12.1%). The prevalence was 8.8% if the 118I mutation was excluded. By drug class, the estimated prevalence of mutations conferring resistance to nucleoside reverse-transcriptase inhibitors was 7.8%, and the prevalence was 3.0% for nonnucleoside reverse-transcriptase inhibitors and 0.7% for protease inhibitors. In a multiple logistic regression analysis, non-Hispanic white subjects were twice as likely than African American subjects to have resistance (odds ratio [OR], 2.1; 95% CI, 1.1-4.1; P=.03), and there was a 40% increase per year in prevalence of mutations by later year of enrollment (OR, 1.4; 95% CI, 1.0-2.1; P=.05).These results demonstrate the persistence of drug resistance mutations in chronically HIV-infected patients and an increasing prevalence of resistance over time, and they support genotyping of virus at baseline for chronically HIV-infected patients.

    View details for DOI 10.1086/427212

    View details for PubMedID 15668873

  • HIV drug resistance and HIV transmission risk behaviors among active injection drug users. Journal of acquired immune deficiency syndromes (1999) Kozal, M. J., Amico, K. R., Chiarella, J., Cornman, D., Fisher, W., Fisher, J., Friedland, G. 2005; 40 (1): 106-9


    HIV(+) injection drug users in clinical care may harbor and transmit drug-resistant HIV. We performed a retrospective study of HIV drug resistance and risk behavior among HIV(+) injection drug users in care to determine the number of needle-sharing events that involved and the proportion of sharing partners exposed to drug-resistant HIV. Among 180 HIV injection drug users, 55 (31%) reported injecting drugs in the previous month, and 22 of these (40%) shared needles and/or works 148 times with 296 partners, of whom 271 (92%) were thought to be HIV(-) or status unknown. Further, 55 (31%) drug users harbored resistant HIV, including 5 (3% of total) who also shared needles and/or works a total of 27 times with 44 partners (18% of all sharing events and 15% of all exposed partners). A small proportion of injection drug users receiving clinical care engage in injection risk behavior and carry resistant HIV; however, because of multiple partners and needle-sharing events, they expose a substantial number of individuals to drug-resistant HIV. Strategies to reduce injection drug use risk behaviors among patients in clinical care are needed to reduce the transmission of sensitive and resistant HIV.

    View details for DOI 10.1097/01.qai.0000159666.95455.d2

    View details for PubMedID 16123691

  • Cross-resistance patterns among HIV protease inhibitors. AIDS patient care and STDs Kozal, M. 2004; 18 (4): 199-208


    Acquired resistance to antiretroviral agents is an established sequela of HIV pharmacotherapy. Viral mutations can confer reduced susceptibility to antiretroviral medications, resulting in virologic and clinical failure in more than half of treated patients. Cross-resistance that can develop within each drug class leads to the progressive loss of future therapeutic options for individual patients. Although protease inhibitors (PIs) are a potent class of antiretrovirals, resistance can still develop rapidly, and multiple-PI resistance has become a serious, growing clinical problem. Development of rational treatment strategies that recognize specific patterns of cross-resistance among PIs are needed to help clinicians choose the most appropriate PI. Rational sequencing of PI use should be based on genotypic and phenotypic resistance testing. Maintaining higher drug plasma levels or using specific PI combinations may also diminish PI cross-resistance. New agents that are less likely to induce or be susceptible to cross-resistance will be of value in HIV treatment. This article reviews the acquisition of resistance to currently available PIs, discussing the drug-specific mutational patterns and evidence of clinical cross-resistance. The resistance profiles of two newer PIs, atazanavir and tipranavir, are also presented.

    View details for DOI 10.1089/108729104323038874

    View details for PubMedID 15142350

  • Antiretroviral resistance and high-risk transmission behavior among HIV-positive patients in clinical care. AIDS (London, England) Kozal, M. J., Amico, K. R., Chiarella, J., Schreibman, T., Cornman, D., Fisher, W., Fisher, J., Friedland, G. 2004; 18 (16): 2185-9


    HIV-positive patients receiving antiretroviral therapy (ART) who engage in HIV transmission behaviors may harbor and transmit drug-resistant HIV. However, little is known about the risk behaviors of these patients, potential partners exposed and the relationship of these to ART resistance.To determine the relationship of HIV drug resistance and continuing HIV transmission risk behavior among HIV-positive patients in care.A retrospective, cross-sectional study of HIV transmission risk behavior and HIV drug resistance data from 333 HIV-positive patients.Among a diverse population of 333 HIV-positive patients, 75 (23%) had unprotected sex during the previous 3-months, resulting in 1126 unprotected sexual events with 191 partners of whom 155 were believed by patients to be HIV-negative or of unknown status. Eighteen of the 75 (24%) had resistant HIV and 207 unprotected sexual events, exposing 18% of the HIV- or status unknown partners. There was no difference in the proportion of patients engaging in unprotected sex who had undetectable viral load (VL) (22%): VL > 400 copies/ml without resistance (20%) and VL > 400 copies/ml with resistance (26%). Resistance and risk behavior was predicted only by lower mental health scores (odds ratio, 10.3; 95% confidence interval, 1.7-18.6).A substantial minority (23%) of patients in clinical care engaged in HIV sexual transmission risk behavior. A small subset of these also had ART-resistant HIV. However, this core group (approximately 5% of all patients) accounted for a large number of high-risk HIV transmission events with resistant virus, exposing a substantial number of partners.

    View details for DOI 10.1097/00002030-200411050-00011

    View details for PubMedID 15577652

  • The effect of high-dose saquinavir on viral load and CD4(+) T-cell counts in HIV-infected patients ANNALS OF INTERNAL MEDICINE Schapiro, J. M., Winters, M. A., Stewart, F., Efron, B., Norris, J., Kozal, M. J., Merigan, T. C. 1996; 124 (12): 1039-1050


    To evaluate the efficacy and safety of high-dose therapy with the human immunodeficiency virus (HIV) protease inhibitor saquinavir and to establish the duration of the effect of this therapy.Open-label study.Clinical research referral center.40 adults with human immunodeficiency virus type 1 (HIV-1) infection and CD4+ T-cell counts of 200 to 500 cells/mm3.Monotherapy with 3600 mg or 7200 mg of saquinavir per day, in six divided doses, for 24 weeks.Patients were monitored for adverse events and were evaluated monthly for CD4+ T-cell count, HIV-1 viral load (as measured by reverse transcriptase polymerase chain reaction [PCR] for plasma HIV RNA levels), immune-complex-disassociated p24 antigen levels, peripheral blood mononuclear cell viral DNA levels (as measured by PCR), and resistance mutations to saquinavir. Quantitative peripheral blood mononuclear cell cultures were also done every 2 months.The low-dose saquinavir regimen (3600 mg/d) resulted in a maximal mean decrease in plasma HIV RNA levels of 1.06 log RNA copies/mL of plasma and a mean maximal increase in CD4 counts of 72 cells/mm3. At week 24, the plasma HIV RNA level remained 0.48 log RNA copies/mL of plasma lower than baseline (P < 0.001) and the CD4 count remained 31 cells/mm3 higher than baseline (P = 0.165). The high-dose saquinavir regimen (7200 mg/d) produced a mean maximal decrease in the plasma HIV RNA level of 1.34 log RNA copies/mL of plasma and a mean maximal increase in CD4 count of 121 cells/mm3. At week 24, the plasma HIV RNA level remained 0.85 log RNA copies/mL of plasma lower than baseline (P < 0.001) and the CD4 count remained 82 cells/mm3 higher than baseline (P = 0.002). The high-dose regimen produced a greater reduction in plasma HIV RNA level (P = 0.08), a greater reduction in peripheral blood mononuclear cell cultures (P = 0.008), and a greater increase in CD4 count (P = 0.002) than did the low-dose regimen. Higher plasma drug concentrations in individual patients correlated with greater reductions in plasma HIV RNA levels over the two doses. Nine patients receiving the low-dose regimen and four patients receiving the high-dose regimen developed key saquinavir resistance mutations. Adverse reactions, most commonly gastrointestinal problems and elevated serum aminotransferase levels, were more common in patients receiving the high-dose regimen, but most adverse events were mild and all were reversible.Saquinavir is a potent antiviral agent that has a favorable toxicity profile at high doses. Higher doses produce a greater and more durable suppression of viral load and elevation in CD4+ T-cell counts and may delay the development of resistance mutations. Therapy with high-dose saquinavir alone or in combination with other antiretroviral agents should be investigated further.

    View details for Web of Science ID A1996UQ65800003

    View details for PubMedID 8633817

  • Using oligonucleotide probe arrays to access genetic diversity. BioTechniques Lipshutz, R. J., Morris, D., Chee, M., Hubbell, E., Kozal, M. J., Shah, N., Shen, N., Yang, R., Fodor, S. P. 1995; 19 (3): 442-7


    As the Human Genome Project and related efforts identify and determine the DNA sequences of human genes, it is important that highly reliable and efficient mechanisms are found to access individual genetic variation. It is only through a greater understanding of genetic diversity that the true benefit of the Human Genome Project will be realized. One approach, hybridization to high-density arrays of oligonucleotides, is a fast and effective means of accessing this genetic variation. Light-directed chemical synthesis has been used to generate miniaturized, high-density arrays of oligonucleotide probes. Application-specific oligonucleotide probe array designs have been developed for the rapid screening of characterized genes. Dedicated instrumentation and software have been developed for array hybridization, fluorescence detection and data acquisition and analysis. In a specific and challenging application, oligonucleotide probe arrays have been used to screen the reverse transcriptase and protease genes of the highly polymorphic HIV-1 genome to explore genetic diversity and detect mutations conferring resistance to antiviral drugs. Results from this application strongly suggest that oligonucleotide probe arrays will be a powerful tool for rapid investigations in sequence checking, pathogen detection, expression monitoring and DNA molecular recognition.

    View details for PubMedID 7495558



    Different tissues or body fluids in which human immunodeficiency virus type 1 (HIV-1) can reside may contain viruses with distinct characteristics. Sixteen HIV-1-infected patients receiving zidovudine or didanosine were studied cross-sectionally and 1 patient who switched from zidovudine to didanosine was followed sequentially to determine if drug resistance mutations within the HIV-1 pol gene at codons 74 and 215 differed depending on the compartment from which the gene was isolated (plasma, seminal fluid, peripheral blood mononuclear cells, or seminal nonspermatozoal mononuclear cells). Cell-free virus in plasma and semen developed detectable mutations first, followed by proviral DNA in seminal nonspermatozoal and peripheral blood mononuclear cells. Study of the appearance of HIV-1 mutations in various compartments may help elucidate how the populations and dynamics of the virus differ throughout the body and determine whether seminal cell-free virus or provirus is the major sexually transmitted form.

    View details for Web of Science ID A1994PN66800038

    View details for PubMedID 7963730



    To determine the frequency and pattern of development of specific drug resistance mutations for human immunodeficiency virus (HIV) reverse transcriptase in patients switched from zidovudine to didanosine therapy and to examine the relation of the didanosine resistance mutation at codon 74 of the HIV reverse-transcriptase gene to CD4+ T-cell changes and virus burden.Retrospective analysis of all patients enrolled at Stanford University in protocols where patients were switched from zidovudine to didanosine monotherapy.A university hospital.64 patients infected with HIV who were switched from zidovudine to didanosine monotherapy. Patients had the acquired immunodeficiency syndrome (AIDS), AIDS-related complex, or were asymptomatic (mean [+/- SD] starting CD4+ T-cell count of 129 +/- 88 cells/mm3).Serial serum specimens were tested for the didanosine resistance mutation at codon 74 of the HIV reverse-transcriptase gene and for a zidovudine resistance mutation at codon 215 using selective polymerase chain reactions (PCR). Serum HIV RNA levels were determined by quantitative PCR. CD4+ T-cell counts were determined at serial time points.By 24 weeks of didanosine therapy, the proportion of patients with the didanosine resistance mutation at codon 74 increased from 0% to 56% (36 of 64). In contrast, the proportion of patients with the zidovudine resistance mutation at codon 215 decreased from 84% at the start to 59% after 24 weeks of didanosine therapy (a 25% decrease, 95% lower CI, 15%; P < 0.0001). Patients who developed the codon 74 mutation had a greater decrease in CD4+ T cells after the development of the mutation than did patients without the mutation (P < 0.001). In addition, after 24 weeks of didanosine, patients who developed the codon 74 mutation had a greater serum HIV RNA burden than patients who remained wild type (did not have the mutation) at codon 74 (225,000 compared with 82,400 HIV RNA copies/mL serum; P = 0.01).Among patients infected with HIV who had advanced disease and were switched from zidovudine to didanosine therapy, more than one half developed the didanosine resistance mutation at codon 74 by 24 weeks of didanosine therapy. Patients who developed the codon 74 mutation had a greater decline in CD4+ T cells after the development of the mutation and had a greater serum virus burden than did patients without the codon 74 mutation.

    View details for Web of Science ID A1994PB10200005

    View details for PubMedID 7518658



    The variable rate of disease progression in HIV-1-infected patients treated with zidovudine may be related to certain viral characteristics, such as, antiviral drug resistance, virus burden, and viral syncytium-inducing (SI) capacity. Thirty-two HIV-1-infected patients treated with zidovudine (mean of 34 months) were studied to determine the relationship of SI phenotype and the codon 215 pol gene mutation (a marker of zidovudine resistance) to virus burden and CD4 cell decline. Patients with SI strains and the codon 215 mutation in their proviral DNA had a 54% decline in CD4 cells and a virus burden of 21,480 proviral DNA copies/10(6) CD4 cells. In contrast, patients with non-SI (NSI) strains and wild-type at codon 215 had a 10% increase in CD4 cells and had a viral burden 1/46 that of patients with SI and the 215 mutation. Among patients with NSI strains, changes in CD4 cells depended on the presence of the codon 215 mutation (-160 CD4 cells/microliters), compared with those wild-type at codon 215 (+28 CD4 cells/microliters) (p < 0.01). There was a concordant rise in virus burden between proviral DNA and plasma HIV RNA depending on HIV phenotype and genotype. Using multiple linear regression, SI phenotype and the codon 215 mutation were found to independently predict CD4 cell decline and increased virus burden in zidovudine-treated patients.

    View details for Web of Science ID A1994NX17100007

    View details for PubMedID 7517448

  • PREVALENCE OF HIV-1 SYNCYTIUM-INDUCING PHENOTYPE ANNALS OF INTERNAL MEDICINE Kozal, M. J., Ramachandran, R. V., Shafer, W. 1994; 120 (9): 811-811

    View details for Web of Science ID A1994NH25100019

    View details for PubMedID 7908508



    Drug resistance conferred by specific human immunodeficiency virus type 1 (HIV-1) pol gene mutations has been associated with clinical progression in HIV-infected patients receiving anti-retroviral therapy. This study examined drug susceptibilities and pol mutations of HIV-1 strains from patients treated for 1 year with zidovudine, didanosine (ddI), or zidovudine and ddI. Ten (42%) of 24 patients receiving combination therapy versus 8/26 (31%) receiving only zidovudine had HIV-1 strains with phenotypic zidovudine resistance or a zidovudine resistance pol mutation at codon 215 (P = .6). In contrast, a ddI resistance mutation at codon 74 was less common among patients receiving combination therapy (2/24) than among those receiving ddI only (17/26; P < .001). Two patients receiving combination therapy developed resistance to zidovudine and ddI; they had HIV strains with amino acid mutations at codons 62, 75, 77, 116, and 151. Combination therapy with zidovudine and ddI selects for zidovudine-resistant HIV-1 strains lacking a ddI resistance mutation and for multidrug-resistant strains containing novel pol mutations.

    View details for Web of Science ID A1994NP11100002

    View details for PubMedID 8133086



    Quantification of viral load in HIV disease has become increasingly important as a marker of antiviral efficacy. We applied gene amplification techniques in vivo to asses antiretroviral activity of combination therapy. Five HIV-infected subjects, four of whom were drug naive, were administered combination therapy with zidovudine (ZDV) and didanosine (ddI). Plasma and peripheral blood mononuclear cells (PBMC) were obtained twice at baseline and then at 1, 3, 6, 9, and 12 months after the initiation of therapy. Results show that plasma HIV RNA copy number fell from 2,170 +/- 660/ml to undetectable at 1 month, with continued suppression at 12 months. HIV proviral DNA copy number decreased from 3.9 to 3.0 log10/10(6) CD4+ T cells at 12 months. Cell dilution cultures were positive in 4 of 5 subjects at baseline and in only 1 of 5 after 12 months. CD4+ T-cell count increased from 390 +/- 30/mm3 pretherapy, to 505 +/- 66/mm3 after 6 months of therapy, but returned to baseline levels after 12 months of therapy. No mutations were detected from PBMC DNA for codon 215 and 74 in the HIV pol gene from the drug-naive subjects. These findings suggest that gene amplification techniques can be used to study changes in viral load or genotype and can be applied in real time to samples from patients involved in clinical trials.

    View details for Web of Science ID A1993KU22100007

    View details for PubMedID 8095981



    A nested polymerase chain reaction assay was used to define the sequence of a specific codon, amino acid 215, of the human immunodeficiency virus (HIV) pol gene in DNA from peripheral blood mononuclear cells (PBMC) and viral RNA from serum from 38 patients treated with zidovudine for > or = 2 years. After treatment for a mean of 34 months, 17 patients with sequences with a codon 215 mutation had a mean 50% decrease in CD4 cells, compared with 21 patients with sequences wild-type at codon 215, who had a mean 11% increase in CD4 cells (P < .0001). Patients with a mutation at 215 had a ninefold higher provirus burden in PBMC. Detection of the codon 215 mutation in plasma viral RNA preceded detection of the mutation in DNA from PBMC and decline in CD4 cells. The appearance of a mutation at codon 215 in the HIV reverse transcriptase gene in patients receiving zidovudine may be a marker for impending immunologic decline.

    View details for Web of Science ID A1993KN15200002

    View details for PubMedID 7680058



    Traditional antiviral susceptibility testing methods using cell lines can be applied to no more than about 30% of clinical HIV isolates (Larder et al., 1989a; Fenyo et al., 1989). We tested the cell-free supernatant from low passage clinical HIV isolates using donor peripheral blood mononuclear cells (PBMC). Drug susceptibility was assessed by measuring the effect of increasing zidovudine (ZDV) concentrations on HIV P24 antigen production. Susceptibility results were obtained on 24/27 consecutive clinical isolates and 6/6 laboratory isolates. The mean IC90 of isolates from untreated patients was 0.008 microM ZDV (range: 0.002-0.038). The IC90s of isolates from ZDV-treated patients ranged from 0.007 to greater than 10 microM ZDV. All isolates with an IC90 < 0.1 microM ZDV had a wild type sequence at codon 215 of the HIV pol gene; 11/12 isolates with an IC90 > 0.1 microM ZDV had a mutation at codon 215 (P < 0.001). Among 16 ZDV-treated patients, there was a modest correlation between the change in CD4 count from the start of ZDV treatment and the IC90 of the patient's isolate following treatment (r = 0.51). Susceptibility testing using donor PBMC can be a sensitive means of testing a broad range of clinical HIV isolates.

    View details for Web of Science ID A1993KR99500004

    View details for PubMedID 8097199