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Martits-Chalangari K, Spak CW, Askar M, Killian A, Fisher TL, Atillasoy E, Marshall WL, McNeel D, Miller MD, Mathai SK, Gottlieb RL. ALVR109, an off-the-shelf partially HLA matched SARS-CoV-2-specific T cell therapy, to treat refractory severe COVID-19 pneumonia in a heart transplant patient: Case report. Am J Transplant 2022; 22:1261-1265. [PMID: 34910857 PMCID: PMC9303326 DOI: 10.1111/ajt.16927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 12/10/2021] [Indexed: 01/25/2023]
Abstract
An unvaccinated adult male heart transplant recipient patient with recalcitrant COVID-19 due to SARS-CoV-2 delta variant with rising nasopharyngeal quantitative viral load was successfully treated with ALVR109, an off-the-shelf SARS-CoV-2-specific T cell therapy. Background immunosuppression included 0.1 mg/kg prednisone, tacrolimus, and mycophenolate mofetil 1 gm twice daily for historical antibody-mediated rejection. Prior therapies included remdesivir, corticosteroids, and tocilizumab, with requirement for high-flow nasal oxygen. Lack of clinical improvement and acutely rising nasopharyngeal viral RNA more than 3 weeks into illness prompted the request of ALVR109 through an emergency IND. The day following the first ALVR109 infusion, the patient's nasopharyngeal SARS-CoV-2 RNA declined from 7.43 to 5.02 log10 RNA copies/ml. On post-infusion day 4, the patient transitioned to low-flow oxygen. Two subsequent infusions of ALVR109 were administered 10 and 26 days after the first; nasopharyngeal SARS-CoV-2 RNA became undetectable on Day 11, and he was discharged the following day on low-flow oxygen 5 weeks after the initial diagnosis of COVID-19. The clinical and virologic improvements observed in this patient following administration of ALVR109 suggest a potential benefit that warrants further exploration in clinical trials.
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Affiliation(s)
- Katalin Martits-Chalangari
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA
| | - Cedric W. Spak
- Baylor University Medical Center, Dallas, Texas, USA,Texas A&M Health Science Center, Dallas, Texas, USA
| | - Medhat Askar
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA,Texas A&M Health Science Center, Dallas, Texas, USA
| | - Aaron Killian
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA
| | - Tammy L. Fisher
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA
| | | | | | | | | | - Susan K. Mathai
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA,Texas A&M Health Science Center, Dallas, Texas, USA
| | - Robert L. Gottlieb
- Baylor University Medical Center, Dallas, Texas, USA,Baylor Scott & White Research Institute, Dallas, Texas, USA,Texas A&M Health Science Center, Dallas, Texas, USA,TCU and University of North Texas Health Science Center, Fort Worth, Texas, USA,Correspondence Robert L. Gottlieb, Center for Advanced Heart and Lung Disease, Baylor University Medical Center, Dallas, TX, USA.
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Bodkin SG, Hertel J, Diduch DR, Saliba SA, Novicoff WM, Brockmeier SF, Miller MD, Gwathmey FW, Werner BC, Hart JM. Predicting ACL Reinjury from Return to Activity Assessments at 6-months Post-Surgery: A Prospective Cohort Study. J Athl Train 2021; 57:325-333. [PMID: 35439312 PMCID: PMC9020598 DOI: 10.4085/1062-6050-0407.20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CONTEXT Return to activity(RTA) assessments are commonly administered following ACL-Reconstruction(ACLR) to manage post-operative progressions back to activity. To date, there is little knowledge on the clinical utility of these assessments to predict patient outcomes such as secondary ACL injury once returned to activity. OBJECTIVE To identify what measures of patient function at 6-months post-ACLR best predict return to activity and second ACL injury at a minimum of 2-years following ACLR. DESIGN Prospective-cohort Setting: Laboratory Patients: A total of 234 patients with primary, unilateral ACLR completed functional assessments at approximately 6-months post-ACLR. A total of 192(82%) completed follow-up ≥ 2-years post ACLR. MAIN OUTCOME MEASURES Six-month functional assessments consisted of patient reported outcomes, isokinetic knee flexor and extensor strength, and single-leg hopping. The ability to return to activity and secondary ACL injury were collected at a minimum of two-years following ACLR. RESULTS In patients who did RTA(n=155), a total of 44(28%) individuals had a subsequent ACL injury; graft n=24(15.5%), contralateral ACL n=20(13%). A greater proportion of females had a secondary injury to the contralateral ACL(15/24, 63%) whereas a greater proportion of males reinjured the ipsilateral ACL graft(15/20, 75%, P=.017) Greater knee extension symmetry at 6-months increased the probability of reinjury(B=.016, P=.048). In patients who RTA before 8-months, every 1% increase in quadriceps strength symmetry at 6-months increased the risk of reinjury by 2.1%(B=.021, P=.05). In patients who RTA after 8-months, every month that RTA was delayed reduced the risk of reinjury by 28.4%(B=-284, P=.042). CONCLUSIONS Patients with more symmetric quadriceps strength at 6-months post ACLR were more likely to experience another ACL rupture, especially in those who returned to sport earlier than 8-months after the index surgery. Clinicians should be cognizant that returning high functioning patients to activity earlier than 8-months post-ACLR may place them at an increased risk for reinjury.
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Affiliation(s)
- S G Bodkin
- Department of Physical Medicine and Rehabilitation. University of Colorado Anschutz Medical Campus. Aurora, CO
| | - J Hertel
- Department of Kinesiology. University of Virginia, Charlottesville, VA
| | - D R Diduch
- Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
| | - S A Saliba
- Department of Kinesiology. University of Virginia, Charlottesville, VA
| | - W M Novicoff
- Public Health Sciences, University of Virginia, Charlottesville, VA
| | - S F Brockmeier
- Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
| | - M D Miller
- Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
| | - F W Gwathmey
- Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
| | - B C Werner
- Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
| | - J M Hart
- Department of Kinesiology. University of Virginia, Charlottesville, VA.,Department of Orthopaedic Surgery. University of Virginia, Charlottesville, VA
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Miller MD, Kokko C, Ballard CS, Dann HM, Fustini M, Palmonari A, Formigoni A, Cotanch KW, Grant RJ. Influence of fiber degradability of corn silage in diets with lower and higher fiber content on lactational performance, nutrient digestibility, and ruminal characteristics in lactating Holstein cows. J Dairy Sci 2020; 104:1728-1743. [PMID: 33309368 DOI: 10.3168/jds.2020-19088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/22/2020] [Indexed: 11/19/2022]
Abstract
The effect of neutral detergent fiber (NDF) degradability of corn silage in diets containing lower and higher NDF concentrations on lactational performance, nutrient digestibility, and ruminal characteristics in lactating Holstein cows was measured. Eight ruminally cannulated Holstein cows averaging 91 ± 4 (standard error) days in milk were used in a replicated 4 × 4 Latin square design with 21-d periods (7-d collection periods). Dietary treatments were formulated to contain either conventional (CON; 48.6% 24-h NDF degradability; NDFD) or brown midrib-3 (BM3; 61.1% 24-h NDFD) corn silage and either lower NDF (LNDF) or higher NDF (HNDF) concentration (32.0 and 35.8% of ration dry matter, DM) by adjusting the dietary forage content (52 and 67% forage, DM basis). The dietary treatments were (1) CON-LNDF, (2) CON-HNDF, (3) BM3-LNDF, and (4) BM3-HNDF. Data were analyzed as a factorial arrangement of diets within a replicated Latin square design with the MIXED procedure of SAS (SAS Institute Inc., Cary, NC) with fixed effects of NDFD, NDF, NDFD × NDF, period(square), and square. Cow within square was the random effect. Time and its interactions with NDFD and NDF were included in the model when appropriate. An interaction between NDFD and NDF content resulted in the HNDF diet decreasing dry matter intake (DMI) with CON corn silage but not with BM3 silage. Cows fed the BM3 corn silage had higher DMI than cows fed the CON corn silage, whereas cows fed the HNDF diet consumed less DM than cows fed the LNDF diet. Cows fed the BM3 diets had greater energy-corrected milk yield, higher milk true protein content, and lower milk urea nitrogen concentration than cows fed CON diets. Additionally, cows fed the BM3 diets had greater total-tract digestibility of organic matter and NDF than cows fed the CON diets. Compared with CON diets, the BMR diets accelerated ruminal NDF turnover. When incorporated into higher NDF diets, corn silage with greater in vitro 24-h NDFD and lower undegradable NDF at 240 h of in vitro fermentation (uNDF240) allowed for greater DMI intake than CON. In contrast, for lower NDF diets, NDFD of corn silage did not affect DMI, which suggests that a threshold level of inclusion of higher NDFD corn silage is necessary to observe enhanced lactational performance. Results suggest that there is a maximum gut fill of dietary uNDF240 and that higher NDFD corn silage can be fed at greater dietary concentrations.
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Affiliation(s)
- M D Miller
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - C Kokko
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - C S Ballard
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - H M Dann
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - M Fustini
- Department of Veterinary Medicine, Università di Bologna, 40064 Bologna, Italy
| | - A Palmonari
- Department of Veterinary Medicine, Università di Bologna, 40064 Bologna, Italy
| | - A Formigoni
- Department of Veterinary Medicine, Università di Bologna, 40064 Bologna, Italy
| | - K W Cotanch
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - R J Grant
- William H. Miner Agricultural Research Institute, Chazy, NY 12921.
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Miller MD, Lanier JS, Kvidera SK, Dann HM, Ballard CS, Grant RJ. Evaluation of source of corn silage and trace minerals on rumen characteristics and passage rate of Holstein cows. J Dairy Sci 2020; 103:8864-8879. [PMID: 32747108 DOI: 10.3168/jds.2020-18490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022]
Abstract
The effects of source of corn silage and trace mineral on rumen fermentation, turnover, and particle passage rates were evaluated with 8 ruminally cannulated Holstein cows averaging 83 (standard error = 5) days in milk in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and 28-d periods. The diets consisted (dry basis) of 55% conventional (CON) or brown midrib-3 (BM3) corn silage, 2% chopped wheat straw, and 43% grain mix with either sulfate (STM) or hydroxy (HTM) source of Cu, Zn, and Mn trace minerals. The targeted supplemental amount of Cu, Zn, and Mn was 194, 1,657, and 687 mg/d, respectively. The dietary treatments were (1) CON-STM, (2) CON-HTM, (3) BM3-STM, and (4) BM3-HTM. Dietary nutrient composition of BM3 diets averaged 32.1% amylase neutral detergent fiber on an organic matter basis (aNDFom) and 6.9% undigested neutral detergent fiber at 240 h of in vitro fermentation (uNDF240om; % of dry matter), and CON diets averaged 36.2% aNDFom and 8.6% uNDF240om (% of dry matter). Data were summarized by period and analyzed as a replicated Latin square design with fixed model effects for corn silage, trace mineral, corn silage and trace mineral interaction, period within replicated square, and replicated square using the MIXED procedure of SAS (version 9.4, SAS Institute Inc., Cary, NC). Cow within replicate was a random effect. Daily mean, standard deviation, minimum, and maximum for rumen pH were unaffected by corn silage or trace mineral source. Cows fed the CON diets had greater rumen acetate percentage than cows fed the BM3 diets (65.7 vs. 64.7 molar %). In contrast, cows fed the BM3 diets had greater rumen propionate percentage than cows fed the CON diets (21.4 vs. 20.4 molar %). Total volatile fatty acid concentration was lower for cows fed STM versus HTM in BM3 diets, but not for the cows fed the CON diets. Cows fed the BM3 diets had faster turnover rate and shorter turnover time for uNDF240om than cows fed the CON diets (3.12 vs. 2.86%/h and 33.3 vs. 36.5 h, respectively). Cows fed the BM3 diets had a faster passage rate of small and medium corn silage neutral detergent fiber particles than cows fed the CON diets (5.73 vs. 5.37%/h and 4.74 vs. 4.31%/h, respectively). We observed a corn silage by source of trace mineral interaction on organic matter and uNDF240om rumen pool size and organic matter turnover. Overall, source of corn silage had a pronounced influence on rumen dynamics presumably related to greater in vitro neutral detergent fiber digestibility and lower uNDF240om content of BM3 corn silage that allowed for faster turnover of indigestible neutral detergent fiber and greater passage rate of corn silage particles. In contrast, the source of trace mineral had much less significant effects on rumen fermentation, turnover, and particle passage rates. Corn silage-based diets intended to enhance rumen fiber fermentation, turnover, and passage are more affected by source and digestibility of neutral detergent fiber than source of dietary trace minerals.
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Affiliation(s)
- M D Miller
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - J S Lanier
- Micronutrients USA LLC, Indianapolis, IN 46241
| | - S K Kvidera
- Micronutrients USA LLC, Indianapolis, IN 46241
| | - H M Dann
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - C S Ballard
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - R J Grant
- William H. Miner Agricultural Research Institute, Chazy, NY 12921.
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Miller MD, Lanier JS, Kvidera SK, Dann HM, Ballard CS, Grant RJ. Evaluation of source of corn silage and trace minerals on lactational performance and total-tract nutrient digestibility in Holstein cows. J Dairy Sci 2020; 103:3147-3160. [PMID: 32037164 DOI: 10.3168/jds.2019-17716] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/15/2019] [Indexed: 11/19/2022]
Abstract
We evaluated the effects of source of corn silage and trace minerals on lactational performance and total-tract digestibility (TTD) of nutrients in 16 Holstein cows averaging 82 (standard error = 3) days in milk in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments with 28-d periods. The diets consisted [dry matter (DM) basis] of 55% conventional (CON) or brown midrib-3 (BM3) corn silage, 2% chopped wheat straw, and 43% grain mix with either sulfate (STM) or hydroxy (HTM) sources of copper, manganese, and zinc trace minerals. The targeted supplemental concentrations of copper, zinc, and manganese were 194, 1,657, and 687 mg/d, respectively. The dietary treatments were CON-STM, CON-HTM, BM3-STM, and BM3-HTM. The dietary nutrient composition of the BM3 diets averaged 32.1% amylase neutral detergent fiber on an organic matter basis (aNDFom) and 6.9% undigested neutral detergent fiber at 240 h (uNDF240om; % of DM), and CON diets averaged 36.2% aNDFom and 8.6% uNDF240om (% of DM). The average supplemental concentrations of copper, zinc, and manganese for the STM diets were 10, 41, and 64 mg/kg, respectively, and the average supplemental concentrations of copper, zinc, and manganese for the HTM diets were 10, 40, and 62 mg/kg, respectively. The average total dietary concentrations of copper, zinc, and manganese for the STM diets were 17, 104, and 60 mg/kg, respectively, and the average total dietary concentrations of copper, zinc, and manganese for the HTM diets were 17, 91, and 66 mg/kg, respectively. Data were summarized by period and analyzed as a replicated Latin square design with fixed model effects for corn silage, trace minerals, corn silage × trace mineral interaction, period within replicated square, and replicated square using the MIXED procedure of SAS. Cow within replicated square was a random effect. Cows fed the BM3 diets had greater dry matter intake (DMI) and milk yield (28.1 and 47.0 kg/d) than cows fed the CON diets (27.5 and 44.7 kg/d). We found no significant interaction between corn silage and trace minerals for DMI and milk yield. Cows fed the HTM diets (28.1 kg/d) had a greater DMI than cows fed the STM diets (27.5 kg/d). Cows fed the BM3 diets had greater TTD of DM and OM (72.8 and 74.1% of DM) than cows fed the CON diets (71.1 and 72.3% of DM). Cows fed the HTM diets had a tendency for greater TTD of aNDFom than cows fed the STM diets (56.8 vs. 54.9% of DM). Cows fed the CON diets ruminated longer during the day than cows fed the BM3 diets (524 vs. 496 min/d). Corn silage with greater NDF digestibility and lower uNDF240om enhanced DMI, milk yield, and TTD of DM and OM, and hydroxy trace minerals improved DMI and tended to improve TTD of aNDFom. The source of corn silage and trace minerals should be taken into consideration when formulating diets for high-producing dairy cows.
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Affiliation(s)
- M D Miller
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - J S Lanier
- Micronutrients USA LLC, Indianapolis, IN 46241
| | - S K Kvidera
- Micronutrients USA LLC, Indianapolis, IN 46241
| | - H M Dann
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - C S Ballard
- William H. Miner Agricultural Research Institute, Chazy, NY 12921
| | - R J Grant
- William H. Miner Agricultural Research Institute, Chazy, NY 12921.
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Miller MD. Isolation and Identification of Lysergic Acid Amide and Isolysergic Acid Amide as the Principal Ergoline Alkaloids in Argyreia nervosa, a Tropical Wood Rose. J AOAC Int 2020. [DOI: 10.1093/jaoac/53.1.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Lysergic acid amide and isolysergic acid amide have been extracted and isolated from the seed of Hawaiian baby wood rose. The ergoline alkaloids were identified by TLC, melting point determination, and UV and IR spectrophotometry.
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Affiliation(s)
- Michael D Miller
- Bureau of Narcotics and Dangerous Drugs, Department of Justice, Dallas Regional Laboratory, Dallas, Tex. 75202
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Lawitz E, Yang JC, Stamm LM, Taylor JG, Cheng G, Brainard DM, Miller MD, Mo H, Dvory-Sobol H. Characterization of HCV resistance from a 3-day monotherapy study of voxilaprevir, a novel pangenotypic NS3/4A protease inhibitor. Antivir Ther 2019; 23:325-334. [PMID: 29063860 DOI: 10.3851/imp3202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Voxilaprevir (VOX; GS-9857) is a pangenotypic HCV NS3/4A protease inhibitor (PI) with potent antiviral activity against HCV genotypes (GTs) 1-6 and improved coverage of GT1 NS3 resistance-associated substitutions (RAS) associated with other HCV PIs. In a 3-day Phase Ib monotherapy study in patients infected with HCV GT1a, 1b, 2, 3 and 4, VOX was well-tolerated and resulted in maximal mean viral load reduction >3 log10 IU/ml at the 100 mg dose across all genotypes evaluated. This report characterizes the HCV NS3 RAS in the study. METHODS The NS3 gene was amplified and successfully deep sequenced using MiSeq for 66 patients at baseline and 61 patients post-baseline using 15% and 1% assay cutoffs. RESULTS With a 15% assay cutoff, pretreatment HCV NS3 RAS were present in the HCV of 38% (9/24) of patients with GT1a and 5% (1/19) with GT3a; there were no pretreatment NS3 RAS present in patients with GT1b (n=6), GT2 (n=7) or GT4 (n=4). In patients with and without pretreatment NS3 RAS, ≥3.4 log10 mean maximal viral load reductions over 3 days of VOX administration were observed. The majority of patients did not have detectable treatment-emergent NS3 RAS and only 12% (7/53) and 26% (14/53) had emergent NS3 RAS using 15% and 1% cutoffs, respectively. No NS3 RAS were detected in patients with GT2 or GT4. A156T or A156V were the most prevalent emergent NS3 RAS in patients with GT1a or GT1b infection, but were not observed in patients with GT3 infection. CONCLUSIONS The lack of selection of NS3 RAS in the majority of patients demonstrates a high resistance barrier for VOX. ClinicalTrails.gov identifier NCT02185794.
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Affiliation(s)
- Eric Lawitz
- Texas Liver Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | | | | | | | | | | | | | - Hongmei Mo
- Gilead Sciences, Inc., Foster City, CA, USA
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Wyles D, Mangia A, Cheng W, Shafran S, Schwabe C, Ouyang W, Hedskog C, McNally J, Brainard DM, Doehle BP, Svarovskaia E, Miller MD, Mo H, Dvory-Sobol H. Long-term persistence of HCV NS5A resistance-associated substitutions after treatment with the HCV NS5A inhibitor, ledipasvir, without sofosbuvir. Antivir Ther 2019. [PMID: 28650844 DOI: 10.3851/imp3181] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Data on persistence of NS5A resistance-associated substitutions (RASs) may have implications for resistance testing approaches and selection of initial and retreatment strategies. METHODS Long-term persistence of NS5A RASs in HCV genotype (GT) 1 infected subjects (n=76) who did not achieve sustained virological response after receiving ledipasvir (LDV) without sofosbuvir (SOF) and were subsequently enrolled in an ongoing 3-year follow-up registry study was investigated by population or deep sequencing. RESULTS Of the 76 subjects enrolled, 67 and 9 subjects had GT1a and GT1b infection, respectively. At pretreatment, NS5A RASs were detected in 14% of subjects (11/76) by population sequencing, with three subjects having >1 RAS. All RASs that were detected at pretreatment persisted and were observed at the 96 week visit in the follow-up study (FU96). For the remaining subjects with no detectable RASs at pretreatment, RASs were detected in 98% (63/64) of subjects at virological failure in the parent study and persisted at detectable levels through FU96 in 86% of subjects by deep sequencing (1% cutoff). However, a decline in the quasispecies frequency of most RASs and the number of RASs per subject was observed over time. Phenotypic analysis demonstrated that the majority of NS5A RASs confer similar levels of resistance to LDV and daclatasvir. CONCLUSIONS The majority of NS5A RASs can persist at detectable levels for >96 weeks post-treatment in subjects who failed treatment with regimens containing an NS5A inhibitor without SOF, suggesting relatively high fitness of NS5A RASs even in the absence of drug pressure.
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Affiliation(s)
- David Wyles
- Division of Infectious Diseases, Denver Health and Hospital Authority, Denver, CO, USA
| | - Alessandra Mangia
- Liver Unit, Department of Medical Sciences IRCCS 'Casa Sollievo della Sofferenza', San Giovanni Rotondo, Italy
| | - Wendy Cheng
- Gastroenterology and Hepatology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Stephen Shafran
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | | - Wen Ouyang
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | | | | | | | | | | | - Hongmei Mo
- Gilead Sciences, Inc., Foster City, CA, USA
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Lim SY, Osuna CE, Hraber PT, Hesselgesser J, Gerold JM, Barnes TL, Sanisetty S, Seaman MS, Lewis MG, Geleziunas R, Miller MD, Cihlar T, Lee WA, Hill AL, Whitney JB. TLR7 agonists induce transient viremia and reduce the viral reservoir in SIV-infected rhesus macaques on antiretroviral therapy. Sci Transl Med 2019; 10:10/439/eaao4521. [PMID: 29720451 DOI: 10.1126/scitranslmed.aao4521] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/19/2017] [Indexed: 12/18/2022]
Abstract
Antiretroviral therapy (ART) can halt HIV-1 replication but fails to target the long-lived latent viral reservoir. Several pharmacological compounds have been evaluated for their ability to reverse HIV-1 latency, but none has demonstrably reduced the latent HIV-1 reservoir or affected viral rebound after the interruption of ART. We evaluated orally administered selective Toll-like receptor 7 (TLR7) agonists GS-986 and GS-9620 for their ability to induce transient viremia in rhesus macaques infected with simian immunodeficiency virus (SIV) and treated with suppressive ART. In an initial dose-escalation study, and a subsequent dose-optimization study, we found that TLR7 agonists activated multiple innate and adaptive immune cell populations in addition to inducing expression of SIV RNA. We also observed TLR7 agonist-induced reductions in SIV DNA and measured inducible virus from treated animals in ex vivo cell cultures. In a second study, after stopping ART, two of nine treated animals remained aviremic for more than 2 years, even after in vivo CD8+ T cell depletion. Moreover, adoptive transfer of cells from aviremic animals could not induce de novo infection in naïve recipient macaques. These findings suggest that TLR7 agonists may facilitate reduction of the viral reservoir in a subset of SIV-infected rhesus macaques.
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Affiliation(s)
- So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christa E Osuna
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Peter T Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | | | - Srisowmya Sanisetty
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | - Tomas Cihlar
- Gilead Sciences Inc., Foster City, CA 94404, USA
| | | | - Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
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Taljanovic MS, Gimber LH, Omar IM, Klauser AS, Miller MD, Wild JR, Chadaz TS. Imaging of Postoperative Infection at the Knee Joint. Semin Musculoskelet Radiol 2018; 22:464-480. [PMID: 30134470 DOI: 10.1055/s-0038-1667119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Postoperative infections of the knee are uncommon but may occur with joint arthroplasties, fracture fixation, or after arthroscopic procedures. The ultimate diagnosis is made by joint aspiration or tissue sampling. Joint aspiration and tissue sampling can be performed under imaging guidance or intraoperatively. Imaging is an important adjunct to clinical and laboratory findings and should start with radiographs. Cross-sectional imaging including magnetic resonance (MR) imaging, computed tomography (CT), nuclear studies, and ultrasound (US) are frequently used if the diagnosis is in doubt and to evaluate the extent of disease. We discuss the current algorithm in the diagnosis of various postoperative infections of the knee joint. The article addresses the utility of radiography, MR imaging, CT, US, and the most commonly used nuclear studies in the diagnosis of various postoperative knee infections and the imaging appearances of these infections on each of these diagnostic modalities.
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Affiliation(s)
- Mihra S Taljanovic
- Department of Medical Imaging, Banner University Medical Center, The University of Arizona, College of Medicine, Tucson, Arizona
| | - Lana H Gimber
- Department of Medical Imaging, Banner University Medical Center, The University of Arizona, College of Medicine, Tucson, Arizona
| | - Imran M Omar
- Department of Musculoskeletal Imaging, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrea S Klauser
- Section of Rheumatology and Sports Imaging, Department of Radiology, Medical University Innsbruck, Innsbruck, Austria
| | - Michael D Miller
- Department of Orthopedic Surgery, Banner University Medical Center, The University of Arizona, College of Medicine, Tucson, Arizona
| | - Jason R Wild
- Department of Orthopaedic Surgery, The University of Arizona, College of Medicine, Banner, University Medical Center Tucson, Tucson, Arizona
| | - Tyson S Chadaz
- Department of Medical Imaging, Banner University Medical Center, The University of Arizona, College of Medicine, Tucson, Arizona
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11
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Lai MT, Tawa P, Auger A, Wang D, Su HP, Yan Y, Hazuda DJ, Miller MD, Asante-Appiah E, Melnyk RA. Identification of novel bifunctional HIV-1 reverse transcriptase inhibitors. J Antimicrob Chemother 2018; 73:109-117. [PMID: 29029095 DOI: 10.1093/jac/dkx332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/12/2017] [Indexed: 02/01/2023] Open
Abstract
Objectives The increasing prevalence of mutations in HIV-1 reverse transcriptase (RT) that confer resistance to existing NRTIs and NNRTIs underscores the need to develop RT inhibitors with novel mode-of-inhibition and distinct resistance profiles. Methods Biochemical assays were employed to identify inhibitors of RT activity and characterize their mode of inhibition. The antiviral activity of the inhibitors was assessed by cell-based assays using laboratory HIV-1 isolates and MT4 cells. RT variants were purified via avidin affinity columns. Results Compound A displayed equal or greater potency against many common NNRTI-resistant RTs (K103N and Y181C RTs) relative to WT RT. Despite possessing certain NNRTI-like properties, such as being unable to inhibit an engineered variant of RT lacking an NNRTI-binding pocket, we found that compound A was dependent on Mg2+ for binding to RT. Optimization of compound A led to more potent analogues, which retained similar activities against WT and K103N mutant viruses with submicromolar potency in a cell-based assay. One of the analogues, compound G, was crystallized in complex with RT and the structure was determined at 2.6 Å resolution. The structure indicated that compound G simultaneously interacts with the active site (Asp186), the highly conserved primer grip region (Leu234 and Trp229) and the NNRTI-binding pocket (Tyr188). Conclusions These findings reveal a novel class of RT bifunctional inhibitors that are not sensitive to the most common RT mutations, which can be further developed to address the deficiency of current RT inhibitors.
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Affiliation(s)
- Ming-Tain Lai
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Paul Tawa
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Anick Auger
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Deping Wang
- Department of Modeling, MRL, West Point, PA 19486, USA
| | - Hua-Poo Su
- Department of Structure Determination, MRL, West Point, PA 19486, USA
| | - Youwei Yan
- Department of Structure Determination, MRL, West Point, PA 19486, USA
| | - Daria J Hazuda
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Michael D Miller
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Ernest Asante-Appiah
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Roman A Melnyk
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
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12
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Crossland WL, Tedeschi LO, Callaway TR, Miller MD, Smith WB, Cravey M. Effects of rotating antibiotic and ionophore feed additives on volatile fatty acid production, potential for methane production, and microbial populations of steers consuming a moderate-forage diet. J Anim Sci 2018; 95:4554-4567. [PMID: 29108045 DOI: 10.2527/jas2017.1665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Ionophores and antibiotics have been shown to decrease ruminal methanogenesis both in vitro and in vivo but have shown little evidence toward a sustainable means of mitigation. Feed additive rotation was proposed and investigated for methane, VFA, and microbial population response. In the present study, cannulated steers ( = 12) were fed a moderate-forage basal diet in a Calan gate facility for 13 wk. In addition to the basal diet, steers were randomly assigned to 1 of 6 treatments: 1) control, no additive; 2) bambermycin, 20 mg bambermycin/d; 3) monensin, 200 mg monensin/d; 4) the basal diet + weekly rotation of bambermycin and monensin treatments (B7M); 5) the basal diet + rotation of bambermycin and monensin treatments every 14 d (B14M); and 6) the basal diet + rotation of bambermycin and monensin treatments every 21 d (B21M). Steers were blocked by weight in a randomized complete block design where the week was the repeated measure. Rumen fluid was collected weekly for analysis ( = 13), and results were normalized according to individual OM intake (OMI; kg/d). Potential activity of methane production was not significantly different among treatments ( > 0.05). However, treatment tended to affect the CH-to-propionate ratio ( = 0.0565), which was highest in the control and lowest in the monensin, B21M, and B14M treatments (0.42 vs. 0.36, 0.36, and 0.33, respectively). The CH:propionate ratio was lowest in wk 2 and 3 ( < 0.05) but the ratio in wk 4 to 12 was not different from the ratio in wk 0. Week also affected total VFA, with total VFA peaking at wk 3 and plummeting at wk 4 (4.02 vs. 2.86 m/kg OMI; < 0.05). A significant treatment × week interaction was observed for the acetate-to-propionate (A:P) ratio, where bambermycin- and rotationally fed steers did not have a reduced A:P ratio compared with monensin-fed steers throughout the feeding period ( < 0.0001). Microbial analysis revealed significant shifts, but several predominant classes showed adaptation between 4 and 6 wk after additive initiation. There was no significant evidence to suggest that rotations of monensin and bambermycin provided additional benefits to steers consuming a moderate-forage diet at the microbial/animal and environmental level versus those continuously fed.
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13
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Moores CJ, Bell LK, Miller J, Damarell RA, Matwiejczyk L, Miller MD. A systematic review of community-based interventions for the treatment of adolescents with overweight and obesity. Obes Rev 2018; 19:698-715. [PMID: 29345042 DOI: 10.1111/obr.12660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/09/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022]
Abstract
Adolescent obesity is a risk factor for obesity and other chronic disease in adulthood. Evidence for the effectiveness of community-based obesity treatment programs for adolescents is required to inform policy and clinical decisions. This systematic review aims to evaluate recent effective and scalable community-based weight management programs for adolescents (13-17 years) who are overweight or obese. Eight databases (Medline, Embase, PsycINFO, CINAHL, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Informit, and Scopus) were searched for studies published between January 2011-2 March 2017 which are scalable in a community setting and reported primary outcome measures relating to weight. Following deduplication, 10,074 records were screened by title/abstract with 31 publications describing 21 programs included in this review. Programs were heterogeneous in nature (including length, number and frequency of sessions, parent-involvement and technology involvement). Reduction in adolescent BMIz ranged from 2 to 9% post-program and from 2 to 11% after varied lengths of follow-up. Study quality varied (n = 5 weak; n = 8 moderate; n = 8 high), and findings are limited by the risk of selection and retention bias in the included studies. Factors including the effectiveness and acceptability to the target population must be considered when selecting such community programs.
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Affiliation(s)
- C J Moores
- Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - L K Bell
- Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - J Miller
- Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - R A Damarell
- Gus Fraenkel Medical Library, Flinders University, Adelaide, South Australia, Australia
| | - L Matwiejczyk
- Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - M D Miller
- Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
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Miller MD, Sharma RA, Rivas J, Robbins R, Seixas A, Giardin J, de Leon MJ, Varga AW, Ayappa I, Rapoport D, Osorio RS, Godinho A. 0281 Decreased Objective Total Sleep Time in APOE Ɛ4 Positive Cognitively Normal Elderly. Sleep 2018. [DOI: 10.1093/sleep/zsy061.280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - J Rivas
- New York University, New York, NY
| | | | - A Seixas
- New York University, New York, NY
| | | | - M J de Leon
- Mount Sinai School of Medicine, New York, NY
| | - A W Varga
- Mount Sinai School of Medicine, New York, NY
| | - I Ayappa
- Mount Sinai School of Medicine, New York, NY
| | - D Rapoport
- Mount Sinai School of Medicine, New York, NY
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15
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Rivas J, Sharma R, Miller MD, Godinho A, Ayappa I, Jean-Louis G, Varga AW, Convit A, Osorio RS. 0143 Associations Between Slow Wave Sleep Duration, Insulin Resistance, and Respiratory Effort-Related Arousals in Young Adults. Sleep 2018. [DOI: 10.1093/sleep/zsy061.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- J Rivas
- NYU School of Medicine, New York, NY
| | - R Sharma
- NYU School of Medicine, New York, NY
| | | | - A Godinho
- NYU School of Medicine, New York, NY
| | - I Ayappa
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - A W Varga
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - A Convit
- NYU School of Medicine, New York, NY
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16
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Varga AW, Kam K, Parekh A, Sharma RA, Castillo B, Miller MD, Bagchi N, Rapoport DM, Ayappa I, Osorio RS. 0292 Sleep Spindle Characteristics and Their Association with Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease in Cognitively Normal Older Adults. Sleep 2018. [DOI: 10.1093/sleep/zsy061.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A W Varga
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - K Kam
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - A Parekh
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - R A Sharma
- NYU Center for Brain Health, New York, NY
| | - B Castillo
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - M D Miller
- NYU Center for Brain Health, New York, NY
| | - N Bagchi
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - D M Rapoport
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - I Ayappa
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - R S Osorio
- NYU Center for Brain Health, New York, NY
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17
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Sharma RA, Miller MD, Kam K, Parekh A, Rivas J, Bubu OM, Varga AW, Iosifescu DV, Osorio RS. 0970 Sleep Spindle Count In Subsyndromal Depressed vs Normal Elderly: A Protective Effect Of Sleep Spindles? Sleep 2018. [DOI: 10.1093/sleep/zsy061.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- R A Sharma
- New York University School of Medicine, New York, NY
| | | | - K Kam
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - A Parekh
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - J Rivas
- New York University, New York, NY
| | - O M Bubu
- University of South Florida, Tampa, FL
| | - A W Varga
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - D V Iosifescu
- New York University School of Medicine, New York, NY
| | - R S Osorio
- New York University School of Medicine, New York, NY
- New York University School of Medicine, New York, NY
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18
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Sharma RA, Miller MD, Kam K, Parekh A, Bubu OM, Rivas J, Ayappa I, Rapoport DM, Varga AW, Osorio RS. 0695 Objectively Measured Total Sleep Time as a Tool to Detect Longitudinal Changes In Alzheimer’s Disease Neuroimaging Biomarker (FDG PET). Sleep 2018. [DOI: 10.1093/sleep/zsy061.694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - K Kam
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - A Parekh
- Icah School of Medicine, Mount Sinai, New York, NY
| | - O M Bubu
- University of South Florida, Tampa, FL
| | - J Rivas
- New York University, New York, NY
| | - I Ayappa
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - D M Rapoport
- Icahn School of Medicine, Mount Sinai, New York, NY
| | - A W Varga
- Icahn School of Medicine, Mount Sinai, New York, NY
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19
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Margot N, Cox S, Das M, McCallister S, Miller MD, Callebaut C. Rare emergence of drug resistance in HIV-1 treatment-naïve patients receiving elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide for 144 weeks. J Clin Virol 2018; 103:37-42. [PMID: 29627709 DOI: 10.1016/j.jcv.2018.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/17/2018] [Accepted: 03/31/2018] [Indexed: 11/20/2022]
Abstract
BACKGROUND The single tablet regimen (STR) composed of elvitegravir (E), cobicistat (C), emtricitabine (F), and tenofovir alafenamide (TAF) (E/C/F/TAF) was compared to the STR composed of E, C, F, and tenofovir disoproxil fumarate (TDF) (E/C/F/TDF) in 2 phase 3 studies in 1733 HIV-1 infected treatment-naïve adults. Superior efficacy of E/C/F/TAF compared to E/C/F/TDF was demonstrated at Week 144 with 84% treatment success compared to 80%, respectively, along with significantly better outcomes of bone and renal safety. OBJECTIVES Analyze the emergence of HIV-1 resistance in treatment-naïve adults receiving E/C/F/TAF for 144 weeks. STUDY DESIGN We conducted an integrated resistance analysis of the 2 Phase 3 studies, comprising pretreatment HIV-1 sequencing for all participants (N = 1733) and post-baseline HIV-1 resistance analysis for participants with virologic failure (HIV-1 RNA ≥400 copies/mL). RESULTS Primary resistance-associated mutations (RAMs) were observed pre-treatment in 7.4% (NRTI-RAMs), 18.1% (NNRTI-RAMs), and 3.3% (PI-RAMs) of enrolled subjects. Baseline HIV-1 subtype or pre-existing RAMs did not affect E/C/F/TAF treatment response at week 144. Virologic failure resistance analyses were conducted for 28/866 (3.2%) and 30/867 (3.5%) patients in the E/C/F/TAF and E/C/F/TDF arms, respectively. Over the 3-year study, the rate of resistance emergence remained low at 1.4% in each group (12/866 in E/C/F/TAF; 12/867 in E/C/F/TDF). Resistant virus emerged in 24 patients who developed resistance to antiretrovirals in the regimens (E/C/F/TAF: M184V/I [1.3%], INSTI-RAMs [0.9%], K65R/N [0.2%]; E/C/F/TDF: M184V/I [1.0%], INSTI-RAMs [0.9%], K65R/N [0.5%]). CONCLUSIONS Resistance emergence was rare (1.4%) with similar patterns of emergent mutations in both groups. M184V/I was the most prevalent RAM (1.2% overall).
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Affiliation(s)
- Nicolas Margot
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.
| | - Stephanie Cox
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
| | - Moupali Das
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
| | - Scott McCallister
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
| | - Michael D Miller
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
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20
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Bhardwaj N, Ragonnet-Cronin M, Murrell B, Chodavarapu K, Martin R, Chang S, Miller MD, Feld JJ, Sulkowski M, Mangia A, Wertheim JO, Osinusi A, McNally J, Brainard D, Mo H, Svarovskaia ES. Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens. J Viral Hepat 2018; 25:344-353. [PMID: 29112331 DOI: 10.1111/jvh.12825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/02/2017] [Indexed: 12/27/2022]
Abstract
Treatment with the direct-acting antiviral agent (DAA) sofosbuvir (SOF), an NS5B inhibitor, and velpatasvir (VEL), an NS5A inhibitor, demonstrates viral cure rates of ≥95% in hepatitis C virus (HCV) genotypes (GT) 1-6. Here, we investigated intrapatient HCV diversity in NS5A and NS5B using Shannon entropy to examine the relationship between viral diversity and treatment outcome. At baseline, HCV diversity was lowest in patients infected with HCV GT3 as compared to the other GTs, and viral diversity was greater in NS5A than NS5B (P < .0001). Treatment outcome with SOF/VEL or the comparator regimen of SOF with ribavirin (RBV) was not correlated with baseline diversity. However, among persons treated with SOF/VEL, a decrease in diversity from baseline was observed at relapse in the majority virologic failures, consistent with a viral bottleneck event at relapse. In contrast, an increase in diversity was observed in 27% of SOF+RBV virologic failures. We investigated whether the increase in diversity was due to an increase in the transition rate, one mode of potential RBV-mediated mutagenesis; however, we found no evidence of this mechanism. Overall, we did not observe that viral diversity at baseline influenced treatment outcome, but the diversity changes observed at relapse can improve our understanding of RBV viral suppression in vivo.
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Affiliation(s)
- N Bhardwaj
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | | | - B Murrell
- University of California San Diego, San Diego, CA, USA
| | - K Chodavarapu
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - R Martin
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - S Chang
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - M D Miller
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - J J Feld
- Toronto Centre for Liver Disease, University of Toronto, Toronto, ON, Canada
| | - M Sulkowski
- Johns Hopkins University, Baltimore, MD, USA
| | - A Mangia
- Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - J O Wertheim
- University of California San Diego, San Diego, CA, USA
| | - A Osinusi
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - J McNally
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - D Brainard
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
| | - H Mo
- Clinical Virology, Gilead Sciences, Foster City, CA, USA
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21
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Parsons IL, Johnson JR, Kayser WC, Miller MD, Carstens GE. 25 Prediction of Residual Feed Intake in Feedlot Steers Based on Phenotypic Associations with Feeding Behavior and Carcass Ultrasound Traits. J Anim Sci 2018. [DOI: 10.1093/jas/sky027.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- I L Parsons
- Department of Animal Science, Texas A&M University, College Station, TX
| | | | - W C Kayser
- Department of Animal Science, Texas A&M University, College Station, TX
| | - M D Miller
- Texas A&M University, College Station, TX
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22
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Camus G, Han B, Asselah T, Hsieh D, Dvory-Sobol H, Lu J, Svarovskaia E, Martin R, Parhy B, Miller MD, Brainard DM, Kersey K, Abergel A, Mo H. Resistance characterization of ledipasvir and velpatasvir in hepatitis C virus genotype 4. J Viral Hepat 2018; 25:134-143. [PMID: 28984067 DOI: 10.1111/jvh.12795] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/01/2017] [Indexed: 01/22/2023]
Abstract
HCV genotype 4 (GT4) has often been overlooked in drug development, even though it infects ~20 million people worldwide. Ledipasvir/sofosbuvir and sofosbuvir/velpatasvir were highly efficacious in GT4 HCV-infected patients from GS-US-337-1119 and GS-US-342-1138. Here, we characterize the resistance profile of ledipasvir (LDV) and velpatasvir (VEL) in patients with GT4 HCV infection. NS5A deep-sequencing was performed for 454 patients infected with HCV GT4 at baseline, including 44 patients enrolled in GS-US-337-1119 and 116 patients enrolled in GS-US-342-1138, and at relapse for patients with virologic failure. LDV and VEL susceptibilities of 56 patient isolates were determined. In GS-US-337-1119, SVR12 rates were 100% for all subtypes except 4b and 4r. Phenotypic assessment of 56 HCV NS5A patient isolates from various GT4 subtypes indicated that LDV had high potency for the common subtypes 4a/d, and subtypes 4c/f/k/l/m/n/o/p/r/t despite the presence of resistance-associated substitutions (RASs). For the rare GT4b, LDV median EC50 was higher, but with a broad range of individual values. Importantly, all GT4b isolates tested had 2-4 NS5A RASs, some including Y93H. Similarly, the 2 GT4r infected patients who had virologic relapse had rare triple RASs. Reversion of these substitutions to the consensus residue significantly increased LDV susceptibility. In GS-US-342-1138, all patients achieved SVR12, regardless of their subtype or presence of RASs. In vitro data confirmed that VEL is potent against all GT4 isolates tested. LDV and VEL are potent antiviral drugs, estimated to be effective against >95% and >99%, respectively, of GT4 HCV isolates.
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Affiliation(s)
- G Camus
- Gilead Sciences, Inc., Foster City, CA, USA
| | - B Han
- Gilead Sciences, Inc., Foster City, CA, USA
| | - T Asselah
- Department of Hepatology, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Université Paris-Diderot and INSERM UMR1149, Clichy, France
| | - D Hsieh
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | - J Lu
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | - R Martin
- Gilead Sciences, Inc., Foster City, CA, USA
| | - B Parhy
- Gilead Sciences, Inc., Foster City, CA, USA
| | - M D Miller
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | - K Kersey
- Gilead Sciences, Inc., Foster City, CA, USA
| | - A Abergel
- UMR CNRS 6284, Department of Hepatology and Gastroenterology, Centre Hospitalier Universitaire Estaing, Université d'Auvergne, Clermont-Ferrand, France
| | - H Mo
- Gilead Sciences, Inc., Foster City, CA, USA
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Kitrinos KM, Corsa AC, Worth A, Hedskog C, Brainard DM, Miller MD, Mo H. Nonstructural protein 5A resistance profile in patients with chronic hepatitis C treated with ledipasvir-containing regimens without sofosbuvir. J Viral Hepat 2018; 25:126-133. [PMID: 28833932 DOI: 10.1111/jvh.12783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
Abstract
The study aimed to evaluate the effects of baseline hepatitis C virus (HCV) nonstructural protein 5A (NS5A) resistance-associated substitutions (RASs) on sustained virologic response to ledipasvir (LDV)-containing regimens in the absence of sofosbuvir (SOF) in patients with HCV genotype (GT) 1 infection across 6 phase 2 clinical studies. We analysed data from 1103 patients who received either LDV + vedroprevir (NS3 protease inhibitor) + tegobuvir (NS5B inhibitor) ± ribavirin or LDV + ribavirin + pegylated interferon. Population sequencing of HCV NS5A was performed at baseline and at virologic failure from patient plasma samples. Of 1045 patients with available baseline sequences, 747 (67.7%) had GT1a, and 298 (26.9%) had GT1b infection. The overall prevalence of NS5A RASs at baseline was 9.4%; 7.6% (57/747) and 13.8% (41/298) of patients with GT1a and GT1b infection, respectively. The majority of GT1a-infected patients with NS5A RASs at baseline had a single NS5A RAS (78.9%) at NS5A positions K24R, M28T, Q30H/L, L31M and Y93H/N/C/S. The spectrum of NS5A RASs detected in GT1b patients was much less diverse compared to GT1a patients, with all patients harbouring a single NS5A RAS either L31M or Y93H/C. For patients treated with LDV-containing regimens in the absence of SOF, the presence of baseline NS5A RASs was associated with low SVR rates. In patients with virologic failure, nearly all had either pre-existing and/or emergent NS5A RASs: 287/287 (100%) and 40/42 (95.2%) patients with GT1a and GT1b infection, respectively. Three novel NS5A substitutions were identified as emergent NS5A RASs: K26E and S38F in GT1a; and L31I in GT1b. In conclusion, the presence of NS5A RASs at baseline reduced the SVR rate in patients treated with LDV in combination vedroprevir + tegobuvir ± ribavirin or ribavirin + pegylated interferon. Virologic failure was associated with the detection of NS5A RASs in nearly all patients. These results suggest that the resistance barrier may differ depending on HCV drug combination and may be more important than that of the individual DAAs.
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Affiliation(s)
| | - A C Corsa
- Gilead Sciences, Inc., Foster City, CA, USA
| | - A Worth
- Gilead Sciences, Inc., Foster City, CA, USA
| | - C Hedskog
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | - M D Miller
- Gilead Sciences, Inc., Foster City, CA, USA
| | - H Mo
- Gilead Sciences, Inc., Foster City, CA, USA
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24
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Bungard CJ, Williams PD, Schulz J, Wiscount CM, Holloway MK, Loughran HM, Manikowski JJ, Su HP, Bennett DJ, Chang L, Chu XJ, Crespo A, Dwyer MP, Keertikar K, Morriello GJ, Stamford AW, Waddell ST, Zhong B, Hu B, Ji T, Diamond TL, Bahnck-Teets C, Carroll SS, Fay JF, Min X, Morris W, Ballard JE, Miller MD, McCauley JA. Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors. ACS Med Chem Lett 2017; 8:1292-1297. [PMID: 29259750 DOI: 10.1021/acsmedchemlett.7b00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/13/2017] [Indexed: 12/19/2022] Open
Abstract
Using the HIV-1 protease binding mode of MK-8718 and PL-100 as inspiration, a novel aspartate binding bicyclic piperazine sulfonamide core was designed and synthesized. The resulting HIV-1 protease inhibitor containing this core showed an 60-fold increase in enzyme binding affinity and a 10-fold increase in antiviral activity relative to MK-8718.
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Affiliation(s)
- Christopher J. Bungard
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Peter D. Williams
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Jurgen Schulz
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Catherine M. Wiscount
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - M. Katharine Holloway
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - H. Marie Loughran
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Jesse J. Manikowski
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Hua-Poo Su
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - David J. Bennett
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Lehua Chang
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xin-Jie Chu
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Alejandro Crespo
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Michael P. Dwyer
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Kartik Keertikar
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Gregori J. Morriello
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Andrew W. Stamford
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Sherman T. Waddell
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Bin Zhong
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Bin Hu
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Tao Ji
- WuXi AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Tracy L. Diamond
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Carolyn Bahnck-Teets
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Steven S. Carroll
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - John F. Fay
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Xu Min
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - William Morris
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jeanine E. Ballard
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Michael D. Miller
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - John A. McCauley
- Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
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25
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Camus G, Xu S, Han B, Lu J, Dvory-Sobol H, Yu M, Cheng G, Miller MD, Doehle BP, Mo H. Establishment of robust HCV genotype 4d, 5a, and 6a replicon systems. Virology 2017; 514:134-141. [PMID: 29175627 DOI: 10.1016/j.virol.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/25/2017] [Accepted: 11/02/2017] [Indexed: 12/29/2022]
Abstract
Hepatitis C Virus (HCV) is a diverse human pathogen which displays ~15% divergence at the subtype level. To facilitate development of antivirals with pan-genotype activity, we developed the first genotype 4d subgenomic replicon, as well as new replicons for genotypes 5a, and 6a. Adaptive mutations developed in these replicons differ greatly across genotypes. Their impacts on the replication capacity were tested using site-directed mutants. In the genotype 4d replicon, single mutations have moderate effect, but the double mutation NS4A-Q34R+NS5A-S232G increased the replication capacity by 161-fold. These new stable replicon cell lines were used to determine the antiviral activity of HCV inhibitors. The NS3 protease inhibitor voxilaprevir, NS5A second generation inhibitor velpatasvir, and NS5B nucleoside analog inhibitor sofosbuvir, had similar antiviral activities across the different genotypes/subtypes tested, while the NS5A first generation inhibitor, ledipasvir, had very good antiviral activity against GT1, 4, 5, and 6 in vitro.
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Affiliation(s)
| | - Simin Xu
- Gilead Sciences, Foster City, CA, USA
| | - Bin Han
- Gilead Sciences, Foster City, CA, USA
| | - Julia Lu
- Gilead Sciences, Foster City, CA, USA
| | | | - Mei Yu
- Gilead Sciences, Foster City, CA, USA
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26
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Welzel TM, Bhardwaj N, Hedskog C, Chodavarapu K, Camus G, McNally J, Brainard D, Miller MD, Mo H, Svarovskaia E, Jacobson I, Zeuzem S, Agarwal K. Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses. J Hepatol 2017; 67:224-236. [PMID: 28343981 DOI: 10.1016/j.jhep.2017.03.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/10/2017] [Accepted: 03/06/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND & AIMS HCV genotype, subtype, and presence of resistance-associated substitutions (RASs) are key determinants for the selection of direct-acting antiviral (DAA) treatment regimens. However, current HCV genotyping assays have limitations in differentiating between HCV subtypes, and RAS prevalence is largely undefined. The aim of this study was to investigate HCV epidemiology in 12,615 patient samples from 28 different countries across five geographic regions. METHODS We compared HCV genotype and subtypes using INNO-LiPA 2.0 vs. amplicon sequencing among 8,945 patients from phase II/III clinical trials of DAAs. Global HCV molecular epidemiology in 12,615 patients was investigated. Subtype RAS prevalence was determined by population or deep sequencing, and phylogenetic analyses investigating subtype diversity were performed. RESULTS Although there was high concordance between INNO-LiPA and sequencing for genotype determination, INNO-LiPA was insufficient for subtype determination for genotype 2, 3, 4, and 6. Sequencing provided subtype refinement for 42%, 10%, 81%, and 78% of genotype 2, 3, 4, and six patients, respectively. Genotype discordance (genotype 2-genotype 1) was observed in 28 of 950 (3%) genotype 2 patients, consistent with inter-genotype recombinants. Sequencing-based analyses demonstrated variations in regional subtype prevalence, notably within genotype 2, 4 and 6. RAS prevalence varied by subtype, with the clinically relevant NS3 RAS Q80K found in genotype 1a, 5a and 6a and the NS5A RAS Y93H in genotype 1b, 3a, 4b, 4r and 7. CONCLUSIONS Together, these analyses provide an understanding of subtyping accuracy and RAS distribution that are crucial for the implementation of global HCV treatment strategies. LAY SUMMARY Hepatitis C virus (HCV) is highly variable, with seven genotypes and 67 subtypes characterized to date. The aim of this study was to i) compare two different methods of discriminating between genotypes; ii) investigate the prevalence of HCV subtypes for each genotype around the world; iii) find the prevalence of resistance-associated substitutions (RASs) in different subtypes. We found that both methods showed high concordance in genotype discrimination, but specific subtypes were not always identified accurately. Sequencing-based analyses demonstrated variations in regional subtype prevalence for some genotypes, notably within GT2, 4 and 6. RAS prevalence also varied by subtype. These variations could determine how successful different drugs are for treating HCV.
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Affiliation(s)
- Tania M Welzel
- Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | | | | - Ira Jacobson
- Mount Sinai Beth Israel Medical Center, New York, USA
| | - Stefan Zeuzem
- Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
| | - Kosh Agarwal
- King's College Hospital Foundation Trust, London, UK
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27
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Kulkarni R, Hodder SL, Cao H, Chang S, Miller MD, White KL. Week 48 resistance analysis of Elvitegravir/Cobicistat/Emtricitabine/Tenofovir DF versus Atazanavir + Ritonavir + Emtricitabine/Tenofovir DF in HIV-1 infected women (WAVES study GS-US-236-0128). HIV Clin Trials 2017; 18:164-173. [PMID: 28891788 PMCID: PMC5942200 DOI: 10.1080/15284336.2017.1370059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Background Women and those with non-B subtype HIV-1 are typically underrepresented in clinical trials. WAVES (GS-US-236-0128) was a double-blind phase 3b study among treatment-naïve HIV-1-infected women that demonstrated that elvitegravir/cobicistat/emtricitabine/tenofovir DF (EVG/COBI/FTC/TDF; N = 289) was superior to atazanavir + ritonavir + FTC/TDF (ATV + RTV + FTC/TDF; N = 286) for HIV-1 RNA < 50 copies/mL by FDA snapshot analysis at week 48. Here, we describe resistance development through week 48 in women with virologic failure and determine the impact of pre-existing mutations and HIV-1 subtype on viral suppression. Methods Genotypic analyses (population and deep sequencing) and phenotypic analyses of HIV-1 protease, reverse transcriptase (RT), and integrase (IN) were performed. The resistance analysis population (participants with HIV-1 RNA ≥ 400 copies/mL at confirmed virologic failure, at discontinuation ≥ week 8, or at week 48) had genotypic and phenotypic analyses at failure and baseline. Results The proportion of women qualifying for resistance analyses was similar between treatment groups (6.2% EVG/COBI/FTC/TDF; 7.3% ATV + RTV + FTC/TDF). Emergent resistance was rare (0% EVG/COBI/FTC/TDF; 1% ATV + RTV + FTC/TDF - 3 with M184V/I in RT). Deep sequencing of HIV-1 did not detect additional resistance development. Pre-existing mutations did not lead to virologic failure; most with the polymorphic primary IN substitution T97A (92%), or with substitutions in RT (i.e. A62V, V90I, K103N, or E138A/G/K/Q; 68-82%) demonstrated virologic suppression at week 48, with no resistance development except for one patient with M184V and pre-existing K103N in the ATV + RTV + FTC/TDF group. Most participants (74%) had non-B HIV-1, and subtype did not affect outcome. Conclusions Emergent resistance to study drugs was rare in this study of women, with no resistance observed among EVG/COBI/FTC/TDF-treated participants, despite a high proportion of participants with natural or transmitted viral mutations and non-B HIV-1 subtypes.
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Affiliation(s)
- Rima Kulkarni
- Clinical Virology, Gilead Sciences, Inc., Foster City, CA, USA
| | - Sally L. Hodder
- Health Sciences Center, West Virginia Clinical and Translational Science Institute, Morgantown, WV, USA
| | - Huyen Cao
- Clinical Research, Gilead Sciences, Inc., Foster City, CA, USA
| | - Silvia Chang
- Clinical Virology, Gilead Sciences, Inc., Foster City, CA, USA
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28
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Margot NA, Wong P, Kulkarni R, White K, Porter D, Abram ME, Callebaut C, Miller MD. Commonly Transmitted HIV-1 Drug Resistance Mutations in Reverse-Transcriptase and Protease in Antiretroviral Treatment-Naive Patients and Response to Regimens Containing Tenofovir Disoproxil Fumarate or Tenofovir Alafenamide. J Infect Dis 2017; 215:920-927. [PMID: 28453836 DOI: 10.1093/infdis/jix015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/05/2017] [Indexed: 11/12/2022] Open
Abstract
Background The presence of transmitted drug resistance mutations (TDRMs) in antiretroviral treatment (ART)-naive patients can adversely affect the outcome of ART. Methods Resistance testing was conducted in 6704 ART-naive subjects predominantly from the United States and Europe in 9 clinical studies conducted by Gilead Sciences from 2000 to 2013. Results The presence of TDRMs increased during this period (from 5.2% to 11.4%), primarily driven by an increase in nonnucleoside reverse-transcriptase (RT) inhibitor (NNRTI) resistance mutations (from 0.3% to 7.1%), particularly K103N/S (increase from 0.3% to 5.3%). Nucleoside/nucleotide RT inhibitor mutations were found in 3.1% of patients. Only 1 patient had K65R (0.01%) and 7 had M184V/I (0.1%), despite high use of tenofovir disoproxil fumarate (TDF), emtricitabine, and lamivudine and potential transmission of resistance to these drugs. At least 1 thymidine-analogue mutations was present in 2.7% of patients with 0.07% harboring T215Y/F and 2.7% harboring T215 revertant mutations (T215rev). Patients with the combination of M41L + L210W + T215rev showed full human immunodeficiency virus RNA suppression while receiving a TDF- or tenofovir alafenamide-containing regimen. Conclusions There was an overall increase of TDRMs among patients enrolling in clinical trials from 2000 through 2013, driven primarily by an increase in NNRTI resistance. However, the presence of common TDRMs, including thymidine-analogue mutations/T215rev, showed no impact on response to TDF- or tenofovir alafenamide-containing regimens.
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Affiliation(s)
| | - Pamela Wong
- Gilead Sciences, Foster City, California, USA
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29
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Zeuzem S, Mizokami M, Pianko S, Mangia A, Han KH, Martin R, Svarovskaia E, Dvory-Sobol H, Doehle B, Hedskog C, Yun C, Brainard DM, Knox S, McHutchison JG, Miller MD, Mo H, Chuang WL, Jacobson I, Dore GJ, Sulkowski M. NS5A resistance-associated substitutions in patients with genotype 1 hepatitis C virus: Prevalence and effect on treatment outcome. J Hepatol 2017; 66:910-918. [PMID: 28108232 DOI: 10.1016/j.jhep.2017.01.007] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 12/22/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS The efficacy of NS5A inhibitors for the treatment of patients chronically infected with hepatitis C virus (HCV) can be affected by the presence of NS5A resistance-associated substitutions (RASs). We analyzed data from 35 phase I, II, and III studies in 22 countries to determine the pretreatment prevalence of various NS5A RASs, and their effect on outcomes of treatment with ledipasvir-sofosbuvir in patients with genotype 1 HCV. METHODS NS5A gene deep sequencing analysis was performed on samples from 5397 patients in Gilead clinical trials. The effect of baseline RASs on sustained virologic response (SVR) rates was assessed in the 1765 patients treated with regimens containing ledipasvir-sofosbuvir. RESULTS Using a 15% cut-off, pretreatment NS5A and ledipasvir-specific RASs were detected in 13% and 8% of genotype 1a patients, respectively, and in 18% and 16% of patients with genotype 1b. Among genotype 1a treatment-naïve patients, SVR rates were 91% (42/46) vs. 99% (539/546) for those with and without ledipasvir-specific RASs, respectively. Among treatment-experienced genotype 1a patients, SVR rates were 76% (22/29) vs. 97% (409/420) for those with and without ledipasvir-specific RASs, respectively. Among treatment-naïve genotype 1b patients, SVR rates were 99% for both those with and without ledipasvir-specific RASs (71/72 vs. 331/334), and among treatment-experienced genotype 1b patients, SVR rates were 89% (41/46) vs. 98% (267/272) for those with and without ledipasvir-specific RASs, respectively. CONCLUSIONS Pretreatment ledipasvir-specific RASs that were present in 8-16% of patients have an impact on treatment outcome in some patient groups, particularly treatment-experienced patients with genotype 1a HCV. LAY SUMMARY The efficacy of treatments using NS5A inhibitors for patients with chronic hepatitis C virus (HCV) infection can be affected by the presence of NS5A resistance-associated substitutions (RASs). We reviewed results from 35 clinical trials where patients with genotype 1 HCV infection received treatments that included ledipasvir-sofosbuvir to determine how prevalent NS5A RASs are in patients at baseline, and found that ledipasvir-specific RASs were present in 8-16% of patients prior to treatment and had a negative impact on treatment outcome in subset of patient groups, particularly treatment-experienced patients with genotype 1a HCV.
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Affiliation(s)
| | | | - Stephen Pianko
- Monash Health and Monash University, Melbourne, Australia
| | - Alessandra Mangia
- IRCCS Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo, Italy
| | - Kwang-Hyub Han
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ross Martin
- Gilead Sciences, Inc., Foster City, CA, United States
| | | | | | - Brian Doehle
- Gilead Sciences, Inc., Foster City, CA, United States
| | | | - Chohee Yun
- Gilead Sciences, Inc., Foster City, CA, United States
| | | | - Steven Knox
- Gilead Sciences, Inc., Foster City, CA, United States
| | | | | | - Hongmei Mo
- Gilead Sciences, Inc., Foster City, CA, United States
| | - Wan-Long Chuang
- Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ira Jacobson
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gregory J Dore
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mark Sulkowski
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
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30
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Xu S, Doehle B, Rajyaguru S, Han B, Barauskas O, Feng J, Perry J, Dvory-Sobol H, Svarovskaia ES, Miller MD, Mo H. In vitro selection of resistance to sofosbuvir in HCV replicons of genotype-1 to -6. Antivir Ther 2017; 22:587-597. [PMID: 28248189 DOI: 10.3851/imp3149] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Sofosbuvir is a nucleoside analogue inhibitor of the HCV NS5B polymerase approved for treatment of HCV-infected patients in combination with ribavirin or with other antivirals. It has activity against all genotypes of HCV. Resistance to sofosbuvir in genotype-1 and -2 HCV is conferred by the S282T substitution in NS5B. METHODS To begin to define the correlates of resistance to sofosbuvir in other genotypes, we performed selection experiments in cell culture using cell lines containing subgenomic replicons derived from genotypes-1b, -2a, -3a and -4a, or chimeric replicons in a genotype-1b background but encoding genotype-2b, -5a and -6a NS5B polymerase. RESULTS In every case, S282T was selected following passage in the presence of increasing concentrations of sofosbuvir for 10 to 15 weeks. When introduced as a site-directed mutant, S282T conferred reductions in sofosbuvir susceptibility of between 2.4 and 19.4-fold. Other substitutions observed during the selections had relatively less impact on susceptibility, such as N237S in genotype-6a (2.5-fold). Replication capacity was affected by the introduction of S282T in all genotypes to variable extents (3.2% to 22% of wild type). CONCLUSIONS These results confirm that S282T is the primary sofosbuvir resistance-associated substitution and that replication capacity is reduced when it is present in all genotypes of HCV.
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Affiliation(s)
- Simin Xu
- Gilead Sciences, Foster City, CA, USA
| | | | | | - Bin Han
- Gilead Sciences, Foster City, CA, USA
| | | | - Joy Feng
- Gilead Sciences, Foster City, CA, USA
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31
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Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ, Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N, Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J, Steele TG, Wai J, Walji A, Xu M, Coleman PJ. Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV. Bioorg Med Chem Lett 2017; 27:2038-2046. [PMID: 28285916 DOI: 10.1016/j.bmcl.2017.02.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naïve patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles. Herein, we detail medicinal chemistry efforts on a novel class of 2-pyridinone aminal InSTIs, inpsired by MK-0536, which led to the discovery of important lead molecules for our program. Systematic optimization carried out at the amide and aminal positions on the periphery of the core provided the necessary balance of antiviral activity and physiochemical properties. These efforts led to a novel aminal lead compound with the desired virological profile and preclinical pharmacokinetic profile to support a once-daily human dose prediction.
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Affiliation(s)
- John D Schreier
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States.
| | - Mark W Embrey
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Izzat T Raheem
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Guillaume Barbe
- Merck Frost Centre for Therapeutic Research, Kirkland, QC, Canada
| | - Louis-Charles Campeau
- Discovery Process Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - David Dubost
- Discovery Pharmaceutical Sciences, Merck Research Laboratories, West Point, PA 19486, United States
| | - Jamie McCabe Dunn
- Discovery Process Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Jay Grobler
- Infectious Disease Biology, Merck Research Laboratories, West Point, PA 19486, United States
| | - Timothy J Hartingh
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Daria J Hazuda
- Infectious Disease Biology, Merck Research Laboratories, West Point, PA 19486, United States
| | - Daniel Klein
- Global Structural Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Michael D Miller
- Infectious Disease Biology, Merck Research Laboratories, West Point, PA 19486, United States
| | - Keith P Moore
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Natalie Nguyen
- Merck Frost Centre for Therapeutic Research, Kirkland, QC, Canada
| | - Natasa Pajkovic
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, West Point, PA 19486, United States
| | - David A Powell
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States; Merck Frost Centre for Therapeutic Research, Kirkland, QC, Canada
| | - Vanessa Rada
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - John M Sanders
- Global Structural Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - John Sisko
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Thomas G Steele
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - John Wai
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Abbas Walji
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
| | - Min Xu
- In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, United States
| | - Paul J Coleman
- Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States
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Mo H, Hedskog C, Lawitz E, Brainard DM, Yang J, Delaney W, Worth A, Miller MD. Antiviral response and resistance analysis of treatment-naïve HCV infected patients receiving multiple doses of the NS3 protease inhibitor GS-9256. Antiviral Res 2017; 140:151-157. [PMID: 28132867 DOI: 10.1016/j.antiviral.2017.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/23/2017] [Indexed: 01/14/2023]
Abstract
The NS3 protease inhibitor (PI) GS-9256 has demonstrated antiviral activity in a monotherapy study and in combination with other DAAs for treatment of chronic hepatitis C virus (HCV) infection. The resistance profile of GS-9256 was investigated in a phase 1 monotherapy study of patients with HCV genotype (GT) 1 infection. No PI resistance associated substitutions (RASs) at positions 36, 155, 156, 168 and 170 were observed at baseline by population sequencing (15% cutoff) in the 54 patients enrolled in the study, however the PI RAS Q80K were detected in 41% of patients at baseline. In patients who received 75 mg of the investigational protease inhibitor (PI) GS-9256 BID, 300 mg of GS-9256 QD and 200 mg of GS-9256 BID for three days, NS3 RASs (A156V, R155K, D168G/E/N/V) were observed in 9/21, 3/7 and 8/8 post-treatment, respectively. Q80K was not selected in any patients post-treatment. The mean maximal viral load response was -3.0 ± 0.42 log10 IU/mL HCV RNA in the 200 mg BID cohort. In more than 50% of the patients with RASs detected at Day 4, mutations were no longer detectable by population sequencing at Day 14. One patient had the R155K mutation persist to Week 24. Phenotypic analyses showed that substitutions at R155, A156 and D168 significantly reduced susceptibility to GS-9256. In conclusion, NS3 PI RASs were rapidly selected in the majority of patients receiving GS-9256 as monotherapy, despite undetectable levels at baseline. The R155, A156 and D168 substitutions identified in patients confer reduced susceptibility to GS-9256 and other PIs in vitro.
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Affiliation(s)
- Hongmei Mo
- Gilead Sciences Inc, Foster City, CA, USA.
| | | | - Eric Lawitz
- Texas Liver Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | | | - Jenny Yang
- Gilead Sciences Inc, Foster City, CA, USA
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Porter DP, Kulkarni R, Garner W, Miller MD, White KL. Viral blips were infrequent in treatment-naive adults treated with rilpivirine/emtricitabine/tenofovir DF or efavirenz/emtricitabine/tenofovir DF through 96 weeks. Antivir Ther 2017; 22:495-502. [PMID: 28091393 DOI: 10.3851/imp3128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The clinical impact of transient episodes of HIV viraemia (viral blips) on virological failure and resistance development is not fully understood. Here we investigated the blip frequency and virological outcomes of HIV-1-infected subjects experiencing viral blips among treatment-naive subjects initiating therapy on rilpivirine (RPV)/emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF) or efavirenz (EFV)/FTC/TDF through 96 weeks of treatment. METHODS Subjects treated with at least one dose of study drug and with at least one post-baseline HIV-1 RNA value were included in this analysis. All on-drug HIV-1 RNA data points and FDA snapshot outcome data through week 96 were utilized. A viral blip was defined as after achieving confirmed suppression (two consecutive HIV-1 RNA values <50 copies/ml), any HIV-1 RNA value ≥50 copies/ml preceded and followed by HIV-1 RNA <50 copies/ml. RESULTS Of the 717 subjects with confirmed suppression, 67 (9.3%) experienced ≥1 blip through week 96 with similar blip frequencies occurring in both treatment arms (10.7% RPV/FTC/TDF versus 8.0% EFV/FTC/TDF; P=0.25). A significantly higher proportion of subjects with baseline HIV-1 RNA >100,000 copies/ml experienced blips compared to subjects with baseline HIV-1 RNA ≤100,000 copies/ml and this was observed in both arms. Of 72 total blip events, 61 (85%) were low-level (50-199 copies/ml). Overall, among subjects with blips, 79% were virological successes at week 96, similar to those subjects without blips (83%; P=0.50). More subjects with blips ≥200 copies/ml experienced virological failure compared to subjects with blips <200 copies/ml (36.4% versus 7.1%; P=0.02). CONCLUSIONS Viral blips were infrequent and similar among subjects treated with RPV/FTC/TDF or EFV/FTC/TDF. Most blips were low-level and most subjects with blips remained virologically suppressed through week 96 without experiencing virological failure.
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Margot N, Cox S, Das M, McCallister S, Miller MD, Callebaut C. Infrequent development of drug resistance in HIV-1-infected treatment-naive subjects after 96 weeks of treatment with elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide or elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate. Antivir Ther 2017; 22:443-446. [PMID: 28076335 DOI: 10.3851/imp3125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tenofovir alafenamide (TAF) is a novel prodrug of the nucleotide reverse transcriptase inhibitor tenofovir (TFV) that loads lymphocytes with TFV-diphosphate more efficiently than tenofovir disoproxil fumarate (TDF). The single-tablet regimen (STR) comprising elvitegravir, cobicistat, emtricitabine and TAF (E/C/F/TAF) has demonstrated non-inferiority to the STR of E/C/F/TDF in clinical studies, with high proportions of subjects achieving HIV-1 RNA <50 copies/ml at week 48 that were maintained through week 96. A resistance analysis of the combined Phase III clinical studies through 96 weeks is described here. METHODS Genotypic and phenotypic susceptibility to antiretrovirals (ARVs) was evaluated for subjects with HIV-1 RNA ≥400 copies/ml at time of virological failure (VF) or early discontinuation. RESULTS Through week 96, VF resistance analyses were conducted for 24 subjects in each arm (2.8%, 24/866 and 2.8%, 24/867; for E/C/F/TAF and E/C/F/TDF arms, respectively). Primary resistance development to ARVs of the regimen occurred in 10 of 24 subjects in the E/C/F/TAF arm, and 8 of 24 subjects in the E/C/F/TDF arm (E/C/F/TAF: M184V/I, n=9; integrase strand-transfer inhibitor resistance-associated mutations [INSTI-RAMs], n=8; K65R/N, n=2; E/C/F/TDF: M184V/I, n=6; INSTI-RAMs, n=5; K65R/N, n=3). The emergent resistance mutations were similar between the treatment arms. CONCLUSIONS E/C/F/TAF achieved a high level of virological suppression in HIV-1 treatment-naive subjects through 96 weeks of treatment, with infrequent resistance development and comparable genotypic changes across both the E/C/F/TAF and E/C/F/TDF treatment groups.
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Liu Y, Corsa AC, Buti M, Cathcart AL, Flaherty JF, Miller MD, Kitrinos KM, Marcellin P, Gane EJ. No detectable resistance to tenofovir disoproxil fumarate in HBeAg+ and HBeAg- patients with chronic hepatitis B after 8 years of treatment. J Viral Hepat 2017; 24:68-74. [PMID: 27658343 DOI: 10.1111/jvh.12613] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/10/2016] [Indexed: 12/12/2022]
Abstract
A major hurdle in the long-term treatment of chronic hepatitis B (CHB) patients is to maintain viral suppression in the absence of drug resistance. To date, no evidence of resistance to tenofovir disoproxil fumarate (TDF) has been observed. A cumulative evaluation of CHB patients who qualified for resistance surveillance over 8 years of TDF treatment was conducted. Patients in studies GS-US-174-0102 (HBeAg-) and GS-US-174-0103 (HBeAg+) were randomized 2:1 to receive TDF or adefovir dipivoxil (ADV) for 48 weeks followed by open-label TDF through year 8. Population sequencing of HBV pol/RT was attempted for all TDF-treated patients at baseline and, annually if viremic, at discontinuation, or with addition of emtricitabine. Overall, 88/641 (13.7%) patients qualified for sequence analysis at one or more time points. The percentage of patients qualifying for sequence analysis declined over time, from 9 to 11% in years 1-2 to <4% over years 3-8. Forty-one episodes of virologic breakthrough (VB) occurred throughout the study, with most (n=29, 70%) associated with nonadherence to study medication. Fifty-nine per cent of VB patients with an opportunity to resuppress HBV achieved HBV DNA resuppression. A minority of patients who qualified for sequencing had polymorphic (41/165, 24.8%) or conserved (17/165, 10.3%) site changes in pol/RT, with six patients developing lamivudine and/or ADV resistance-associated mutations. No accumulation of conserved site changes was detected. The long-term treatment of CHB with TDF monotherapy maintains effective suppression of HBV DNA through 8 years, with no evidence of TDF resistance or accumulation of conserved site changes.
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Affiliation(s)
- Y Liu
- Gilead Sciences, Inc, Foster City, CA, USA
| | - A C Corsa
- Gilead Sciences, Inc, Foster City, CA, USA
| | - M Buti
- Hospital General Universitari Vall d'Hebron, Barcelona, Spain
| | | | | | - M D Miller
- Gilead Sciences, Inc, Foster City, CA, USA
| | | | - P Marcellin
- Hôpital Beaujon, University Paris-Diderot, Clichy, France
| | - E J Gane
- Auckland City Hospital, Auckland, New Zealand
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Liu Y, Miller MD, Kitrinos KM. Tenofovir alafenamide demonstrates broad cross-genotype activity against wild-type HBV clinical isolates and maintains susceptibility to drug-resistant HBV isolates in vitro. Antiviral Res 2016; 139:25-31. [PMID: 28017761 DOI: 10.1016/j.antiviral.2016.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/19/2022]
Abstract
Tenofovir alafenamide (TAF) is a novel prodrug of tenofovir (TFV). This study evaluated the antiviral activity of TAF against wild-type genotype A-H HBV clinical isolates as well as adefovir-resistant, lamivudine-resistant, and entecavir-resistant HBV isolates. Full length HBV genomes or the polymerase/reverse transcriptase (pol/RT) region from treatment-naïve patients infected with HBV genotypes A-H were amplified and cloned into an expression vector under the control of a CMV promoter. In addition, 11 drug resistant HBV constructs were created by site-directed mutagenesis of a full length genotype D construct. Activity of TAF was measured by transfection of each construct into HepG2 cells and assessment of HBV DNA levels following treatment across a range of TAF concentrations. TAF activity in vitro was similar against wild-type genotype A-H HBV clinical isolates. All lamivudine- and entecavir-resistant isolates and 4/5 adefovir-resistant isolates were found to be sensitive to inhibition by TAF in vitro as compared to the wild-type isolate. The adefovir-resistant isolate rtA181V + rtN236T exhibited low-level reduced susceptibility to TAF. TAF is similarly active in vitro against wild-type genotype A-H HBV clinical isolates. The TAF sensitivity results for all drug-resistant isolates are consistent with what has been observed with the parent drug TFV. The in vitro cell-based HBV phenotyping assay results support the use of TAF in treatment of HBV infected subjects with diverse HBV genotypes, in both treatment-naive and treatment-experienced HBV infected patients.
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Affiliation(s)
- Yang Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.
| | - Michael D Miller
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
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Sarrazin C, Isakov V, Svarovskaia ES, Hedskog C, Martin R, Chodavarapu K, Brainard DM, Miller MD, Mo H, Molina JM, Sulkowski MS. Late Relapse Versus Hepatitis C Virus Reinfection in Patients With Sustained Virologic Response After Sofosbuvir-Based Therapies. Clin Infect Dis 2016; 64:44-52. [PMID: 27737953 DOI: 10.1093/cid/ciw676] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The development of direct-acting antivirals in recent years has dramatically enhanced rates of viral eradication to >90% in patients with chronic hepatitis C virus (HCV) infection. To determine true treatment efficacy and define the most appropriate retreatment, it is important to distinguish virologic relapse from reinfection when patients in whom HCV is eradicated during treatment become infected with a new HCV strain after treatment. METHODS We investigated the prevalence of late recurrent viremia (patients with sustained virologic response 12 weeks after the end of treatment but detectable HCV RNA at follow-up week 24) and used refined phylogenetic analysis of multiple HCV genes to distinguish virologic relapse from reinfection. RESULTS Across 11 phase 3 clinical trials of ledipasvir-sofosbuvir (SOF) and SOF, only 12 of 3004 patients had detectable HCV RNA following sustained virologic response 12 weeks after the end of treatment. Of these 12 patients with late recurrent viremia, 11 had the same HCV genotype/subtype at baseline and at recurrence. Phylogenetic analysis demonstrated that 58% (7 of 12) of these patients were successfully treated with the SOF-based regimen, with HCV eradication achieved, but became reinfected with a different HCV strain after treatment. The remaining 5 patients with late recurrent viremia had virologic relapse in which the HCV present at baseline persisted in the liver or another compartment and reemerged in the blood 24 weeks after treatment. CONCLUSIONS The incidence of late recurrent viremia was low. Distinguishing reinfection from virologic relapse has implications for determining true treatment efficiency and selecting optimal retreatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hongmei Mo
- Gilead Sciences, Foster City, California
| | | | - Mark S Sulkowski
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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Mizokami M, Dvory-Sobol H, Izumi N, Nishiguchi S, Doehle B, Svarovskaia ES, De-Oertel S, Knox S, Brainard DM, Miller MD, Mo H, Sakamoto N, Takehara T, Omata M. Resistance Analyses of Japanese Hepatitis C-Infected Patients Receiving Sofosbuvir or Ledipasvir/Sofosbuvir Containing Regimens in Phase 3 Studies. J Viral Hepat 2016; 23:780-8. [PMID: 27196675 DOI: 10.1111/jvh.12549] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/21/2016] [Indexed: 12/11/2022]
Abstract
High rates of sustained virologic response (SVR) has been achieved in Japanese patients with chronic hepatitis C virus (HCV) genotype (GT)1 and GT2 infection treated with ledipasvir/sofosbuvir (LDV/SOF) ±ribavirin (RBV) and SOF+RBV, respectively. We evaluated the effect of baseline HCV NS5A and NS5B resistance-associated variants (RAVs) on treatment outcome and characterized variants at virologic failure. Baseline deep sequencing for NS5A and NS5B genes was performed for all GT1 patients. Deep sequencing of NS5A (GT1 only) and NS5B (GT1 and GT2) was performed for patients who failed treatment or discontinued early with detectable HCV RNA (i.e., >25 IU/mL). In patients with HCV GT1 infection, 22.3% (GT1a: 2/11; GT1b: 74/330) had ≥1 baseline NS5A RAV. The most frequent NS5A RAVs in GT1b were Y93H (17.9%, 59/330) and L31M (2.4%, 8/330). Despite the presence of NS5A RAVs at baseline, 100% and 97% of patients achieved SVR12, compared with 100% and 99% for those with no NS5A RAVs with LDV/SOF and LDV/SOF+RBV, respectively. All patients with NS5B RAVs at baseline achieved SVR12. Of the 153 patients with GT2 infection (GT2a 60.1%, GT2b 39.9%), 3.3% (5/153) experienced viral relapse. No S282T or other NS5B RAVs were detected at baseline or relapse; no change in susceptibility to SOF or RBV was observed at relapse. In conclusion, LDV/SOF and SOF+RBV demonstrate a high barrier to resistance in Japanese patients with HCV GT1 and GT2 infection. The presence of baseline NS5A RAVs did not impact treatment outcome in GT1 Japanese patients treated with LDV/SOF for 12 weeks.
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Affiliation(s)
- M Mizokami
- The Research Center for Hepatitis & Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | | | - N Izumi
- Musashino Red Cross Hospital, Tokyo, Japan
| | | | - B Doehle
- Gilead Sciences Inc., Foster City, CA, USA
| | | | | | - S Knox
- Gilead Sciences Inc., Foster City, CA, USA
| | | | - M D Miller
- Gilead Sciences Inc., Foster City, CA, USA
| | - H Mo
- Gilead Sciences Inc., Foster City, CA, USA
| | | | | | - M Omata
- Yamanashi Prefectural Hospital Organization, Yamanashi, Japan
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Sarrazin C, Dvory-Sobol H, Svarovskaia ES, Doehle BP, Pang PS, Chuang SM, Ma J, Ding X, Afdhal NH, Kowdley KV, Gane EJ, Lawitz E, Brainard DM, McHutchison JG, Miller MD, Mo H. Prevalence of Resistance-Associated Substitutions in HCV NS5A, NS5B, or NS3 and Outcomes of Treatment With Ledipasvir and Sofosbuvir. Gastroenterology 2016; 151:501-512.e1. [PMID: 27296509 DOI: 10.1053/j.gastro.2016.06.002] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS We evaluated the effects of baseline hepatitis C virus (HCV) NS5A, NS5B, and NS3 resistance-associated substitutions (RASs) on response to the combination of ledipasvir and sofosbuvir, with or without ribavirin, in patients with HCV genotype 1 infection. METHODS We analyzed data from 2144 participants in phase 2 and 3 studies of patients with HCV genotype 1a or b infection who received the combination of ledipasvir (90 mg) and sofosbuvir (400 mg) (ledipasvir/sofosbuvir) once daily, with or without ribavirin twice daily. Population and/or deep sequence analyses of the HCV NS3, NS5A, and NS5B genes were performed on blood samples collected at baseline. RESULTS Overall, 16.0% of patients had detectable baseline RASs in NS5A. Among patients with HCV genotype 1b infection, there was no significant effect of baseline RASs in NS5A on sustained viral response 12 weeks after the end of treatment (SVR12) with ledipasvir/sofosbuvir and only a small effect in patients with HCV genotype 1a infection. RASs in NS5A that increased the half-maximal effective concentration to ledipasvir by more than 100-fold reduced the rate of SVR12 in treatment-naive patients given ledipasvir/sofosbuvir for 8 weeks (P = .011), but not for 12 weeks. These same baseline NS5A RASs reduced the percentage of treatment-experienced patients who achieved an SVR12 to 12 weeks (but not 24 weeks) ledipasvir/sofosbuvir (P < .001). These RASs had a small effect in patients given ledipasvir/sofosbuvir in combination with ribavirin for 12 weeks. Overall, 2.5% of patients had baseline NS5B nucleotide inhibitor RASs (L159F, N142T, S282G, or L320S) and all achieved an SVR12. Of patients previously treated with protease inhibitors, 53.7% had RASs in NS3 and 96.5% achieved an SVR12. CONCLUSIONS Baseline RASs in NS5A have minimal effects on patient responses to ledipasvir/sofosbuvir therapy. When these RASs do have effects, they could be largely overcome by extending treatment duration or through treatment intensification.
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Affiliation(s)
| | | | | | | | | | | | - Julie Ma
- Gilead Sciences, Inc, Foster City, California
| | - Xiao Ding
- Gilead Sciences, Inc, Foster City, California
| | - Nezam H Afdhal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Edward J Gane
- New Zealand Liver Transplant Unit, Auckland City Hospital, Auckland, New Zealand
| | - Eric Lawitz
- Texas Liver institute, University of Texas Health Science Center, San Antonio, Texas
| | | | | | | | - Hongmei Mo
- Gilead Sciences, Inc, Foster City, California
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Abstract
This study examined the effects of a contiguity learning model which posited one-trial learning based upon accurate knowledge of results as a reinforcer. A reconceptualization of reinforcing stimuli in the resistance to persuasion paradigm is experimentally tested. Repetition of the persuasive message was tested as part of the developed learning model and as a replication of earlier research. Knowledge of correct results and message repetition were manipulated to overcome resistance to persuasion created by pretreatment inoculation. Inoculation and persuasive attack messages were carefully created to control for a number of important message variables. A pilot study with 219 subjects tested effectiveness of the message. The actual experiment included 162 subjects in a three-way factorial analysis of variance design with inoculation, reinforcement, and repetition of message as predictor variables. Predicted main effects for each independent variable on posttest attitudes were found. Moreover, the pattern of posttest attitude means was exactly as posited. Discussion centered on the use of this learning model in research on persuasion.
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Affiliation(s)
- Michael Burgoon
- Department of Psychology, Harvard University Department of Communication, University of Arizona
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Mo H, Hedskog C, Svarovskaia E, Sun SC, Jacobson IM, Brainard DM, McHutchison JG, Miller MD. Antiviral response and resistance analysis of treatment-naïve HCV-infected patients receiving single and multiple doses of GS-9190. J Viral Hepat 2016; 23:644-51. [PMID: 27004425 DOI: 10.1111/jvh.12536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/17/2016] [Indexed: 01/03/2023]
Abstract
GS-9190 is a NS5B non-nucleoside analogue with demonstrated effectiveness in a Phase 1 monotherapy study and in combination with other DAAs for treatment of chronic HCV infection. Here, the resistance profile of GS-9190 monotherapy in a Phase 1b study was investigated. Resistance analysis was performed by population sequencing and allele-specific PCR (AS-PCR) for Y448H with an assay cut-off of 0.5%. Phenotypic susceptibility analyses were performed on patient isolates as well as site-directed mutagenesis of mutations selected during monotherapy. No resistance-associated variants were observed in patients before or after receiving single doses of GS-9190 by population sequencing. In contrast, in patients who received GS-9190 for 8 days, mutations Y448H and Y452H in NS5B were observed by population sequencing in 21/36 (58%) and 2/36 (5.6%) patients, respectively, at Day 8 or Day 14. Among the remaining 15 patients who had no detectable Y448H at Day 8 or Day 14 by population sequencing, low frequencies of Y448H ranging from 1.3 to 9.7% were detected in 14 of 15 patients by AS-PCR. By AS-PCR, Y448H remained detectable at reduced frequency in the majority of patients analysed through 4-6 months of follow-up. Chimeric HCV replicons constructed with the NS5B sequence from patients with Y448H and Y448H + Y452H/Y demonstrated 27-fold and 78.5-fold reduced susceptibility to GS-9190. In conclusion, Y448H was rapidly selected in the majority of patients receiving multiple doses of GS-9190 as monotherapy, despite undetectable levels in pretreatment samples. Y448H confers reduced susceptibility to GS-9190 and other NNIs and persisted in most patients for months post-treatment.
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Affiliation(s)
- H Mo
- Gilead Sciences Inc, Foster City, CA, USA
| | - C Hedskog
- Gilead Sciences Inc, Foster City, CA, USA
| | | | - S-C Sun
- Gilead Sciences Inc, Foster City, CA, USA
| | - I M Jacobson
- Mount Sinai Beth Israel Medical Center, New York, NY, USA
| | | | | | - M D Miller
- Gilead Sciences Inc, Foster City, CA, USA
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Massud I, Mitchell J, Babusis D, Deyounks F, Ray AS, Rooney JF, Heneine W, Miller MD, García-Lerma JG. Chemoprophylaxis With Oral Emtricitabine and Tenofovir Alafenamide Combination Protects Macaques From Rectal Simian/Human Immunodeficiency Virus Infection. J Infect Dis 2016; 214:1058-62. [DOI: 10.1093/infdis/jiw312] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/18/2016] [Indexed: 11/13/2022] Open
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Margot NA, Kitrinos KM, Fordyce M, McCallister S, Miller MD, Callebaut C. Rare emergence of drug resistance in HIV-1 treatment-naïve patients after 48 weeks of treatment with elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide. HIV Clin Trials 2016; 17:78-87. [PMID: 26892863 DOI: 10.1080/15284336.2016.1142731] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Tenofovir alafenamide (TAF), a novel prodrug of the NtRTI tenofovir (TFV), delivers TFV-diphosphate (TFV-DP) to target cells more efficiently than the current prodrug, tenofovir disoproxil fumarate (TDF), with a 90% reduction in TFV plasma exposure. TAF, within the fixed dose combination of elvitegravir /cobicistat / emtricitabine (FTC)/TAF (E/C/F/TAF), has been evaluated in one Phase 2 and two Phase 3 randomized, double-blinded studies in HIV-infected treatment-naive patients, comparing E/C/F/TAF to E/C/F/TDF. In these studies, the TAF-containing group demonstrated non-inferior efficacy to the TDF-containing comparator group with 91.9% of E/C/F/TAF patients having <50 copies/mL of HIV-1 RNA at week 48. An integrated resistance analysis across these three studies was conducted, including HIV-1 genotypic analysis at screening, and genotypic/phenotypic analysis for patients with HIV-1 RNA>400 copies/mL at virologic failure. Pre-existing primary resistance-associated mutations (RAMs) were observed at screening among the 1903 randomized and treated patients: 7.5% had NRTI-RAMs, 18.2% had NNRTI-RAMs, and 3.4% had primary PI-RAMs. Pre-treatment RAMs did not influence treatment response at Week 48. In the E/C/F/TAF group, resistance development was rare; seven patients (0.7%, 7/978) developed NRTI-RAMs, five of whom (0.5%, 5/978) also developed primary INSTI-RAMs. In the E/C/F/TDF group, resistance development was also rare; seven patients (0.8%, 7/925) developed NRTI-RAMs, four of whom (0.4%, 4/925) also developed primary INSTI-RAMs. An additional analysis by deep sequencing in virologic failures revealed minimal differences compared to population sequencing. Overall, resistance development was rare in E/C/F/TAF-treated patients, and the pattern of emergent mutations was similar to E/C/F/TDF.
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Affiliation(s)
- Nicolas A Margot
- a Gilead Sciences Inc. , 333 Lakeside Drive, Foster City , CA , 94404 , USA
| | - Kathryn M Kitrinos
- a Gilead Sciences Inc. , 333 Lakeside Drive, Foster City , CA , 94404 , USA
| | - Marshall Fordyce
- a Gilead Sciences Inc. , 333 Lakeside Drive, Foster City , CA , 94404 , USA
| | - Scott McCallister
- a Gilead Sciences Inc. , 333 Lakeside Drive, Foster City , CA , 94404 , USA
| | - Michael D Miller
- a Gilead Sciences Inc. , 333 Lakeside Drive, Foster City , CA , 94404 , USA
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Porter DP, Toma J, Tan Y, Solberg O, Cai S, Kulkarni R, Andreatta K, Lie Y, Chuck SK, Palella F, Miller MD, White KL. Clinical Outcomes of Virologically-Suppressed Patients with Pre-existing HIV-1 Drug Resistance Mutations Switching to Rilpivirine/Emtricitabine/Tenofovir Disoproxil Fumarate in the SPIRIT Study. HIV Clin Trials 2016; 17:29-37. [PMID: 26899540 DOI: 10.1080/15284336.2015.1115585] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Antiretroviral regimen switching may be considered for HIV-1-infected, virologically-suppressed patients to enable treatment simplification or improve tolerability, but should be guided by knowledge of pre-existing drug resistance. The current study examined the impact of pre-existing drug resistance mutations on virologic outcomes among virologically-suppressed patients switching to Rilpivirine (RPV)/emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF). METHODS SPIRIT was a phase 3b study evaluating the safety and efficacy of switching to RPV/FTC/TDF in virologically-suppressed HIV-1-infected patients. Pre-existing drug resistance at baseline was determined by proviral DNA genotyping for 51 RPV/FTC/TDF-treated patients with known mutations by historical RNA genotype and matched controls and compared with clinical outcome at Week 48. RESULTS Drug resistance mutations in protease or reverse transcriptase were detected in 62.7% of patients by historical RNA genotype and in 68.6% by proviral DNA genotyping at baseline. Proviral DNA sequencing detected 89% of occurrences of NRTI and NNRTI resistance-associated mutations reported by historical genotype. Mutations potentially affecting RPV activity, including E138A/G/K/Q, Y181C, and H221Y, were detected in isolates from 11 patients by one or both assays. None of the patients with single mutants had virologic failure through Week 48. One patient with pre-existing Y181Y/C and M184I by proviral DNA genotyping experienced virologic failure. Nineteen patients with K103N present by historical genotype were confirmed by proviral DNA sequencing and 18/19 remained virologically-suppressed. DISCUSSION Virologic success rates were high among virologically-suppressed patients with pre-existing NRTI and NNRTI resistance-associated mutations who switched to RPV/FTC/TDF in the SPIRIT study. While plasma RNA genotyping remains preferred, proviral DNA genotyping may provide additional value in virologically-suppressed patients for whom historical resistance data are unavailable.
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Margot NA, Liu Y, Miller MD, Callebaut C. High resistance barrier to tenofovir alafenamide is driven by higher loading of tenofovir diphosphate into target cells compared to tenofovir disoproxil fumarate. Antiviral Res 2016; 132:50-8. [PMID: 27208653 DOI: 10.1016/j.antiviral.2016.05.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/16/2022]
Abstract
Tenofovir alafenamide (TAF) is a new oral prodrug of tenofovir (TFV) recently approved for the treatment of HIV-1 as part of the single-tablet regimen containing elvitegravir, cobicistat, emtricitabine, and TAF. Clinical dosing with TAF vs. tenofovir disoproxil fumarate (TDF) has shown improved bone and kidney safety, and has been associated with an increased concentration of the anti-HIV active moiety tenofovir diphosphate (TFV-DP) in the PBMCs of treated patients and a reduction of TFV systemic exposure. We have studied the potential benefit of this increased concentration of TFV-DP observed clinically in an in vitro model system. Using a newly developed virus breakthrough assay with TAF exposure set at physiological concentrations, we show that HIV-1 clinical isolates harboring TFV resistance mutations such as K65R, 3 or 4 thymidine-analog mutations (TAMs), Q151M/K65R, or T69 insertion complex could be inhibited by TAF, but not by TFV when used at clinically relevant concentrations for TDF. These data suggest that the inhibitory quotient (IQ) of TAF is projected to be higher than the IQ of TDF, and that TAF has the potential to inhibit viruses containing TDF resistance in the clinic.
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Affiliation(s)
- Nicolas A Margot
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.
| | - Yang Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
| | - Michael D Miller
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA
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Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA, Abeywickrema P, Barbe G, Bennet A, Childers K, Christensen M, Clas SD, Dubost D, Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ, Kuethe JT, McCabe Dunn J, Miller MD, Moore KP, Nolting A, Pajkovic N, Patel S, Peng Z, Rada V, Rearden P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu M, Coleman PJ. Correction to Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors. J Med Chem 2015; 59:486. [PMID: 26709958 DOI: 10.1021/acs.jmedchem.5b01957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Porter DP, Daeumer M, Thielen A, Chang S, Martin R, Cohen C, Miller MD, White KL. Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study. Viruses 2015; 7:6360-70. [PMID: 26690199 PMCID: PMC4690866 DOI: 10.3390/v7122943] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023] Open
Abstract
At Week 96 of the Single-Tablet Regimen (STaR) study, more treatment-naïve subjects that received rilpivirine/emtricitabine/tenofovir DF (RPV/FTC/TDF) developed resistance mutations compared to those treated with efavirenz (EFV)/FTC/TDF by population sequencing. Furthermore, more RPV/FTC/TDF-treated subjects with baseline HIV-1 RNA >100,000 copies/mL developed resistance compared to subjects with baseline HIV-1 RNA ≤100,000 copies/mL. Here, deep sequencing was utilized to assess the presence of pre-existing low-frequency variants in subjects with and without resistance development in the STaR study. Deep sequencing (Illumina MiSeq) was performed on baseline and virologic failure samples for all subjects analyzed for resistance by population sequencing during the clinical study (n = 33), as well as baseline samples from control subjects with virologic response (n = 118). Primary NRTI or NNRTI drug resistance mutations present at low frequency (≥2% to 20%) were detected in 6.6% of baseline samples by deep sequencing, all of which occurred in control subjects. Deep sequencing results were generally consistent with population sequencing but detected additional primary NNRTI and NRTI resistance mutations at virologic failure in seven samples. HIV-1 drug resistance mutations emerging while on RPV/FTC/TDF or EFV/FTC/TDF treatment were not present at low frequency at baseline in the STaR study.
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Affiliation(s)
| | - Martin Daeumer
- Seq-IT GmbH & Co. KG, Pfaffplatz 10, 67655 Kaiserslautern, Germany.
| | | | - Silvia Chang
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Ross Martin
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Cal Cohen
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Michael D Miller
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Kirsten L White
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
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48
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Svarovskaia ES, Gane E, Dvory-Sobol H, Martin R, Doehle B, Hedskog C, Jacobson IM, Nelson DR, Lawitz E, Brainard DM, McHutchison JG, Miller MD, Mo H. L159F and V321A Sofosbuvir-Associated Hepatitis C Virus NS5B Substitutions. J Infect Dis 2015; 213:1240-7. [PMID: 26603202 DOI: 10.1093/infdis/jiv564] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/09/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Sofosbuvir (SOF) exhibits a high barrier to resistance, with no S282T NS5B substitution or phenotypic resistance detected in phase 3 registration studies. METHODS Here, emergence of the NS5B variants L159F and V321A and possible association with resistance was evaluated in 8 studies of SOF (NEUTRINO, FISSION, POSITRON, FUSION, VALENCE, PHOTON-1, PHOTON-2, and P7977-2025) and 5 studies of combination ledipasvir (LDV) and SOF (LDV/SOF; LONESTAR, ELECTRON [LDV/SOF arms], ION1, ION2, and ION3), using deep sequencing. RESULTS Deep sequencing detected L159F in 15% (53 of 353) and V321A in 5% (17 of 353) of patients with virologic failure in the SOF studies. Intensification of SOF treatment with LDV reduced the emergence of L159F or V321A to 2% (1 of 50 each) at virologic failure. L159F and V321A did not influence the outcome of retreatment with SOF, ribavirin, and pegylated interferon. At baseline, L159F was detected only in genotype 1-infected patients (1%) and was only associated with increased virologic failure in patients treated for short durations with SOF and ribavirin. CONCLUSIONS Deep-sequencing analysis confirmed that NS5B variants L159F and V321A emerged in a subset of patients treated with SOF at virologic failure. These variants had no impact on retreatment outcome with SOF, ribavirin, and pegylated interferon. Baseline L159F in genotype 1 did not affect the treatment outcome with LDV/SOF.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eric Lawitz
- Texas Liver Institute, University of Texas Health Science Center, San Antonio
| | | | | | | | - Hongmei Mo
- Gilead Sciences, Foster City, California
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Hedskog C, Dvory-Sobol H, Gontcharova V, Martin R, Ouyang W, Han B, Gane EJ, Brainard D, Hyland RH, Miller MD, Mo H, Svarovskaia E. Evolution of the HCV viral population from a patient with S282T detected at relapse after sofosbuvir monotherapy. J Viral Hepat 2015; 22:871-81. [PMID: 25784085 DOI: 10.1111/jvh.12405] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 02/06/2015] [Indexed: 12/12/2022]
Abstract
Clinical phase II/III studies of the nucleotide analogue HCV NS5B inhibitor sofosbuvir (SOF) have demonstrated high efficacy in HCV-infected patients in combination therapy. To date, resistance to SOF (S282T in NS5B) has rarely been detected in patients. In this study, we investigated the evolution of S282T viral variants detected in one HCV genotype 2b-infected patient who relapsed following 12 weeks of SOF monotherapy. Deep sequencing of the NS5B gene was performed on longitudinal plasma samples at baseline, days 2 and 3 on SOF, and longitudinal samples post-SOF treatment through week 48. Intrapatient HCV evolution was analysed by maximum-likelihood phylogenetic analysis. Deep sequencing analysis revealed a low level pre-existence of S282T at 0.05% of viral sequences (4/7755 reads) at baseline and 0.03% (6/23 415 reads) at day 2 on SOF. Viral relapse was detected at week 4 post-treatment where 99.8% of the viral population harboured S282T. Follow-up analysis determined that S282T levels diminished post-treatment reaching undetectable levels 24-48 weeks post-SOF. Phylogenetic analysis together with the persistence of unique post-treatment mutations in all post-SOF samples suggested that growth of wild type resulted from reversion of the S282T mutant to a wild type and not outgrowth of the baseline wild-type population. Our data suggest that a very low level of pre-existing S282T at baseline in this patient was enriched and transiently detected following SOF monotherapy. Despite relapse with drug resistance to SOF, this patient was successfully retreated with SOF plus ribavirin for 12 weeks and is now cured from HCV infection.
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Affiliation(s)
- C Hedskog
- Gilead Sciences Inc., Foster City, CA, USA
| | | | | | - R Martin
- Gilead Sciences Inc., Foster City, CA, USA
| | - W Ouyang
- Gilead Sciences Inc., Foster City, CA, USA
| | - B Han
- Gilead Sciences Inc., Foster City, CA, USA
| | - E J Gane
- New Zealand Liver Transplant Unit, Auckland City Hospital, Auckland, New Zealand
| | - D Brainard
- Gilead Sciences Inc., Foster City, CA, USA
| | - R H Hyland
- Gilead Sciences Inc., Foster City, CA, USA
| | - M D Miller
- Gilead Sciences Inc., Foster City, CA, USA
| | - H Mo
- Gilead Sciences Inc., Foster City, CA, USA
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50
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Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA, Abeywickrema P, Barbe G, Bennet A, Childers K, Christensen M, Clas SD, Dubost D, Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ, Kuethe JT, McCabe Dunn J, Miller MD, Moore KP, Nolting A, Pajkovic N, Patel S, Peng Z, Rada V, Rearden P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu M, Coleman PJ. Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors. J Med Chem 2015; 58:8154-65. [PMID: 26397965 DOI: 10.1021/acs.jmedchem.5b01037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The search for new molecular constructs that resemble the critical two-metal binding pharmacophore required for HIV integrase strand transfer inhibition represents a vibrant area of research within drug discovery. Here we present the discovery of a new class of HIV integrase strand transfer inhibitors based on the 2-pyridinone core of MK-0536. These efforts led to the identification of two lead compounds with excellent antiviral activity and preclinical pharmacokinetic profiles to support a once-daily human dose prediction. Dose escalating PK studies in dog revealed significant issues with limited oral absorption and required an innovative prodrug strategy to enhance the high-dose plasma exposures of the parent molecules.
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Affiliation(s)
| | | | | | | | - David A Powell
- Merck Frosst Centre for Therapeutic Research , Kirkland, QC Canada
| | | | - Guillaume Barbe
- Merck Frosst Centre for Therapeutic Research , Kirkland, QC Canada
| | | | - Karla Childers
- Department of Process Chemistry, Merck & Co., Inc., Rahway, NJ 07065
| | | | | | | | | | | | | | | | | | - Jeffrey T Kuethe
- Department of Process Chemistry, Merck & Co., Inc., Rahway, NJ 07065
| | - Jamie McCabe Dunn
- Department of Process Chemistry, Merck & Co., Inc., Rahway, NJ 07065
| | | | | | - Andrew Nolting
- Department of Process Chemistry, Merck & Co., Inc., Rahway, NJ 07065
| | | | | | - Zuihui Peng
- Department of Process Chemistry, Merck & Co., Inc., Rahway, NJ 07065
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