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

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.

Predicting ACL Reinjury from Return to Activity Assessments at 6-months Post-Surgery: A Prospective Cohort Study

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.

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

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.

Evaluation of source of corn silage and trace minerals on rumen characteristics and passage rate of Holstein cows

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.

Evaluation of source of corn silage and trace minerals on lactational performance and total-tract nutrient digestibility in Holstein cows

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.

Isolation and Identification of Lysergic Acid Amide and Isolysergic Acid Amide as the Principal Ergoline Alkaloids in Argyreia nervosa, a Tropical Wood Rose

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.

Characterization of HCV resistance from a 3-day monotherapy study of voxilaprevir, a novel pangenotypic NS3/4A protease inhibitor

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.

Long-term persistence of HCV NS5A resistance-associated substitutions after treatment with the HCV NS5A inhibitor, ledipasvir, without sofosbuvir

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.

Imaging of Postoperative Infection at the Knee Joint

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.

Identification of novel bifunctional HIV-1 reverse transcriptase inhibitors

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.

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

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.

TLR7 agonists induce transient viremia and reduce the viral reservoir in SIV-infected rhesus macaques on antiretroviral therapy

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.

A systematic review of community-based interventions for the treatment of adolescents with overweight and obesity

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.

Rare emergence of drug resistance in HIV-1 treatment-naïve patients receiving elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide for 144 weeks

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).

Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens

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.

Resistance characterization of ledipasvir and velpatasvir in hepatitis C virus genotype 4

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.

Nonstructural protein 5A resistance profile in patients with chronic hepatitis C treated with ledipasvir-containing regimens without sofosbuvir

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.

Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors

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.

Establishment of robust HCV genotype 4d, 5a, and 6a replicon systems

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.