deLIVER: Direct Acting Antiviral Effects on the Liver (deLIVER)

Open-label, partially-randomized plasma and liver sampling study to assess hepatitis C virus (HCV) kinetics during treatment with two (Sofosbuvir/Velpatasvir) or three (Sofosbuvir/Velpatasvir/Voxilaprevir) direct acting antivirals (DAAs)

Primary Objective: The primary objective is to estimate the 1-week change in the proportion of HCV-infected hepatocytes in participants with HCV monoinfection and HIV/HCV coinfection on therapy with two or three DAAs with different mechanisms of action using single cell laser microdissection (scLCM). Secondary Objectives: Estimate the change over the first week in plasma HCV RNA in subjects with HCV monoinfected and HIV/HCV coinfected participants on therapy with two or three DAAs Estimate the 1 week change in the amount of HCV RNA per infected hepatocyte using scLCM on liver biopsy specimens, obtained just prior to treatment initiation (pre-treatment), and after the first week of DAA therapy. Estimate the change in the proportion of HCV-infected hepatocytes that express interferon-stimulated genes (ISGs) within the first week of DAA therapy using scLCM. Measure the change in expression of ISGs in non-parenchymal intrahepatic immune cells (Kupffer cells, plasmacytoid dendritic cells) within the first week of DAA therapy using scLCM. Exploratory Objectives: Estimate the 1 week change in expression of ISGs from peripheral blood mononucleated cells (PBMCs) within the first week of DAA+ribavirin (RBV) therapy using scLCM. Compare sequence(s) of HCV protease, nonstructural protein 5A (NS5A), and nonstructural protein 5B (NS5B) depending on the peripheral sequence) of intrahepatic HCV RNA in single cells and bulk tissue, before and during week 1 of DAA+RBV therapy. Estimate the week 1 change in the sizes and numbers of HCV-infected clusters on DAA therapy to test whether clearance of HCV-infected hepatocytes occurs in spatially random patterns or within specific clusters.

Monoinfected: Sofosbuvir/Velpatasvir/Voxilaprevir SOF/VEL/VOX days 0-7 Paired liver biopsy at days 0 and 7 (cohort 1) or days 0 and 4 (cohort 2). SOF/VEL days 8 (week 2) through 84 (week 12). Post-treatment follow up through week 12.

Monoinfected: Sofosbuvir/Velpatasvir (SOF/VEL) days 0 through 7 and Paired liver biopsy at days 0 and 7 (cohort 1) or days 0 and 4 (cohort 2). SOF/VEL on day 8 (week 2) through 84 (week 12) . Post-Treatment follow up through week 12.

HIV/HCV Co-infection: Sofosbuvir/Velpatasvir (SOF/VEL) days 0 through 7 and Paired liver biopsy at days 0 and 7 (cohort 1) or days 0 and 4 (cohort 2). SOF/VEL on day 8 (week 2) through 84 (week 12) . Post-Treatment follow up through week 12.

Total Number of HCV-infected Hepatocytes Measured in Liver Tissue Obtained by Liver Biopsy at Day 0 (Pre-treatment) and at Day 7 of Antiviral Therapy

Estimate the total number of HCV-infected Hepatocytes (virus burden) for each participant between pre-treatment liver biopsy and post treatment liver biopsy samples using HCV Quantitative real time PCR. Comparison of total number of HCV-infected Hepatocytes (virus burden) were reported between HCV mono infection and co infection groups.

During one week after treatment with direct-acting antivirals, the decline from the baseline plasma HCV RNA levels observed for each individual participant using HCV Quantitative real time PCR. The level of HCV RNA decline compared to those treated with Sofosbuvir/Velpatasvir (SOF/VEL) vs Sofosbuvir/Velpatasvir/Voxilaprevir (SOF/VEL/VOX) and between HCV mono infection and HIV/HCV co infection groups.

Total Number of HCV-infected Hepatocytes That Express Interferon-stimulated Genes (ISGs) Within the First Week of DAA Therapy Using Single Cell Laser Micro Dissection (scLCM).

Total number of hepatocytes that express interferon-stimulated genes (ISGs) were estimated using Quantitative real time PCR for each participant on pre-treatment and post treatment liver biopsy samples. Comparison of total number of hepatocytes that express interferon-stimulated genes (ISGs) were reported between HCV mono infection and co infection groups.

Amount of HCV RNA Per Infected Hepatocyte Using Single Cell Laser Micro Dissection (scLCM) on Liver Biopsy Specimens, Obtained Just Prior to Treatment Initiation (Pre-treatment), and After the First Week of DAA Therapy.

The HCV RNA levels (viral burden) from each infected hepatocytes were measured using Quantitative Real-Time Polymerase Chain Reaction (PCR) from each participants at pre-treatment and post-treatment. The level of HCV RNA (viral burden) decline were reported from intracellular hepatocytes and compared to those treated with Sofosbuvir/Velpatasvir (SOF/VEL) vs Sofosbuvir/Velpatasvir/Voxilaprevir (SOF/VEL/VOX) and between HCV mono infection and HIV/HCV co infection groups.

Inclusion Criteria Participants must meet all of the following inclusion criteria to be eligible for participation Ability and willingness of participant to provide written informed consent. Men and women age ≥18 to ≤70 years at study entry Body mass index (BMI) ≥ 18 kg/m2 HCV RNA ≥ 10,000 IU/mL at Screening HCV genotype 1a at Screening or within 6 months of screening Chronic HCV infection (≥ 6 months) documented by prior medical history HCV treatment-naïve with no prior treatment with any IFN, RBV, or approved or experimental HCV-specific DAA Absence of cirrhosis as defined as transient elastography (FibroScan®) liver stiffness measurement < 12.5 kPa within 6 months of screening The following laboratory values obtained within 42 days prior to study entry. • Hemoglobin > 10 g/dL for men and > 9 g/dL for women • Platelet count ≥90,000/mm3 • International normalized ratio (INR) ≤1.5 • Calculated creatinine clearance (CrCl) ≥ 30 mL/min • Alanine aminotransferase (ALT) and aspartate aminotransferase level ≤ 10 x upper limit of the normal range (ULN) • Total bilirubin <3 mg/dL • Albumin ≥3.5 g/dL CD4+ cell count ≥200 cells/uL and CD4+ cell percentage ≥14% within 42 days of study entry at any US laboratory that has a Clinical Laboratory Improvement Amendments (CLIA) certification [HIV seropositive participants only] HIV RNA < 400 copies/mL prior to study entry by any US laboratory that has a CLIA certification or its equivalent [HIV seropositive participants only] On a qualifying antiretroviral therapy (ART) regimen which is permitted with SOF/VEL. This allows for antiretroviral regimen that does not include Efavirenz, Nevirapine, or Tipranavir. Women of childbearing potential must have a negative serum pregnancy test at Screening and a negative urine pregnancy test on Day 0 prior to liver biopsy All participants must agree not to participate in a conception process (e.g., active attempt to become pregnant or to impregnate, sperm donation, in vitro fertilization). If participating in sexual activity that could lead to pregnancy, the participant (men and women) must also agree to use two reliable methods of contraception simultaneously while receiving study treatment and for 30 days after stopping study treatment. A combination of TWO of the following contraceptives MUST be used appropriately: • Condoms (male or female) with or without a spermicidal agent • Diaphragm or cervical cap with spermicide • IUD (intrauterine device) Participants who are not of reproductive potential (women who have been post-menopausal for at least 24 consecutive months or have undergone hysterectomy, bilateral tubal ligation, and/or bilateral oophorectomy or men who have documented azoospermia) are eligible without requiring the use of contraceptives. Acceptable documentation of sterilization and menopause is specified below. Written or oral documentation communicated by clinician or clinician's staff of one of the following: Physician report/letter Laboratory report of azoospermia Follicle stimulating hormone-release factor (FSH) measurement elevated into the menopausal range as established by the reporting laboratory. Participants must be able to adhere to dosing instructions for study drug administration and able to complete the study schedule of assessments, in the opinion of the investigator. Exclusion Criteria Subjects who meet any of the following exclusion criteria are not to be enrolled in this study: Breastfeeding. Known allergy/sensitivity or any hypersensitivity to components of study drugs or their formulation. Acute or serious illness requiring systemic treatment and/or hospitalization within 42 days prior to study entry. Active hepatitis B infection (positive HBsAg) within 42 days prior to study entry. History of decompensated liver disease (including but not limited to encephalopathy, variceal bleeding, or ascites) prior to study entry. Any cause of liver disease other than chronic HCV infection, including but not limited to the following: • Hemochromatosis Alpha-1 antitrypsin deficiency Wilson's disease Autoimmune hepatitis Alcoholic liver disease Drug-related liver disease Uncontrolled or active depression or other psychiatric disorder within 24 weeks prior to study entry that in the opinion of the investigator might preclude adherence to study requirements. Active drug or alcohol use or dependence that, in the opinion of the investigator, would interfere with adherence to study requirements. Serious illness including uncontrolled seizure disorders, active coronary artery disease within 24 weeks prior to study entry, or other chronic medical conditions that in the opinion of the investigator might preclude completion of the protocol. Presence of active or acute AIDS-defining opportunistic infections within 12 weeks prior to study entry. Active or history of malignancy within 2 years prior to study entry other than basal cell carcinoma of the skin and/or cutaneous Kaposi's sarcoma (KS) and/or cervical or anal dysplasia or carcinoma in situ. 13. Infection with any HCV genotype other than genotype 1a, or mixed genotype infection any time prior to study entry. 14. History of major organ transplantation with an existing functional graft any time prior to study entry. 15. History of acquired or hereditary bleeding disorder (e.g., hemophilia, warfarin use) or any other cause of or tendency toward excessive bleeding time prior to study entry. 16. Gastrointestinal disorder or post-operative condition that could interfere with the absorption of the study drug 17. Difficulty with blood collection and/or poor venous access for the purposes of phlebotomy 18. Planning to take any of the following medications or supplements from Day -7 to the end of treatment: Proton pump inhibitors (patients may switch to H2 blockers up to Day -7) Inducers of P-gp (including, but not limited to, dexamethasone, morphine, ritonavir, saquinavir, tipranavir) Moderate to potent inducers of CYP2B6, CYP2C8, or CYP3A4 (including, but not limited to, efavirenz, etavirine, modafinil, rifampin, St. John's Wort, carbamazepine, phenytoin) 19. History of taking any dose of amiodarone within 6 months (180 days) of Day 0