Proviral DNA as a Target for HIV-1 Resistance Analysis (HIV)

In summary, in this project the investigators propose to study the proviral DNA genotyping to implement a lower cost and wider than the commercial systems currently in use, in order to analyze all HIV genes that are therapeutic targets of antiretroviral drugs. Using HIV proviral DNA we can obtain information for: HIV-1 Viral Tropism, Mutations associated to Integrase Inhibitors, Mutations associated to Transcriptase reverse Inhibitors, Mutations associated to Protease Inhibitors, and Mutations associated to GP41 Inhibitors.

Along with this the investigators propose to validate the proviral DNA as starting material for genotyping which is independent of the patient's viral load and achieve a greater number of patients living with HIV have access to this important test that is essential in monitoring the HIV infection.

3.2 RESEARCH QUESTIONs Is proviral DNA a genetic compartment suitable for carrying out a genotypic resistance test in patients with low or undetectable viral load? Does proviral DNA have the same clinical validity that RNA? 3.3.- HYPOTHESIS A resistance genotyping test carried out by Proviral DNA detects the same mutations associated to resistance that viral RNA.

3.4.- OBJECTIVES: General/Specific General objective Develop a methodology to assess the proviral HIV-1 DNA or RNA as the genetic material for genotyping assays in genes that are targets of pharmacological interest as TR reverse transcriptase and protease (PRO), Integrase or GP41 Inhibitors and HIV tropism. Specific Objectives

1. Carry out genotyping by proviral DNA and compare it with the same genes genotyping performed with viral RNA. 2. Once the correlation between proviral DNA and RNA has shown, standardize a method to use the technique for clinical use in monitoring HIV patients according to each patient's needs. RNA for patients with viral load above 1,000 copies/mL. Proviral DNA for patients with low or undetectable viral load.

Study Overview

• Status: Unknown
• Conditions: HIV Infections; HIV/AIDS; HIV Seropositivity; Viral Infection

Detailed Description

A prospective longitudinal observational study, the objective is to observe and describe the prevalence of INRT, INNRT, Protease and INIS mutations detected by proviral DNA in patients with virologic failure and low level viremia.

Inclusion/Exclusion: Our Study will include only patients with HIV that had been confirmed by "Instituto de Salud Pública de Chile" (ISP-Chile). Children less than 18 years are excluded.

Number of Patients: A total of 1,200 patients will be included in a period of three years (Including statistical justification, if appropriate).

1. - Only patients who have signed informed consent will be admitted to our study.
2. - The admitted patients will have a blood sample taken for an HIV genotypic resistance test.
3. - from the clinical record of each patient admitted, some relevant clinical data will be taken to interpret the results such as CD4 T lymphocyte count, Viral Load, date of HIV diagnosis, date of initiation of therapy in addition to number and type of treatments antiretrovirals
4. - By way of genotype control, a second blood sample will be taken every year.

Detailed Description

Detection of Resistance Mutations in Proviral DNA in HIV-1 Infection

Background The genetic test HIV proviral DNA (HPD) for resistance to antiretroviral drugs is very useful to detect mutations in patients under antiretroviral therapy who has failed to achieve undetectable viral loads levels or with low level viremia (LLV).

HPD allows the detection of circulating resistant variants and archived which could not be detected in the plasma.

HPD is independent of the viral load of patients. This makes it very useful for studies of primary resistance as it can detect resistance mutations in recently diagnosed patients with low baseline viral loads (<1,000 copies/mL).

HPD is recommended by the European AIDS Clinical Society EACS for cases where there is not HIV RNA for analysis (Barcelona, October 2015).

HPD is able to analyze resistance to all antiretroviral drugs currently available in the market. Therefore, with the HPD innovation we can carry out the following genetic resistance tests: HIV Tropism (Maraviroc), resistance to Integrase Inhibitors (Dolutegravir) and resistance to Transcriptase reversa/Proteasa (Abacavir).

Size Sample and Methodology

During a period of two years, we will study a population of 1,200 patients. These include all patients we have analyzed in our HIV center until December 2012. The methodology includes nucleic acid extraction, amplification of HIV-1 genes that are targets of therapeutic interest and sequencing by traditional and new generation sequencing methods.

Patient Recruitment: a Total of 1.200 (400 by year)

Obtaining blood samples: two samples: sample to the start and one sample to the end after one year

DNA and viral RNA extraction:

RT-PCR amplification:

Electrophoresis visualization in agarose gels

Sending samples to Macrogen for sequencing services

Automatic sequencing by Sanger method in Macrogen USA

Sequencing by deep sequencing (NGS) in Chile or Macrogen USA

Sequence Analysis

Quality Analysis and assemble of raw sequences in software ReCall

Registry of mutations of clinical interest

Report on resistance to antiretroviral drugs

Biostatistical analysis

Results Report and Publications

Preliminary results Preliminary analysis of 100 patients with viral load <1,000 copies/mL, detected 10% of patients with mutations of resistance to drugs that inhibit reverse transcriptase and viral protease. This valuable information enabled earlier therapeutic intervention by changing the drug scheme before they reach higher levels of viral load with consequent improvement in the clinical management.

Projections Project Due to the success and immediate application of this preliminary study, we believe it become very important to validate this technique as a daily routine genetic testing for HIV clinic patients in the public health system. Permanent financing for this genetic HIV test for HIV proviral DNA should be given by the Ministry of Health, Government of Chile.

In conclusion, at present HPD is very useful tool to study virologic failure and LLV in order to an early change of the antiretroviral therapy.

• Study Type: Observational
• Enrollment (Anticipated): 1200

Contacts and Locations

Study Locations

• Chile
  • Metropolitana
    • Santiago, Metropolitana, Chile
      • Recruiting
      • Immunology, HIV and Allergy Section
      • Contact: pablo ferrer, phd; Phone Number: +56950269199; Email: pferrer@hcuch.cl
    • Santiago, Metropolitana, Chile
      • Recruiting
      • Molecular Medicine Laboratory
      • Contact: pablo ferrer, phd; Phone Number: +56950269199; Email: pferrer@hcuch.cl

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 99 years (ADULT, OLDER_ADULT)
• Accepts Healthy Volunteers: Yes
• Genders Eligible for Study: All

• Sampling Method: Probability Sample

Study Population

Inclusion/Exclusion: Our Study will include only patients with HIV that had been confirmed by "Instituto de Salud Pública de Chile" (ISP-Chile). Children less than 18 years are excluded.

Number of Patients: A total of 1,200 patients will be included in a period of three years (Including statistical justification, if appropriate)

Description

Inclusion Criteria:

Clinical diagnosis of HIV

viral load <1.000 copies/mL

under antiretroviral tratment

Exclusion Criteria:

HIV negative

viral load >1.000 copies/mL

Study Plan

How is the study designed?

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Proviral DNA as a Target for HIV-1 Resistance Analysis	Develop a methodology to assess the proviral HIV-1 DNA or RNA as the genetic material for genotyping assays in genes that are targets of pharmacological interest as TR reverse transcriptase and protease (PRO), Integrase or GP41 Inhibitors and HIV tropism	3 years

Collaborators and Investigators

• Sponsor: University of Chile
• Collaborators: ViiV Healthcare
• Investigators: Principal Investigator: Pablo Ferrer, Dr, University of Chile

Study record dates

Study Major Dates

• Study Start (ACTUAL): October 15, 2018
• Primary Completion (ACTUAL): September 8, 2019
• Study Completion (ANTICIPATED): December 31, 2022

Study Registration Dates

• First Submitted: September 11, 2019
• First Submitted That Met QC Criteria: September 11, 2019
• First Posted (ACTUAL): September 13, 2019

Study Record Updates

• Last Update Posted (ACTUAL): September 17, 2019
• Last Update Submitted That Met QC Criteria: September 12, 2019
• Last Verified: September 1, 2019

More Information

Terms related to this study

• Keywords: HIV; Resistance; genotyping; ADNproviral
• Additional Relevant MeSH Terms: Pathologic Processes; RNA Virus Infections; Blood-Borne Infections; Sexually Transmitted Diseases, Viral; Sexually Transmitted Diseases; Lentivirus Infections; Retroviridae Infections; Immunologic Deficiency Syndromes; Immune System Diseases; Disease Attributes; HIV Infections; Infections; Communicable Diseases; Virus Diseases; HIV Seropositivity
• Other Study ID Numbers: Nº OAIC 986/18

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No