Oligonucleotide Ligation Assay (OLA) Resistance Study

Durable suppression of HIV replication is critical to (1) improving the health of infected individuals, (2) to reducing HIV transmission to sexual partners and from mothers to their infants, and (3) to maintaining the effectiveness of the current 1st-line non-nucleoside reverse transcriptase inhibitors (NNRTI)- based ART. Across multiple trials, individuals with NNRTI-resistance, even at low-concentrations, have substantially greater virologic failure when treated with NVP- vs PI-ART. A cost-effective strategy is needed to detect and manage ARV-resistant HIV infections. A simple low-cost innovative assay the investigators developed and successfully transferred to Asian and African countries (oligonucleotide ligation assay (OLA)) can detect NNRTI+lamivudine (3TC) resistant HIV using reagents that costs <$7.00/person. Furthermore, detection of NNRTI-resistance by OLA is highly (P<0.001) associated with virologic failure of nevirapine (NVP)-ART in two retrospective studies; one of Thai women who had been previously randomized to single-dose NVP and the second of ARV-naïve Kenyan adults.

The investigators hypothesize that implementation of OLA into routine care will allow Kenyan clinicians to appropriately target protease inhibitor (PI)-based ART and improve rates of durable suppression of viral replication, and thus improve CD4 cell gains and individuals' health, reduce the transmission of ARV-resistant HIV within the community, and maintain the utility of NNRTI-ART. In addition, the investigators hypothesize that programmatically OLA-guided ART will be more cost-efficient compared to the current strategy of empiric use of NNRTI-ART as initial treatment.

• Pre-ART Oligonucleotide Assay (OLA) (Other), also known as Pre-ART OLA: Block randomization (1:1) to pre-ART OLA testing or OLA testing after 12mo on ART

Primary outcomes

• Number of Participants With Virologic Failure With OLA-guided ART vs. Standard of Care [12 months]: The primary endpoint will be a comparison of the rates of viral non-suppression >400 copies/mL between study arms at 12 months

Secondary outcomes

• The Difference in Virologic Failure Among Participants With Transmitted Drug-resistance (TDR) ≥10% Associated With Use of OLA-guided ART vs. SOC [15 months]: We did not analyze and report outcome of people with TDR ≥10%, instead we reported pretreatment drug resistance (PDR) as this parameter could be determined but antiretroviral history was not reliably available. Thus, PDR ≥10% is considered below in place of TDR ≥10%. Chung et al. Lancet HIV 2020; 7: e104-12.
• Difference in Virologic Failure in the Subgroup of Participants With Prior or Ongoing ART Use Associated With Use of OLA-guided ART vs. SOC [15 months]: The primary outcome was virologic failure defined as plasma HIV RNA of at least 400 copies per mL after initiation of antiretroviral therapy (ART).
• Prevalence of TDR by Consensus Sequencing and OLA [15 months]: We did not analyze and report outcome of people with TDR, instead we reported pretreatment drug resistance (PDR) as this parameter could be determined but antiretroviral history was not reliably available. Thus, PDR is considered below in place of TDR. PDR was assessed by OLA and confirmed by consensus sequence or next-generation sequencing.
• Proportion of Subgroup With TDR With Virologic Failure by Randomization Arm [15 months]: We did not analyze and report outcome of people with TDR, instead we reported pretreatment drug resistance (PDR) as this parameter could be determined but antiretroviral history was not reliably available. Thus, PDR is considered below in place of TDR. The primary outcome for this analysis was the difference in virologic failure, defined as plasma HIV-1 RNA of at least 400 copies per mL following ART initiation, by PDR. \[Chung et al. Lancet HIV 2020; 7: e104-12\]
• Estimates of Medical Resource Utilization During the One-year Trial Period [15 months]: Estimates of medical resource utilization during was not calculated. No data available (data on medical resource utilization was not collected during the one-year trial)
• An Assessment of the Potential Long-term Cost-effectiveness of OLA-guided Testing Over a Patient's Lifetime [15 months]: This was not calculated as the model could not test for a period longer than 15 years due to computing limitations.
• Determination of Whether Low-level ARV Resistance (<5%) Detected by PYRO But Not by OLA is Associated With Virologic Failure [24 months]: The prespecified outcomes of this study included differences in the rate of virologic failure over 24 months of efavirenz-based ART between participants by frequency of drug-resistant variants detected by next-generation sequencing at enrollment. Drug-resistance frequency was defined as the proportion of a nucleotide variant encoding a drug-resistant codon in specimens with at least 100 viral templates sequenced. Virologic failure was defined as plasma HIV RNA of at least 400 copies/ml in sequential specimens or at the final study visit in participants prescribed efavirenz-based ART. \[Milne et al. AIDS 2022 Nov 15;36(14):1949-1958\]

Other outcomes

• Descriptions of Technology Transfer of OLA to the Hope Center Laboratory, Including Intra- and Inter-assay the Reproducibility, and Discussion of Obstacles and Possible Solutions [15 months]: Technology transfer of OLA to the Hope Center Laboratory in Kenya is described, including intra- and inter-assay the reproducibility, and discussion of obstacles and possible solutions. Duarte et a. AIDS 2018, 32:2301-2308
• A Comparison of OLA Results Obtained Using DBS in Kenya to Retesting of Same Specimens With Input of Viral Templates Measured in Seattle [15 months]: DBS were not tested in Kenya and thus, the comparison of OLA results obtained using DBS in Kenya to retesting of same specimens with input of viral templates measured in Seattle was not evaluated.
• Detection of Resistance Mutations at OLA Codons by OLA vs. Consensus Sequencing [Enrollment]: Rates of pre-treatment drug resistance among all study participants in the study were assessed by OLA but not by consensus sequencing (CS) due to the high cost of sequencing the entire population. However, all mutations detected by OLA were confirmed by CS in Seattle, and if not detected by CS were confirmed by next generation Illumina sequencing. Participants with any indeterminate OLA results were also sequenced to determine the genotype at the indeterminate codon.

Sex: All, ages: 2 Years to any

Inclusion Criteria:

1. Confirmed HIV infection
2. >2 years of age
3. Qualifying for 1st-line ART based on Kenyan Guidelines
4. Plan to reside in area for >1 year
5. Adult patient or parent of minor agrees to study and provides informed consent

Exclusion Criteria:

1. Received ART previously from Hope Center
2. Ongoing ART
3. Plan to start 2nd-line ART

Participant flow

Outcome results

• Number of Participants With Virologic Failure With OLA-guided ART vs. Standard of Care (Primary), Count of participants, Participants: Pre-ART Oligonucleotide Assay (OLA) 34; No OLA (Standard of Care [SOC]) 39
• The Difference in Virologic Failure Among Participants With Transmitted Drug-resistance (TDR) ≥10% Associated With Use of OLA-guided ART vs. SOC (Secondary), Count of participants, Participants: Pre-ART Oligonucleotide Assay (OLA) 5; No OLA (Standard of Care [SOC]) 13
• Difference in Virologic Failure in the Subgroup of Participants With Prior or Ongoing ART Use Associated With Use of OLA-guided ART vs. SOC (Secondary), Count of participants, Participants: Pre-ART Oligonucleotide Assay (OLA) With Prior ART Use 1; No OLA (Standard of Care [SOC]) With Prior ART Use 1
• Prevalence of TDR by Consensus Sequencing and OLA (Secondary), Count of participants, Participants: Pre-ART Oligonucleotide Assay (OLA) 51; No OLA (Standard of Care [SOC]) 42
• Proportion of Subgroup With TDR With Virologic Failure by Randomization Arm (Secondary), Count of participants, Participants: Pre-ART Oligonucleotide Assay (OLA) 5; No OLA (Standard of Care [SOC]) 13
• Estimates of Medical Resource Utilization During the One-year Trial Period (Secondary)
• An Assessment of the Potential Long-term Cost-effectiveness of OLA-guided Testing Over a Patient's Lifetime (Secondary)
• Determination of Whether Low-level ARV Resistance (<5%) Detected by PYRO But Not by OLA is Associated With Virologic Failure (Secondary), Count of participants, Participants: Participants With Viral Suppression at 24 Months of ART 301; Participants With Virologic Failure by 24 Months of ART 20
• Descriptions of Technology Transfer of OLA to the Hope Center Laboratory, Including Intra- and Inter-assay the Reproducibility, and Discussion of Obstacles and Possible Solutions (Other pre specified)
• A Comparison of OLA Results Obtained Using DBS in Kenya to Retesting of Same Specimens With Input of Viral Templates Measured in Seattle (Other pre specified)
• Detection of Resistance Mutations at OLA Codons by OLA vs. Consensus Sequencing (Other pre specified), Count of participants, Participants: Oligonucleotide Assay (OLA) 69; Consensus Sequencing (CS) 44

Adverse events

Time frame: 2 years

Serious adverse events by term

Other adverse events by term

• Results publication: Chung MH, McGrath CJ, Beck IA, Levine M, Milne RS, So I, Andersen N, Dross S, Coombs RW, Chohan B, Yatich N, Kiptinness C, Sakr SR, Kiarie JN, Frenkel LM. Evaluation of the management of pretreatment HIV drug resistance by oligonucleotide ligation assay: a randomised controlled trial. Lancet HIV. 2020 Feb;7(2):e104-e112. doi: 10.1016/S2352-3018(19)30337-6. Epub 2019 Dec 7. PMID 31818716
• Results publication: Silverman RA, Beck IA, Kiptinness C, Levine M, Milne R, McGrath CJ, Bii S, Richardson BA, John-Stewart G, Chohan B, Sakr SR, Kiarie JN, Frenkel LM, Chung MH. Prevalence of Pre-antiretroviral-Treatment Drug Resistance by Gender, Age, and Other Factors in HIV-Infected Individuals Initiating Therapy in Kenya, 2013-2014. J Infect Dis. 2017 Dec 19;216(12):1569-1578. doi: 10.1093/infdis/jix544. PMID 29040633

• Lisa Frenkel, MD, Principal investigator, University of Washington, Seattle Children's Research Institute
• Michael H Chung, MD, MPH, Principal investigator, Department of Global Health, University of Washington