1282. Detection of HIV Transmitted Drug Resistance by Next-Generation Sequencing in a CRF01_AE Predominant Epidemic

Abstract

BackgroundThe Philippines has the fastest growing HIV epidemic in the Asia-Pacific. Concurrent with this is a subtype shift from B to CRF01_AE. We have previously documented transmitted drug resistance (TDR) locally. However, the lack of drug pressure and the insensitivity of Sanger-based sequencing (SBS) may leave archived drug-resistance mutations (DRMs) undetected. To better detect TDR, we performed next-generation sequencing (NGS) on treatment-naïve patients and compared this with SBS.MethodsFollowing ethics approval, newly-diagnosed adult Filipino HIV patients were recruited from the Philippine General Hospital HIV treatment hub. Demographic data were collected, and blood samples underwent SBS with a WHO-approved protocol. Whole-genome NGS was performed using Illumina HiSeq through a commercial provider (Macrogen, Korea). Genotype and DRMs were analyzed and scored using the Stanford HIV Drug Resistance Database.Results113 patients were analyzed. Median age was 29 years (range 19–68), mean CD4 count was 147 cells/µL (range 0–556) and median viral load was 2.8 × 106 copies/mL. Genotype distribution was: CRF01_AE (93), B (13), possible CRF01_AE/B recombinants (5), CRF02_AG (1), possible URF (1). TDR prevalence by SBS and NGS at different minority variant cutoffs are shown in Table 1. All DRMs on SBS were found on NGS. Some samples had multiple DRMs. No factors were significantly associated with TDR, genotype, viral load or baseline CD4 count.ConclusionNGS is a more sensitive tool for detecting TDR compared with SBS. Nearly double the DRMs were found at an NGS cutoff of ≥5%, including INSTI DRMs. With increasing HIV drug resistance worldwide, switching to NGS may help decrease rates of initial treatment failure, especially in settings with limited repertoires of ARVs.Table 1. TDR Prevalence by SBS and NGS (N = 113).MethodAll (%)NRTI (%)NNRTI (%)PI (%)INSTI (%)SBS11 (9.7)2 (1.8)7 (6.2)3 (2.7)0 (0)*NGS≥1%59 (52.2)15 (13.3)29 (25.7)19 (16.8)17 (15.0)≥2%39 (34.5)7 (6.2)19 (16.8)9 (8.0)10 (8.8)≥5%22 (19.5)3 (2.7)15 (13.3)5 (4.4)2 (1.8)≥10%19 (16.8)1 (0.9)14 (12.4)4 (3.5)2 (1.8)≥15%15 (13.3)1 (0.9)12 (10.6)3 (2.7)1 (0.9)≥20%13 (11.5)1 (0.9)10(8.8)2 (1.8)1 (0.9)*SBS for INSTI only done for those with INSTI DRM on NGS ≥ 1% minority variantDisclosures All authors: No reported disclosures.

Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008-2018

“…It would be interesting to investigate whether this increased CRF01_AE R e and N e in 2013 was simultaneous with the date of increased usage of mobile dating services in the country. CRF01_AE R e remaining higher than that of B from 2013 to 2016 could have given CRF01_AE ample time to grow even more predominant in the MSM population, reaching 82% of cases since that time [66]. It is possible that the sequences in this dataset are less informative of N e closer to the latest sample collection date, or that increases in R e are not immediately reflected in N e .…”

Multidrug-resistant tuberculosis (MDR-TB) and multidrug-resistant HIV (MDR-HIV) syndemic: challenges in resource limited setting

“…On the other hand, NRTI mutations are less prevalent, ranging from 1.6%38 to 4%39 among ART-experienced and ART-naïve, respectively. In the Philippines, overall HIV-1 TDR by conventional Sanger-based sequencing is 9.7% overall (NNRTI: 6.2%, NRTI: 1.8% and PI: 2.7%) and was even higher on next-generation sequencing at 5% minority variant cut-off (19.5% overall, NNRTI: 13.3%, NRTI: 2.7%, PI: 4.4%, INSTI 1.8%) 40. In our case, the patient had M184 mutations conferring resistance to 3TC, emtricitabine (FTC), didanosine (ddI) and abacavir (ABC), while K65R causes intermediate to high-level phenotypic and clinical resistance to TDF, ddI, ABC and d4T and low level to intermediate phenotypic and clinical resistance to 3TC and FTC.…”