1282. Detection of HIV Transmitted Drug Resistance by Next-Generation Sequencing in a CRF01_AE Predominant Epidemic
Session: Poster Abstract Session: HIV: Molecular Epidemiology
Friday, October 5, 2018
Room: S Poster Hall
  • Salvana NGS TDR 1282 IDWeek2018.pdf (581.9 kB)
  • Background: The 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.

    Methods: Following ethics approval, newly-diagnosed adult Filipino HIV patients were recruited from the Philippine General Hospital HIV treatment hub. Demographic data was 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.

    Results: 113 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 x 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.

    Conclusion: NGS is a more sensitive tool for detecting TDR compared to 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).


    All (%)

    NRTI (%)

    NNRTI (%)

    PI (%)

    INSTI (%)


    11 (9.7)

    2 (1.8)

    7 (6.2)

    3 (2.7)

    0 (0)*



    59 (52.2)

    15 (13.3)

    29 (25.7)

    19 (16.8)

    17 (15.0)


    39 (34.5)

    7 (6.2)

    19 (16.8)

    9 (8.0)

    10 (8.8)


    22 (19.5)

    3 (2.7)

    15 (13.3)

    5 (4.4)

    2 (1.8)


    19 (16.8)

    1 (0.9)

    14 (12.4)

    4 (3.5)

    2 (1.8)


    15 (13.3)

    1 (0.9)

    12 (10.6)

    3 (2.7)

    1 (0.9)


    13 (11.5)

    1 (0.9)


    2 (1.8)

    1 (0.9)

    *SBS for INSTI only done for those with INSTI DRM on NGS ≥ 1% minority variant

    Edsel Maurice Salvana, MD, DTM&H, FIDSA1,2,3, Nina Dungca, MS1, Geraldine Arevalo, BS1, Katerina Leyritana, MD4, Christian Francisco, MD, FPCP2, Christine Penalosa, MD2, Raul Destura, MD1,2,3, Jodor Lim, MD, FPCP, FPSMID5 and Brian Schwem, PhD1, (1)Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines (UP-NIH), Manila, Philippines, (2)Department of Medicine, Section of Infectious Diseases, University of the Philippines - Philippine General Hospital, Manila, Philippines, (3)Philippine Genome Center, Quezon City, Philippines, (4)Sustained Health Initiatives of the Philippines (SHIP), Mandaluyong City, Philippines, (5)Section of Infectious Diseases, University of the Philippines-Philippine General Hospital, Manila, Philippines


    E. M. Salvana, None

    N. Dungca, None

    G. Arevalo, None

    K. Leyritana, None

    C. Francisco, None

    C. Penalosa, None

    R. Destura, None

    J. Lim, None

    B. Schwem, None

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