Clinical evaluation of a low cost, in-house developed real-time RT-PCR human immunodeficiency virus type 1 (HIV-1) quantitation assay for HIV-1 infected patients

• Main Authors: Kaur, Palvinder, Khong, Wei Xin, Wee, Sue Yuen, Tan, Eng Lee, Pipper, Juergen, Koay, Evelyn, Ng, Kah Ying, Yap, Joe Kwan, Chew, Kuan Kiat, Tan, Mei Ting, Leo, Yee Sin, Inoue, Masafumi, Ng, Oon Tek
• Other Authors: Kumar, Anil
• Format: Article
• Language: English
• Published: 2014
• Subjects: DRNTU::Science::Medicine
• Online Access: https://hdl.handle.net/10356/104049; http://hdl.handle.net/10220/19482
• Institution: Nanyang Technological University

Objectives HIV-1 viral quantitation is essential for treatment monitoring. An in-house assay would decrease financial barriers to access. Materials and Methods A real-time competitive RT-PCR in house assay (Sing-IH) was developed in Singapore. Using HXB2 as reference, the assay's primers and probes were designed to generate a 183-bp product that overlaps a portion of the LTR region and gag region. A competitive internal control (IC) was included in each assay to monitor false negative results due to inhibition or human error. Clinical evaluation was performed on 249 HIV-1 positive patient samples in comparison with the commercially available Generic HIV Viral Load assay. Correlation and agreement of results were assessed for plasma HIV-1 quantification with both assays. Results The assay has a lower limit of detection equivalent to 126 copies/mL of HIV-1 RNA and a linear range of detection from 100–1000000 copies/mL. Comparative analysis with reference to the Generic assay demonstrated good agreement between both assays with a mean difference of 0.22 log10 copies/mL and 98.8% of values within 1 log10 copies/mL range. Furthermore, the Sing-IH assay can quantify HIV-1 group M subtypes A–H and group N isolates adequately, making it highly suitable for our region, where subtype B and CRF01_AE predominate. Conclusions With a significantly lower running cost compared to commercially available assays, the broadly sensitive Sing-IH assay could help to overcome the cost barriers and serve as a useful addition to the currently limited HIV viral load assay options for resource-limited settings.