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
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 pri...
| Main Authors: | , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2014
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/104049 http://hdl.handle.net/10220/19482 |
| _version_ | 1811693270926884864 |
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| author | 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 |
| author2 | Kumar, Anil |
| author_facet | Kumar, Anil 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 |
| author_sort | Kaur, Palvinder |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T06:49:01Z |
| format | Journal Article |
| id | ntu-10356/104049 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:49:01Z |
| publishDate | 2014 |
| record_format | dspace |
| spelling | ntu-10356/1040492022-02-16T16:26:30Z 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 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 Kumar, Anil Lee Kong Chian School of Medicine (LKCMedicine) DRNTU::Science::Medicine 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. Published version 2014-06-02T01:58:38Z 2019-12-06T21:25:15Z 2014-06-02T01:58:38Z 2019-12-06T21:25:15Z 2014 2014 Journal Article Kaur, P., Khong, W. X., Wee, S. Y., Tan, E. L., Pipper, J., Koay, E., et al. (2014). 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. PLoS ONE, 9(3). 1932-6203 https://hdl.handle.net/10356/104049 http://hdl.handle.net/10220/19482 10.1371/journal.pone.0089826 24603460 en PLoS ONE © 2014 Kaur et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. application/pdf |
| spellingShingle | DRNTU::Science::Medicine 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 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 |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | DRNTU::Science::Medicine |
| url | https://hdl.handle.net/10356/104049 http://hdl.handle.net/10220/19482 |
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