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A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting
BACKGROUND: Human Immunodeficiency Virus Type 1 (HIV-1) viral load testing at regular intervals is an integral component of disease management in Acquired Immunodeficiency Syndrome (AIDS) patients. The need in countries like India is therefore an assay that is not only economical but efficient and h...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101728/ https://www.ncbi.nlm.nih.gov/pubmed/25028193 http://dx.doi.org/10.1186/0717-6287-47-22 |
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author | Acharya, Arpan Vaniawala, Salil Shah, Parth Parekh, Harsh Misra, Rabindra Nath Wani, Minal Mukhopadhyaya, Pratap N |
author_facet | Acharya, Arpan Vaniawala, Salil Shah, Parth Parekh, Harsh Misra, Rabindra Nath Wani, Minal Mukhopadhyaya, Pratap N |
author_sort | Acharya, Arpan |
collection | PubMed |
description | BACKGROUND: Human Immunodeficiency Virus Type 1 (HIV-1) viral load testing at regular intervals is an integral component of disease management in Acquired Immunodeficiency Syndrome (AIDS) patients. The need in countries like India is therefore an assay that is not only economical but efficient and highly specific for HIV-1 sub type C virus. This study reports a SYBR Green-based HIV-1 real time PCR assay for viral load testing and is designed for enhanced specificity towards HIV-1 sub type C viruses prevalent in India. RESULTS: Linear regression of the observed and reference concentration of standards used in this study generated a correlation coefficient of 0.998 (p < 0.001). Lower limit of detection of the test protocol was 50 copies/ml of plasma. The assay demonstrated 100% specificity when tested with negative control sera. The Spearman coefficient of the reported assay with an US-FDA approved, Taqman probe-based commercial kit was found to be 0.997. No significant difference in viral load was detected when the SYBR Green based assay was used to test infected plasma stored at -20°C and room temperature for 7 days respectively (Wilcoxon signed rank test, p = 0.105). In a comparative study on 90 pretested HIV-1 positive samples with viral loads ranging from 5,000–25,000 HIV-1 RNA copies/ml and between two commercial assays it was found that the later failed to amplify in 13.33% and 10% samples respectively while in 7.77% and 4.44% samples the copy number values were reduced by >0.5 log value, a figure that is considered clinically significant by physicians. CONCLUSION: The HIV-1 viral load assay reported in this study was found to be robust, reliable, economical and effective in resource limited settings such as those existing in India. PCR probes specially designed from HIV-1 Subtype C-specific nucleotide sequences originating from India imparted specificity towards such isolates and demonstrated superior results when compared to two similar commercial assays widely used in India. |
format | Online Article Text |
id | pubmed-4101728 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41017282014-07-18 A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting Acharya, Arpan Vaniawala, Salil Shah, Parth Parekh, Harsh Misra, Rabindra Nath Wani, Minal Mukhopadhyaya, Pratap N Biol Res Research Article BACKGROUND: Human Immunodeficiency Virus Type 1 (HIV-1) viral load testing at regular intervals is an integral component of disease management in Acquired Immunodeficiency Syndrome (AIDS) patients. The need in countries like India is therefore an assay that is not only economical but efficient and highly specific for HIV-1 sub type C virus. This study reports a SYBR Green-based HIV-1 real time PCR assay for viral load testing and is designed for enhanced specificity towards HIV-1 sub type C viruses prevalent in India. RESULTS: Linear regression of the observed and reference concentration of standards used in this study generated a correlation coefficient of 0.998 (p < 0.001). Lower limit of detection of the test protocol was 50 copies/ml of plasma. The assay demonstrated 100% specificity when tested with negative control sera. The Spearman coefficient of the reported assay with an US-FDA approved, Taqman probe-based commercial kit was found to be 0.997. No significant difference in viral load was detected when the SYBR Green based assay was used to test infected plasma stored at -20°C and room temperature for 7 days respectively (Wilcoxon signed rank test, p = 0.105). In a comparative study on 90 pretested HIV-1 positive samples with viral loads ranging from 5,000–25,000 HIV-1 RNA copies/ml and between two commercial assays it was found that the later failed to amplify in 13.33% and 10% samples respectively while in 7.77% and 4.44% samples the copy number values were reduced by >0.5 log value, a figure that is considered clinically significant by physicians. CONCLUSION: The HIV-1 viral load assay reported in this study was found to be robust, reliable, economical and effective in resource limited settings such as those existing in India. PCR probes specially designed from HIV-1 Subtype C-specific nucleotide sequences originating from India imparted specificity towards such isolates and demonstrated superior results when compared to two similar commercial assays widely used in India. BioMed Central 2014-05-30 /pmc/articles/PMC4101728/ /pubmed/25028193 http://dx.doi.org/10.1186/0717-6287-47-22 Text en © ACHARYA et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Acharya, Arpan Vaniawala, Salil Shah, Parth Parekh, Harsh Misra, Rabindra Nath Wani, Minal Mukhopadhyaya, Pratap N A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title | A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title_full | A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title_fullStr | A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title_full_unstemmed | A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title_short | A robust HIV-1 viral load detection assay optimized for Indian sub type C specific strains and resource limiting setting |
title_sort | robust hiv-1 viral load detection assay optimized for indian sub type c specific strains and resource limiting setting |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101728/ https://www.ncbi.nlm.nih.gov/pubmed/25028193 http://dx.doi.org/10.1186/0717-6287-47-22 |
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