Comparative Evaluation of RT-LAMP and RT-PCR for Detection of HIV-1 in the Sudan

Abstract

Abstract Introduction/Objective Rapid, simple, cost effective, nucleic acid based test for detecting HIV-1 in areas with limited resources is badly needed. Loop-mediated isothermal amplification (LAMP) is a technique that allows the amplification of nucleic acids DNA and RNA with high specificity, sensitivity and rapidity under isothermal conditions. This study was conducted to evaluate RT-LAMP method for HIV-1 detection in comparison with RT-PCR. Methods In the present study, ninety EDTA blood samples were studied; seventy samples were collected from HIV-1 infected patients and 20 samples from HIV-1 negative participants. All samples subjected to RT-LAMP and RT-PCR assay targeting HIV-1 p24 gene. Additionally nine positive samples were subjected to viral load measurement using COBAS® TaqMan® HIV-1 Test, version 2.0 (v2.0), and five samples were subjected to direct DNA sequencing of p24 gene phylogenetic analysis. Results Of the 70 HIV-1 positive samples, 68 (97.1%) and 61 (87.1%) positive samples were detected using RT-LAMP and RT-PCR respectively. Whereas, all the 20 HIV-1 negative samples were confirmed negative by RT- LAMP, 2 (10%) were positive by RT-PCR. Furthermore, the limit of detection (LOD) for both RT-LAMP and RT-PCR assays was determined to be 130 and 325 copies/ml respectively. The viral loads for the nine samples ranged between 1.92E+4 C/ml – 1.04C6/ml. The sequencing of five samples showed similarity of the Sudanese isolates with the neighboring countries Uganda, Saudi Arabia and also Senegal and even more closely sub-grouped with the Tanzanian counterpart. Conclusion RT-LAMP was successfully performed under minimal laboratory conditions demonstrating it as a very useful for use in fields setting and limited resources region.