COMPARATIVE EVALUATION OF RT-LAMP AND RT-PCR FOR DETECTION OF HIV-1 IN THE SUDAN.
Mustafa E Yassin1, Khalid A Enan2, Bashir Salim3, Walid A Eldaif1, Imad Fadl-Elmula4, Isam M Elkhidir6
1Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Alneelain University, Khartoum, Sudan
2Department of Virology, Central Laboratory, Ministry of science and Communication, P.O. Box 7099, Khartoum, Sudan.
3Parasites, Vectors and Vector-Borne Diseases, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa
4Faculty of Medicine, Al Neelain University, Khartoum, Sudan.
5Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
Aim: This study was conducted to evaluate RT-LAMP method for HIV-1 detection in comparison with RT-PCR.
Background: 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.
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+4C/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.
Keywords: RT-LAMP, RT-PCR, HIV, Sudan, COBAS TaqMan, Phylogeny.
Dr. MUSTAFA ELTIGANI MUSTAFA YASSIN, Assistant professor of Medical Microbiology.
Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Alneelain University, Khartoum, Sudan