title: Detection of HIV-1 minority variants containing the K103N drug-resistance mutation using a simple method to amplify RNA targets (SMART).
abstract: The simple method for amplifying RNA targets (SMART) was used to detect K103N, a common HIV-1 reverse transcriptase drug-resistance mutation. Novel amplifiable SMART probes served as reporter molecules for RNA sequences that are captured and separated on a microfluidic platform under zero-flow conditions. Assays were performed both off chip and in a microchip reservoir using a modified version of real-time nucleic acid sequence-based amplification, without the noncyclic phase, and 65°C preheat. A total of 6000 copies/mL of the synthetic sequences were detected within 180 minutes of amplification. Although the sensitivity of research platforms is higher, SMART has the potential to offer comparable sensitivity and speed to commercially available viral load and HIV detection kits. Furthermore, SMART uses an inexpensive, practical, and more accurate isothermal exponential amplification technique. The use of molecular beacons resulted in relatively fast real-time detection (<180 minutes); however, they were also shown to hinder the amplification process when compared with end point detection. Finally, SMART probes were used for modeling of K103N concentrations within an unknown sample. Only 1% of the SMART probes was detected within the wild-type population (6 × 10(8) copies/mL). These results establish the groundwork for point-of-care drug resistance and viral load monitoring in clinical samples, which can revolutionize HIV patient care globally.
authors.affiliation: Center for Biomedical Engineering, School of Engineering, Alpert Medical School, Brown University, Providence, RI, USA.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Morabito
authors.forename: Rami
authors.initials: R
authors.lastname: Kantor
authors.forename: Warren
authors.initials: W
authors.lastname: Tai
authors.forename: Leeann
authors.initials: L
authors.lastname: Schreier
authors.forename: Anubhav
authors.initials: A
authors.lastname: Tripathi
mesh_terms: D024882:Drug Resistance, Viral / Q000235:genetics*; D023381:Endpoint Determination; D005838:Genotype; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification*; D009154:Mutation; D009693:Nucleic Acid Hybridization; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D015203:Reproducibility of Results; D021161:Self-Sustained Sequence Replication / Q000379:methods*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA; D019562:Viral Load
chemical_list: D012367:RNA, Viral; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase
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