Cross-subtype detection of HIV-1 using reverse transcription and recombinase polymerase amplification

• Published in: Journal of virological methods 2016-04, Vol.230, p.28-35
• Main Authors: Lillis, Lorraine, Lehman, Dara A., Siverson, Joshua B., Weis, Julie, Cantera, Jason, Parker, Mathew, Piepenburg, Olaf, Overbaugh, Julie, Boyle, David S.
• Format: Article
• Language: English
• Subjects: Diagnostic; HIV Infections - diagnosis; HIV Infections - virology; HIV-1 - isolation & purification; Human immunodeficiency virus; Human immunodeficiency virus 1; Humans; Infant; Infant HIV; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques - methods; Point of care; Recombinases - analysis; Recombinases - genetics; Reverse Transcription; Reverse transcription recombinase polymerase amplification; Sensitivity and Specificity; Viral Proteins - analysis; Viral Proteins - genetics
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2016.01.010

•RT RPA can detect low copies of HIV-1 proviral DNA and genomic RNA.•Result scoring via fluorescence or visual detection have similar sensitivity.•An HIV-1 assay that can detect variant target sequences in groups M and O.•The test result is available in 20min. A low complexity diagnostic test that rapidly and reliably detects HIV infection in infants at the point of care could facilitate early treatment, improving outcomes. However, many infant HIV diagnostics can only be performed in laboratory settings. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that can rapidly amplify proviral DNA from multiple subtypes of HIV-1 in under twenty minutes without complex equipment. In this study we added reverse transcription (RT) to RPA to allow detection of both HIV-1 RNA and DNA. We show that this RT-RPA HIV-1 assay has a limit of detection of 10–30 copies of an exact sequence matched DNA or RNA, respectively. In addition, at 100 copies of RNA or DNA, the assay detected 171 of 175 (97.7%) sequence variants that represent all the major subtypes and recombinant forms of HIV-1 Groups M and O. This data suggests that the application of RT-RPA for the combined detection of HIV-1 viral RNA and proviral DNA may prove a highly sensitive tool for rapid and accurate diagnosis of infant HIV.