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

Lillis, Lorraine; Lehman, Dara A.; Siverson, Joshua B.; Weis, Julie F.; Cantera, Jason L.; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie; Boyle, David S.

doi:10.1016/j.jviromet.2016.01.010

Cited by 38 publications

(39 citation statements)

References 39 publications

(69 reference statements)

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“…RPA has the ability to tolerate mismatches, and the highest mismatch tolerability reported so far is nine nucleotide base pairs across the primer and probe binding sites. [82][83][84][85][86][87][88][89] Studies also showed that the mismatches at the 5′-end or centre of primers only mildly affect the RPA reaction, but mismatches located at the 3′-end of primers significantly affect the reaction. 84,86 This is consistent with the RPA reaction mechanism (see section 2.2), since the polymerase extends the primers and probe (once cleaved) from the 3′-terminus.…”

Section: Tolerability To Mismatches Inhibitors and Background Dnamentioning

confidence: 99%

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

Macdonald

Stetten

2019

Analyst

454

365

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Section: Tolerability To Mismatches Inhibitors and Background Dnamentioning

confidence: 99%

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

Macdonald

Stetten

2019

Analyst

454

365

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“…PCR assays are difficult to implement in POC devices due to the significant power demands of thermocycling and the need for highly purified nucleic acids. Other options may include isothermal amplification techniques, such as loop-mediated isothermal amplification (LAMP) (84,85), helicase dependent amplification (86), and recombinase polymerase amplification (87). Isothermal assays do not require thermal cycling and therefore have reduced power demands and require less time for amplification.…”

Section: Technologies To Advance Next-generation Testsmentioning

confidence: 99%

Point-of-Care HIV Viral Load Testing: an Essential Tool for a Sustainable Global HIV/AIDS Response

et al. 2019

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SUMMARY The global public health community has set ambitious treatment targets to end the HIV/AIDS pandemic. With the notable absence of a cure, the goal of HIV treatment is to achieve sustained suppression of an HIV viral load, which allows for immunological recovery and reduces the risk of onward HIV transmission. Monitoring HIV viral load in people living with HIV is therefore central to maintaining effective individual antiretroviral therapy as well as monitoring progress toward achieving population targets for viral suppression. The capacity for laboratory-based HIV viral load testing has increased rapidly in low- and middle-income countries, but implementation of universal viral load monitoring is still hindered by several barriers and delays. New devices for point-of-care HIV viral load testing may be used near patients to improve HIV management by reducing the turnaround time for clinical test results. The implementation of near-patient testing using these new and emerging technologies may be an essential tool for ensuring a sustainable response that will ultimately enable an end to the HIV/AIDS pandemic. In this report, we review the current and emerging technology, the evidence for decentralized viral load monitoring by non-laboratory health care workers, and the additional considerations for expanding point-of-care HIV viral load testing.

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“…The RPA reaction can tolerate a few base mismatches between the template and the primers or the probe (Daher, Stewart, Boissinot, Boudreau, & Bergeron, 2015; Lillis et al., 2016). This feature left us some room to modify the sequences of the primers and the probe.…”

Section: Resultsmentioning

confidence: 99%

An improved recombinase polymerase amplification assay for visual detection of Vibrio parahaemolyticus with lateral flow strips

Yang¹,

Zhao

Yü³

et al. 2020

Journal of Food Science

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Vibrio parahaemolyticus is an important pathogenic bacterium in both food safety management and mariculture. Rapid and accurate detection technologies are critical for effective control of its outbreak and spreading. Conventional technologies and polymerase chain reaction (PCR)‐based approaches have limited usage because of the requirement of laboratory instruments and trained personnel. Using the isothermal recombinase polymerase amplification (RPA) technology, several detection assays have been developed with added convenience. Combining the lateral flow strip (LFS) test with RPA can further simplify the detection. In this study, an improved RPA assay using LFS for visual detection of V. parahaemolyticus was developed. Primers were designed targeting the virulence genes and screened for amplification efficiency, nonspecific amplification, and primer–dimer formation. Probes were designed for the best primer pairs, and the weakness of LFS tests, being easily affected by primer‐dependent artifacts, was overcome by sequence modifications on primers and probe. The RPA–LFS assay took 25 min at 35 to 45 °C, and showed excellent specificity. It detected as low as one colony forming unit (CFU) of V. parahaemolyticus per reaction without DNA purification, or 10 CFU/10 g spiked food samples with 2 hr of enrichment. The detection limit was better than the currently available RPA‐based detection methods. Application of the RPA–LFS assay for simulated samples or real clinical samples showed accurate and consistent detection results compared to bioassay and quantitative PCR. The RPA–LFS assay provided a rapid, accurate, and convenient V. parahaemolyticus detection method suitable for on‐site detection in resource‐limited conditions. Practical Application This research developed a rapid and visual detection technology for Vibrio parahaemolyticus that is not dependent on complicated equipment. The detection process takes 25 min and the result is read with the naked eye. A detection kit can be developed based on this technology for on‐site detection of V. parahaemolyticus in resource‐limited regions for food safety management and mariculture.

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

Cited by 38 publications

References 39 publications

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

Point-of-Care HIV Viral Load Testing: an Essential Tool for a Sustainable Global HIV/AIDS Response

An improved recombinase polymerase amplification assay for visual detection of Vibrio parahaemolyticus with lateral flow strips

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