Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay
by
Sanchita Bhadra 1,*
, Miguel A. Saldaña 2, Hannah Grace Han 1, Grant L. Hughes 3,† and Andrew D. Ellington 1
Sanchita Bhadra 1,*, Miguel A. Saldaña 2, Hannah Grace Han 1, Grant L. Hughes 3,† and Andrew D. Ellington 1
1
Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
2
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
3
Department of Pathology, Institute for Human Infections and Immunity, Center for Tropical Diseases, Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555, USA
*
Author to whom correspondence should be addressed.
†
Present Address: Department of Vector Biology and Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
Viruses 2018, 10(12), 714; https://doi.org/10.3390/v10120714
Received: 20 October 2018 / Revised: 8 December 2018 / Accepted: 11 December 2018 / Published: 14 December 2018
(This article belongs to the Special Issue New Advances on Zika Virus Research)
We have developed a generalizable “smart molecular diagnostic” capable of accurate point-of-care (POC) detection of variable nucleic acid targets. Our isothermal assay relies on multiplex execution of four loop-mediated isothermal amplification reactions, with primers that are degenerate and redundant, thereby increasing the breadth of targets while reducing the probability of amplification failure. An easy-to-read visual answer is computed directly by a multi-input Boolean OR logic gate (gate output is true if either one or more gate inputs is true) signal transducer that uses degenerate strand exchange probes to assess any combination of amplicons. We demonstrate our methodology by using the same assay to detect divergent Asian and African lineages of the evolving Zika virus (ZIKV), while maintaining selectivity against non-target viruses. Direct analysis of biological specimens proved possible, with crudely macerated ZIKV-infected Aedes aegypti mosquitoes being identified with 100% specificity and sensitivity. The ease-of-use with minimal instrumentation, broad programmability, and built-in fail-safe reliability make our smart molecular diagnostic attractive for POC use.
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Keywords:
point-of-care diagnostics; isothermal nucleic acid amplification; nucleic acid computation; nucleic acid strand exchange; zika virus; mosquito; mosquito surveillance; multiplex nucleic acid detection; boolean logic-processing nucleic acid probes
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MDPI and ACS Style
Bhadra, S.; Saldaña, M.A.; Han, H.G.; Hughes, G.L.; Ellington, A.D. Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay. Viruses 2018, 10, 714.
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