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Viruses. 2018 Dec 14;10(12). pii: E714. doi: 10.3390/v10120714.

Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay.

Author information

1
Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA. sanchitabhadra@utexas.edu.
2
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA. misaldan@utmb.edu.
3
Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA. whitehannahhan@gmail.com.
4
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. Grant.Hughes@lstmed.ac.uk.
5
Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA. ellingtonlab@gmail.com.

Abstract

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.

KEYWORDS:

boolean logic-processing nucleic acid probes; isothermal nucleic acid amplification; mosquito; mosquito surveillance; multiplex nucleic acid detection; nucleic acid computation; nucleic acid strand exchange; point-of-care diagnostics; zika virus

PMID:
30558136
PMCID:
PMC6316447
DOI:
10.3390/v10120714
[Indexed for MEDLINE]
Free PMC Article

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