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      Field-deployable viral diagnostics using CRISPR-Cas13

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          Abstract

          Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015-2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

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          Human antibody responses after dengue virus infection are highly cross-reactive to Zika virus.

          Lalita Priyamvada, Kendra Quicke, William Hudson … (2016)
          Zika virus (ZIKV) is an emerging mosquito-borne flavivirus of significant public health concern. ZIKV shares a high degree of sequence and structural homology compared with other flaviviruses, including dengue virus (DENV), resulting in immunological cross-reactivity. Improving our current understanding of the extent and characteristics of this immunological cross-reactivity is important, as ZIKV is presently circulating in areas that are highly endemic for dengue. To assess the magnitude and functional quality of cross-reactive immune responses between these closely related viruses, we tested acute and convalescent sera from nine Thai patients with PCR-confirmed DENV infection against ZIKV. All of the sera tested were cross-reactive with ZIKV, both in binding and in neutralization. To deconstruct the observed serum cross-reactivity in depth, we also characterized a panel of DENV-specific plasmablast-derived monoclonal antibodies (mAbs) for activity against ZIKV. Nearly half of the 47 DENV-reactive mAbs studied bound to both whole ZIKV virion and ZIKV lysate, of which a subset also neutralized ZIKV. In addition, both sera and mAbs from the dengue-infected patients enhanced ZIKV infection of Fc gamma receptor (FcγR)-bearing cells in vitro. Taken together, these findings suggest that preexisting immunity to DENV may impact protective immune responses against ZIKV. In addition, the extensive cross-reactivity may have implications for ZIKV virulence and disease severity in DENV-experienced populations.
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            Genomic epidemiology reveals multiple introductions of Zika virus into the United States

            Nathan Grubaugh, Jason T. Ladner, Moritz Ug Kraemer … (2017)
            Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes 1,2 . In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida 3,4 . To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.
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              SNP genotyping: technologies and biomedical applications.

              S. H. Kim, Ashish Misra (2006)
              Single nucleotide polymorphisms (SNPs) are the most frequently occurring genetic variation in the human genome, with the total number of SNPs reported in public SNP databases currently exceeding 9 million. SNPs are important markers in many studies that link sequence variations to phenotypic changes; such studies are expected to advance the understanding of human physiology and elucidate the molecular bases of diseases. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis, yielding a large number of distinct approaches. This article presents a review of SNP genotyping techniques and examines their principles of genotype determination in terms of allele differentiation strategies and detection methods. Further, several current biomedical applications of SNP genotyping are discussed.
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                Author and article information

                Journal
                Title: Science
                Abbreviated Title: Science
                Publisher: American Association for the Advancement of Science (AAAS)
                ISSN (Print): 0036-8075
                ISSN (Electronic): 1095-9203
                Publication date Created: April 26 2018
                Publication date (Electronic): April 26 2018
                Publication date (Print): April 27 2018
                Volume: 360
                Issue: 6387
                Pages: 444-448
                Article
                DOI: 10.1126/science.aas8836
                PMC ID: 6197056
                PubMed ID: 29700266
                ArXiV ID: http://science.sciencemag.org/content/360/6387/444.full.pdf
                SO-VID: 17cded66-3b8f-4b7a-b12e-cc75b5a4f718
                Copyright © © 2018
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                http://www.sciencemag.org/about/science-licenses-journal-article-reuse

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