Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field-deployable. Here, 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 down to 1 copy/μl. We develop 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 4 DENV serotypes as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid design and testing (<1 week) of instrument-free assays to detect clinically relevant viral single nucleotide polymorphisms.

Pyrethroid insecticides are critical for malaria control in Africa. However, resistance to this insecticide class in the malaria vector Anopheles funestus is spreading rapidly across Africa, threatening the success of ongoing and future malaria control programs. The underlying resistance mechanisms driving the spread of this resistance in wild populations remain largely unknown. Here, we show that increased expression of two tandemly duplicated P450 genes, CYP6P9a and CYP6P9b, is the main mechanism driving pyrethroid resistance in Malawi and Mozambique, two southern African countries where this insecticide class forms the mainstay of malaria control. Genome-wide transcription analysis using microarray and quantitative RT-PCR consistently revealed that CYP6P9a and CYP6P9b are the two genes most highly overexpressed (>50-fold; q < 0.01) in permethrin-resistant mosquitoes. Transgenic expression of CYP6P9a and CYP6P9b in Drosophila melanogaster demonstrated that elevated expression of either of these genes confers resistance to both type I (permethrin) and type II (deltamethrin) pyrethroids. Functional characterization of recombinant CYP6P9b confirmed that this protein metabolized both type I (permethrin and bifenthrin) and type II (deltamethrin and Lambda-cyhalothrin) pyrethroids but not DDT. Variability analysis identified that a single allele of each of these genes is predominantly associated with pyrethroid resistance in field populations from both countries, which is suggestive of a single origin of this resistance that has since spread across the region. Urgent resistance management strategies should be implemented in this region to limit a further spread of this resistance and minimize its impact on the success of ongoing malaria control programs. metabolic resistance | P450 allelic variation | heterologous expression | GAL4/UAS expression