PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs.

BACKGROUND: CRISPR-Cas based diagnostic assays provide a portable solution which bridges the benefits of qRT-PCR and serological assays in terms of portability, specificity and ease of use. CRISPR-Cas assays are rapidly fieldable, specific and have been rigorously validated against a number of targets, including HIV and vector-borne pathogens. Recently, CRISPR-Cas12 and CRISPR-Cas13 diagnostic assays have been granted FDA approval for the detection of SARS-CoV-2. A critical step in utilizing this technology requires the design of highly-specific and efficient CRISPR RNAs (crRNAs) and isothermal primers. This process involves intensive manual curation and stringent parameters for design in order to minimize off-target detection while also preserving detection across divergent strains. As such, a single, streamlined bioinformatics platform for rapidly designing crRNAs for use with the CRISPR-Cas12 platform is needed. Here we offer PrimedSherlock, an automated, computer guided process for selecting highly-specific crRNAs and primers for targets of interest. RESULTS: Utilizing PrimedSherlock and publicly available databases, crRNAs were designed against a selection of Flavivirus genomes, including West Nile, Zika and all four serotypes of Dengue. Using outputs from PrimedSherlock in concert with both wildtype A.s Cas12a and Alt-R Cas12a Ultra nucleases, we demonstrated sensitive detection of nucleic acids of each respective arbovirus in in-vitro fluorescence assays. Moreover, primer and crRNA combinations facilitated the detection of their intended targets with minimal off-target background noise. CONCLUSIONS: PrimedSherlock is a novel crRNA design tool, specific for CRISPR-Cas12 diagnostic platforms. It allows for the rapid identification of highly conserved crRNA targets from user-provided primer pairs or PrimedRPA output files. Initial testing of crRNAs against arboviruses of medical importance demonstrated a robust ability to distinguish multiple strains by exploiting polymorphisms within otherwise highly conserved genomic regions. As a freely-accessible software package, PrimedSherlock could significantly increase the efficiency of CRISPR-Cas12 diagnostics. Conceptually, the portability of detection kits could also be enhanced when coupled with isothermal amplification technologies.

Aedes japonicus japonicus in Nebraska and Texas.

Aedes japonicus japonicus continues to spread westward and in this study, its presence is documented in 8 counties in Nebraska and in Bowie County, TX. In 1998, Ae. japonicus was collected in Connecticut, New Jersey, and New York for the 1st records of this species in North America. Except for Louisiana, it has been reported from all states that border or are east of the Mississippi River. In Canada, it has been reported in Ontario and all eastern provinces. In the Pacific Northwest, it has been reported in Washington, Oregon, and British Columbia, and in the midwestern states that do not border the Mississippi River, Kansas, Oklahoma, and South Dakota are the only states to have reported its presence in peer-reviewed journals.

Distribution of Culex coronator in the USA.

In 1920, Culex coronator was reported from San Benito, Texas, and later in Arizona, New Mexico, and Oklahoma. In 2005, this species was reported to be spreading across the southeastern USA. Now reported in 14 states, it has been found as far north as northern Oklahoma; Memphis, TN; and Suffolk, VA. The public health significance of Cx. coronator is not firmly established, even though it has been implicated as a potential vector of several arboviral diseases. This study aims to document additional Cx. coronator county-level records, to provide information about its continued expansion across the southern USA, and to provide a short research update into its vector potential. Data acquired through multistate collaborations and author collections resulted in 146 new county records from Alabama, Arkansas, Florida, Georgia, Louisiana, Mississippi, North Carolina, Oklahoma, South Carolina, and Texas. No new county records were presented for Arizona, New Mexico, Tennessee, or Virginia, which had previously reported this species. With these new data, this species has been documented in 386 counties in 14 states of the continental USA.

Feeding Habits of Vector Mosquitoes in Harris County, TX, 2018.

Mosquito-borne pathogens contribute significantly to the global burden of infectious diseases and are a continuing public health concern in the United States. Blood feeding by vector mosquitoes is a critical step in the transmission of human pathogens. Continuous surveillance of mosquito feeding patterns, especially in major population centers, is necessary for sustainable, effective control strategies. To better understand female feeding habits in Harris County, TX, we trapped mosquitoes from various locations, distributed among urban and semi-urban environments. Bloodmeal hosts were determined using a cytochrome C oxidase I DNA barcoding strategy. We identified a diverse array of vertebrate hosts with a high degree of avian host utilization, most surprisingly from anthropophilic species like Aedes aegypti (L.). We also detected sequences from two different vertebrate hosts in about half of specimens examined, suggesting that multiple bloodmeals had been acquired in the same feeding cycle by a sizable fraction of females in both urban and semi-urban locations. The high proportion of feeding on domestic chickens may indicate that a significant number of homeowners are rearing chickens within close proximity to study trap sites. As non-amplifying hosts, chickens may have a diluting effect on West Nile virus, as well as a zooprophylactic effect in their immediate vicinities. Ultimately, spatial and temporal host utilization patterns add insight into potential disease transmission dynamics, thereby informing vector control strategies in Harris County and other metropolitan areas.