![]() There are two probes per pathogen-specific gene target, allowing sufficient sequencing to determine (1) if the pathogen is present and (2) if the pathogen nucleic acid sequence matches known isolates or is a new variant. We have finished the design of probes for 12 tick-borne pathogens: Borrelia burgdorferi, Borrelia miyamotoi, Powassan virus, Deer Tick virus, Anaplasma phagocytophilum, Bartonella henselae, Erhlichia chaffeensis, Rickettsia rickettsii, Ehrlichia muris, Babesia microti, Heartland virus and Bourbon virus. Our bioinformatics pipeline that we will use for data analysis is nearly completed. The first sequencing dataset from known tick sampleswas generated on 12/01/20. A total of 238 probes were designed against two tick gene targets (cytochrome oxidase 1, 16S ribosomal DNA). In 2020, we completed the first design of a tick molecular diagnostic platform and are currently in process of validating it with previously identified specimens of seven tick species: Amblyomma americanum, Dermacentor variabilis, Haemaphysalis longicornis, Ixodes marxi, Ixodes cookei, Ixodes muris andIxodes scapularis. Impacts What was accomplished under these goals? Our goal in 2021 will be to combine these first sets of validatedtick and tick-borne pathogen probes into a single sequencing reaction to identify unknown tick specimens and to detect the presence of pathogens in these tick specimens. What do you plan to do during the next reporting period to accomplish the goals?In 2021, we will complete the development of our bioinformatics pipeline for data analysis andinitiate validation of our first set of pathogen probes. How have the results been disseminated to communities of interest?The diagnostic platform is still under development and validation, so no results have been disseminated yet. What opportunities for training and professional development has the project provided? ![]() We expect that the pandemic will continue to impact the campus through mid-2021, but hope that we can keep the project moving forward. We have, however, made progress in the design phase of the work and have recently completed the first sequencing run. Changes/Problems:COVID-19 was a major impediment to our progress in 2020 because personnel, equipment and resources in our genomics core have been committed to virus testing for the University of Idaho. Progress 12/01/19 to 09/30/20 Outputs Target Audience:The target audiences for these efforts include researchers in vector-borne diseases within and beyond the multi-state project as well as public health professionals. Such an approach can beused to establish a nationally available platform that is uniform, cost-effective, and accessible to both researchers and publichealth officials. Specifically, I will leverage our expertise in new technology that enables interrogation ofup to 100,000 targets and biomarkers in a single assay reaction with a single sample. To address these issues, I will work with themulti-state project directors and participants to develop an assay platform for improveddiagnostics for arthropods and associated pathogensof medical importance. Furthermore, assay capacity is typically limited to a few targets of interest (e.g., <20, limitedmulti-plexing) or, if thousands of targets can be analyzed, this is most often from a single organism (e.g., RNA-seq), with thechallenge that analyses of infecting pathogens that are rare in the background of arthropod sequences are confounded by this approach. Non Technical Summary Cutting-edge diagnostic assays for vector-borne disease samples (vectors, pathogens, hosts) are largely limited to researchlaboratories or a few commercial entities in the U.S., are expensive, and difficult to compare across laboratories due to use ofplatforms that vary significantly.
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