Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.

We employed high throughput sequencing to survey the microbiomes of Ixodes scapularis collected in New York and Connecticut. We examined 197 individual I. scapularis adults and pools from 132 adults and 197 nymphs.

Genotyping and Quantifying Lyme Pathogen Strains by Deep Sequencing of the Outer Surface Protein C () Locus.

A mixed infection of a single tick or host by Lyme disease spirochetes is common and a unique challenge for the diagnosis, treatment, and surveillance of Lyme disease. Here, we describe a novel protocol for differentiating Lyme strains on the basis of deep sequencing of the hypervariable outer surface protein C locus (). Improving upon the traditional DNA-DNA hybridization method, the next-generation sequencing-based protocol is high throughput, quantitative, and able to detect new pathogen strains.

Identification of Novel Viruses in , , and Ticks.

Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including ( 1,138), ( 720), and ( 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species.

Detection of , , , , and Powassan Virus in Ticks by a Multiplex Real-Time Reverse Transcription-PCR Assay.

ticks are implicated in transmission of , , , , and Powassan virus. We describe the establishment and implementation of the first multiplex real-time PCR assay with the capability to simultaneously detect and differentiate all five pathogens in a single reaction. The application of this assay for analysis of ticks at sites in New York and Connecticut revealed a high prevalence of in ticks from Suffolk County, NY.