Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen

Jerome Bouquet,Robert S Lane,Andrea Swei,Michael Melgar,Charles Y Chiu,Eric Delwart

doi:10.1038/s41598-017-12047-6

Abstract

An increasing number of emerging tick-borne diseases has been reported in the United States since the 1970s. Using metagenomic next generation sequencing, we detected nucleic acid sequences from 2 novel viruses in the family Bunyaviridae and an emerging human rickettsial pathogen, Rickettsia philipii, in a population of the Pacific Coast tick, Dermacentor occidentalis in Mendocino County sampled annually from 2011 to 2014. A total of 250 adults of this human-biting, generalist tick were collected from contiguous chaparral and grassland habitats, and RNA from each individually extracted tick was deep sequenced to an average depth of 7.3 million reads. We detected a Francisella endosymbiont in 174 ticks (70%), and Rickettsia spp. in 19 ticks (8%); Rickettsia-infected ticks contained R. rhipicephali (16 of 250, 6.4%) or R. philipii (3 of 250,1.2%), the agent of eschar-associated febrile illness in humans. The genomes of 2 novel bunyaviruses (>99% complete) in the genera Nairovirus and Phlebovirus were also identified and found to be present in 20–91% of ticks, depending on the year of collection. The high prevalence of these bunyaviruses in sampled Dermacentor ticks suggests that they may be viral endosymbionts, although further studies are needed to determine whether they are infectious for vertebrate hosts, especially humans, and their potential role in tick ecology.

Highlights

Dermacentor is a genus of hard-bodied ticks in the family Ixodidae that utilizes small and large mammals as primary hosts
An average of 7.3 (±5.06) million reads per tick were obtained, with an average of 76.2% host sequences being aligned and subtracted by SURPI, followed by an average of 230,000 reads per sample aligning to a sequence in the National Center for Biotechnology Information (NCBI) nt database and an average of 327 reads per sample mapping to a viral protein database by translated nucleotide alignment (Fig. 2)
We used metagenomic next-generation sequencing to individually screen 250 D. occidentalis adults collected in northern California from 2011–2014 for the presence of viruses and bacteria

Summary

Introduction

Dermacentor is a genus of hard-bodied ticks in the family Ixodidae that utilizes small and large mammals as primary hosts. D. occidentalis is though to be the primary vector for R. philipii (previously known as the unclassified Rickettsia 364D), a recently recognized cause of eschar-associated illness in California[2]. Unlike PCR amplicon sequencing, which is limited to a few predefined targets, unbiased metagenomic next-generation sequencing (mNGS), otherwise known as deep sequencing, can be used to identify novel and emerging human pathogens circulating in the tick vector. Deep sequencing was recently used to identify Bourbon virus, a novel virus in the genus Thogotovirus associated with a fatal case of febrile tick-borne illness in Kansas in 20155. We performed longitudinal field sampling, mNGS, and SURPI analysis of individual D. occidentalis ticks collected in Mendocino County, California from 2011–2014 to explore their viral and bacterial diversity and to detect both known and potential tick-borne pathogens afflicting humans

Methods

Results

Conclusion