Integrated Jingmenvirus Polymerase Gene in Ixodes ricinus Genome

Abstract

Members of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia and Antarctica. Two viruses of this group were isolated from patients with fever after a tick bite. Using a nested RT-PCR assay targeting a jingmenvirus polymerase gene fragment, we screened ticks collected in seven regions of Russia and found that the abundant jingmenvirus-positive were of Ixodes ricinus species, with the prevalence ranging from 19.8% to 34.3%. In all cases, DNase/RNase treatment suggested that the detected molecule was DNA and subsequent next generation sequencing (NGS) proved that the viral polymerase gene was integrated in the I. ricinus genome. The copy number of the integrated polymerase gene was quantified by qPCR relative to the ITS2 gene and estimated as 1.32 copies per cell. At least three different genetic variants of the integrated polymerase gene were found in the territory of Russia. Phylogenetic analysis of the integrated jingmenvirus polymerase gene showed the highest similarity with the sequence of the correspondent gene obtained in Serbia from I. ricinus.

Vector-borne pathogen surveillance in a metagenomic world

“…Evidence for host genome integration of particular nonretroviral RNA viruses has also been documented in vector mosquitoes, ticks, and sandflies [ 9 ]. Recently, integrated virus replicase sequences from the tick-borne human pathogen Jingmen tick virus have been identified in ticks, with implications for nucleic acid screening targeting this region [ 10 ].…”

Effective Methods of Estimation of Pathogen Prevalence in Pooled Ticks

“…The maximum-likelihood estimate of pooled prevalence (EPP) is defined as the infection rate most likely observed given the test results and an assumed probabilistic model (i.e., a binomial distribution of infected individuals in a positive pool). This method could be set both with fixed or variable pool size and, assuming perfect 100% test sensitivity and specificity, permits to estimate prevalence and confidence limits [28,29].…”