RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qīnghăi Province, China

Abstract

Ticks are a major parasite on the Qīnghăi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species in this area remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qīnghăi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xīnjiāng tick-associated virus 1 (XJTAV1), and three novel viruses: Qīnghăi Lake virus 1, Qīnghăi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qīnghăi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses in the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. ​nuttalli ticks. A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses from sequencing data of other tick pools by ​using the putative M segment sequence of QHLV3. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.

Keywords: Dermacentor nuttalli; M segment; Qīnghăi Province; Uukuvirus; Virome.

Fig. 1

Viral abundance of Dermacentor nuttalli ticks according to metagenomics analysis. A Proportions of the numbers of reads assigned to eukaryotes, bacteria, and viruses, and number of unassigned reads in each of the six pools shown as pie charts. B Heatmap of the TPM of viruses identified from 2015 to 2017. TPM, transcripts per million.

Fig. 2

Phylogenetic relationships and genome organizations of QHLV3. A Genome organizations of QHLV3. Black lines represent contigs, yellow arrows represent ORFs, and purple regions represent conserved domains. B Phylogenetic trees of QHLV3 L and S segments. Red font indicates the uukuvirus lacking the M segment. QHLV3, Qīnghăi Lake virus 3; ORF, open reading frame.

Fig. 3

Putative M segment encoding a glycoprotein with similar features to the viral glycoprotein belonging to family Phenuiviridae. A Glycoprotein features of family Phenuiviridae. Yellow line represents the glycoprotein, “SP” represents the signal peptide cleavage site, green slash represents the glycoprotein cleavage site, red asterisk represents the N-glycosylation site, and purple region represents the transmembrane region. B Alignment of glycoprotein cleavage sites. C Western blot result of Gn and Gc glycosylation after treatment with tunicamycin. Primary antibodies for Gn and Gc were anti-strep and anti-flag, respectively.

Fig. S1

The phylogenetic tree constructed by using the ITS2 genes of different tick species, including those collected from Qīnghăi Lake (in red).

Fig. S2

A heatmap showing the abundance of viruses identified from 5 pools in 2016 and 2017.

Fig. S3

Genome organizations of XJTAV1, QHLV1, and QHLV2. Black lines represent contigs, yellow arrows represent ORFs, and purple regions represent conserved domains.

Fig. S4

Pairwise comparison of viral protein sequence identities of RdRp, GP, and NP among phenuiviruses.