Diverse virome and potential pathogens in five tick species from metropolis surroundings of Beijing and Tianjin, China

Abstract

Rapid urbanization and dense populations in metropolitan areas increase the risk of tick-borne disease transmission. We profiled 139 RNA libraries of 1697 adult ticks belonging to Haemaphysalis longicornis, Haemaphysalis concinna, Dermacentor silvarum, Dermacentor sinicus, and Rhipicephalus sanguineus, field-collected in the Hebei region. Among 179 viral species, four human pathogens (a novel Bandavirus dabieense genotype, Orthonairovirus nairobiense, Thogotovirus thogotoense, and Xue-Cheng virus) were identified, highlighting potential emerging tick-borne disease threats. Four viruses infecting animals (Lagovirus europaeus, Ovine parvovirus, canine parvovirus, and Psittaciform Parvoviridae sp.) were discovered for the first time in ticks, suggesting the role of ticks as a potential reservoir. Hebei bunya-like virus 1, Dandong tick virus 1, and Zhejiang mosquito virus 3 were genetically closely related to mosquito-associated viruses, suggesting a potential transmission route for these viruses through both mosquitoes and ticks. The diverse tick virome in metropolitan surroundings contained potential human and animal pathogens, highlighting the need for proactive surveillance of emerging tick-borne viruses.

Fig. 1. Geographic map of sample collections in the Hebei region, China.

The color of the circle represents the species of tick samples collected in the area: dark blue for H. longicornis, light blue for H. concinna, pink for D. silvarum, yellow for D. sinicus, and green for R. sanguineus.

Fig. 2. The sequencing libraries and sample distribution of tick specimens.

a Virus abundance (top) and the number of identified viruses with genome sequences (bottom). b The viral α-diversity of H. longicornis, H. concinna, and D. silvarum was assessed. Shannon index was calculated, multiple comparisons were performed by bilateral Kruskal-Wallis test, and P-values were adjusted by Bonferroni method. c Beta diversity analysis of virome compositions across H. longicornis, H. concinna, and D. silvarum using t-SNE.

Fig. 3. Maximum likelihood phylogenies of viruses identified in this study based on protein sequences.

a Phylogenetic analysis of RdRp protein from ssRNA(+) viruses. b Phylogenetic analysis of RdRp protein from ssRNA(-) viruses. c Phylogenetic analysis of RdRp protein from dsRNA viruses. d Phylogenetic analysis of the non-structural replicase proteins in ssDNA viruses. e Phylogenetic analysis of RdRp protein from ormycovirus. The red pentagrams indicate a novel virus in this study. The color of the circle represents the species of tick. Tip are color-coded based on the tick species from which the viral sequences were collected: dark blue (H. longicornis), light blue (H. concinna), pink (D. silvarum), yellow (D. sinicus), and green (R. sanguineus). The circle represents a sequence, while the triangles represent multiple sequences.

Fig. 4

Taxonomic distribution of the 179 viruses identified in this study.

Fig. 5. Phylogenetic analysis of human pathogenic viruses.

a Phylogenetic relationship of segment L RdRp gene nt sequences of Bandavirus dabieense. b Phylogenetic relationship of segment L of Orthonairovirus. c Phylogenetic relationship of PB1 protein of Thogotovirus. The dark blue circle represents a sequence from H. longicornis, while the dark blue and light blue triangles represent multiple sequences from H. longicornis and H. concinna, respectively.

Fig. 6. Phylogenetic and recombination analysis of Rabbit hemorrhagic disease virus 2 (RHDV2).

a Phylogenetic relationship in the genus Lagovirus based on VP60 protein. b Phylogenetic relationship in the genus Lagovirus based on ORF1 protein except VP60. c Genome structure and recombination analysis of the RHDV2 strain. The horizontal axis represents the nt position of the genome, whereas the vertical axis represents the similarity to the two putative parental strains. The green plot indicates the closest major parent, EBHSV strain NC_002615, donor of the NS genes, whereas the orange plot indicates RHDV2 MT505389 strain, the closest minor parent, donor of the VP60 gene. A window size of 400 bp with a step size of 20 bp was used.

Fig. 7. Phylogenetic analysis of animal-infecting viruses and mosquito-associated viruses, including.

a Family Parvoviridae based on NS1. b Hebei bunya-like virus 1 based on RdRp protein. c Dandong tick virus 1 based on RdRp protein. d Zhejiang mosquito virus based on RdRp gene 3. The color of the circles represents the tick species, dark blue for H. longicornis, pink for D. silvarum, and green for R. sanguineus. The names of viruses infecting humans and mosquito-related viruses from the NCBI database are highlighted in red and cyan, respectively.