Tick virome diversity in Hubei Province, China, and the influence of host ecology

Abstract

Ticks are important vector hosts of pathogens which cause human and animal diseases worldwide. Diverse viruses have been discovered in ticks; however, little is known about the ecological factors that affect the tick virome composition and evolution. Herein, we employed RNA sequencing to study the virome diversity of the Haemaphysalis longicornis and Rhipicephalus microplus ticks sampled in Hubei Province in China. Twelve RNA viruses with complete genomes were identified, which belonged to six viral families: Flaviviridae, Matonaviridae, Peribunyaviridae, Nairoviridae, Phenuiviridae, and Rhabdoviridae. These viruses showed great diversity in their genome organization and evolution, four of which were proposed to be novel species. The virome diversity and abundance of R. microplus ticks fed on cattle were evidently high. Further ecological analyses suggested that host species and feeding status may be key factors affecting the tick virome structure. This study described a number of novel viral species and variants from ticks and, more importantly, provided insights into the ecological factors shaping the virome structures of ticks, although it clearly warrants further investigation.

Keywords: JMTV; ecology; evolution; ticks; virome; virus diversity.

Figure 1.

Sampling sites in Hubei Province and the tick species composition. Abbreviations of sampling sites: Wanhe (WH) and Yindian (YD) towns in Suizhou City (SZ), and Huahe (HH), Yonghe (YH), Shunhe (SH), Yantianhe (YTH), Baimiaohe (BMH), and Shengli (SL) towns in Huanggang City (HG). The number of samples at each site was marked. The types of ticks are represented by different colors: blue: H. longicornis fed on goats (H. longicornis—goat), yellow: H. longicornis free (H. longicornis—free), green: R. microplus fed on goats (R. microplus—goat), and orange: R. microplus fed on cattle (R. microplus—cattle).

Figure 2.

Viral presence and abundance across the libraries. (A) Virus counts identified in each library. (B) Total and (C) proportions of the RPM (non-rRNA) of the twelve identified viruses shown in different colors.

Figure 3.

Phylogenetic analyses of flaviviruses and jingmenviruses. Phylogenetic trees were constructed based on the RdRP protein sequences of representative viruses in the family Flaviviridae (A) and the segment 3 of jingmenviruses (B). In panel A, viruses obtained in ticks here are marked with red-filled circles and highlighted in red, and the closest referenced viruses are also highlighted in bold font. In panel B, the strains described here are shown using the same colors as those in Fig. 1, representing the type of the ticks. The hosts of JMTVs discovered previously are marked as follows: black-filled circles, ticks; grey-filled circles, other arthropods; and grey-filled rectangles, mammals. The accession numbers of the viral sequences used in the trees are shown in Supplementary Table S3.

Figure 4.

Phylogenetic analyses of hepeliviruses. Phylogenetic trees were constructed based on the RdRP protein sequences of representative viruses in the order Hepelivirales (A) and the HTHLV strains (B). Viruses identified in ticks here are marked with red-filled circles and are formatted in bold red font, and the closest referenced viruses are shown in bold font. The strains described in this study are shown using the same colors as those in Fig. 1, representing the type of the ticks. The accession numbers of the viral sequences used in the trees are shown in Supplementary Table S3.

Figure 5.

Phylogenetic tree generated based on the RdRP protein sequences of peribunyaviruses. Viruses identified in ticks here are marked with red-filled circles and are formatted in bold red font, and the closest referenced viruses are shown in bold font. The accession numbers of the viral sequences used in the tree are shown in Supplementary Table S3.

Figure 6.

Phylogenetic analyses of nairoviruses. Phylogenetic trees were constructed based on the RdRP protein sequences of viruses in Nairoviridae (A) and S segments of known NSDVs (B). In panel A, viruses obtained in ticks here are marked with red-filled circles and highlighted in red, and the closest referenced viruses are shown in bold font. In panel B, the strains described here are shown using the same colors as those in Fig. 1, representing the type of the ticks. The hosts of NSDVs discovered previously are marked as follows: black-filled circles, ticks; and grey-filled rectangles, mammals. The accession numbers of the viral sequences used in the trees are shown in Supplementary Table S3.

Figure 7.

Phylogenetic analyses of phenuiviruses. Phylogenetic trees were constructed based on the RdRP protein sequences (A) of viruses in Phenuiviridae and S segments of SFTSV found in China (B), LHTVs (C), and DBSTVs (D). In panel A, viruses obtained in ticks here were marked with red-filled circles and highlighted in red, and the closest referenced viruses are also highlighted in bold font. In panel B, the hosts of SFTSVs discovered previously are marked as follows: black-filled circles, ticks; grey-filled circles, other arthropods; black-filled rectangles, humans; and grey-filled rectangles, mammals. The strains described here are shown using the same colors as those in Fig. 1, representing the type of the ticks. The accession numbers of the viral sequences used in the trees are shown in Supplementary Table S3.

Figure 8.

Phylogenetic analyses of rhabdoviruses. Phylogenetic trees were constructed based on the RdRP protein sequences of viruses in Rhabdoviridae (A) and full-length genomes of WHTV2 (B) and WHTV1 (C) found in China. In panel A, viruses identified in ticks here are marked with red-filled circles and are formatted in bold red font, and the closest referenced viruses are shown in bold font. In panel B, the strains described in this study are shown using the same colors as those in Fig. 1, representing the type of the ticks. The accession numbers of the viral sequences used in the trees are shown in Supplementary Table S3.

Figure 9.

Comparison of the viral diversity between tick species and feeding statuses. (A) Virome richness, (B) Shannon, and (C) Shannon effective indices. The numbers of libraries of the four types of ticks are as follows: H. longicornis—goat (n = 35), H. longicornis—unfed (n = 3), R. microplus—cattle (n = 8), and R. microplus—goat (n = 4).

Figure 10.

Beta diversity analysis of the viromic composition among libraries.