From 2014 to 2017, a total of 58, 932 tick samples were collected from 17 counties in four geographic ecosystems in Xinjiang, including the arid desert area in Junggar Basin and Tarim Basin, the north slope forest grassland of the Tianshan Mountain, and drought desert grassland in hilly south slope of the Altai Mountain. Among the collected ticks, 10, 840 samples of H. asiaticum asiaticum were grouped into 130 pools, 47, 608 D. nuttalli samples were grouped into 464 pools, and 454 H. detritum samples were grouped into 18 pools, and all pools were screened for the presence of CCHFV RNA by nested RT-PCR (Guo et al. 2017). The distribution of CCHFV in four geographical ecosystems was assessed; H. asiaticum asiaticum was mainly distributed in the arid desert region in Tarim and Junggar basins, whereas D. nuttalli and H. detritum were mainly distributed in the north slope forest grassland of the Tianshan Mountain and the drought desert grassland in the hilly south slope of the Altai Mountain. The CCHFVpositive percentage was 5.26%, 6.85%, 1.94%, and 5.56% in Tarim Basin, Junggar Basin, Tianshan Mountain, and Altai Mountain, respectively. The results are shown in Table 1.
Table 1. Molecular detection of CCHFV from ticks isolated from different regions in Xinjiang, China.
The tick populations in the abovementioned ecosystems were different. H. asiaticum asiaticum was the predominant tick species in the arid desert region in Tarim and Junggar basins, whereas D. nuttalli and H. detritum were dominant in the north slope forest grassland of the Tianshan Mountain and the drought desert grassland in the hilly south slope of the Altai Mountain (Table 1). CCHFV was mainly detected in H. asiaticum asiaticum, D. nuttalli, and H. detritum, and the CCHFV-positive samples included 8 of 130 (6.15%) H. asiaticum asiaticum pools, 9 of 464 (1.94%) D. nuttalli pools, and 1 of 18 (5.56%) H. detritum pools. The results showed that the positive detection rate of CCHFV in H. asiaticum asiaticum and H. detritum was significantly higher (χ2 = 6.948, P = 0.031) than that in D. nuttalli (Table 1), suggesting that the Hyalomma tick is the major CCHFV vector in Xinjiang. Nevertheless, this study was the first to detect CCHFV in H. detritum and D. nuttalli in the Altai Mountain and Tianshan Mountain.
The PCR product obtained using the CCHFV-S primers was recovered and sequenced. Eighteen partial S segments obtained from this study were analyzed. The results indicated that the amplified fragment (220 bp) from 18 Chinese strains had high similarity in terms of nucleic acid (85%– 99.5% identity) and amino acid sequences (88.9%–100% identity).
Sequences of CCHFV S segment obtained in this study were submitted to GenBank and used for a phylogenetic analysis (Supplementary Table S1). Figure 2 shows the phylogenetic tree based on the 18 partial S segments from this study and 44 representative CCHFV sequences from GenBank (Supplementary Table S2). Among the 18 partial sequences, nine were from D. nuttali, eight from H. asiaticum asiaticum, and one from H. detritum (Supplementary Table S1).
Our results showed that CCHFV strains could be generally grouped into eight clades: Europe 1, Asia 2, Asia 1, Africa 3, Europe 3, Africa 2, Africa 1, and Europe 2 (Fig. 2). This result is in agreement with that of previous studies (Hewson et al. 2004; Guo et al. 2017; OrKun et al. 2017). Based on the result of the sequencing and phylogenetic analyses, CCHFV strains obtained in this study were clustered into two clades. Eleven newly detected Chinese strains from Wusu Ganjiahu, Wusu Guertu, and Jinghe Bayinamen in the Junggar Basin, and from Yuli in the Tarim Basin were clustered in the Asia 2 clade, which contains strains from Xinjiang, China, as well as from Uzbekistan, Tajikistan, India, and other countries. Other novel Chinese strains from Wusu Guertu and Urumqi Midong in the Junggar Basin, and Fuhai in the Altai prefecture were clustered in the Asia 1 clade, which also contains strains from Xinjiang, China, as well as from Pakistan, Oman, Kazakhstan, and others. In both clades, sequences from different tick species appeared to be grouped together, indicating that emergence of the two CCHFV clades may be independent of their vectors.
Figure 2. Phylogenetic tree of CCHFV strains based on sequences of the 220-nucleotide S RNA fragment. Strains are displayed in the format of "GenBank accession number, strain, country, year, and origin". The tree was constructed using the maximum likelihood method with MEGA6 software. Values lower than 50% are not shown. The red and black circles indicate sequences obtained in this study (detailed information in Supplementary Table S1), while others are from reference strains (detailed information in Supplementary Table S2).
Geographical Distribution of CCHFV
Distribution of CCHFV Host Ticks
Phylogenetic Tree Mapping Based on CCHFV S Fragment Sequences
Table S1. Xinjiang CCHFV strains detected in the present study
Table S2. CCHFV isolates from GenBank used for the phylogenetic analysis