Fig 1.
Sampling sites of ticks in northeastern China.
The number of ticks collected at each site was marked, and species was shown by different colors. Yellow, Ixodes persulcatus; Green, Dermacentor silvarum; Brown, Haemaphysalis concinna; Orange, Haemaphysalis japonica. The link to the base layer of the map is http://bzdt.ch.mnr.gov.cn/index.html.
Table 1.
Viruses identified in the present study.
Fig 2.
Viral presence and abundance across the libraries.
(A) Viral number identified in each library. (B) Heatmap based on the normalized numbers of sequence reads for 8 viral families and one unclassified RNA virus in each library. Tick species and location information were listed at the bottom, and names of the viral families and species were indicated on the left. Log10 relative abundance of the viruses in each species in each location were indicated as a heat map ranging from low (blue) to high (red) based on the normalized average viral genome size and total sequencing reads in each library. The libraries from XXAM, DXAM, and CBM are marked with blue, red, and black, respectively.
Fig 3.
Phylogenetic analyses of flaviviruses.
Phylogenetic trees were constructed based on the RdRp sequence of representative viruses in the family Flaviviridae (A), the segment 3 of ALSV and other representative viral strains in the Jingmenvirus group (B), the E protein of TBEV in NE China (C), and the RdRp of BLTV4 (D). All the viruses obtained in ticks here were highlighted in red. In panel A, closest referenced viruses were highlighted in bold font, and the virus genera or groups were marked with different colors of background. In panel B, ALSV isolated from humans were marked with blue. ALSV were highlighted with light green background. The host tick species of the viruses and the countries that the viruses discovered were also labeled. In panel C, TBEV isolated from CBM and XXAM were marked with blue-filled circles, while strains found in DXAM were marked with red-filled circles. In panel D, the strain names of BLTV4 were labeled. The host tick species and the countries that BLTV4 discovered were also marked. ALSV, Alongshan virus; TBEV, Tick-borne encephalitis virus; BLTV4, Bole tick virus 4. The accession numbers of the viral sequences are shown in S2 and S3 Tables.
Fig 4.
Phylogenetic analyses of nairoviruses.
Phylogenetic trees were constructed based on the RdRp protein sequences of representative viruses in the Nairoviridae family (A), the S segment of JANV and SGLV (B), and the S segment of BJNV and YCNV (C). All the viruses obtained in ticks here were highlighted in red, and the closest referenced viruses were also highlighted in bold font. In panel B and C, viral strains identified in this study were marked with red-filled circles, while strains found in humans were marked with blue-filled circles. JANV, Ji’an nariovirus; SGLV, Songling virus; TCTV1, Tacheng tick virus 1; SXTV2, Shanxi tick virus 2; HNTV, Henan tick virus; YCNV, Yichun nariovirus; BJNV, Beiji nariovirus; GKTV, Gakugsa tick virus; PTV, Pustyn virus; NWNV1, Norway nairovirus 1; GTV, Grotenhout virus. The accession numbers of the viral sequences are shown in S2 and S3 Tables.
Fig 5.
Phylogenetic analyses of phenuiviruses.
Phylogenetic trees constructed based on the RdRp sequences of representative viruses in the family Phenuiviridae (A), the S segment of MKWV and MJPV (B), and the S segment of STPV and OTPV (C). All the viruses obtained in ticks here were highlighted in red, and the closest referenced viruses were highlighted in bold font. Abbreviations: MKWV, Mukawa virus; KYV, Kuriyama virus; MJPV, Mudanjiang phlebovirus; BTPV1, Blacklegged tick phlebovirus-1; NWPV1, Norway phlebovirus 1; STPV, Sara tick phlebovirus; OTPV, Onega tick phlebovirus. The accession numbers of the viral sequences are shown in S2 and S3 Tables.
Fig 6.
Phylogenetic analyses of rhabdoviruses.
Phylogenetic trees constructed based on the RdRp sequences of representative viruses in the family Rhabdoviridae (A), the RdRp sequences of novel identified Tahe rhabdoviruses (B). All the viruses obtained in ticks here were highlighted in red, and the closest referenced viruses were also highlighted in bold font. Abbreviations: THRV1, Tahe rhabdovirus 1; THRV2, Tahe rhabdovirus 2; THRV3, Tahe rhabdovirus 3. The accession numbers of the viral sequences are shown in S2 and S3 Tables.
Fig 7.
Phylogenetic analyses of chuviruses.
Phylogenetic trees were constructed based on the RdRp sequences of representative viruses in the family Chuviridae (A), the RdRp sequences of NUMV (B) and JLCV (C). All the viruses obtained in ticks here were highlighted in red, and the closest referenced viruses were also highlighted in bold font. In panel B, NUMV viral strains discovered from ticks were marked with red-filled circles, while strains found in tick-bite patients were marked with blue-filled circles. Abbreviations: NUMV, Nuomin virus; YCMV, Yichun mivirus. The accession numbers of the viral sequences are shown in S2 and S3 Tables.
Fig 8.
Phylogenetic analyses of plant-related viruses.
Phylogenetic trees constructed based on the RdRp protein sequences of representative viruses in the family Partitiviridae (A), Tombusviridae (B), Solemoviridae (C), and ISAV3 (D). All the viruses obtained in ticks here were highlighted in red, and the closest referenced viruses were also highlighted in bold font. Abbreviations: JPLV1, Jilin partiti-like virus 1; NPLV1, Norway partiti-like virus 1; FTLV, Fangzheng tombus-like virus; ISAV3, Ixodes scapularis associated virus 3; ISAV4, Ixodes scapularis associated virus 4; XTAV2, Xinjiang tick associated virus 2; ADTV, American dog tick associated virus 2. The accession numbers of the viral sequences are shown in S2 and S3 Tables.