Metatranscriptomic analysis reveals the diversity of RNA viruses in ticks in Inner Mongolia, China

Abstract

Background: Ticks are widely distributed throughout China and are the second most prevalent pathogen vectors in the world, following only mosquitoes. Tick bites can lead to Lyme disease, forest encephalitis, and other illnesses that may result in death under severe circumstances. Materials and methods: Ticks collected from March 2021 to May 2023 were pooled and used in metatranscriptomic analyses to gain insight into the diversity and distribution of tick-borne viruses in Inner Mongolia. Next-generation sequencing (NGS) outcomes were validated, and viral prevalence across distinct tick species was determined through the application of polymerase chain reaction (PCR) paired with Sanger sequencing.

Results: A total of 20 RNA viruses belonging to at least 8 families, including Chuviridae, Flaviviridae, Solemoviridae, Nairoviridae, Partitiviridae, Phenuiviridae, Rhabdoviridae, and Totiviridae, and to unclassified families were identified by NGS. Five of the identified RNA viruses (Nuomin virus, Yezo virus, tick-borne encephalitis virus, Alongshan virus, and Beiji nairovirus) are considered human pathogens. A potential human pathogen, Mukawa virus, was also among the identified viruses. Ixodes persulcatus carried a significantly greater number of viral species than did Dermacentor nuttalli, Hyalomma marginatum, and Haemaphysalis concinna. The prevalence of coinfection with multiple viruses differed in I. persulcatus from Hinggan League and Hulun Buir, and Beiji nairovirus was the codominant virus species.

Conclusions: There is a remarkable diversity of RNA viruses harboured by ticks in Inner Mongolia, with variations observed in the distribution of these tick-borne viruses across different regions and tick hosts.

Fig 1. Map showing tick collection sites in Inner Mongolia, China.

The map was created using the ArcGIS software program. Map source: Xinliang Xu, Multiyear administrative division boundary data of Chinese cities and municipalities, Resource and Environmental Science Data Registration and Publication System (http://www.resdc.cn/DOI, DOI: 10.12078/2023010102).

Fig 2. Phylogenetic analysis of novel strains of Bunyavirales, Flaviviridae and Nairoviridae.

ML tree of representative viruses based on the RdRp genes. (A) ML tree of Bunyavirales viruses. (B) ML tree of viruses of Flaviviridae. (C) ML tree of viruses of Nairoviridae. The viruses newly identified in this study and previously identified viruses are shown in red and black, respectively. The best-fit amino acid substitution model for each phylogenetic tree was LG + F + R10 for Bunyavirales, LG + F + R7 for Flaviviridae, and LG + F + G4 for Nairoviridae.

Fig 3. Phylogenetic analysis of the novel strains of Chuviridae, Partitiviridae and Phenuiviridae.

ML tree of representative viruses based on the RdRp genes. (A) ML tree of Chuviridae viruses. (B) ML tree of Partitiviridae viruses. (C) ML tree of Phenuiviridae viruses (Fold clade 1 includes several members of the genus Phlebovirus. Fold clade 2 includes Phasivirus, Beidivirus, Hudivirus, Pidchovirus, Hudovirus, Tenuivirus, Mechlorovirus, and Horwuvirus. Fold clade 3 includes Goukovirus and Mobuvirus. Fold clade 4 includes Coguvirus, Laulavirus, Lentinuvirus, Entovirus, and Rubodvirus). The viruses newly identified in this study and previously identified viruses are shown in red and black, respectively. The best-fit amino acid substitution model for each phylogenetic tree was LG + I + G4 for Chuviridae, LG + F + I + G4 for Partitiviridae, and LG + F + R10 for Phenuiviridae.

Fig 4. Phylogenetic analysis of the novel strains of Rhabdoviridae, Solemoviridae and Totiviridae.

ML tree of representative viruses based on the RdRp genes. (A) ML tree of Rhabdoviridae (Fold clade 1 includes Hapavirus, Arurhavirus, Curiovirus, Ephemerovirus, Tibrovirus, Vesiculovirus, Sprivivirus, Perhabdovirus, Siniperhavirus, Cetarhavirus, Scophrhavirus, Sigmaviris, Alphapaprhavirus, Ohlsrhavirus, Merhavirus, Caligrhavirus, Sunrhavirus, Sripuvirus, Tupavirus, Ledantevirus, and Thriprhavirus. Fold clade 2 includes Lyssavirus, Replylivirus, and Amplylivirus. Fold clade 3 includes Betanucleorhabdovirus, Dichorhavirus, Alphanucleorhabdovirus, Gammanucleorhabdovirus, Varicosavirus, Cytorhabdovirus, Alphahymrhavirus, Betanemrhavirus, Alphacrustrhavirus, Betaricinrhavirus, Aphadrosrhavirus, Betahymrhavirus, and Betanemrhavirus). (B) ML tree of Solemoviridae. (C) ML tree of Totiviridae. The viruses newly identified in this study and previously identified viruses are shown in red and black, respectively. The best-fit amino acid substitution model for each phylogenetic tree was LG + F + R10 for Rhabdoviridae, LG + F + R5 for Solemoviridae, and LG + F + I + G4 for Totiviridae.