Virome analysis of ticks and tick-borne viruses in Heilongjiang and Jilin Provinces, China

Detection of tick-borne pathogens in blood-fed ticks from animals across nine Asian countries

Climate change, land development, and increased outdoor human activity have increased the prevalence and distribution of tick-borne pathogens, causing public health issues. Asia is a pivotal region of emerging infectious diseases caused by zoonotic disease. Therefore, this study aimed to construct effective surveillance systems and establish preventive strategies against novel tick-borne diseases. Next-generation sequencing (NGS) was performed to detect tick-borne pathogens from animal blood-fed ticks. Ticks (n = 261) were collected from different animals across nine Asian countries between 2022 and 2023. Five genera of adults and nymphal ticks were used, namely, Amblyomma, Haemaphysalis, Hyalomma, Rhipicephalus, and Ixodes. The animals from which the ticks were collected were wild, domestic animals, birds, and reptiles, living in the natural environment. After NGS, clean reads of 18,382,262-30,460,619 DNA viruses, 22,744,384-32,400,471 RNA viruses, 134,506-286,282 16S rRNA of bacteria, and 147,154-352,826 18S rRNA of protozoa were obtained from nine Asian countries. After analysis of the species, 28 RNA, 13 DNA viruses, 16 bacteria, and 4 protozoa were detected. Several tick-borne pathogens, including those in families that cause zoonotic diseases, such as Phenuiviridae, Nairoviridae, Rickettsiaceae, and Borreliaceae, were identified. This study is distinctive in that it involved cooperative studies with nine Asian countries to prevent the spread of tick-borne diseases. The results suggest that pathogens, which were detected in animal blood-fed ticks, can circulate in animals and may be transmitted to humans. In addition, this study can provide a basis for effective surveillance systems to prevent novel pathogens.

IMPORTANCE

Surveillance systems against novel tick-borne diseases are significant for global health. Climate and other environmental changes have contributed to an expanding range of ticks and tick-borne diseases. Areas in Asia constitute key areas of emerging infectious diseases. Through analysis of blood-fed ticks, collected from various animals living in the natural environment, we suggest that tick-borne pathogens may harbor animals and environment and have potential risk of transmission in humans. Understanding the distribution of tick-borne pathogens requires cooperative studying and, thus, can construct standardized surveillance systems.

Exploring the potential of tick transcriptomes for virus screening: A data reuse approach for tick-borne virus surveillance

BACKGROUND

We set out to investigate the utility of publicly available tick transcriptomic data to identify and characterize known and recently described tick-borne viruses, using de novo assembly and subsequent protein database alignment and taxonomical binning.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 127 virus contigs were recovered from 35 transcriptomes, originating from cell lines (40%), colony-reared ticks (25.7%) or field-collected ticks (34.2%). Generated virus contigs encompass DNA (n = 2) and RNA (n = 13) virus families, with 3 and 28 taxonomically distinct isolates, respectively. Known human and animal pathogens comprise 32.8% of the contigs, where Beiji nairovirus (BJNV) was the most prevalent tick-borne pathogenic virus, identified in 22.8% of the transcriptomes. Other pathogens included Nuomin virus (NUMV) (2.8%), African swine fever virus (ASFV) (5.7%), African horse sickness virus 3 (AHSV-3) (2.8%) and Alongshan virus (ALSV) (2.8%).

CONCLUSIONS

Previously generated transcriptome data can be leveraged for detecting tick-borne viruses, as exemplified by new descriptions of ALSV and BJNV in new geographic locations and other viruses previously detailed in screening reports. Monitoring pathogens using publicly available data might facilitate biosurveillance by directing efforts to regions of preliminary spillover and identifying targets for screening. Metadata availability is crucial for further assessments of detections.

Development of a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Beiji nairovirus

Beiji nairovirus (BJNV) is a recently discovered tick-borne RNA virus associated with human febrile illness. This study aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the precise detection of BJNV, with a specific focus on assessing its effectiveness with clinical samples. The optimal molecular target was identified as the BJNV small (S) segment gene, and the ideal reaction conditions were established at 65 °C for 50 min. A neutral red stain concentration of 300 μM was determined to be optimal for visualizing the LAMP reaction. The LAMP method demonstrated an impressive lower limit of detection at 10 copies/μL, highlighting a sensitivity level 10,000 times higher than traditional PCR methods. Moreover, it showed no cross-reactivity with three other viruses. The LAMP assay demonstrated results consistent with those of semi-nested PCR when applied to clinical samples, thereby validating its suitability for field testing. In conclusion, the LAMP assay developed in this study represents a significant advancement in the rapid detection of BJNV. Its high sensitivity, specificity, and ease of use make it a valuable tool for the establishment of effective prevention and control strategies against this emerging pathogen.

Prevalence of three important tick-borne pathogens in ticks and humans in Shaanxi Province, Northwest China

The investigation of important prevalent tick-borne pathogens is central to the control of tick-borne diseases. To understand the prevalence of Borrelia burgdorferi s.l., Borrelia miyamotoi, and the Alongshan virus in ticks and patients in Shaanxi Province, China, a total of 670 adult ticks and 524 patient blood samples were collected in the region between 2022 and 2023. In this study, PCR was used to estimate the prevalence of the three pathogens. The results revealed that the overall positive rates of B. burgdorferi s.l, B. miyamotoi, and ALSV infection in the collected ticks were 13.58 %, 2.46 %, and 4.17 %, respectively. Three genospecies of B. burgdorferi s.l. were detected in this study, namely, B. garinii, B. afzelii, and B. bavariensis, with positive rates of 4.63 %, 3.58 %, and 5.37 %, respectively. The prevalence rates of B. miyamotoi, ALSV  and B. burgdorferi s.l. in the patients were 0.38 %, 0.95 %, and 15 %, respectively. Moreover, B. burgdorferi s.l. and ALSV coinfection was also detected in three patients. Evolutionary analysis revealed that the isolate of B. miyamotoi belongs to the Asian type (Siberian type) and that of ALSV is closely related to that of Finland. To our knowledge, this is the first report on B. miyamotoi and ALSV detection in both ticks and humans in Shaanxi Province; the prevalence indicates that the regions in this province might be endemic areas. The results also suggest that humans in these regions are at risk of infection with these three tick-borne diseases.

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

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.

Development of a LAMP assay for the rapid visual detection of the emerging tick-borne Songling virus

BACKGROUND

Songling virus (SGLV) within the genus Orthonairovirus, family Nairoviridae, is an emerging tick-borne virus associated with human febrile illness. However, no rapid detection method for SGLV has been established.

METHODS

In this study, four primer sets targeting the nucleocapsid protein gene of SGLV were designed for use in the LAMP assay and evaluated to identify the optimal primer set. Recombinant plasmids were constructed and utilized for assessing the sensitivity of the assay. Tacheng tick virus 1 (TcTV-1)-, Beiji nairovirus (BJNV)-, Yezo virus (YEZV)-, severe fever with thrombocytopenia syndrome virus (SFTSV)-, and tick-borne encephalitis virus (TBEV)-positive tick samples were utilized to assess the specificity. Field-collected ticks were also evaluated as biological specimens to validate the assay.

RESULTS

A SGLV-specific LAMP assay was established with a detection limit of 1 × 10-2 copies/μl and could be visually confirmed by a color change from purple to blue in SGLV-positive samples. No cross-reactivity was observed in the detection of TcTV-1, BJNV, YEZV, SFTSV, and TBEV using the LAMP assay. In addition to the detection of the same seven high-copy numbers of SGLV as the SYBR Green quantitative RT-PCR assay within a reduced timeframe, the developed LAMP method also effectively identified an additional sample with a low copy number in the field-collected tick samples.

CONCLUSIONS

We successfully developed a sensitive, specific, and cost-effective visual method for the rapid detection of SGLV using the LAMP assay, which can be applied in pathogenesis and epidemiological surveillance studies of SGLV.

Diversity of species and geographic distribution of tick-borne viruses in China

Introduction

Tick-borne pathogens especially viruses are continuously appearing worldwide, which have caused severe public health threats. Understanding the species, distribution and epidemiological trends of tick-borne viruses (TBVs) is essential for disease surveillance and control.

Methods

In this study, the data on TBVs and the distribution of ticks in China were collected from databases and literature. The geographic distribution of TBVs in China was mapped based on geographic locations of viruses where they were prevalent or they were detected in vector ticks. TBVs sequences were collected from The National Center for Biotechnology Information and used to structure the phylogenetic tree.

Results

Eighteen TBVs from eight genera of five families were prevalent in China. Five genera of ticks played an important role in the transmission of TBVs in China. According to phylogenetic analysis, some new viral genotypes, such as the Dabieshan tick virus (DTV) strain detected in Liaoning Province and the JMTV strain detected in Heilongjiang Province existed in China.

Discussion

TBVs were widely distributed but the specific ranges of viruses from different families still varied in China. Seven TBVs belonging to the genus Orthonairovirus of the family Nairoviridae such as Nairobi sheep disease virus (NSDV) clustered in the Xinjiang Uygur Autonomous Region (XUAR) and northeastern areas of China. All viruses of the family Phenuiviridae except Severe fever with thrombocytopenia syndrome virus (SFTSV) were novel viruses that appeared in the last few years, such as Guertu virus (GTV) and Tacheng tick virus 2 (TcTV-2). They were mainly distributed in the central plains of China. Jingmen tick virus (JMTV) was distributed in at least fourteen provinces and had been detected in more than ten species of tick such as Rhipicephalus microplus and Haemaphysalis longicornis, which had the widest distribution and the largest number of vector ticks among all TBVs. Parainfluenza virus 5 (PIV5) and Lymphatic choriomeningitis virus (LCMV) were two potential TBVs in Northeast China that could cause serious diseases in humans or animals. Ixodes persulcatus carried the highest number of TBVs, followed by Dermacentor nuttalli and H. longicornis. They could carry as many as ten TBVs. Three strains of Tick-borne encephalitis (TBEV) from Inner Mongolia Province clustered with ones from Russia, Japan and Heilongjiang Province, respectively. Several SFTSV strains from Zhejiang Province clustered with strains from Korea and Japan. Specific surveillance of dominant TBVs should be established in different areas in China.

Metatranscriptomics Reveals the RNA Virome of Ixodes Persulcatus in the China-North Korea Border, 2017

In recent years, numerous viruses have been identified from ticks, and some have been linked to clinical cases of emerging tick-borne diseases. Chinese northeast frontier is tick infested. However, there is a notable lack of systematic monitoring efforts to assess the viral composition in the area, leaving the ecological landscape of viruses carried by ticks not clear enough. Between April and June 2017, 7101 ticks were collected to perform virus surveillance on the China-North Korea border, specifically in Tonghua, Baishan, and Yanbian. A total of 2127 Ixodes persulcatus were identified. Further investigation revealed the diversity of tick-borne viruses by transcriptome sequencing of Ixodes persulcatus. All ticks tested negative for tick-borne encephalitis virus. Transcriptome sequencing expanded 121 genomic sequence data of 12 different virus species from Ixodes persulcatus. Notably, a new segmented flavivirus, named Baishan Forest Tick Virus, were identified, closely related to Alongshan virus and Harz mountain virus. Therefore, this new virus may pose a potential threat to humans. Furthermore, the study revealed the existence of seven emerging tick-borne viruses dating back to 2017. These previously identified viruses included Mudanjiang phlebovirus, Onega tick phlebovirus, Sara tick phlebovirus, Yichun mivirus, and three unnamed viruses (one belonging to the Peribunyaviridae family and the other two belonging to the Phenuiviridae family). The existence of these emerging tick-borne viruses in tick samples collected in 2017 suggests that their history may extend further than previously recognized. This study provides invaluable insights into the virome of Ixodes persulcatus in the China-North Korea border region, enhancing our ongoing efforts to manage the risks associated with tick-borne viruses.

Genomic annotation for vaccine target identification and immunoinformatics-guided multi-epitope-based vaccine design against Songling virus through screening its whole genome encoded proteins

Songling virus (SGLV), a newly discovered tick-borne orthonairovirus, was recently identified in human spleen tissue. It exhibits cytopathic effects in human hepatoma cells and is associated with clinical symptoms including headache, fever, depression, fatigue, and dizziness, but no treatments or vaccines exist for this pathogenic virus. In the current study, immunoinformatics techniques were employed to identify potential vaccine targets within SGLV by comprehensively analyzing SGLV proteins. Four proteins were chosen based on specific thresholds to identify B-cell and T-cell epitopes, validated through IFN-γ epitopes. Six overlap MHC-I, MHC-II, and B cell epitopes were chosen to design a comprehensive vaccine candidate, ensuring 100% global coverage. These structures were paired with different adjuvants for broader protection against international strains. Vaccine constructions' 3D models were high-quality and validated by structural analysis. After molecular docking, SGLV-V4 was selected for further research due to its lowest binding energy (-66.26 kcal/mol) and its suitable immunological and physiochemical properties. The vaccine gene is expressed significantly in E. coli bacteria through in silico cloning. Immunological research and MD simulations supported its molecular stability and robust immune response within the host cell. These findings can potentially be used in designing safer and more effective experimental SGLV-V4 vaccines.

Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens

Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10'286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.

Quantitative Polymerase Chain Reaction System for Alongshan Virus Detection

The recently discovered Jingmenvirus group includes viruses with a segmented genome, RNA of a positive polarity, and several proteins with distant homology to the proteins of the members of the genus Orthoflavivirus. Some Jingmenvirus group members, namely the Alongshan virus (ALSV) and Jingmen tick virus, are reported to be tick-borne human pathogens that can cause a wide variety of symptoms. The ALSV is widely distributed in Eurasia, yet no reliable assay that can detect it exists. We describe a qPCR system for ALSV detection. Our data showed that this system can detect as little as 104 copies of the ALSV in a sample. The system showed no amplification of the common tick-borne viruses circulating in Eurasia, i.e., the Yanggou tick virus-which is another Jingmenvirus group member-or some known members of the genus Orthoflavivirus. The qPCR system was tested and had no nonspecific signal for the Ixodes ricinus, I. persulcatus, Dermacentor reticulatus, D. marginatus, Haemaphysalis concinna, and H. japonica ticks. The qPCR system had no nonspecific signal for human and sheep serum as well. Overall, the qPCR system described here can be used for reliable and quantitative ALSV detection.

Analysis of the diversity of tick-borne viruses at the border areas in Liaoning Province, China

Ticks play a significant role in transmitting arboviruses, which pose a risk to human and animal health. The region of Liaoning Province, China, with abundant plant resources with multiple tick populations, has reported several tick-borne diseases. However, there remains a scarcity of research on the composition and evolution of the tick virome. In this study, we conducted the metagenomic analysis of 561 ticks in the border area of Liaoning Province in China and identified viruses related to known diseases in humans and animals, including severe fever with thrombocytopenia syndrome virus (SFTSV) and nairobi sheep disease virus (NSDV). Moreover, the groups of tick viruses were also closely related to the families of Flaviviridae, Parvoviridae, Phenuiviridae, and Rhabdoviridae. Notably, the Dabieshan tick virus (DBTV) of the family Phenuiviridae was prevalent in these ticks, with the minimum infection rate (MIR) of 9.09%, higher than previously reported in numerous provinces in China. In addition, sequences of tick-borne viruses of the family Rhabdoviridae have first been reported from the border area of Liaoning Province, China, after being described from Hubei Province, China. This research furthered the insight into pathogens carried by ticks in the northeastern border areas of China, offering epidemiological information for possible forthcoming outbreaks of infectious diseases. Meanwhile, we provided an essential reference for assessing the risk of tick bite infection in humans and animals, as well as for exploring into the evolution of the virus and the mechanisms of species transmission.