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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. https://doi.org/10.1371/journal.pntd.0011017.g005
Source publication
Background:
Ticks act as important vectors of infectious agents, and several emerging tick-borne viruses have recently been identified to be associated with human diseases in northeastern China. However, little is known about the tick virome in northeastern China.
Methods:
Ticks collected from April 2020 to July 2021 were pooled for metagenomic...
Context in source publication
Context 1
... MKWV and MJPV, together with STPV and OTPV identified here, fell within the genera Phlebovirus and Ixovirus of the family Phenuiviridae, respectively (Fig 5A). MKWV NE strains were clustered together with the strain MKW73 identified in I. persulcatus ticks in Japan, with nt identities of 92.4-100% for L segment, 90.7-100% for M segment, and 93.5-99.9% ...
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Crimean-Congo haemorrhagic fever orthonairovirus (CCHFV) is a negative-sense, single-stranded RNA virus with a segmented genome and the causative agent of a severe Crimean-Congo haemorrhagic fever (CCHF) disease. The virus is transmitted mainly by tick species in Hyalomma genus but other ticks such as representatives of genera Dermacentor and Rhipi...
Citations
... In light of extensive tick virus diversity and incidence, including TBEV, uncovered through metagenomic sequencing efforts in China [19][20][21][22][23][24], we sought to further understand the diversity of tick-borne orthoflaviviruses in the country. To achieve this, we conducted high-throughput metatranscriptomics and subsequent screening of wild samples. ...
Tick-borne orthoflaviviruses (TBFs) are classified into three conventional groups based on genetics and ecology: mammalian, seabird and probable-TBF group. Recently, a fourth basal group has been identified in Rhipicephalus ticks from Africa: Mpulungu flavivirus (MPFV) in Zambia and Ngoye virus (NGOV) in Senegal. Despite attempts, isolating these viruses in vertebrate and invertebrate cell lines or intracerebral injection of newborn mice with virus-containing homogenates has remained unsuccessful. In this study, we report the discovery of Xinyang flavivirus (XiFV) in Haemaphysalis flava ticks from Xìnyáng, Henan Province, China. Phylogenetic analysis shows that XiFV was most closely related to MPFV and NGOV, marking the first identification of this tick orthoflavivirus group in Asia. We developed a reverse transcriptase quantitative PCR assay to screen wild-collected ticks and egg clutches, with absolute infection rates of 20.75 % in adult females and 15.19 % in egg clutches, suggesting that XiFV could be potentially spread through transovarial transmission. To examine potential host range, dinucleotide composition analyses revealed that XiFV, MPFV and NGOV share a closer composition to classical insect-specific orthoflaviviruses than to vertebrate-infecting TBFs, suggesting that XiFV could be a tick-only orthoflavivirus. Additionally, both XiFV and MPFV lack a furin cleavage site in the prM protein, unlike other TBFs, suggesting these viruses might exist towards a biased immature particle state. To examine this, chimeric Binjari virus with XIFV-prME (bXiFV) was generated, purified and analysed by SDS-PAGE and negative-stain transmission electron microscopy, suggesting prototypical orthoflavivirus size (~50 nm) and bias towards uncleaved prM. In silico structural analyses of the 3′-untranslated regions show that XiFV forms up to five pseudo-knot-containing stem-loops and a prototypical orthoflavivirus dumbbell element, suggesting the potential for multiple exoribonuclease-resistant RNA structures.
... Beiji nairovirus (BJNV), also a new nairo-like virus, was first mentioned in high-throughput sequencing, and then it was detected in a febrile patient in Inner Mongolia Province. Researchers identified BJNV infections in several tick-bitten patients in Heilongjiang and Jilin Provinces, and BJNV was also detected in local ticks, including I. persulcatus, I. crenulatus, Demacentor silvarum, D. nuttalli, H. concinna and H. longicornis (Wang YC et al., 2021;Liu et al., 2022). Yezo virus (YEZV) is a new Orthonairovirus first detected in Japan in 2019 and is currently only reported in Japan and China (Kodama et al., 2021). ...
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.
... Initial detection of SGLV occurred in patients in China in 2021 [15]. Subsequently, the virus nucleic acid was detected in ticks in the Greater and Lesser Khingan Mountains in northeast China, and in great gerbils in Xinjiang [15,[17][18][19]. SGLV encompasses typical characteristics of orthonairoviruses. ...
... Initially reported in northeast China in 2021 as a novel tick-borne virus, SGLV has been linked to human diseases. Further investigations have revealed the presence of SGLV nucleic acid in H. concinna ticks and great gerbils in the northeastern and northwestern region of China [15,[17][18][19] [15]. Further research is warranted to elucidate the specific mechanisms underlying SGLV transmission by H. concinna and its potential implications for public health. ...
Background
Songling virus (SGLV) is a spherical, enveloped, fragmented, negative-stranded RNA virus belonging to the genus Orthonairovirus in the Nairoviridae family. SGLV is transmitted by ticks and can cause disease in humans. This study identified and characterized SGLV in Haemaphysalis concinna ticks collected in 2023 in the Yanbian Korean Autonomous Prefecture (China) near the China-North Korea border.
Methods
A real-time quantitative polymerase chain reaction (RT-qPCR) was used to screen for SGLV nucleic acid in ticks. Baby hamster kidney (BHK-21) and African green monkey kidney (Vero) cells were used to isolate strains of SGLV from nucleic acid-positive samples through three successive passages. Next-generation sequencing and phylogenetics methods were used to characterize the SGLVs.
Results
Of the 1659 ticks collected from 6 towns in the Yanbian Korean Autonomous Prefecture near the China-North Korea border, positive SGLV nucleic acid results were identified in 19 H. concinna tick pools from Helong and Longjing towns. This discovery led to the extraction of 17 SGLV genome sequences. Homology analysis that compare the newly discovered L, M, and S segments of SGLV strain HLJ1202 revealed nucleotide similarities ranging from 95.5%–97.1%, 91.9%–98.9%, and 98.3%–99.2%, respectively, and amino acid similarities ranging from 95.7%–97.4%, 97.1%–98.8%, and 98.2%–98.9%, respectively. Six distinct clades, characterized by specific geographic locations and host organisms, were identified on the Maximum Likelihood tree of the L segment. The YB129 and YB150 isolates demonstrated SGLV nucleic acid replication across three successive passages in Vero cells, as evidenced by the decrease in RT-qPCR Ct values.
Conclusion
This study marks the initial identification of SGLV in H. concinna within the Yanbian Korean Autonomous Prefecture.
... Located within the transnational area of Changbai Mountain, these border cities are characterized by a temperate monsoon climate and is abundant in forests and wildlife resources. These environmental characteristics provide favorable conditions for tick proliferation and the circulation of tick-borne viruses [6]. TBEV has been prevalent in this region for a considerable time [7,8]. ...
... While differences were identified in the I. persulcatus virome among different regions, no apparent distinction was found for viruses with the potential to infect humans. Although previous metagenomic studies have explored the tick-borne pathogen spectrum in the region [5,6], we provided a more comprehensive understanding of tick-borne virus diversity across the three regions. Alpha and beta diversity analyses revealed that Yanbian shows significantly greater diversity at the viral family and species levels compared to Baishan, and the viral spectrum composition of I. persulcatus also differs between these two regions. ...
... Although our study only identified three new YEZV strains with a low positive rate, it is important to note that our pooled sequencing cannot determine the individual tick-level positivity rate. Beiji nairovirus has exclusively been found in northeastern China, with the earliest detection dating back to 2015 in I. persulcatus [6,21,41]. In our study, Beiji nairovirus was detected in 25 out of 53 libraries, indicating a relatively high positivity rate. ...
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.
... Due to its ability to cause severe and fatal disease in humans, RVFV has been listed as a priority pathogen by the World Health Organization (WHO) [6]. Since the 2000s, novel phleboviruses have been continuously identified and classified based on their genetic and serological characterization [7][8][9]. In 2018, the Mukawa virus (MKWV), a newly discovered member of the genus Phlebovirus, was detected and isolated from Ixodes persulcatus ticks collected in Hokkaido, Japan [7]. ...
... Our own group's study, as well as others', confirmed the presence of MKWV in I. persulcatus and Haemaphysalis concinna in northern China [10]. Recently, another new species within the Phlebovirus genus, the Mudanjiang phlebovirus (MJPV), was identified through next-generation sequencing (NGS) from I. persulcatus in Mudanjiang city, Heilongjiang province, China [9]. Given that Phlebovirus members have a wide geographic distribution across East Asia, we aimed to determine molecular evidence of MJPV by studying a diverse range of ticks and wild small mammals across an expanded geographic area in China. ...
... ON408133.1 and ON408134.1) [9], we conducted a pairwise similarity analysis. The nucleotide acid identity for full L, M, and S sequences was found to be 99.11%, ...
Mudanjiang phlebovirus (MJPV) is a newly discovered phlebovirus, initially detected from Ixodes persulcatus ticks in China in 2022. In this study, by next-generation sequencing (NGS) on a wide variety of ticks and wild small animals in China, we detected MJPV from I. persulcatus and Meriones meridianus. Additionally, we conducted RT-PCR and sequencing on 1815 adult ticks and 805 wild small mammals collected from eight provinces in China between 2017 and 2021. MJPV RNA-positive results were found in 0.22% (4/1815) of tick samples, as well as in 0.12% (1/805) of rodent samples. All positive detections were obtained from Heilongjiang and Inner Mongolia. Sequencing analysis revealed nucleotide similarities ranging from 98.23% to 99.11%, as well as amino acid similarities ranging from 99.12% to100%, between the current MJPV strain and previously reported strains of MJPV. Phylogenetic tree analysis demonstrated that the previously reported MJPV strain along with our two variants clustered together with other tick-borne phenuiviruses, indicating their close relationship within this viral group. This study represents the first detection of MJPV infection in wild rodents, expanding the known host range for this virus in the endemic regions.
... MDJV-like/Alsace and MDJV-like/Iasi presented the same trisegmented genome architecture specific to phleboviruses. Comparison of the RdRp sequences of Alsace and Iasi MDJV strains demonstrated a 99% amino-acid identity between each other, and a lower (around 90%) degree of conservation with the two strains of MDJV identified in Ixodes persulcatus in China [43]. MDJV-like/Alsace and [43,44] and Japan (Mukawa and Kuriyama virus) [45], respectively, except for Pangolin phlebovirus for which the vector is yet unknown. ...
... Comparison of the RdRp sequences of Alsace and Iasi MDJV strains demonstrated a 99% amino-acid identity between each other, and a lower (around 90%) degree of conservation with the two strains of MDJV identified in Ixodes persulcatus in China [43]. MDJV-like/Alsace and [43,44] and Japan (Mukawa and Kuriyama virus) [45], respectively, except for Pangolin phlebovirus for which the vector is yet unknown. This clade is rooted by Alxa phlebovirus, a tick-borne phlebovirus detected in Chinese tick metagenomes in 2016 and 2019, forming a distinct but well-supported clade within the Phlebovirus genus ( Figure 4). ...
... In contrast, our serological research indicated that MDJV does not appear to have the ability to infect small ruminants, or at very low prevalence. Therefore, we cannot exclude that this virus could constitute tick endosymbionts that represent viral ancestors of the known trisegmented tick-borne phleboviruses, as previously suggested [43]. ...
Tick-borne pathogens are responsible for many vector-borne diseases in Europe, causing important problems for human and animal health. The composition of viral communities in ticks and their interactions with pathogens is little understood, especially in Eastern Europe, an area that represents a major hub for animal-arthropod vectors exchanges. In this study, we used metatran-scriptomics to characterize the virome of 2,753 Ixodes ricinus ticks collected from France and Romania, focusing on viruses that could potentially have implications for human or animal health. Among the great viral diversity of viruses identified, we reported a novel strain of Tribec virus, an important human pathogen that was found in Romanian ticks. We detected viruses belonging to the Phenuiviridae and Nairoviridae families close to human and animal pathogens, suggesting that these viruses could constitute novel arboviruses. We used luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Sedoreoviridae, Phenuiviridae, and Nairoviridae families to screen serum samples from small ruminants' exposed to tick bites. The results suggest that part (approximately 12%, 95% CI 9.1-16.2) of the small ruminant population from Danube Delta, was exposed to viruses related to bi-or tri-segmented nairoviruses, but cross-reactive viruses could not be confirmed with certainly. The strategy developed in this study serves as a key step in predicting potential new disease outbreaks and can be readily adapted to study other reservoirs, vectors, and interfaces involving susceptible hosts.
... Our analysis of the bat-tick C. vespertilionis virome revealed the family Nairoviridae (Bunyavirales) as the most abundant and prevalent in the libraries of recently blood-fed ticks (Fig. 1). Similar findings have been reported in recent metagenomic studies on different tick and host species across a variety of geographical locations [44][45][46][47], suggesting that ticks might be competent hosts and vectors for the replication and transmission of nairoviruses in nature. Among the members of the Nairoviridae found here, we identified ISKV [48,49], a zoonotic virus associated with outbreaks of acute febrile illness in humans. ...
Ticks harbour a high diversity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle (Pipistrellus pygmaeus, Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae, while other invertebrate-associated viruses included members of the Dicistroviridae, Iflaviridae, Nodaviridae, Partitiviridae, Permutotetraviridae, Polycipiviridae and Solemoviridae. Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable diversity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
The incidence of numerous vector-borne diseases (VBDs) has recently increased alarmingly due to various widespread factors, including unplanned urbanization, greater human mobility, environmental changes, vector resistance to insecticides, and evolving pathogens. In this context, the World Health Organization (WHO) has repositioned effective and sustainable vector control as a key approach to prevent and eliminate VBDs. It has been shown that the microbiome influences development, nutrition, and pathogen defense in disease-transmitting vectors such as mosquitoes, sandflies, tsetse flies, triatomine bugs, and ticks. Consequently, understanding the endogenous regulation of vector biology can aid in developing effective approaches for vector control. In this respect, a metatranscriptomic approach analyzes all the expressed RNAs in an environmental sample (meta-RNAs) and can thus reveal how the metabolic activities of the microbiome influence vector biology. This review includes an extensive analysis of available literature on microbial and viral studies for some of the major hematophagous disease-transmitting arthropods, with a focus on studies that used next generation sequencing (NGS) approaches. Since a consensus terminology for these “meta-sequencing analyses” has not yet been established, a definition of these terms is presented here to provide the framework for systematically sorting the available information for each of the VBDs analyzed here to single out metatranscriptomic analyses. Finally, key gaps in knowledge were identified for some of these hematophagous disease-transmitting arthropods which will prove very useful for driving future studies.
It is a volume of the Journal of the Florida Mosquito Control Association. The JFMCA Vol. 71, 2024 included 4 reviews and opinions, 5 articles, 2 scientific notes, and annual meeting abstracts.
Tick‐associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta‐genomic and ‐transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta‐genomic and ‐transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick‐associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick‐associated viruses using a genome composition‐based machine learning model. We found five high‐risk tick‐associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick‐associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick‐associated diseases.
