Diversity and circulation of Jingmen tick virus in ticks and mammals

Latitude-driven patterns and dynamics in Jingmen group viral lineages: Spatial correlation, recombination, and phylogeography

The global emergence of Jingmen group viruses (JMVs), including Jingmen tick virus (JMTV), Alongshan virus (ALSV), and Yanggou tick virus (YGTV), has significantly broadened our perspective on the potential public health risks posed by segmented flaviviruses. However, the global evolutionary and genetic epidemiology of JMVs remains unclear. In this study, we conducted a comprehensive analysis of the spatial correlation, recombination, and phylogeography of JMVs. Our phylogenetic analysis identified three latitudinal lineages: (1) a mid-high-latitude group with YGTV and ALSV, prevalent in Europe and Asia; (2) a mid-latitude group with JMTV in Romania, Turkey, Kosovo, Trinidad, and Tobago; and (3) a mid-low-latitude group with JMTV and the Sichuan tick virus in Brazil, Japan, China, Kenya, and Uganda. The strong correlation between genetic distance and latitude also supports a latitude-dependent evolutionary pattern. Notably, concordance between the phylogenies of dominant tick species and JMVs underscores the pivotal role of tick species in the evolution of JMVs. Furthermore, the detection of frequent intra-lineage recombination and global migration events underscores the ecological pressures and tick-mediated evolutionary mechanisms that propel the global dissemination of emerging segmented flaviviruses. Additionally, the complex interplay of JMV recombination and migration events of JMVs identified here, particularly the recombination between JMTV and ALSV from disparate regions and viral migration across different regions and continents, complicates their evolutionary interrelationships and heightens potential health risks. Overall, our study provides valuable insights into ecological factors and tick species-mediated evolution and transmission that shape the global spread of emerging segmented flaviviruses.

Distribution prediction of the habitat of Jingmen tick virus in China

Jingmen tick virus (JMTV) is widely distributed in China, and human cases have been reported. Therefore, the objectives of this study were to understand the distribution of the JMTV in suitable areas in China under the current and projected future climates. We used two pairs of JMTV primers to detect ticks in Guizhou Province via PCR and obtained data on JMTV detection in other regions through literature research. We obtained climate data from China. Finally, maximum entropy, a boosted regression tree model, and a random forest model were used for prediction. The predictive performance of the model was evaluated by the area under the curve (AUC) of the receiver operating characteristic (ROC) curve. The JMTV positivity rate in Guizhou Province was 11.02%, which was lower than the overall national positivity rate of 16.9%. The predicted probability increased monotonically with increasing monthly mean temperature. China's high JMTV habitat is concentrated in the Daxinganling region of Heilongjiang, Shanghai, and Hainan Provinces, with the total area of high JMTV habitat accounting for 1.94% of the country's total land area. In the future, from 2021 to 2040, the area of JMTV habitat area in China will show an expanding trend. Our maps of JMTV distributions provide effective early warning information for monitoring JMTV and rapidly detecting outbreaks. The potential distribution of JMTV in China is expected to increase in size in the future, requiring continuous attention and surveillance.IMPORTANCESince the first detection of the Jingmen tick virus (JMTV) in ticks in 2014, it has been detected on several continents around the world. JMTV has also been detected in several regions of China, and human cases have been reported. JMTV has many types of hosts, including ticks, mice, bats, and turtles. It can be spread with these hosts in close proximity or over long distances. As a segmented virus, JMTV is capable not only of genetic mutation and recombination but also of genetic reassortment, resulting in changes in viral infectivity or pathogenicity. However, many uninvestigated areas still exist in China. Therefore, we investigated ticks carrying JMTV in Guizhou Province. We also predicted the distribution of JMTV in China by combining previous data.

Molecular detection of novel Jingmen tick virus in hard ticks from diverse hosts in Guangxi, southwestern China

BACKGROUND

Ticks are the second most important vectors of arboviruses after mosquitoes, and they also serve as reservoir hosts for some zoonotic diseases. It is essential to understand the prevalence of tick-borne viruses in ticks from different sampling sites and vectors, as this information can facilitate the surveillance and prevention of arboviral infectious diseases.

METHODS

We systematically collected ticks from a variety of animals, including wildlife and domestic livestock, across 18 distinct regions in Guangxi Zhuang Autonomous Region(Guangxi). We then identified the ticks using traditional morphological classification and molecular biology methods to investigate the diversity of ticks in the regionWe also systematically examined the diversity of viruses carried by ticks using comprehensive virological methods based on viral metagenomics. We performed phylogenetic and recombination analyses for the assembled viral sequences.

RESULTS

We collected 1286 Ixodidae from 18 sampling sites in 17 districts of Guangxi. We identified 4 genera and 6 species of Ixodidae. We annotated 2 unclassified viruses and 13 known viral families. We assembled 208 nucleotide sequences and obtained six near full-length sequences of Jingmen tick virus (JMTV). Among these sequences, GXTV-PC4.2 and GXTV-43 were new mutant strains of JMTV. We detected genetic recombination of JMTV in segments 2, 3, and 4 of JMTV.

CONCLUSIONS

Our study uncovers a diverse tick fauna in Guangxi, including 4 genera and 6 species, and a broad virome with 13 viral families and 2 novel viruses. The JMTV, in particular, shows significant genetic diversity and potential for cross-species transmission, marked by new strains and recombination events. These findings underscore the need for vigilant tick-borne disease surveillance in Guangxi.

Strange relatives: the enigmatic arbo-jingmenviruses and orthoflaviviruses

Arthropod - and vertebrate-associated jingmenviruses (arbo-JMV) have segmented positive-strand RNA genomes and are provisional members of the genus Orthoflavivirus (family Flaviviridae). Current investigations have described arbo-JMV infection in vertebrate hosts in proximity to humans. This raises concerns about the virus host range and public health implications. This review explores the genomic and evolutionary relationship between arbo-JMV and orthoflaviviruses and evaluates the potential of arbo-JMV to pose a public health threat.

High Diversity and Prevalence of Rickettsial Agents in Rhipicephalus microplus Ticks from Livestock in Karst Landscapes of Southwest China

Ticks and tick-borne pathogens pose a significant threat to human and animal health, yet the diversity and prevalence of tick-borne microorganisms in karst regions remains inadequately explored. In October 2023, a total of 274 Rhipicephalus microplus ticks were collected from livestock in Guizhou Province, which boasts the largest karst area in China. Pathogen identification was subsequently performed using PCR amplification, Sanger sequencing, and phylogenetic analysis. High microbial diversity was noted, with five bacterial species from the order Rickettsiales detected, including those from the genera Rickettsia (family Rickettsiaceae), Anaplasma, and Ehrlichia (family Anaplasmataceae). The overall prevalence of infection with at least one pathogen was remarkably high at 94.5%. The highest positive rate was observed for Candidatus Rickettsia jingxinensis at 90.9%. A novel Ehrlichia species, provisionally designated as Candidatus Ehrlichia carsus, was identified with a positive rate of 16.8%. In addition, Anaplasma marginale, Ehrlchia minasensis and Ehrlichia canis were detected in 15.3%, 4.7% and 1.5%, respectively. The co-infections involving two or three rickettsial species were observed in 34.3% ticks. These findings highlight the high diversity and prevalence of tick-borne rickettsial agents in the karst area, underscoring the need for enhanced surveillance and effective tick control to mitigate disease risks to both humans and livestock.

Detection of multiple novel viruses in argasid and ixodid ticks in Mexico

We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.

Geographical distribution and characterization of Jingmen tick virus in wild boars in China

•JMTV RNA was identified in 9 out of 26 provinces with an average wild boar infection rate of 5.45% (25/459). •Phylogenetic analysis indicated that JMTV strains could be divided into two groups, but have a complex evolutionary history. •Wild boars are a potential reservoir host for JMTV.

Identification and phylogenetic analysis of Jingmen tick virus in ticks and sheep from Henan Province, China

Jingmen tick virus (JMTV) is a novel segmented Flavivirus that was first identified from Rhipicephalus microplus in the Jingmen region of Hubei Province, China, in 2010. Subsequently, it was detected in a variety of countries and regions around the world. Meanwhile, JMTV has been proved to be pathogenic to humans and animals and could cause viremia in animals. However, the pathogenic mechanism of JMTV and what role animals play in the viral cycle have not yet been elucidated. In this study, 38 sheep sera were collected from Xinyang region of Henan Province, China and 204 ticks attached to the sheep were collected. The qRT-PCR and nested PCR were used to confirm the presence of JMTV in serum and tick samples. The results showed that the positive rate of JMTV in serum and ticks was 13.16% (5/38) and 7.84% (16/204), respectively. Phylogenetic analysis showed that JMTV sequences in sheep and ticks shared a high degree of identity with each other, and JMTV was relatively conserved in evolution. These results enriched the evidence for the prevalence of JMTV in animals and further deepened our understanding of the mechanisms and routes of JMTV transmission.

Epidemiology and global spread of emerging tick-borne Alongshan virus

The emergence and spread of novel viral pathogens is a major threat to human health, particularly in the context of climate and human-induced change in land use. Alongshan virus (ALSV) is a tick-borne virus associated with human disease, which was first identified in northeast China. More recently, several studies reported the emergence of ALSV in mammalian and arthropod hosts in multiple different countries outside of Asia, and the first viral genome sequencing data has become available. ALSV is a member of the Jingmenvirus group closely related to the Flaviviridae family. Unusually, the positive-sense, single-stranded RNA genome of ALSV is segmented and consists of four distinct segments, two of which show homology with the NS3 and NS5 protein encoding regions of non-segmented flaviviruses. Transmission of arthropod-borne pathogens will likely increase in the future due to environmental change mediated by a variety of environmental and ecological factors and increasing human encroachment into wild animal habitats. In this review, we present current knowledge of global ALSV distribution and emergence patterns, highlight genetic diversity, evolution and susceptible species. Finally, we discuss the role of this emerging tick-borne virus in the context of urbanization and global health.

Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China

Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.

First detection of Jingmen tick virus in Corsica with a new generic RTqPCR system

Jingmen tick virus (JMTV) is a recently discovered segmented RNA virus, closely related to flaviviruses. It was identified for the first time in 2014, in China and subsequently in Brazil. Following this discovery, JMTV-related sequences have been identified in arthropods, vertebrates (including humans), plants, fungus, and environmental samples from Asia, America, Africa, Europe, and Oceania. Several studies suggest an association between these segmented flavi-like viruses, termed jingmenviruses, and febrile illness in humans. The development of rapid diagnostic assays for these viruses is therefore crucial to be prepared for a potential epidemic, for the early detection of these viruses via vector surveillance or hospital diagnosis. In this study, we designed a RT-qPCR assay to detect tick-associated jingmenviruses, validated it and tested its range and limit of detection with six tick-associated jingmenviruses using in vitro transcripts. Then, we screened ticks collected in Corsica (France) from different livestock species, in order to determine the distribution of these viruses on the island. In total, 6269 ticks from eight species were collected from 763 cattle, 538 horses, 106 sheep, and 218 wild boars and grouped in 1715 pools. We report the first detection of JMTV in Corsica, in Rhipicephalus bursa, Hyalomma marginatum and R. sanguineus ticks collected from cattle and sheep. The highest prevalence was found in the Rhipicephalus genus. The complete genome of a Corsican JMTV was obtained from a pool of Rhipicephalus bursa ticks and shares between 94.7% and 95.1% nucleotide identity with a JMTV sequence corresponding to a human patient in Kosovo and groups phylogenetically with European JMTV strains. These results show that a Mediterranean island such as Corsica could act as a sentinel zone for future epidemics.

First Detection of the Jingmen Tick Virus in Amblyomma testudinarium Ticks from the Kanto Region, Japan

In 2010, Jingmen tick virus (JMTV) was discovered in ticks in China and has been shown to be distributed in several regions worldwide. Recently, cases of JMTV infection in humans have been reported in China and Kosovo, and have attracted much attention as an emerging tick-borne disease. In this study, we detected the JMTV genome in Amblyomma testudinarium ticks collected in Kanagawa Prefecture, Japan, during tick-borne virus surveillance conducted in the Kanto Region. Phylogenetic analysis revealed that the new JMTV strain was closely related to previous strains detected in Japan. This suggests that JMTV may have been maintained during an independent natural transmission cycle in Japan. In addition, unlike other countries and regions, all JMTV strains in Japan were detected only in A. testudinarium ticks, suggesting that this tick species is the primary JMTV vector in Japan. This is the first report of JMTV in the Kanto Region. Further studies are required to elucidate the potential risk of infection with this tick-borne virus in Japan. In particular, the prevalence of JMTV in wild animals should be examined to clarify its geographical distribution, host range, and transmission cycle.

Identification and phylogenetic analysis of Jingmen tick virus in Jiangxi Province, China

Jingmen tick virus (JMTV) is a newly identified segmented flavivirus that has been recognized in multiple hosts, such as humans, buffalos, bats, rodents, mosquitos and ticks. Various clinical cases and studies manifested that JMTV is a true arbovirus with wide host spectrum and showed potential threats toward public health. JMTV has been reported in multiple countries in Asia, Europe, Africa, and America. Moreover, wild boars serve as an important intermediary between humans and the wild ecological system. In China, it has been reported in nine provinces, while the prevalence and the distribution of JMTV in most regions including Jiangxi Province are still unknown. Thus, to profile the distribution of JMTV in Jiangxi Province, an epidemiological investigation was carried out from 2020 to 2022. In current study, 66 ticks were collected from 17 wild boars in Jiangxi Province. The results showed that 12 out of 66 ticks were JMTV positive, indicating JMTV is prevalent in ticks and boars in Jiangxi Province. The genome sequences of JMTV strain WY01 were sequenced to profile viral evolution of JMTV in China. Phylogenetic analysis divided JMTV strains into two genotypes, Group I and Group II. WY01 belongs to Group II and it shares the closest evolutionary relationship with the Japan strains rather than the strains from neighboring provinces in China suggesting that JMTV might have complex transmission routes. Overall, current study, for the first time, reported that JMTV is prevalent in Jiangxi Province and provided additional information concerning JMTV distribution and evolution in China.

Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks

Haemaphysalis longicornis ticks, commonly found in East Asia, can transmit various pathogenic viruses, including the severe fever with thrombocytopenia syndrome virus (SFTSV) that has caused febrile diseases among humans in Hubei Province. However, understanding of the viromes of H. longicornis was limited, and the prevalence of viruses among H. longicornis ticks in Hubei was not well clarified. This study investigates the viromes of both engorged (fed) and free (unfed) H. longicornis ticks across three mountainous regions in Hubei Province from 2019 to 2020. RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging to unclassified viruses and seven RNA viral families, namely Chuviridae, Nairoviridae, Orthomyxoviridae, Parvoviridae, Phenuiviridae, Rhabdoviridae, and Totiviridae. Viral abundance and diversity in these ticks were analysed, and phylogenetic characteristics of the Henan tick virus (HNTV), Dabieshan tick virus (DBSTV), Okutama tick virus (OKTV), and Jingmen tick virus (JMTV) were elucidated based on their full genomic sequences. Prevalence analysis demonstrated that DBSTV was the most common virus found in individual H. longicornis ticks (12.59%), followed by HNTV (0.35%), whereas JMTV and OKTV were not detected. These results improve our understanding of H. longicornis tick viromes in central China and highlight the role of tick feeding status and geography in shaping the viral community. The findings of new viral strains and their potential impact on public health raise the need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.

First detection of Jingmen tick virus in Corsica, France and development of a real time detection system for multiple tick-associated jingmenviruses

Jingmen tick virus (JMTV) is a recently discovered segmented RNA virus, closely related to flaviviruses. It was identified for the first time in 2014, in China and subsequently in Brazil. Following this discovery, JMTV-related sequences have been identified in arthropods, vertebrates (including humans), plants, fungus and environmental samples from Asia, America, Africa, Europe and Oceania. Several studies suggest an association between these segmented flavi-like viruses, termed jingmenviruses, and febrile illness in humans. The development of rapid diagnostic assays for these viruses is therefore crucial to be prepared for a potential epidemic, for the early detection of these viruses via vector surveillance or hospital diagnosis. In this study, we designed a RT-qPCR assay to detect tick-associated jingmenviruses, validated it and tested its range and limit of detection with six tick-associated jingmenviruses using in vitro transcripts. Then we screened ticks collected in Corsica (France) from different livestock species, in order to determine the distribution of these viruses on the island. In total, 6,269 ticks from eight species were collected from 763 cattle, 538 horses, 106 sheep and 218 wild boars and grouped in 1,715 pools. We report the first detection of JMTV in Corsica, in Rhipicephalus bursa, Hyalomma marginatum and R. sanguineus ticks collected from cattle and sheep. The highest prevalence was found in the Rhipicephalus genus. The complete genome of a Corsican JMTV was obtained from a pool of Rhipicephalus bursa ticks and shares between 94.7% and 95.1% nucleotide identity with a JMTV sequence corresponding to a human patient in Kosovo and groups phylogenetically with European JMTV strains. These results show that a Mediterranean island such as Corsica could act as a sentinel zone for future epidemics.

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.

Prevalence, genomic characteristics, and pathogenicity of fowl adenovirus 2 in Southern China

In recent years, the occurrence of fowl adenovirus 2 (FAdV-2) has been on the rise in China, posing a significant threat to the poultry industry. This study aimed to investigate the epidemiology, phylogenetic relationship, genomic characteristics, and pathogenicity of FAdV-2. The epidemiological analysis revealed the detection of multiple FAdV serotypes, including FAdV-1, FAdV-2, FAdV-3, FAdV-4, FAdV-8a, FAdV-8b, and FAdV-11 serotypes. Among them, FAdV-2 exhibited the highest proportion, accounting for 21.05% (8/38). The complete genomes of these 8 FAdV-2 strains were sequenced. Genetic evolution analysis indicated that these FAdV-2 strains formed a separate branch within the FAdV-D group, sharing 94.60 to 97.90% nucleotide similarity with the reference FAdV-2 and FAdV-11 strains. Notably, the recombination analysis revealed that 5 out of the 8 FAdV-2 strains, exhibited recombination events between FAdV-2 and FAdV-11. The recombination regions involved Hexon, Fiber, ORF19 genes and 3' end. Furthermore, pathogenicity experiments demonstrated that recombinant FAdV-2 XX strain is capable of inducing mortality rate of 66.70% and causing more severe hepatitis hydropericardium syndrome (HHS) in 6-wk-old specific-pathogen-free chickens. These findings contribute to our understanding of the prevalence, genomic characteristics, and the pathogenicity of FAdV-2, providing foundations for FAdV-2 vaccine development.

Meta-transcriptomics for the diversity of tick-borne virus in Nujiang, Yunnan Province

Ticks, an arthropod known for transmitting various pathogens such as viruses, bacteria, and fungi, pose a perpetual public health concern. A total of 2,570 ticks collected from Nujiang Prefecture in Yunnan Province between 2017 and 2022 were included in the study. Through the meta-transcriptomic sequencing of four locally distributed tick species, we identified 13 RNA viruses belonging to eight viral families, namely, Phenuiviridae, Nairoviridae, Peribunyaviridae, Flaviviridae, Chuviridae, Rhabdoviridae, Orthomyxoviridae, and Totiviridae. The most prevalent viruses were members of the order Bunyavirales, including three of Phenuiviridae, two were classified as Peribunyaviridae, and one was associated with Nairoviridae. However, whether they pose a threat to human health still remains unclear. Indeed, this study revealed the genetic diversity of tick species and tick-borne viruses in Nujiang Prefecture based on COI gene and tick-borne virus research. These data clarified the genetic evolution of some RNA viruses and furthered our understanding of the distribution pattern of tick-borne pathogens, highlighting the importance and necessity of monitoring tick-borne pathogens.

Genomics evolution of Jingmen viruses associated with ticks and vertebrates

Jingmen virus (JMV) associated with ticks and vertebrates have been found to be related to human disease. We obtained the genome of a Jingmen tick virus (JMTV) strain from Rhipicephalus microplus in Guizhou province and compared the genomes of seven JMV species associated with ticks and vertebrates to understand the evolutionary relationships. The topology of the phylogenetic tree of segment 1 and segment 3 is similar, and segment 2 and segment 4 formed two different topologies, with the main differences being between Alongshan virus (ALSV), Takachi virus, Yanggou tick virus and Pteropus lylei jingmen virus (PLJV), and the possibility of genetic reassortment among these viruses. Moreover, we detected recombination within JMTV and between PLJV and ALSV. The genetic reassortment and recombination that occurs during cross-species transmission of these JMV associated with ticks and vertebrates not only complicates their evolutionary relationships, but also raises the risk of these viruses to humans.

Jingmen tick virus: an emerging arbovirus with a global threat

Jingmen tick virus (JMTV), belonging to the Flaviviridae family, is a novel segmented RNA virus identified in 2014 in the Jingmen region of Hubei Province, China. Up to now, JMTV has been detected in a variety of countries or regions in Asia, Europe, Africa, and the Americas, involving a wide range of arthropods and mammals, and even humans. The JMTV genome is composed of four linear RNA segments, two of which are derived from flaviviruses, while the other two segments are unique to JMTV and has no matching virus. Currently, JMTV has been shown to have a pathogenic effect on humans. Humans who had been infected would develop viremia and variable degrees of clinical symptoms. However, the pathogenic mechanism of JMTV has not been elucidated yet. Therefore, it is crucial to strengthen the epidemiological surveillance and laboratory studies of JMTV.

RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance

Background

The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored.

Methods

A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing.

Findings

This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments.

Interpretation

RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time.

Funding

UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.

Identification of novel Jingmen tick virus from parasitic ticks fed on a giant panda and goats in Sichuan Province, southwestern China

Introduction

Tick-borne viruses (TBVs) pose a significant risk to the health of humans and other vertebrates. A class of multisegmented flavi-like viruses, Jingmen tick virus (JMTV) was first discovered in Rhipicephalus microplus ticks collected from Jingmen of Hubei Province, China in 2010. JMTV has been confirmed to have a relatively wide distribution in vectors and hosts and is associated with human diseases.

Methods

Parasitic and host-seeking ticks were collected in Wolong Nature Reserve, Sichuan Province. Total RNA was extracted and then enriched the viral RNA. The DNA library was constructed and then were sequenced with MGI High-throughput Sequencing Set (PE150). After the adaptor sequences,low-quality bases and host genome were removed, resulting reads classified as a virus were subsequently de novo assembled into contigs, which were then compared to the NT database. Those annotated under the kingdom virus were initially identified as potential virus-associated sequences. Phylogenetic and Reassortment analysis of sequences were performed using MEGA and SimPlot software, respectively.

Results and discussion

Two host-seeking ticks and 17 ticks that fed on giant pandas and goats were collected. Through high-throughput sequencing, whole virus genomes were attained from four tick samples (PC-13, PC-16, PC-18, and PC-19) that shared 88.7-96.3% similarity with known JMTV. Phylogenetic tree showed that it was a novel JMTV-like virus, referred to as Sichuan tick virus, which also had the signals of reassortment with other JMTV strains, suggesting a cross-species transmission and co-infection of segmented flavi-like viruses among multiple tick hosts.

Conclusion

We discovered and confirmed one new Jingmen tick virus, Sichuan tick virus. Further investigation is required to determine the pathogenicity of Sichuan tick virus to humans and animals, as well as its epidemiological characteristics in nature.

Impact of nanopore-based metagenome sequencing on tick-borne virus detection

Introduction

We evaluated metagenomic nanopore sequencing (NS) in field-collected ticks and compared findings from amplification-based assays.

Methods

Forty tick pools collected in Anatolia, Turkey and screened by broad-range or nested polymerase chain reaction (PCR) for Crimean-Congo Hemorrhagic Fever Virus (CCHFV) and Jingmen tick virus (JMTV) were subjected to NS using a standard, cDNA-based metagenome approach.

Results

Eleven viruses from seven genera/species were identified. Miviruses Bole tick virus 3 and Xinjiang mivirus 1 were detected in 82.5 and 2.5% of the pools, respectively. Tick phleboviruses were present in 60% of the pools, with four distinct viral variants. JMTV was identified in 60% of the pools, where only 22.5% were PCR-positive. CCHFV sequences characterized as Aigai virus were detected in 50%, where only 15% were detected by PCR. NS produced a statistically significant increase in detection of these viruses. No correlation of total virus, specific virus, or targeted segment read counts was observed between PCR-positive and PCR-negative samples. NS further enabled the initial description of Quaranjavirus sequences in ticks, where human and avian pathogenicity of particular isolates had been previously documented.

Discussion

NS was observed to surpass broad-range and nested amplification in detection and to generate sufficient genome-wide data for investigating virus diversity. It can be employed for monitoring pathogens in tick vectors or human/animal clinical samples in hot-spot regions for examining zoonotic spillover.

Identification and Characterization of Jingmen Tick Virus in Ticks from Yunnan Imported Cattle

Jingmen tick virus (JMTV) is a tick-borne segmented positive-sense ssRNA virus that can cause human disease. This virus has been confirmed to be widespread, having a wide host range. In human it can cause fever, headache, lymphadenopathy, and asthenia. Therefore, JMTV poses a threat to public health. In this study, we collected 478 ticks from imported cattle on three quarantine farms near the Yunnan border to detect medically significant tick-borne viruses. Our findings show that JMTV was the only detected virus, with an incidence rate of 56.67%. Phylogenetic analysis showed that our JMTV is more closely related to previously reported JMTV strains from Yunnan Province and neighboring Laos, implying that the tick-borne virus was most likely imported from Laos. In conclusion, we identified and characterized a novel JMTV strain in tick (Rhipicephalus microplus) from Yunnan imported cattle, emphasizing the importance of arbovirus quarantine of livestock imports.

Detection of Viral Genes in Metarhizium anisopliae JEF-290-infected longhorned tick, Haemaphysalis longicornis using transcriptome analysis

Ticks are carriers of viruses that can cause disease in humans and animals. The longhorned ticks (Haemaphysalis longicornis; LHT), for example, mediates the severe fever with thrombocytopenia syndrome virus (SFTSV) in humans, and the population of ticks is growing due to increases in temperature caused by climate change. As ticks carry primarily RNA viruses, there is a need to study the possibility of detecting new viruses through tick virome analysis. In this study, viruses in LHTs collected in Korea were investigated and virus titers in ticks exposed to the entomopathogenic fungus Metarhizium anisopliae JEF-290 were analyzed. Total RNA was extracted from the collected ticks, and short reads were obtained from Illumina sequencing. A total of 50,024 contigs with coding capacity were obtained after de novo assembly of the reads in the metaSPAdes genome assembler. A series of BLAST-based analyses using the GenBank database was performed to screen viral contigs, and three putative virus species were identified from the tick meta-transcriptome, such as Alongshan virus (ALSV), Denso virus and Taggert virus. Measurements of virus-expression levels of infected and non-infected LHTs failed to detect substantial differences in expression levels. However, we suggest that LHT can spread not only SFTSV, but also various other disease-causing viruses over large areas of the world. From the phylogenetic analysis of ALSV glycoproteins, genetic differences in the ALSV could be due to host differences as well as regional differences. Viral metagenome analysis can be used as a tool to manage future outbreaks of disease caused by ticks by detecting unknown viruses.

[Structural Motifs and Spatial Structures of Helicase (NS3) and RNA-dependent RNA-polymerase (NS5) of a Flavi-like Kindia tick virus (unclassified Flaviviridae)]

INTRODUCTION

Kindia tick virus (KITV) is a novel segmented unclassified flavi-like virus of the Flaviviridae family. This virus is associated with ixodes ticks and is potentially pathogenic to humans. The main goal of this work was to search for structural motifs of viral polypeptides and to develop a 3D-structure for viral proteins of the flavi-like KITV.

MATERIALS AND METHODS

The complete genome sequences for KITV, Zika, dengue, Japanese encephalitis, West Nile and yellow fever viruses were retrieved from GenBank. Bioinformatics analysis was performed using the different software packages.

RESULTS

Analysis of the KITV structural proteins showed that they have no analogues among currently known viral proteins. Spatial models of NS3 and NS5 KITV proteins have been obtained. These models had a high level of topological similarity to the tick-borne encephalitis and dengue viral proteins. The methyltransferase and RNA-dependent RNA-polymerase domains were found in the NS5 KITV. The latter was represented by fingers, palm and thumb subdomains, and motifs A-F. The helicase domain and its main structural motifs IVI were identified in NS3 KITV. However, the protease domain typical of NS3 flaviviruses was not detected. The highly conserved amino acid motives were detected in the NS3 and NS5 KITV. Also, eight amino acid substitutions characteristic of KITV/2018/1 and KITV/2018/2 were detected, five of them being localized in alpha-helix and three in loops of nonstructural proteins.

CONCLUSION

Nonstructural proteins of KITV have structural and functional similarities with unsegmented flaviviruses. This confirms their possible evolutionary and taxonomic relationships.

Molecular evidence for potential transovarial transmission of Jingmen tick virus in Haemaphysalis longicornis fed on cattle from Yunnan Province, China

Jingmen tick virus (JMTV) is a novel tick-borne virus first identified from Jingmen city, Hubei Province of China in 2010. It has been proved that JMTV can cause human diseases and is widely distributed both inside and outside of China. However, the survival mode and transmission characteristics of JMTV still need further research, particularly in terms of transovarial transmission. In this study, an investigation was conducted to explore the presence of JMTV from engorged female ticks to their offspring. All engorged female adult ticks were collected from domestic cattle and allowed to lay eggs in appropriate humidity and temperature conditions. Maternal ticks, eggs and larvae were screened for JMTV RNA through real-time polymerase chain reaction (RT-PCR) and nested PCR methods. The results revealed the positive rate of 10.53% (10/95) in engorged ticks, 9.09% (2/22) in eggs and 8% (4/50) in larvae pools, respectively. Phylogenetic analysis confirmed that sequences from eggs and larvae had closer relationship with those isolates from maternal engorged ticks with more than 99.7% homology and JMTV manifested with evolutional conservatism. Our study has identified for the first time that JMTV could be transmitted from mother generation to offspring of Haemaphysalis Longicornis. Nonetheless, the efficiency of transovarial transmission in JMTV and the significance of ticks as amplification hosts still need to be further illustrated.

Skin infectome of patients with a tick bite history

Introduction

Ticks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people.

Methods

A total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings.

Results

Four bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins.

Discussion

Advances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients' skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness.

Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China

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 analysis to investigate the virome diversity in northeastern China.

RESULTS

In total, 22 RNA viruses were identified, including four each in the Nairoviridae and Phenuiviridae families, three each in the Flaviviridae, Rhabdoviridae, and Solemoviridae families, two in the Chuviridae family, and one each in the Partitiviridae, Tombusviridae families and an unclassified virus. Of these, eight viruses were of novel species, belonging to the Nairoviridae (Ji'an nairovirus and Yichun nairovirus), Phenuiviridae (Mudanjiang phlebovirus), Rhabdoviridae (Tahe rhabdovirus 1-3), Chuviridae (Yichun mivirus), and Tombusviridae (Yichun tombus-like virus) families, and five members were established human pathogens, including Alongshan virus, tick-borne encephalitis virus, Songling virus, Beiji nairovirus, and Nuomin virus. I. persulcatus ticks had significant higher number of viral species than H. japonica, H. concinna, and D. silvarum ticks. Significant differences in tick viromes were observed among Daxing'an, Xiaoxing'an and Changbai mountains.

CONCLUSIONS

These findings showed an extensive diversity of RNA viruses in ticks in northeastern China, revealing potential public health threats from the emerging tick-borne viruses. Further studies are needed to explain the natural circulation and pathogenicity of these viruses.

Distribution and Characterisation of Tick-Borne Flavi-, Flavi-like, and Phenuiviruses in the Chelyabinsk Region of Russia

In this work, we presented data from a two-year study of flavi-, flavi-like, and phenuiviruses circulation in the population of ixodid ticks in the Chelyabinsk region. We isolated three tick-borne encephalitis virus (TBEV) strains from I. persulcatus, which was not detected in the ticks of the genus Dermacentor. The virus prevalence ranged from 0.66% to 2.28%. The Yanggou tick virus (YGTV) is widespread in steppe and forest-steppe zones and is mainly associated with ticks of the genus Dermacentor. We isolated 26 strains from D. reticulatus, D. marginatus, and I. persulcatus ticks in the HAE/CTVM8 tick cell line. The virus prevalence ranged from 1.58% to 4.18% in D. reticulatus, ranged from 0.78% to 3.93% in D. marginatus, and was 0.66% in I. persulcatus. There was combined focus of TBEV and YGTV in the territory of the Chelyabinsk region. The Alongshan virus (ALSV) was found to be associated with I. persulcatus ticks and is spread in forest zone. We detected 12 amplicons and isolated 7 strains of ALSV in tick cells. The virus prevalence ranged from 1.13% to 6.00%. The phlebovirus Gomselga and unclassified phenuivirus Stavropol were associated with I. persulcatus and D. reticulatus ticks, respectively. Virus prevalence of the unclassified phenuivirus Stavropol in the Chelyabinsk region is lower than that in neighbouring regions.

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

Identification of Jingmen tick virus (JMTV) in Amblyomma testudinarium from Fujian Province, southeastern China

Background

Jingmen tick virus (JMTV) is a newly discovered tick-borne virus that can cause disease in humans. This virus has been authenticated as being extremely widespread worldwide and as posing a significant threat to public health and safety.

Methods

We collected 35 ticks belonging to two tick species from wild boars in Nanping, Fujian Province, China. JMTV-specific genes were amplified by qRT-PCR and nested PCR to confirm the presence of this pathogen.

Results

More than one third of of all ticks collected (11/35) were positive for JMTV. Viral sequences were obtained from three of the JMTV-positive ticks, including the complete genomic sequence from one tick. This was the first time that JMTV was identified in the hard-bodied tick Amblyomma testudinarium. Phylogenetic analysis revealed that JMTV from Fujian Province shared > 90% identity with other isolates derived from China, but was distinct from those reported in France and Cambodia.

Conclusions

JMTV is characterized by relatively low mutations and has its own local adaptive characteristics in different regions. Our findings provide molecular evidence of the presence of JMTV in an overlooked tick species from an area not unrecognized as being endemic. They also suggest that JMTV occupies a wider geographical distribution than currently believed and is a potential disease vector.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05478-2.

Integrated Jingmenvirus Polymerase Gene in Ixodes ricinus Genome

Members of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia and Antarctica. Two viruses of this group were isolated from patients with fever after a tick bite. Using a nested RT-PCR assay targeting a jingmenvirus polymerase gene fragment, we screened ticks collected in seven regions of Russia and found that the abundant jingmenvirus-positive were of Ixodes ricinus species, with the prevalence ranging from 19.8% to 34.3%. In all cases, DNase/RNase treatment suggested that the detected molecule was DNA and subsequent next generation sequencing (NGS) proved that the viral polymerase gene was integrated in the I. ricinus genome. The copy number of the integrated polymerase gene was quantified by qPCR relative to the ITS2 gene and estimated as 1.32 copies per cell. At least three different genetic variants of the integrated polymerase gene were found in the territory of Russia. Phylogenetic analysis of the integrated jingmenvirus polymerase gene showed the highest similarity with the sequence of the correspondent gene obtained in Serbia from I. ricinus.

Geographical distribution and phylogenetic analysis of Jingmen tick virus in China

Jingmen tick virus (JMTV) is a novel tick-borne segmented RNA virus that is closely related to un-segmental RNA virus in evolution. It has been confirmed that JMTV could be a causative agent of human disease. In this study, a total of 3658 ticks were sampled from 7 provinces of China and then divided into 545 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of JMTV. The results showed JMTV was identified in 5 out of 7 provinces with an average infection rate of 1.4% (51/3658). Phylogenetic analysis indicated that all JMTV strains identified in this study were closely related to each other and formed a well-supported sub-lineage. Our results provide molecular evidence of JMTV in different species of ticks from endemic and non-endemic regions and demonstrate that JMTV, as a natural foci pathogen, may be widely distributed all over China.

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JMTV was first identified in unrecognized endemic regions of China

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Two complete genomes and 13 partial S1 segments of JMTV were sequenced and analyzed

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JMTV was relatively conservative in evolution

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JMTV was widely distributed in China as a potential health threat to humans and animals

Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records

Focusing on the utility of ticks as xenosurveillance sentinels to expose circulating pathogens in Kenyan drylands, host-feeding ticks collected from wild ungulates [buffaloes, elephants, giraffes, hartebeest, impala, rhinoceros (black and white), zebras (Grévy’s and plains)], carnivores (leopards, lions, spotted hyenas, wild dogs), as well as regular domestic and Boran cattle were screened for pathogens using metagenomics. A total of 75 host-feeding ticks [Rhipicephalus (97.3%) and Amblyomma (2.7%)] collected from 15 vertebrate taxa were sequenced in 46 pools. Fifty-six pathogenic bacterial species were detected in 35 pools analyzed for pathogens and relative abundances of major phyla. The most frequently observed species was Escherichia coli (62.8%), followed by Proteus mirabilis (48.5%) and Coxiella burnetii (45.7%). Francisella tularemia and Jingmen tick virus (JMTV) were detected in 14.2 and 13% of the pools, respectively, in ticks collected from wild animals and cattle. This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. Eight fungal species with human pathogenicity were detected in 5 pools (10.8%). The vector-borne filarial pathogens (Brugia malayi, Dirofilaria immitis, Loa loa), protozoa (Plasmodium spp., Trypanosoma cruzi), and environmental and water-/food-borne pathogens (Entamoeba histolytica, Encephalitozoon intestinalis, Naegleria fowleri, Schistosoma spp., Toxoplasma gondii, and Trichinella spiralis) were detected. Documented viruses included human mastadenovirus C, Epstein-Barr virus and bovine herpesvirus 5, Trinbago virus, and Guarapuava tymovirus-like virus 1. Our findings confirmed that host-feeding ticks are an efficient sentinel for xenosurveillance and demonstrate clear potential for wildlife-livestock-human pathogen transfer in the Kenyan landscape.

Dermacentor silvarum, a Medically Important Tick, May Not Be a Competent Vector to Transmit Jingmen Tick Virus

Background: Jingmen tick virus (JMTV) has attracted great attention due to its potential pathogenicity in humans and its transmission by ticks. Dermacentor silvarum (D. silvarum) is one of the dominant tick species in northeastern China, and can transmit many pathogens to humans and animals. However, there have been no report of transmission of JMTV by D. silvarum. Materials and Methods: Ticks were collected from vegetation at the Aershan Port in Inner Mongolia in April 2019. And we do attempt to infect D. silvarum with JMTV by the immersion technique in laboratory conditions. The transmission of JMTV was examined by reverse transcriptase PCR, fluorescence in situ hybridization, and indirect immunofluorescence assay. Statistical analysis was performed using SPSS 24.0. Results: We found that JMTV may only be maintained in the tick without replication, and could not be transmitted to a host following transstadial transmission. Moreover, no virus colonization was found in the midgut or salivary glands of unfed D. silvarum; therefore, D. silvarum may not be susceptible to JMTV infection and therefore unlikely to carry and transmit JMTV. Conclusion: Our study has to some extent filled the knowledge gap regarding the possibility of JMTV transmission by a medically important tick vector, D. silvarum.

Jingmen Tick Virus in Ticks from Kenya

Jingmen tick virus (JMTV) is an arbovirus with a multisegmented genome related to those of unsegmented flaviviruses. The virus first described in Rhipicephalus microplus ticks collected in Jingmen city (Hubei Province, China) in 2010 is associated with febrile illness in humans. Since then, the geographic range has expanded to include Trinidad and Tobago, Brazil, and Uganda. However, the ecology of JMTV remains poorly described in Africa. We screened adult ticks (n = 4550, 718 pools) for JMTV infection by reverse transcription polymerase chain reaction (RT-PCR). Ticks were collected from cattle (n = 859, 18.88%), goats (n = 2070, 45.49%), sheep (n = 1574, 34.59%), and free-ranging tortoises (Leopard tortoise, Stigmochelys pardalis) (n = 47, 1.03%) in two Kenyan pastoralist-dominated areas (Baringo and Kajiado counties) with a history of undiagnosed febrile human illness. Surprisingly, ticks collected from goats (0.3%, 95% confidence interval (CI) 0.1-0.5), sheep (1.8%, 95% CI 1.2-2.5), and tortoise (74.5%, 95% CI 60.9-85.4, were found infected with JMTV, but ticks collected from cattle were all negative. JMTV ribonucleic acid (RNA) was also detected in blood from tortoises (66.7%, 95% CI 16.1-97.7). Intragenetic distance of JMTV sequences originating from tortoise-associated ticks was greater than that of sheep-associated ticks. Phylogenetic analyses of seven complete-coding genome sequences generated from tortoise-associated ticks formed a monophyletic clade within JMTV strains from other countries. In summary, our findings confirm the circulation of JMTV in ticks in Kenya. Further epidemiological surveys are needed to assess the potential public health impact of JMTV in Kenya.

Several Tick-Borne Pathogenic Viruses in Circulation in Anatolia, Turkey

Introduction: We screened host-collected ticks for tick-borne viruses, including those recently documented as human pathogens. Methods: During 2020-2021, ticks removed form cattle, sheep, dogs, and cats in 11 provinces in 5 geographically distinct regions of Anatolia were identified, pooled, and screened using pan-nairovirus, pan-flavivirus and individual assays for Jingmen tick virus (JMTV), and Tacheng tick virus 1 and 2 (TcTV-1 and TcTV-2). Results: A total of 901 tick specimens, comprising 6 species were included. Rhipicephalus sanguineus complex was the most abundant species (44.1%), followed by Rhipicephalus bursa (38.3%), Haemaphysalis parva (7.2%), and others. The specimens were screened in 158 pools with 12 pools (7.6%) being positive. Crimean-Congo hemorrhagic fever virus (CCHFV) lineage Europe 2 (genotype VI) sequences were detected in R. bursa in five (3.2%) of the pools, with similar prevalences in central and Mediterranean Anatolian provinces. JMTV was identified in four R. bursa and one Rhipicephalus turanicus pools, collected from Mediterranean and southeastern Anatolia, with a CCHFV and JMTV coinfected R. bursa pool. The JMTV segment 1 sequences formed a separate cluster with those from Turkey and the Balkan peninsula in the maximum likelihood analysis. TcTV-2 was detected in two Dermacentor marginatus specimens (1.3%) collected in central Anatolia, with nucleocapsid sequences forming a phylogenetically segregated group among viruses from humans and ticks from China and Kazakhstan. Discussion: CCHFV Europe 2 was initially documented in ticks from central Anatolian locations, where related orthonairoviruses had been previously recorded. Ongoing activity and a wider distribution of JMTV and TcTV-2 were observed. These viruses should be screened as potential etiological agents in human infections associated with tick bites.

Detection of Jingmenviruses in Japan with Evidence of Vertical Transmission in Ticks

Jingmen tick virus (JMTV) and the related jingmenvirus-termed Alongshan virus are recognized as globally emerging human pathogenic tick-borne viruses. These viruses have been detected in various mammals and invertebrates, although their natural transmission cycles remain unknown. JMTV and a novel jingmenvirus, tentatively named Takachi virus (TAKV), have now been identified during a surveillance of tick-borne viruses in Japan. JMTV was shown to be distributed across extensive areas of Japan and has been detected repeatedly at the same collection sites over several years, suggesting viral circulation in natural transmission cycles in these areas. Interestingly, these jingmenviruses may exist in a host tick species-specific manner. Vertical transmission of the virus in host ticks in nature was also indicated by the presence of JMTV in unfed host-questing Amblyomma testudinarium larvae. Further epidemiological surveillance and etiological studies are necessary to assess the status and risk of jingmenvirus infection in Japan.

Tick virome diversity in Hubei Province, China, and the influence of host ecology

Ticks are important vector hosts of pathogens which cause human and animal diseases worldwide. Diverse viruses have been discovered in ticks; however, little is known about the ecological factors that affect the tick virome composition and evolution. Herein, we employed RNA sequencing to study the virome diversity of the Haemaphysalis longicornis and Rhipicephalus microplus ticks sampled in Hubei Province in China. Twelve RNA viruses with complete genomes were identified, which belonged to six viral families: Flaviviridae, Matonaviridae, Peribunyaviridae, Nairoviridae, Phenuiviridae, and Rhabdoviridae. These viruses showed great diversity in their genome organization and evolution, four of which were proposed to be novel species. The virome diversity and abundance of R. microplus ticks fed on cattle were evidently high. Further ecological analyses suggested that host species and feeding status may be key factors affecting the tick virome structure. This study described a number of novel viral species and variants from ticks and, more importantly, provided insights into the ecological factors shaping the virome structures of ticks, although it clearly warrants further investigation.

A Novel Subtype of Bovine Hepacivirus Identified in Ticks Reveals the Genetic Diversity and Evolution of Bovine Hepacivirus

Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. New members of the genus Hepacivirus in the family Flaviviridae have recently been identified in a wide variety of host species worldwide. Similar to the Hepatitis C virus (HCV), bovine hepacivirus (BovHepV) is hepatotropic and causes acute or persistent infections in cattle. BovHepVs are distributed worldwide and classified into two genotypes with seven subtypes in genotype 1. In this study, three BovHepV strains were identified in the samples of ticks sucking blood on cattle in the Guangdong province of China, through unbiased high-throughput sequencing. Genetic analysis revealed the polyprotein-coding gene of these viral sequences herein shared 67.7–84.8% nt identity and 76.1–95.6% aa identity with other BovHepVs identified worldwide. As per the demarcation criteria adopted for the genotyping and subtyping of HCV, these three BovHepV strains belonged to a novel subtype within the genotype 1. Additionally, purifying selection was the dominant evolutionary pressure acting on the genomes of BovHepV, and genetic recombination was not common among BovHepVs. These results expand the knowledge about the genetic diversity and evolution of BovHepV distributed globally, and also indicate genetically divergent BovHepV strains were co-circulating in cattle populations in China.

Complete genome sequence of a novel mitovirus from the phytopathogenic fungus Fusarium oxysporum

Fusarium oxysporum is a cosmopolitan plant pathogen that causes fusarium wilt and fusarium root rot in many economically important crops. There is still limited information about mycoviruses that infect F. oxysporum. Here, a novel mitovirus tentatively named "Fusarium oxysporum mitovirus 1" (FoMV1) was identified in F. oxysporum strain B2-10. The genome of FoMV1 is 2,453 nt in length with a predicted AU content of 71.6% and contains one large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF putatively encodes an RNA-dependent RNA polymerase (RdRp) of 723 aa with a molecular mass of 84.98 kDa. The RdRp domain of FoMV1 shares 29.01% to 68.43% sequence identity with the members of the family Mitoviridae. Phylogenetic analysis further suggested that FoMV1 is a new member of a distinct species in the genus Mitovirus.

Revisiting the rules of life for viruses of microorganisms

Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.

Geographical and Tick-Dependent Distribution of Flavi-Like Alongshan and Yanggou Tick Viruses in Russia

The genus Flavivirus includes related, unclassified segmented flavi-like viruses, two segments of which have homology with flavivirus RNA-dependent RNA polymerase NS5 and RNA helicase-protease NS3. This group includes such viruses as Jingmen tick virus, Alongshan virus, Yanggou tick virus and others. We detected the Yanggou tick virus in Dermacentor nuttalli and Dermacentor marginatus ticks in two neighbouring regions of Russia. The virus prevalence ranged from 0.5% to 8.0%. We detected RNA of the Alongshan virus in 44 individuals or pools of various tick species in eight regions of Russia. The virus prevalence ranged from 0.6% to 7.8%. We demonstrated the successful replication of the Yanggou tick virus and Alongshan virus in IRE/CTVM19 and HAE/CTVM8 tick cell lines without a cytopathic effect. According to the phylogenetic analysis, we divided the Alongshan virus into two groups: an Ixodes persulcatus group and an Ixodes ricinus group. In addition, the I. persulcatus group can be divided into European and Asian subgroups. We found amino acid signatures specific to the I. ricinus and I. persulcatus groups and also distinguished between the European and Asian subgroups of the I. persulcatus group.