Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek island

Pathogens Detected in Questing Ixodes ricinus Ticks in a Mountainous Area in Greece

Ixodes ricinus ticks are vectors of a plethora of pathogens. The purpose of this study was to screen 398 I. ricinus ticks for a variety of pathogens. Following the pooling, homogenization, and extraction of total nucleic acids, a real-time PCR was applied for the detection of a panel of tick-borne pathogens, while additional conventional PCRs combined with Sanger sequencing were applied for the detection of viruses and typing of Rickettsia and Borrelia species. At least one pathogen was detected in 60 of the 80 (75%) tick pools. Rickettsia spp. predominated, as it was detected in 63.75% of the pools (51/80; MIR 12.81%), followed by Borrelia spp. (35 pools (45%); MIR 8.79%), while Anaplasma phagocytophilum was detected in 2 pools (2.5%, MIR 0.5%). The ticks of six Rickettsia-positive pools were tested individually (from stored half-ticks); all sequences were identical to those of R. monacensis. Similarly, the ticks of six Borrelia-positive pools were tested individually, and it was shown that four belonged to the genospecies Borrelia garinii and two to Borrelia valaisiana. Phleboviruses were detected in 3 pools (3.75%; MIR 0.75%), with sequences clustering in the Ixovirus genus, while nairoviruses were detected in 7 pools (8.75%; MIR 1.76%), with one sequence clustering in the Orthonairovirus genus, and six clustering in the Norwavirus genus. Although a small number of ticks from only one area in Greece were tested, a variety of pathogens together with recently identified viruses were detected, prompting further studies in ticks and surveillance studies in humans.

Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis

BACKGROUND

Haemaphysalis longicornis is drawing attentions for its geographic invasion, extending population, and emerging disease threat. However, there are still substantial gaps in our knowledge of viral composition in relation to genetic diversity of H. longicornis and ecological factors, which are important for us to understand interactions between virus and vector, as well as between vector and ecological elements.

RESULTS

We conducted the meta-transcriptomic sequencing of 136 pools of H. longicornis and identified 508 RNA viruses of 48 viral species, 22 of which have never been reported. Phylogenetic analysis of mitochondrion sequences divided the ticks into two genetic clades, each of which was geographically clustered and significantly associated with ecological factors, including altitude, precipitation, and normalized difference vegetation index. The two clades showed significant difference in virome diversity and shared about one fifth number of viral species that might have evolved to "generalists." Notably, Bandavirus dabieense, the pathogen of severe fever with thrombocytopenia syndrome was only detected in ticks of clade 1, and half number of clade 2-specific viruses were aquatic-animal-associated.

CONCLUSIONS

These findings highlight that the virome diversity is shaped by internal genetic evolution and external ecological landscape of H. longicornis and provide the new foundation for promoting the studies on virus-vector-ecology interaction and eventually for evaluating the risk of H. longicornis for transmitting the viruses to humans and animals. Video Abstract.

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.

Phlebovirus diversity in ticks from livestock in arid ecologies in Kenya

Phleboviruses are emerging pathogens of public health importance. However, their association with ticks is poorly described, particularly in Africa. Here, adult ticks infesting cattle, goats and sheep were collected in two dryland pastoralist ecosystems of Kenya (Baringo and Kajiado counties) and were screened for infection with phleboviruses. Ticks mainly belonged to the species Rhipicephalus appendiculatus, Hyalomma impeltatum, and Hyalomma rufipes. A fragment of the RNA-dependent RNA polymerase (RdRp) gene was identified in thirty of 671 tick pools, of which twenty-nine were from livestock sampled in Baringo county. Phylogenetic analyses revealed that twenty-five sequences were falling in three clades within the group of tick-associated phleboviruses. The sequences of the three clades showed nucleotide distances 8%, 19% and 22%, respectively, to previously known viruses suggesting that these sequence fragments may belong to three distinct viruses. Viruses of the group of tick-associated phleboviruses have been found in several countries and continents but so far have not been associated with disease in humans or animals. In addition, five sequences were found to group with the sandfly-associated phleboviruses Bogoria virus, Perkerra virus and Ntepes virus recently detected in the same region. Further studies are needed to investigate the transmission and maintenance cycles of these viruses, as well as to assess their potential to infect vertebrates.

Tick-Borne Pathogens and Diseases in Greece

Tick-borne diseases (TBDs) are recognized as a serious and growing public health epidemic in Europe, and are a cause of major losses in livestock production worldwide. This review is an attempt to present a summary of results from studies conducted over the last century until the end of the year 2020 regarding ticks, tick-borne pathogens, and tick-borne diseases in Greece. We provide an overview of the tick species found in Greece, as well as the most important tick-borne pathogens (viruses, bacteria, protozoa) and corresponding diseases in circulation. We also consider prevalence data, as well as geographic and climatic conditions. Knowledge of past and current situations of TBDs, as well as an awareness of (risk) factors affecting future developments will help to find approaches to integrated tick management as part of the ‘One Health Concept’; it will assist in avoiding the possibility of hotspot disease emergencies and intra- and intercontinental transmission. Increased surveillance in Greece is required to ensure clear and effective policies for TBD control.

Prevalence and genetic diversity of Shibuyunji virus, a novel tick-borne phlebovirus identified in Zambia

Tick-borne pathogens are an emerging public health threat worldwide. However, information on tick-borne viruses is scanty in sub-Saharan Africa. Here, by RT-PCR, 363 ticks (Amblyomma, Hyalomma and Rhipicephalus) in the Namwala and Livingstone districts of Zambia were screened for tick-borne phleboviruses (TBPVs). TBPVs (L gene) were detected in 19 (5.2%) Rhipicephalus ticks in Namwala. All the detected TBPVs were Shibuyunji viruses. Phylogenetically, they were closely related to American dog tick phlebovirus. This study highlights the possible role of Rhipicephalus ticks as the main host of Shibuyunji virus and suggests that these viruses may be present outside the area where they were initially discovered.

Discovery and genetic characterization of a novel orthonairovirus in Ixodes ricinus ticks from Danube Delta

Different arthropod species are vectors of a wide array of arboviruses (arthropod-borne viruses) and have likely been central to viral evolution. To better understand the extent of arthropod-borne pathogens, as well as their origin and evolutionary history, it is crucial to uncover the full range of microbial agents, including viruses associated with arthropods. In this study, a collection of ticks obtained in 2016 directly from mammal and bird hosts from several rural and natural sites of Danube Delta was subjected to transcriptome sequencing and amplification assays. Vector surveillance revealed the presence of a novel orthonairovirus species, designated Sulina virus, in Ixodes ricinus ticks. Phylogenetic clustering of each viral protein consistently placed the new virus in the Orthonairovirus genus as a new genogroup closely related to Tamdy orthonairovirus, a genogroup comprising both pathogenic and tick-associated orthonairoviruses. The serological testing of engorged ticks and blood of infected hosts, along with the inoculation of vertebrate cells and mice found no specific antibodies or viral replication, suggesting that Sulina virus is an orthonairovirus associated with the virome of Ixodes ricinus. Finally, the characterization of a novel orthonairovirus identified using high throughput sequencing will advance our knowledge of interactions between viruses and tick vectors, expanding our perspective on fundamental questions regarding orthonairovirus evolution, diversity, ecology and potential of emergence as pathogens.

Phlebovirus sequences detected in ticks collected in Russia: Novel phleboviruses, distinguishing criteria and high tick specificity

Phlebovirus is an abundant and rather heterogeneous genus within the Phenuiviridae family (order Bunyavirales). The genus Phlebovirus is divided into two antigenic complexes, which also correspond to the main vector: sandflies/mosquitoes and ticks. Previously, only sandfly/mosquito-borne phleboviruses were associated with human disease, such as Rift Valley fever virus, Toscana virus, Sicilian and Naples Sandfly fever viruses and others. Until recently, tick-borne phleboviruses were not considered as human pathogens. After the discovery of severe fever with thrombocytopenia syndrome, interest to tick-borne phleboviruses has increased dramatically. In the last decade, many novel phleboviruses have been reported in different regions. Despite this, the diversity, ecology and pathogenicity of these viruses still remain obscure. The aim of this work was to study the diversity of phleboviruses in ticks collected in several regions of Russia. We used pan-phlebovirus RT-PCR assays based on multiple degenerate primers targeting the polymerase gene fragment. Arthropod specimens were collected from 2005 to 2018. A total of 5901 Ixodidae ticks combined into 1116 pools were screened. A total of 160 specific amplicons were produced. In three cases RT-PCR assays amplified two distinct viruses from same tick pools. Direct sequencing of amplicons and subsequent phylogenetic analysis revealed twelve representatives of divergent phlebovirus groups. Based on the distribution of pairwise nucleotide sequence identity values, a cut-off (88%) was suggested to distinguish tick-borne phleboviruses. According to this provisional criterion, two viruses found here could be termed novel, while ten viruses have been described in previous studies. Detected phleboviruses demonstrated almost perfect specificity to a tick species or, at least, a genus. The same pattern was observed for tick-borne phleboviruses found in different studies around the world. Viruses that grouped together on a phylogenetic tree and differed less than this sequence identity threshold suggested above were hosted by ticks from the same genus.

Distribution and phylogenetic analysis of Dabieshan tick virus in ticks collected from Zhoushan, China

Dabieshan tick virus (DBV) belongs to Phlebovirus and its pathogenicity to human and animals is unknown. To investigate the presence of Dabieshan tick virus in Zhoushan, 353 ticks were collected from May 2018 to October 2019. The detection result showed that the average prevalence rate among these samples was 30.3% (107 positives out of 353 samples), which means DBVs are widely distributed in tick populations in Zhoushan of China. In a phylogenetic analysis based on the nucleotide sequences of the L and S segments of the virus (ZS-DBS-2018 tick virus) in the study, it clustered with Dabieshan tick virus (KM817666.1, KM817733.1) with a 97.1% and 99.6% nucleotide identity, respectively. Further studies involving virus isolation are required to characterize Dabieshan tick virus and to expand the geographical distribution of the sampled ticks.

First Report of the Ticks Haemaphysalis punctata Canestrini et Fanzago, 1878, Haemaphysalis parva (Neumann, 1897) and Dermacentor marginatus (Sulzer, 1776) (Acari, Amblyommidae) from Humans in Lebanon

Purpose

Knowledge on ticks infesting humans is scarce for the middle East. In this work, tick specimens (Acari: Amblyommidae) infesting humans in Lebanon were identified.

Methods

Ticks that were found on humans were received in the Lebanese University, Faculty of Sciences. The specimens were preserved in alcohol for their further morphological identification.

Results

Three tick species were identified: a red sheep tick Haemaphysalis punctata Canestrini et Fanzago, 1878, a Mediterranean ear tick H. parva (Neumann, 1897), and an ornate sheep tick Dermacentor marginatus (Sulzer, 1776); all isolated from human hosts.

Conclusion

This is the first report of Haemaphysalis punctata, H. parva and Dermacentor marginatus infesting humans from Central and North Lebanon.

Revisiting new tick-associated viruses: what comes next?

Tick-borne viral infections continue to cause diseases with considerable impact on humans, livestock, companion animals and wildlife. Many lack specific therapeutics and vaccines are available for only a few. Tick-borne viruses will continue to emerge, facilitated by anthroponotic factors related to the modern lifestyle. We persistently identify and are obliged to cope with new examples of emerging tick-borne viral diseases and novel viruses today. Many new strains have been detected in vertebrates and arthropods, some causing severe diseases likely to challenge public and veterinary health. This manuscript aims to provide a narrative overview of recently-described tick-associated viruses, with perspectives on changing paradigms in identification, screening and control.

RNA virome analysis of questing ticks from Hokuriku District, Japan, and the evolutionary dynamics of tick-borne phleboviruses

Tick-borne viruses have emerged recently in many parts of the world, and the discoveries of novel tick-borne viruses have been accelerated by the development of high-throughput sequencing technology. In this study, a cost-efficient small benchtop next-generation sequencer, the Illumina MiniSeq, was used for the RNA virome analysis of questing ticks collected from Hokuriku District, Japan, and assessed for their potential utility in a tick-borne virus surveillance system. We detected two phleboviruses [Kabuto Mountain virus (KAMV) and Okutama tick virus (OKTV)], a coltivirus [Tarumizu tick virus (TarTV)], and a novel iflavirus [Hamaphysalis flava iflavirus (HfIFV)] from tick homogenates and/or cell culture supernatants after virus isolation processes. The number of sequence reads from KAMV and TarTV markedly increased when cell culture supernatants were used, indicating a successful isolation of these viruses. In contrast, OKTV and HfIFV were detected only in tick homogenates but not from cell culture supernatants, suggesting a failure to isolate these viruses. Furthermore, we performed genomic and phylogenetic analyzes of these detected viruses. OKTV and some phleboviruses discovered recently by NGS-based methods were probably deficient in the M genome segment, which are herein proposed as M segment-deficient phlebovirus (MdPV). A phylogenetic analysis of phleboviruses, including MdPV, suggested that Uukuniemi and Kaisodi group viruses and kabutoviruses evolved from an ancestral MdPV, which provides insights into the evolutionary dynamics of phleboviruses as emerging pathogens.

Novel Tick Phlebovirus Genotypes Lacking Evidence for Vertebrate Infections in Anatolia and Thrace, Turkey

We screened ticks and human clinical specimens to detect and characterize tick phleboviruses and pathogenicity in vertebrates. Ticks were collected at locations in Istanbul (Northwest Anatolia, Thrace), Edirne, Kırklareli, and Tekirdağ (Thrace), Mersin (Mediterranean Anatolia), Adiyaman and Şanlıurfa (Southeastern Anatolia) provinces from 2013-2018 and were analyzed following morphological identification and pooling. Specimens from individuals with febrile disease or meningoencephalitic symptoms of an unknown etiology were also evaluated. The pools were screened via generic tick phlebovirus amplification assays and products were sequenced. Selected pools were used for cell culture and suckling mice inoculations and next generation sequencing (NGS). A total of 7492 ticks were screened in 609 pools where 4.2% were positive. A phylogenetic sequence clustering according to tick species was observed. No human samples were positive. NGS provided near-complete viral replicase coding sequences in three pools. A comprehensive analysis revealed three distinct, monophyletic virus genotypes, comprised of previously-described viruses from Anatolia and the Balkans, with unique fingerprints in conserved amino acid motifs in viral replicase. A novel tick phlebovirus group was discovered circulating in the Balkans and Turkey, with at least three genotypes or species. No evidence for replication in vertebrates or infections in clinical cases could be demonstrated.

Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences

The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the continental territory and the islands of São Miguel, in the Azores, and Madeira), as well as in the Spanish western regions of Extremadura and Castilla and León. Phlebovirus sequences were frequently detected (L-segment) from both questing and feeding ticks, but especially in Rhipicephalus sanguineus sensu lato (s.l.) specimens. These sequences were detected in adult ticks, as well as nymphs and eggs, supporting the hypothesis of viral maintenance by vertical transmission. Though multiple genetic groups could be identified in phylogenetic trees (AnLuc, KarMa, RiPar virus 1, and Spanish group 1 and 2), all the sequences from Portugal and Spain shared common ancestry with other viral sequence obtained from samples collected over a large geographic coverage. Spatiotemporal analysis placed Middle-East as the geographic origin of the most recent common ancestor (MRCA) of all phleboviruses analysed in the present study. More recent viral transitions might include migrations from Spain to continental Portugal, and from there to the Portuguese Islands. Our findings suggest that the time of the MRCA of phleboviruses was dated around 225 years ago [95% HPD: 124-387 year before the last sampling date].

Infection of newly identified phleboviruses in ticks and wild animals in Hokkaido, Japan indicating tick-borne life cycles

Recent discoveries of tick-borne pathogens have raised public health concerns on tick-borne infectious diseases and emphasize the need to assess potential risks of unrecognized tick-borne pathogens. First, to determine the existence of tick-borne phleboviruses (TBPVs), genetic surveillance of phleboviruses in ticks was conducted mainly in Hokkaido, the northernmost island in Japan from 2013 to 2015. Genes of two TBPVs, previously reported as Mukawa virus (MKWV) and a newly identified relative of MKWV, Kuriyama virus (KURV), were detected and the viruses were isolated from Ixodes persulcatus collected in Hokkaido, but not in I. persulcatus collected from other areas of Japan. These viruses were phylogenetically and antigenically similar to each other. Next, to investigate the infection of MKWV in mammals, serum samples from wildlife captured in Hokkaido from 2007 to 2011 were used for serological screening. Neutralizing antibodies against MKWV were detected in both Yezo-deer (Cervus nippon yesoensis) (2/50) and raccoons (Procyon lotor) (16/64). However, no infectious MKWV was recovered from laboratory mice in experimental infections, though viral RNAs were detected in their tissues. Thus, MKWV and KURV may maintain tick-mammalian life cycles in Hokkaido, suggesting their potential as causative agents of tick-borne diseases in mammals.

A metagenomic survey identifies Tamdy orthonairovirus as well as divergent phlebo-, rhabdo-, chu- and flavi-like viruses in Anatolia, Turkey

We employed a direct metagenomic approach via next-generation sequencing for a cross-sectional investigation of viruses in 10 tick pools, collected from Aegean, Mediterranean and central Anatolian locations in Turkey. Sequences from all genome segments of Tamdy orthonairovirus (family Nairoviridae) were characterized in ticks collected from a Meriones tristrami. We further obtained near-complete L and partial S segments of several tick-associated phleboviruses (family Phenuiviridae), including Tacheng tick virus 2 and a novel virus, tentatively named as the tick phlebovirus Anatolia. Partial NS5-coding region of recently-described flavi-like virus (Tacheng tick virus 8) was further detected. Moreover, near-complete and polymerase-coding regions of arthropod-associated rhabdoviruses as well as sequences closely-related to the members of the newly-proposed virus family, the Chuviridae, were characterized. Despite origins of the viral sequences could not be fully elucidated, the findings suggest the circulation of diverse arthropod and tick-associated viruses in Anatolia. Occurrence and outcome of vertebrate exposure and probable health impact of these viruses require further investigation. We also report the initial detection of Tamdy orthonairovirus, an established human pathogen, which should be included in the diagnostic workup of infections with unknown etiology.

Detection and phylogenetic analysis of phlebovirus, including severe fever with thrombocytopenia syndrome virus, in ticks collected from Tokyo, Japan

Severe fever with thrombocytopenia syndrome (SFTS) was detected for the first time in China in 2011. Since then, human cases have been reported in endemic regions, including Japan. To investigate the presence of tick-borne pathogens in Tokyo, 551 ticks (266 samples) were collected from October 2015 to October 2016. Although the SFTS virus was not detected by RT-PCR, a novel phlebovirus was detected in one sample. In a phylogenetic analysis based on the partial nucleotide sequences of the L and S segments of the virus, the virus clustered with Lesvos virus (Greece), Yongjia tick virus, and Dabieshan tick virus (China). Further studies involving virus isolation are required to characterize this novel phlebovirus and to expand the epidemiological knowledge of related pathogens.

Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey

Background

Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens.

Results

A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co- infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens.

Conclusions

Widespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2279-1) contains supplementary material, which is available to authorized users.

Emerging arboviral human diseases in Southern Europe

Southern Europe is characterized by unique landscape and climate which attract tourists, but also arthropod vectors, some of them carrying pathogens. Among several arboviral diseases that emerged in the region during the last decade, West Nile fever accounted for high number of human cases and fatalities, while Crimean-Congo hemorrhagic fever expanded its geographic distribution, and is considered as a real threat for Europe. Viruses evolve rapidly and acquire mutations making themselves stronger and naive populations more vulnerable. In an effort to tackle efficiently the emerging arboviral diseases, preparedness and strategic surveillance are needed for the early detection of the pathogen and containment and mitigation of probable outbreaks. In this review, the main human arboviral diseases that emerged in Southern Europe are described.