Novel quaranjavirus and other viral sequences identified from ticks parasitizing hunted wildlife in Trinidad and Tobago

Viral metagenomics of hematophagous insects collected in the Carajas mining complex, Pará State, Brazil

Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3 % of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.

Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe

BACKGROUND

Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many are expanding their geographical range due to changing socioeconomic and climate factors. The Danube Delta, one of Europe's largest wetlands, is an ecosystem that, despite its ecological importance, remains understudied concerning the risk of introducing new tick-borne viruses. This region serves as a critical habitat for migratory birds, which can carry ticks over long distances, potentially introducing exotic tick species and their pathogens into the local ecosystem. Hyalomma marginatum ticks, the primary vector of Crimean-Congo hemorrhagic fever virus (CCHFV), are of particular concern due to their expanding presence in Europe and potential to spread other arboviruses. In addition to being the primary vector for CCHFV, Hyalomma sp. ticks are capable of transmitting other pathogens of medical and veterinary importance, including Dugbe virus, West Nile virus, African horse sickness virus, and Kyasanur forest disease virus. Therefore, it is essential to monitor the presence of Hyalomma sp. ticks while simultaneously surveilling arbovirus circulation in tick populations to mitigate the risk of arboviral outbreaks.

METHODS

In this work, we used an RNA sequencing technique to analyze the virome of H. marginatum ticks collected from the Danube Delta Biosphere Reserve, Romania, one of the major bird migration hubs from Africa to Europe.

RESULTS

Among the viral taxa detected in H. marginatum ticks, sequences belonging to Volzhskoe tick virus (VTV), Balambala tick virus (BMTV) and Bole tick virus 4 (BTV4) were identified. In addition, we report the first identification of a novel Rhabdoviridae-related virus, Hyalomma marginatum rhabdovirus (HMRV). No CCHFV or any CCHFV-related nairovirus were detected in this study.

CONCLUSIONS

To summarize, detecting new viruses is essential for monitoring potential viral outbreaks. Our research expands the understanding of virus diversity in Eastern Europe, including the identification of novel viruses. This insight is crucial for monitoring viruses that may pose risks to both animal and human health, such as CCHFV.

Characterisation of putative novel tick viruses and zoonotic risk prediction

Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.

Diversity of Viruses in Ixodes ricinus in Europe including Novel and Potential Arboviruses

Tick-borne pathogens are responsible for many vector-borne diseases in Europe, causing important problems for human and animal health. The composition of viral communities in ticks and their interactions with pathogens is little understood, especially in Eastern Europe, an area that represents a major hub for animal-arthropod vectors exchanges. In this study, we used metatranscriptomics to characterize the virome of 2,753 Ixodes ricinus ticks collected from France and Romania, focusing on viruses that could potentially have implications for human or animal health. Among the great viral diversity of viruses identified, we reported a novel strain of Tribec virus, an important human pathogen that was found in Romanian ticks. We detected viruses belonging to the Phenuiviridae and Nairoviridae families close to human and animal pathogens, suggesting that these viruses could constitute novel arboviruses. We used luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Sedoreoviridae, Phenuiviridae, and Nairoviridae families to screen serum samples from small ruminants' exposed to tick bites. The results suggest that part (approximately 12%, 95% CI 9.1-16.2) of the small ruminant population from Danube Delta, was exposed to viruses related to bi- or tri-segmented nairoviruses, but cross-reactive viruses could not be confirmed with certainly. The strategy developed in this study serves as a key step in predicting potential new disease outbreaks and can be readily adapted to study other reservoirs, vectors, and interfaces involving susceptible hosts.

The contribution of citizen science in the surveillance of wildlife and related arthropods

Environmental and anthropogenic factors may significantly affect the diffusion of wild animals, enhancing the interface of human–wildlife interactions and driving the spread of pathogens and vector-borne diseases between animals and humans. However, in the last decade, the involvement of citizens in scientific research (the so-called citizen science approach, henceforth abbreviated as CS) provided a network of large-scale and cost-effective surveillance programmes of wildlife populations and their related arthropod species. Therefore, this review aims to illustrate different methods and tools used in CS studies, by arguing the main advantages and considering the limitations of this approach. The CS approach has proven to be an effective method for establishing density and distribution of several wild animal species, in urban, peri-urban and rural environments, as well a source of information regarding vector–host associations between arthropods and wildlife. Extensive efforts are recommended to motivate citizens to be involved in scientific projects to improve both their and our knowledge of the ecology and diseases of wildlife. Following the One Health paradigm, collaborative and multidisciplinary models for the surveillance of wildlife and related arthropod species should be further developed by harnessing the potentiality of the CS approach.

Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia

Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.

Investigating Infectious Organisms of Public Health Concern Associated with Wild Meat

The wild meat trade poses a significant threat to public health as it facilitates the spillover of zoonotic pathogens through high-risk activities such as the hunting, butchering, trade, and consumption of wild animals. Despite the health risks and association with marking epidemics including SARS, Ebola, and COVID-19, the global wild meat trade continues to thrive. To summarize the evidence available, primary literature published between 2000 and 2022 was systematically and critically assessed for evidence of zoonotic pathogens or other infectious organisms detected in samples directly from wild meat, from animals hunted for wild meat, or from humans exposed through high-risk activities. Within the 97 articles analyzed, a total of 114 pathogen genera (15 viruses, 40 bacteria, 54 parasites, and 5 fungi) were detected in wild meat animals belonging to 168 vertebrate species including mammals, reptiles and birds sampled in 32 countries. In the context of wild meat specifically, infectious organisms were differentiated between those with zoonotic potential (32% of reported genera), ectoparasitic vectors (1%), and possible opportunistic or environmental contaminants. Thirteen viral, four bacterial, and one parasitic genera were also documented in humans participating in wild meat trade activities, supporting pathogen spillover potential. Most studies employed a targeted approach to evaluate the presence of (i.e., polymerase chain reaction (PCR); n = 65) or exposure to (i.e., ELISA; n = 19) a specific pathogen, while only one study employed broad-spectrum metabarcoding techniques. The diversity of infectious organisms associated with wild meat are highlighted through this review and could be used to guide policy development. However, the common use of a selected set of targeted detection assays likely biases the exploration of pathogen diversity, therefore potentially preventing the discovery of "disease x". The global health risk demonstrated should make the illegal wild meat trade a priority for law-enforcement agencies and future research.

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.

Metatranscriptomics Reveals the Diversity of the Tick Virome in Northwest China

Blood-sucking ticks are obligate parasites and vectors of a variety of human and animal viruses. Some tick-borne viruses have been identified as pathogens of infectious diseases in humans or animals, potentially imposing significant public health burdens and threats to the husbandry industry. Therefore, identifying the profiles of tick-borne viruses will provide valuable information about the evolution and pathogen ecology of tick-borne viruses. In this study, we investigated the viromes of parasitic ticks collected from the body surfaces of herbivores in Xinjiang Uyghur Autonomous Region and Inner Mongolia Autonomous Region of China, two regions in northwest China. By using a metatranscriptomic approach, 17 RNA viruses with high diversity in genomic organization and evolution were identified. Among them, nine are proposed to be novel species. The classified viruses belonged to six viral families, including Phenuiviridae, Rhabdoviridae, Peribunyaviridae, Lispiviridae, Chuviridae, and Reoviridae, and unclassified viruses were also identified. In addition, although some viruses from different sampling locations shared significant similarities, the abundance and diversity of viruses notably varied among the different collection locations. This study demonstrates the diversity of tick-borne viruses in Xinjiang and Inner Mongolia and provides informative data for further study of the evolution and pathogenicity of these RNA viruses. IMPORTANCE Ticks are widely distributed in pastoral areas in northwestern China and act as vectors that carry and transmit a variety of pathogens, especially viruses. Our study revealed the diversity of tick viruses in Xinjiang and Inner Mongolia and uncovered the phylogenetic relationships of some RNA viruses, especially the important zoonotic tick-borne severe fever with thrombocytopenia syndrome virus in Inner Mongolia. These data suggest a complex and diverse evolutionary history and potential ecological factors associated with pathogenic viruses. The pathogenicity of these tick-borne viruses currently remains unclear. Therefore, future research should focus on evaluating the transmissability and pathogenicity of these tick-borne viruses.

Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China

Tick-borne viruses (TBVs) have increasingly caused a global public health concern. This study collected Rhipicephalus ticks in Guangdong, southern China to identify RNA viruses. Meta-transcriptome analysis revealed the virome in Rhipicephalus ticks, resulting in the discovery of 10 viruses, including Lihan tick virus, Brown dog tick phlebovirus 1 and 2 in the family Phenuiviridae, Mivirus and Wuhan tick virus 2 in the family Chuviridae, Wuhan tick virus 1 in the family Rhabdoviridae, bovine hepacivirus in the family Flaviviridae, Guangdong tick quaranjavirus (GTQV) in the family Orthomyxoviridae, Guangdong tick orbivirus (GTOV) in the family Reoviridae, and Guangdong tick Manly virus (GTMV) of an unclassified family. Phylogenetic analysis showed that most of these TBVs were genetically related to the strains in countries outside China, and GTQV, GTOV, and GTMV may represent novel viral species. These findings provided evidence of the long-distance spread of these TBVs in Guangdong, southern China, suggesting the necessity and importance of TBV surveillance.

Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta

Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The members of the Quaranjavirus genus are mainly associated with argas ticks but recent studies demonstrated the presence of novel quaranjaviruses-like in ixodid ticks. In 2020, 169 Rhipicephalus sanguineus ticks were collected in Southern Romania from small ruminants and analyzed by high-throughput transcriptome sequencing. Among the viral families that infect Romanian ticks, we have identified sequences from Phenuiviridae (Brown dog tick phlebovirus 1 [BDTPV1] and Brown dog tick phlebovirus 2 [BDTPV2]) and Chuviridae families (Cataloi mivirus [CTMV]), and numerous sequences from a new quaranjavirus-like, tentatively named Cataloi tick quaranjavirus (CTQV). Phylogenetic analyses performed on the five segments show that CTQV is phylogenetically positioned within a clade that encompasses Ixodidae-borne viruses associated with iguanas, small ruminants, seabirds, and penguins distributed across different geographical areas. Furthermore, CTQV is positioned differently depending on the segment considered. This is the first report on the detection of a quaranjavirus-like in Eastern Europe. Further investigations are needed to discern its infectivity and pathogenicity against vertebrates.

Jingchuvirales: a New Taxonomical Framework for a Rapidly Expanding Order of Unusual Monjiviricete Viruses Broadly Distributed among Arthropod Subphyla

Technical advances in metagenomics and metatranscriptomics have dramatically accelerated virus discovery in recent years. "Chuviruses" were first described in 2015 as obscure negative-sense RNA viruses of diverse arthropods. Although "chuviruses" first appeared to be members of the negarnaviricot order Mononegavirales in phylogenetic analyses using RNA-directed RNA polymerase sequences, further characterization revealed unusual gene orders in genomes that are nonsegmented, segmented, and/or possibly circular. Consequently, a separate order, Jingchuvirales, was established to include a monospecific family, Chuviridae. Recently, it has become apparent that jingchuvirals are broadly distributed and are therefore likely of ecological and economic importance. Here, we describe recent and ongoing efforts to create the necessary taxonomic framework to accommodate the expected flood of novel viruses belonging to the order.

Ticks and Tick-Borne Diseases in Central America and the Caribbean: A One Health Perspective

Ticks have complex life cycles which involve blood-feeding stages found on wild and domestic animals, with humans as accidental hosts. At each blood-feeding stage, ticks can transmit and/or acquire pathogens from their hosts. Therefore, the circulation of tick-borne pathogens (TBPs), especially the zoonotic ones, should be studied in a multi-layered manner, including all components of the chain of infections, following the 'One Health' tenets. The implementation of such an approach requires coordination among major stakeholders (such as veterinarians, physicians, acarologists, and researchers) for the identification of exposure and infection risks and application of effective prevention measures. In this review, we summarize our current knowledge on the epidemiology of tick-borne diseases in Central America and the Caribbean and the challenges associated with the implementation of 'One Health' surveillance and control programs in the region.