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

Bratuleanu, Bianca Elena; Temmam, Sarah; Munier, Sandie; Chrétien, Delphine; Bigot, Thomas; Werf, Sylvie van der; Savuța, Gheorghe; Éloit, Marc

doi:10.3389/fvets.2022.863814

Cited by 9 publications

(16 citation statements)

References 41 publications

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“…Some quaranjaviruses are associated with avian mortality and demonstrate pathogenicity under experimental conditions (Allison et al, 2015 ; Shearn-Bochsler et al, 2017 ; Mourya et al, 2019 ). Documentation of various quaranjaviruses in several hard tick species in the genera Amblyomma, Haemaphysalis, Ixodes , and Rhipicephalus including this study suggest that unrecognized tick-borne infections may be occurring (Cholleti et al, 2018 ; Sameroff et al, 2021 ; Bratuleanu et al, 2022 ; Kobayashi et al, 2022 ). Furthermore, two reads (279 and 767 base pairs) in a Hae.…”

Section: Resultsmentioning

confidence: 63%

“…Tick-associated phleboviruses identified in the pools include Brown dog tick phlebovirus 2 (BDTP2), phlebovirus Strandja, tick phlebovirus Anatolia, and Lesvos virus ( Table 1 ). Strandja and Anatolia phleboviruses were mainly reported in Rhipicephalus ticks from Bulgaria and Turkey (Emanet et al, 2019 ; Ohlendorf et al, 2019 ), while BDTP2 appears widespread, detected in China, and Trinidad and Tobago as well as the Balkans (Sameroff et al, 2019 ; Bratuleanu et al, 2022 ; Guo et al, 2022 ). Lesvos virus was originally reported from Hae.…”

Section: Resultsmentioning

confidence: 99%

“…BTV3 and tick phleboviruses appear to be a ubiquitous virus in Anatolia, having been detected in various tick species (Dinçer et al, 2017 ; Brinkmann et al, 2018 ; Emanet et al, 2019 ; Ergünay et al, 2020 ). Tick phleboviruses are also widely distributed in Asia, Europe, and America (Ohlendorf et al, 2019 ; Sameroff et al, 2019 ; Bratuleanu et al, 2022 ; Guo et al, 2022 ). As vertebrate in vivo experiments failed to propagate these viruses, they are currently considered non-virulent residents of the tick virome (Emanet et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

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

Ergunay,

Dincer,

Justi

et al. 2023

Front. Microbiol.

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

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Section: Resultsmentioning

confidence: 63%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Ergunay,

Dincer,

Justi

et al. 2023

Front. Microbiol.

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“…Quaranjaviruses have been known to be transmitted to birds mainly by argasid ticks, but a recent study found a quaranjavirus-like sequence in Am. dissimile in Romania (34). In the present study, we identified 4 putative novel Orthomyxo-like tick viruses from ixodid tick metagenomic sequences, 3 of which were sampled from R. sanguineus in Italy, and one from R. haemaphysaloides in China ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

Characterisation and zoonotic risk of tick viruses in public datasets

Lin

Pascall

2022

Preprint

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Tick-borne viruses remain a substantial zoonotic risk worldwide. The advent of next-generation sequencing has significantly broadened our knowledge of viruses. However, large amounts of sequences in public datasets remain unannotated which could represent unrealised or undocumented viruses. This study aimed to assess whether these novel and other understudied viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 136 known tick-borne viruses using a genome composition-based machine learning model. We found five high-risk tick-borne 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 emerging tick-borne viruses. Through bioinformatic analyses, we presented 83 unannotated contigs exhibiting high identity with known tick viruses in public meta-genomic and -transcriptomic datasets. These putative novel viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae, Chuviridae) and one DNA viral family (Asfaviridae). After manual checking, these 83 contigs were reduced to 5 putative novel Alphatetra-like viral contigs, 5 putative novel Orthomyxo-like viral contigs, and 1 Chu-like viral contig which clustered with known tick-borne viruses, forming a separate clade within the viral families. This study added to the knowledge of tick virus diversity and highlighted the importance of surveillance of newly emerging tick-borne diseases.

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“…Raw reads were processed as previously described [ 16 ] with an in-house bioinformatics pipeline, Microseek ( ; accessed on 20 August 2021) [ 17 ], that comprises a quality check and the trimming of raw reads followed by read normalization prior to assembly into contigs and the generation of non-assembled singletons. ORF predictions of both contigs and singletons were performed, and a taxonomic assignation of protein sequences was performed by Blast-based querying using three successive, specialized RVDBs [ 18 ] followed by generalist (NCBI/nr and NCBI/nt) databases.…”

Section: Methodsmentioning

confidence: 99%

A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep

et al. 2023

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Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics to detect the virome, including novel viruses, associated with Ixodes ricinus collected from Romania and France. A bunyavirus-like virus related to the Bronnoya virus was identified for the first time in these regions. It presents a high level of amino-acid conservation with Bronnoya-related viruses identified in I. ricinus ticks from Norway and Croatia and with the Ixodes scapularis bunyavirus isolated from a tick cell line in Japan in 2014. Phylogenetic analyses revealed that the Bronnoya viruses’ sub-clade is distinct from several Bunyavirales families, suggesting that it could constitute a novel family within the order. To determine if Bronnoya viruses could constitute novel tick-borne arboviruses, a Luciferase immunoprecipitation assay for detecting antibodies in the viral glycoprotein of the Romanian Bronnoya virus was used to screen sera from small ruminants exposed to tick bites. No positive serum was detected, suggesting that this virus is probably not able to infect small ruminants. This study represents the first serological investigation of mammalian infections with a Bronnoya-like virus and an initial step in the identification of potential new emergences of tick-borne arboviruses.

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

Cited by 9 publications

References 41 publications

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

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

Characterisation and zoonotic risk of tick viruses in public datasets

A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep

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