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Viruses
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Diversity of RNA Viruses in Arthropod
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Diversity of RNA Viruses in Arthropod

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Insect Viruses".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 13077

Special Issue Editor

Dr. Junmin Li

E-Mail Website
Guest Editor
Institute of Plant Virology, Ningbo University, Ningbo, China
Interests: RNA virus discovery; insect vector - plant virus interaction; virus evolution; non-retroviral endogenous viral element

Special Issue Information

Dear Colleagues,

Viruses are the most abundant microbes on earth, most of those previously discovered and studied being pathogens causing diseases in their plant/animal hosts. Over the past decade, the development of metagenomics next-generation sequencing, such as transcriptome and small RNA sequencing, has led to the discovery of a large number of novel RNA viruses from arthropods, especially for insects. These viruses, known as insect/arthropod-specific viruses (ISVs), are exclusively confined to arthropods/insects, unable to replicate in vertebrates or plant hosts. Nevertheless, considering the enormous abundance of RNA viruses in nature, more investigations are needed to decipher the undescribed RNA viruses in arthropods, which could contribute to the current taxonomy of RNA viruses, as well as the long-term co-evolution with their hosts.

This Special Issue, “Diversity of RNV viruses in arthropod”, intends to provide contemporary research on the diversity of RNA viruses capable of infecting arthropods, the potential effect of ISVs on the fitness/vector competence of their hosts, and the intimate co-evolution between RNA viruses and their arthropod hosts.

Dr. Junmin Li
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA virus discovery
  • insect-specific viruses
  • virus-host co-evolution
  • highthrouput RNA sequencing
  • endogenous viral element
  • RNA virus taxonomy
  • RNA virome
  • arthropod

Published Papers (6 papers)

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Research

25 pages, 3811 KiB  
Article
Enhanced Arbovirus Surveillance with High-Throughput Metatranscriptomic Processing of Field-Collected Mosquitoes
by Jana Batovska, Peter T. Mee, Tim I. Sawbridge, Brendan C. Rodoni and Stacey E. Lynch
Viruses 2022, 14(12), 2759; https://0-doi-org.brum.beds.ac.uk/10.3390/v14122759 - 11 Dec 2022
Cited by 5 | Viewed by 1877
Abstract
Surveillance programs are essential for the prevention and control of mosquito-borne arboviruses that cause serious human and animal diseases. Viral metatranscriptomic sequencing can enhance surveillance by enabling untargeted, high-throughput arbovirus detection. We used metatranscriptomic sequencing to screen field-collected mosquitoes for arboviruses to better [...] Read more.
Surveillance programs are essential for the prevention and control of mosquito-borne arboviruses that cause serious human and animal diseases. Viral metatranscriptomic sequencing can enhance surveillance by enabling untargeted, high-throughput arbovirus detection. We used metatranscriptomic sequencing to screen field-collected mosquitoes for arboviruses to better understand how metatranscriptomics can be utilised in routine surveillance. Following a significant flood event in 2016, more than 56,000 mosquitoes were collected over seven weeks from field traps set up in Victoria, Australia. The traps were split into samples of 1000 mosquitoes or less and sequenced on the Illumina HiSeq. Five arboviruses relevant to public health (Ross River virus, Sindbis virus, Trubanaman virus, Umatilla virus, and Wongorr virus) were detected a total of 33 times in the metatranscriptomic data, with 94% confirmed using reverse transcription quantitative PCR (RT-qPCR). Analysis of metatranscriptomic cytochrome oxidase I (COI) sequences enabled the detection of 12 mosquito and two biting midge species. Screening of the same traps by an established public health arbovirus surveillance program corroborated the metatranscriptomic arbovirus and mosquito species detections. Assembly of genome sequences from the metatranscriptomic data also led to the detection of 51 insect-specific viruses, both known and previously undescribed, and allowed phylogenetic comparison to past strains. We have demonstrated how metatranscriptomics can enhance surveillance by enabling untargeted arbovirus detection, providing genomic epidemiological data, and simultaneously identifying vector species from large, unsorted mosquito traps. Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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11 pages, 1415 KiB  
Article
The Characterization of Three Novel Insect-Specific Viruses Discovered in the Bean Bug, Riptortus pedestris
by Chunyun Guo, Zhuangxin Ye, Biao Hu, Shiqi Shan, Jianping Chen, Zongtao Sun, Junmin Li and Zhongyan Wei
Viruses 2022, 14(11), 2500; https://0-doi-org.brum.beds.ac.uk/10.3390/v14112500 - 11 Nov 2022
Cited by 3 | Viewed by 1312
Abstract
Insect-specific virus (ISV) is one of the most promising agents for the biological control of insects, which is abundantly distributed in hematophagous insects. However, few ISVs have been reported in Riptortus pedestris (Fabricius), one of the major pests threatening soybeans and causing great [...] Read more.
Insect-specific virus (ISV) is one of the most promising agents for the biological control of insects, which is abundantly distributed in hematophagous insects. However, few ISVs have been reported in Riptortus pedestris (Fabricius), one of the major pests threatening soybeans and causing great losses in yield and quality. In this work, field Riptortus pedestris was collected from six soybean-producing regions in China, and their virome was analyzed with the metatranscriptomic approach. Altogether, seven new insect RNA viruses were identified, three of which had complete RNA-dependent RNA polymerase (RdRp) and nearly full-length genome sequences, which were named Riptortus pedestris alphadrosrha-like virus 1 (RpALv1), Riptortus pedestris alphadrosrha-like virus 2 (RpALv2) and Riptortus pedestris almendra-like virus (RiALv). The three identified novel ISVs belonged to the family Rhabdoviridae, and phylogenetic tree analysis indicated that they were clustered into new distinct clades. Interestingly, the analysis of virus-derived small-interfering RNAs (vsiRNAs) indicated that only RiALv-derived siRNAs exhibited 22 nt length preference, whereas no clear 21 or 22 nt peaks were observed for RpALv1 and RpALv2, suggesting the complexity of siRNA-based antiviral immunity in R. pedestris. In conclusion, this study contributes to a better understanding of the microenvironment in R. pedestris and provides viral information for the development of potential soybean insect-specific biocontrol agents. Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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12 pages, 2583 KiB  
Article
Is the Intergenic Region of Aedes aegypti Totivirus a Recombination Hotspot?
by Roseane da Silva Couto, Geovani de Oliveira Ribeiro, Ramendra Pati Pandey and Élcio Leal
Viruses 2022, 14(11), 2467; https://0-doi-org.brum.beds.ac.uk/10.3390/v14112467 - 08 Nov 2022
Cited by 1 | Viewed by 1204
Abstract
The genus totivirus in the family Totiviridae contains double-stranded RNA viruses. Their genome has two open reading frames (ORFs) that encode capsid protein (CP) and RNA-dependent RNA polymerase (RdRp). The toti-like viruses recently identified in Anopheles sp. and Aedes aegypti mosquitoes (AaTV) share [...] Read more.
The genus totivirus in the family Totiviridae contains double-stranded RNA viruses. Their genome has two open reading frames (ORFs) that encode capsid protein (CP) and RNA-dependent RNA polymerase (RdRp). The toti-like viruses recently identified in Anopheles sp. and Aedes aegypti mosquitoes (AaTV) share the same genome organization as other totiviruses. The AaTVs that have been described in distinct geographical regions are monophyletic. In this study, we show that AaTV sequences can be grouped into at least three phylogenetic clades (named A, B, and C). Clades A and B are composed of AaTV sequences from mosquitoes collected in the Caribbean region (Guadeloupe), and clade C contains sequences from the USA. These clades may represent AaTV lineages that are locally adapted to their host populations. We also identified three recombinant AaTV strains circulating in mosquitoes in Guadeloupe. Although these strains have different chimeric patterns, the position of the recombination breakpoint was identical in all strains. Interestingly, this breakpoint is located in a hairpin-like structure in the intergenic region of the AaTV genome. This RNA structure may stall RNA polymerase processivity and consequently induce template switching. In vitro studies should be conducted to further investigate the biological significance of AaTV’s intergenic region as a recombination hotspot Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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64 pages, 16941 KiB  
Article
Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland
by Phuoc T. Truong Nguyen, C. Lorna Culverwell, Maija T. Suvanto, Essi M. Korhonen, Ruut Uusitalo, Olli Vapalahti, Teemu Smura and Eili Huhtamo
Viruses 2022, 14(7), 1489; https://0-doi-org.brum.beds.ac.uk/10.3390/v14071489 - 07 Jul 2022
Cited by 9 | Viewed by 3706
Abstract
RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16–60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis [...] Read more.
RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16–60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date. Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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12 pages, 2053 KiB  
Article
Virome of Three Termite Species from Southern Vietnam
by Alexander G. Litov, Anna I. Zueva, Alexei V. Tiunov, Nguyen Van Thinh, Natalia V. Belyaeva and Galina G. Karganova
Viruses 2022, 14(5), 860; https://0-doi-org.brum.beds.ac.uk/10.3390/v14050860 - 21 Apr 2022
Viewed by 2221
Abstract
Modern metagenomic approaches enable the effective discovery of novel viruses in previously unexplored organisms. Termites are significant ecosystem converters and influencers. As with the majority of tropical forest insects, termites are studied insufficiently, and termite virome remains especially understudied. Here, we studied the [...] Read more.
Modern metagenomic approaches enable the effective discovery of novel viruses in previously unexplored organisms. Termites are significant ecosystem converters and influencers. As with the majority of tropical forest insects, termites are studied insufficiently, and termite virome remains especially understudied. Here, we studied the virome of lichenophagous and mycophagous termites (Hospitalitermes bicolor, Macrotermes carbonarius and Odontotermes wallonensis) collected in the Cat Tien National Park (Vietnam). We assembled four full genomes of novel viruses related to Solemoviridae, Lispiviridae, Polycipiviridae and Kolmioviridae. We also found several contigs with relation to Chuviridae and Deltaflexiviridae that did not correspond to complete virus genomes. All the novel viruses clustered phylogenetically with previously identified viruses of the termites. Deltaflexi-like contigs were identified in the fungi-cultivating M. carbonarius and showed homology with viruses recently discovered in the edible basidiomycete mushrooms. Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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14 pages, 2487 KiB  
Article
Possible Arbovirus Found in Virome of Melophagus ovinus
by Alexander G. Litov, Oxana A. Belova, Ivan S. Kholodilov, Magomed N. Gadzhikurbanov, Larissa V. Gmyl, Natalia D. Oorzhak, Anna A. Saryglar, Aydar A. Ishmukhametov and Galina G. Karganova
Viruses 2021, 13(12), 2375; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122375 - 26 Nov 2021
Cited by 7 | Viewed by 1961
Abstract
Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin [...] Read more.
Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus. Full article
(This article belongs to the Special Issue Diversity of RNA Viruses in Arthropod)
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