Iflavirus Covert Infection Increases Susceptibility to Nucleopolyhedrovirus Disease in .
Viruses
Naturally occurring covert infections in lepidopteran populations can involve multiple viruses with potentially different transmission strategies. In this study, we characterized covert infection by two RNA viruses, Spodoptera exigua iflavirus 1 (SeIV-1) and Spodoptera exigua iflavirus 2 (SeIV-2) (family Iflaviridae) that naturally infect populations of , and examined their influence on susceptibility to patent disease by the nucleopolyhedrovirus Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) (family Baculoviridae). The abundance of SeIV-1 genomes increased up to ten-thousand-fold across insect developmental stages after surface contamination of host eggs with a mixture of SeIV-1 and SeIV-2 particles, whereas the abundance of SeIV-2 remained constant across all developmental stages. Low levels of SeIV-2 infection were detected in all groups of insects, including those that hatched from surface-decontaminated egg masses. SeIV-1 infection resulted in reduced larval weight gain, and an unbalanced sex ratio, whereas larval developmental time, pupal weight, and adult emergence and fecundity were not significantly affected in infected adults. The inoculation of egg masses with iflavirus, followed by a subsequent infection with SeMNPV, resulted in an additive effect on larval mortality. The 50% lethal concentration (LC) of SeMNPV was reduced nearly 4-fold and the mean time to death was faster by 12 h in iflavirus-treated insects. These results suggest that inapparent iflavirus infections may be able to modulate the host response to a new pathogen, a finding that has particular relevance to the use of SeMNPV as the basis for biological pest control products.
10.3390/v12050509
Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus.
Dong Yonghao,Chao Jiangtao,Liu Jinyan,Rice Annabel,Holdbrook Robert,Liu Yongjie,Xu Pengjun
Archives of virology
The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.
10.1007/s00705-017-3622-8
Genome Sequence of a Novel Iflavirus from mRNA Sequencing of the Pupa of Bombyx mori Inoculated with Cordyceps militaris.
Suzuki Tomohiro,Takeshima Yoshino,Mikamoto Toshiyuki,Saeki Jun-David,Kato Tatsuya,Park Enoch Y,Kawagishi Hirokazu,Dohra Hideo
Genome announcements
We discovered a novel iflavirus from the transcriptome of the Bombyx mori pupa inoculated with the insect-pathogenic fungus Cordyceps militaris. The assembled iflavirus genome has 10,119 nucleotides, with a 3'-polyadenylated tail, and it encodes a polyprotein composed of 3,004 amino acids.
10.1128/genomeA.01039-15
Discovery of a novel iflavirus sequence in the eastern paralysis tick Ixodes holocyclus.
O'Brien Caitlin A,Hall-Mendelin Sonja,Hobson-Peters Jody,Deliyannis Georgia,Allen Andy,Lew-Tabor Ala,Rodriguez-Valle Manuel,Barker Dayana,Barker Stephen C,Hall Roy A
Archives of virology
Ixodes holocyclus, the eastern paralysis tick, is a significant parasite in Australia in terms of animal and human health. However, very little is known about its virome. In this study, next-generation sequencing of I. holocyclus salivary glands yielded a full-length genome sequence which phylogenetically groups with viruses classified in the Iflaviridae family and shares 45% amino acid similarity with its closest relative Bole hyalomma asiaticum virus 1. The sequence of this virus, provisionally named Ixodes holocyclus iflavirus (IhIV) has been identified in tick populations from northern New South Wales and Queensland, Australia and represents the first virus sequence reported from I. holocyclus.
10.1007/s00705-018-3868-9
Extended phylogenetic analysis of a new Israeli isolate of Brevicoryne brassicae virus (BrBV-IL) suggests taxonomic revision of the genus Iflavirus.
Luria Neta,Reingold Victoria,Lachman Oded,Sela Noa,Dombrovsky Aviv
Virology journal
BACKGROUND:Brevicoryne brassicae virus (BrBV) is a positive-strand genomic RNA virus which is unassigned tentative member of the genus Iflavirus. BrBv was first identified and characterized in the late 90's in the cabbage aphid in the United Kingdom (UK) (J Gen Virol 88:2590-2595, 2007) and was fully sequenced, using random amplification of encapsidated RNA. No other reports have been published demonstrating detection of this virus outside the UK. FINDINGS:A new isolate of the cabbage aphid virus Brevicoryne brassicae virus was identified from Brevicoryne brassicae aphids growing on wild mustard plants (Sinapis arvensis) in northern Israel. The virus genome was partially assembled from purified siRNA using the Illumina MiSeq Sequencing System with limited success. Combining classical viral RNA purification and RT-PCR amplification followed by traditional Sanger sequencing enabled obtaining the complete genomic sequence. The Israeli strain of BrBV shared 95 % nucleotide sequence identity with the BrBV found in the United Kingdom. CONCLUSIONS:The detection of BrBV in Israel indicates a broader geographical distribution of the virus".
10.1186/s12985-016-0500-z
Sequence analysis and genomic organization of a new insect iflavirus, Sogatella furcifera honeydew virus 1.
Wu Nan,Zhang Peipei,Liu Wenwen,Cao Mengji,Wang Xifeng
Archives of virology
A novel iflavirus, tentatively named "Sogatella furcifera honeydew virus 1" (SFHV1), discovered through transcriptome sequencing analysis of white-backed planthoppers (Sogatella furcifera) collected in southern China, is described here. The full genome of SFHV1 is 10,837 nucleotides (nt) long, including the polyA tail, and shares 65.5% and 64.5% genomic identity with Laodelphax striatellus picorna-like virus 2 and Laodelphax striatella honeydew virus 1, respectively. On the basis of the phylogenetic analysis of the complete genomic sequence and the deduced RdRp amino acid sequence of SFHV1 with other iflaviruses, we suggest that it is a member of a new species in the genus Iflavirus, family Iflaviridae.
10.1007/s00705-018-3817-7
Simultaneous occurrence of covert infections with small RNA viruses in the lepidopteran Spodoptera exigua.
Jakubowska Agata K,D'Angiolo Melania,González-Martínez Rosa M,Millán-Leiva Anabel,Carballo Arkaitz,Murillo Rosa,Caballero Primitivo,Herrero Salvador
Journal of invertebrate pathology
Viral covert infections in invertebrates have been traditionally attributed to sublethal infections that were not able to establish an acute infection. Recent studies are revealing that, although true for some viruses, other viruses may follow the strategy of establishing covert or persistent infections without producing the death of the host. Recently, and due to the revolution in the sequencing technologies, a large number of viruses causing covert infections in all type of hosts have been identified. The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae) is a worldwide pest that causes significant losses to agricultural and ornamental plant industries. In a previous project we used NGS to obtain a comprehensive transcriptome of the larval stage, revealing the presence of an important number of unigenes belonging to novel RNA viruses, most of them from the order Picornavirales. In order to characterize S. exigua viral complex, in this work we have completed the genomic sequences of two picorna-like viruses, and compared them to a SeIV1, a member of Iflaviridae previously described by our group. We performed additional studies to determine virus morphology, horizontal transmission, tissue and life stage distribution and abundance in the hosts. We discuss the role of virus persistent infections on insect populations.
10.1016/j.jip.2014.06.009
Novel Viruses in Mosquitoes from Brazilian Pantanal.
Maia Laura Marina Siqueira,Pinto Andressa Zelenski de Lara,Carvalho Michellen Santos de,Melo Fernando Lucas de,Ribeiro Bergmann Morais,Slhessarenko Renata Dezengrini
Viruses
Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of the Brazilian Pantanal wetland through metagenomics, viral isolation, and RT-PCR. In total, 12 viruses were found, eight putative novel viruses with relatively low similarity with pre-existing species of viruses within their families, named Pirizal iflavirus, Furrundu phlebovirus, Pixé phlebovirus, Guampa vesiculovirus, Chacororé flavivirus, Rasqueado orbivirus, Uru chuvirus, and Bororo circovirus. We also found the already described Lobeira dielmorhabdovirus, Sabethes flavivirus, Araticum partitivirus, and Murici totivirus. Therefore, these findings underscore the vast diversity of culicinae and novel viruses yet to be explored in Pantanal, the largest wetland on the planet.
10.3390/v11100957
Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique.
Cholleti Harindranath,Hayer Juliette,Fafetine Jose,Berg Mikael,Blomström Anne-Lie
Virology journal
BACKGROUND:Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique. METHODS:The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5' and 3' RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay. RESULTS:A near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3' end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates. CONCLUSIONS:The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. mosquitoes from Mozambique. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution.
10.1186/s12985-018-0981-z
A novel picornavirus-like genome from transcriptome sequencing of sugar beet cyst nematode represents a new putative genus.
Lin Jingyu,Ye Rongjian,Thekke-Veetil Thanuja,Staton Margaret E,Arelli Prakash R,Bernard Ernest C,Hewezi Tarek,Domier Leslie L,Hajimorad M R
The Journal of general virology
Analysis of transcriptome sequence data from eggs and second-stage juveniles (J2s) of sugar beet cyst nematode (SBCN, Heterodera schachtii) identified the full-length genome of a positive-sense single-stranded RNA virus, provisionally named sugar beet cyst nematode virus 1 (SBCNV1). The SBCNV1 sequence was detected in both eggs and J2s, indicating its possible vertical transmission. The 9503-nucleotide genome sequence contains a single long open reading frame, which was predicted to encode a polyprotein with conserved domains for picornaviral structural proteins proximal to its amino terminus and RNA helicase, cysteine proteinase and RNA-dependent RNA polymerase (RdRp) conserved domains proximal to its carboxyl terminus, hallmarks of viruses belonging to the order Picornavirales. Phylogenetic analysis of the predicted SBCNV1 RdRp amino acid sequence indicated that the SBCNV1 sequence is most closely related to members of the family Secoviridae, which includes genera of nematode-transmitted plant-infecting viruses. SBCNV1 represents the first fully sequenced viral genome from SBCN.
10.1099/jgv.0.001139
Natural populations of Spodoptera exigua are infected by multiple viruses that are transmitted to their offspring.
Virto Cristina,Navarro David,Tellez M Mar,Herrero Salvador,Williams Trevor,Murillo Rosa,Caballero Primitivo
Journal of invertebrate pathology
Sublethal infections by baculoviruses (Baculoviridae) are believed to be common in Lepidoptera, including Spodoptera exigua. In addition, novel RNA viruses of the family Iflaviridae have been recently identified in a laboratory population of S. exigua (S. exigua iflavirus-1: SeIV-1; S. exigua iflavirus-2: SeIV-2) that showed no overt signs of disease. We determined the prevalence of these viruses in wild populations and the prevalence of co-infection by the different viruses in shared hosts. Infection by S. exigua multiple nucleopolyhedrovirus (SeMNPV) and iflaviruses in S. exigua adults (N=130) from horticultural greenhouses in southern Spain was determined using qPCR and RT-PCR based techniques respectively. The offspring of these insects (N=200) was reared under laboratory conditions and analyzed to determine virus transmission. Overall, 54% of field-caught adults were infected by SeMNPV, 13.1% were infected by SeIV-1 and 7.7% were infected by SeIV-2. Multiple infections were also detected, with 8.4% of individuals harboring SeMNPV and one of the iflaviruses, whereas 2.3% of adults were infected by all three viruses. All the viruses were transmitted to offspring independently of whether the parental female harbored covert infections or not. Analysis of laboratory-reared insects in the adult stage revealed that SeIV-1 was significantly more prevalent than SeMNPV or SeIV-2, suggesting high transmissibility of SeIV-1. Mixed infection involving three viruses was identified in 6.5% of laboratory-reared offspring. We conclude that interspecific interactions between these viruses in co-infected individuals are to be likely frequent, both in the field, following applications of SeMNPV-based insecticides, or in laboratory colonies used for SeMNPV mass production.
10.1016/j.jip.2014.07.007
Complete genome sequences of two iflaviruses from the brown planthopper, Nilaparvata lugens.
Murakami Ritsuko,Suetsugu Yoshitaka,Nakashima Nobuhiko
Archives of virology
The complete genome sequences of two new iflaviruses (genus Iflavirus, family Iflaviridae) were determined. These viral sequences were first identified in RNA-seq contig sequences of Nilaparvata lugens in two distinct colonies: Izumo and Kagoshima. The accuracy of the contig sequences of the two viruses was verified by restriction enzyme digestion of RT-PCR products from viruliferous insects. RT-PCR of RNA extracted from honeydews after viruliferous insect feeding detected the expected viral products, which suggested that viruses were excreted into the honeydews by the insects. Since we previously designated a similar iflavirus as "Nilaparvata lugens honeydew virus 1", the two new viruses have been tentatively named "Nilaparvata lugens honeydew virus 2" and "Nilaparvata lugens honeydew virus 3". The identity of the putative amino acid sequences of the capsid proteins of these viruses met the criterion for iflavirus species demarcation. Therefore, these two viruses are suggested to be members of distinct species in the genus Iflavirus.
10.1007/s00705-013-1850-0
RNA virome analysis of questing ticks from Hokuriku District, Japan, and the evolutionary dynamics of tick-borne phleboviruses.
Kobayashi Daisuke,Murota Katsunori,Itokawa Kentaro,Ejiri Hiroko,Amoa-Bosompem Michael,Faizah Astri Nur,Watanabe Mamoru,Maekawa Yoshihide,Hayashi Toshihiko,Noda Shinichi,Yamauchi Takeo,Komagata Osamu,Sawabe Kyoko,Isawa Haruhiko
Ticks and tick-borne diseases
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.
10.1016/j.ttbdis.2019.101364
Complete genome sequence and structural characterization of a novel iflavirus isolated from Opsiphanes invirae (Lepidoptera: Nymphalidae).
Silva Leonardo A,Ardisson-Araujo Daniel M P,Tinoco Ricardo S,Fernandes Odair A,Melo Fernando L,Ribeiro Bergmann M
Journal of invertebrate pathology
Opsiphanes invirae (Lepidopera: Nymphalidae) is a common pest of the African oil palm tree (Elaeis guineensis) in Brazil. Dead larvae were collected in canopy of oil palm trees cultivated in the amazon region (Para State) and analyzed for viral infection. Electron microscopy of caterpillar extracts showed an icosahedral picorna-like virus particle with 30nm in diameter. Total RNA extracted from partially purified virus particles was sequenced. A contig of 10,083 nucleotides (nt) was identified and showed to encode one single predicted polyprotein with 3185 amino acid residues. Phylogenetic analysis showed that the new virus was closely related to another lepidopteran infective virus Spodoptera exigua iflavirus 1(SeIV-1), with 35% amino acid pairwise identity. The novel virus fulfils all ICTV requirements for a new iflavirus species and was named Opsiphanes invirae Iflavirus 1 (OilV-1).
10.1016/j.jip.2015.08.001
Complete genome sequence and characterization of a new iflavirus from the small brown planthopper (Laodelphax striatellus).
Wu Nan,Zhang Peipei,Liu Wenwen,Cao Mengji,Massart Sebastien,Wang Xifeng
Virus research
A novel iflavirus, tentatively named laodelphax striatellus iflavirus 1 (LsIV1), was identified in Laodelphax striatellus by total RNA-sequencing, and its genome sequence was confirmed by Sanger sequencing. The complete genome consisted of 10,831 nucleotides with a polyA tail and included one open reading frame, encoding a 361.7-kD polyprotein. Conserved motifs for structural proteins, helicase, protease, and RNA-dependent RNA polymerase were identified by aligning the deduced amino acid sequence of LsIV1 with several other iflaviruses. The genome has the highest identity with another planthopper iflavirus, nilaparvata lugens honeydew virus-3 (39.7%), under the species demarcation threshold (90%). Results of the identities and phylogenetic analysis based on the deduced amino acid sequences of the complete polyprotein and helicase of LsIV1 and other iflaviruses, indicated it is a new species belonging to the family Iflaviridae. Furthermore, we did not observe any differences of biological characterizations like development and reproduction between viruliferous and virus-free SBPH. Meanwhile, we found that female could transmit LsIV1 with higher transmission efficiency.
10.1016/j.virusres.2019.197651
Assessment of a cricket, Acheta domesticus, bioassay for Chequa Iflavirus and bunya-like virus from redclaw crayfish Cherax quadricarinatus.
Sakuna Kitikarn,Elliman Jennifer,Owens Leigh
Journal of invertebrate pathology
Chequa iflavirus and a bunya-like virus infect redclaw crayfish (Cherax quadricarinatus) and they may cause mortality reaching 20-40% after about three weeks after a stress event. To complete River's postulates for viruses, virus-free animals are needed. Due to a lack of chequa iflavirus and bunya-like virus-free crayfish (testing shows>85% infection rate) coupled with the facts that iflavirus and bunyaviruses are found in insects and that crickets had been successful alternate hosts for crustacean viruses before, Acheta domesticus was trialled asa bioassay animal. There was no significant difference (P>0.05) in mortality rates between uninfected control crickets and infected crickets. Reverse transcriptase polymerase chain reaction for both viruses failed to find any trace of the RNA viruses in fed or inoculated crickets after 30days. The search for an alternative bioassay host will have to be widened.
10.1016/j.jip.2017.09.005
Isolation and characterization of a new iflavirus from Armigeres spp. mosquitoes in the Philippines.
Kobayashi Daisuke,Isawa Haruhiko,Fujita Ryosuke,Murota Katsunori,Itokawa Kentaro,Higa Yukiko,Katayama Yukie,Sasaki Toshinori,Mizutani Tetsuya,Iwanaga Shiroh,Ohta Nobuo,Garcia-Bertuso Arlene,Sawabe Kyoko
The Journal of general virology
During an entomological surveillance for arthropod-borne viruses in the Philippines, we isolated a previously unrecognized virus from female Armigeres spp. mosquitoes. Whole-genome sequencing, genetic characterization and phylogenetic analysis revealed that the isolated virus, designated Armigeres iflavirus (ArIFV), is a novel member of the iflaviruses (genus Iflavirus, family Iflaviridae) and phylogenetically related to Moku virus, Hubei odonate virus 4, slow bee paralysis virus and Graminella nigrifrons virus 1. To our knowledge, this is the first successful isolation of iflavirus from a dipteran insect. Spherical ArIFV particles of approximately 30 nm in diameter contained at least three major structural proteins. ArIFV multiplied to high titres (~10 p.f.u. ml) and formed clear plaques in a mosquito cell line, C6/36. Our findings provide new insights into the infection mechanism, genetic diversity and evolution of the Iflaviridae family.
10.1099/jgv.0.000929
Full genome sequence of a novel iflavirus from the leafhopper Psammotettix alienus.
Wang Hui,Liu Yan,Liu Wenwen,Cao Mengji,Wang Xifeng
Archives of virology
A novel iflavirus was discovered in Psammotettix alienus by RNA sequencing. The virus genome has 10,826 nucleotides (nt) excluding the poly A tail, encodes a 3187-amino-acid polyprotein, and is tentatively named "Psammotettix alienus iflavirus 1" (PaIV1). PaIV1 has a similar genomic structure, conserved motifs, and a close phylogenetic relationship to members of the genus Iflavirus, but it shows only 41.9-55.2% sequence identity in the full genome and 16.2-49% in the deduced polyprotein. Thus, we suggest that it is a new member of the genus Iflavirus, family Iflaviridae.
10.1007/s00705-018-4041-1
An iflavirus found in stink bugs (Hemiptera: Pentatomidae) of four different species.
Dos Santos Ethiane R,Trentin Luana B,Ecker Assis,Silva Leonardo A,Borges Miguel,Mowery Joseph D,Ribeiro Bergmann M,Harrison Robert L,Ardisson-Araújo Daniel M P
Virology
An analysis of transcriptomes from the antennae of the three South American stink bugs (Euschistus heros, Chinavia ubica, and Dichelops melacanthus) revealed the presence of picorna-like virus genome-length RNAs with high sequence identity to the genome of Halyomorpha halys virus (HhV), originally discovered in the transcriptome of the brown marmorated stink bug, Halyomorpha halys. Features of the genome, phylogenetic relationships to other viruses, and the appearances of virus-like particles isolated from host stink bugs all confirm that these viruses are iflaviruses and isolates of an undescribed species. Iflavirus RNAs were present at high levels (40%-90% of transcriptome reads) in the stink bug antennal transcriptomes. In whole-insect transcriptomes of H. halys, HhV reads were >500-fold more abundant in adults than in nymphs. We identified from field population a subject of species E. heros infected by this iflavirus. The results of the analysis suggest that these iflaviruses are able to produce large quantities of their RNAs without causing any obvious pathology to their hosts.
10.1016/j.virol.2019.06.002
Characterization of a novel member of genus Iflavirus in Helicoverpa armigera.
Yuan He,Xu Pengjun,Yang Xianming,Graham Robert I,Wilson Kenneth,Wu Kongming
Journal of invertebrate pathology
The cotton bollworm, Helicoverpa armigera, is one of the most important agricultural pests of many economic crops worldwide. Herein, we found a novel single-strand RNA virus by RNA-Seq and Polymerase Chain Reaction (PCR) method in H. armigera named Helicoverpa armigera iflavirus (HaIV), which possessed a genome with 10,017 nucleotides in length and contained a single large open reading frame (ORF) encoding a putative polyprotein of 3021 amino acids with a predicted molecular mass of 344.16kDa and a theoretical isoelectric point (pI) of 6.45. The deduced amino acid sequence showed highest similarity (61.0%) with the protein of Lymantria dispar Iflavirus 1. Phylogenetic analysis with putative RdRp amino acid sequences indicated that the virus clustered with members of the genus Iflavirus. The virus was mainly distributed in the fat body of its host and was found to be capable of both horizontal and vertical transmission. The efficiency of perorally horizontal transmission was dose dependent (100% infection rate with a viral dose of 10copies/μl) while vertical transmission efficiency was found to be relatively low (<28.57%). These results suggest that we have found a novel member of genus Iflavirus in H. armigera.
10.1016/j.jip.2017.01.011
Small molecules targeting viral RNA.
Hermann Thomas
Wiley interdisciplinary reviews. RNA
Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug-like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug-like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA-binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect-borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726-743. doi: 10.1002/wrna.1373 For further resources related to this article, please visit the WIREs website.
10.1002/wrna.1373
Plant rhabdoviruses-their origins and vector interactions.
Whitfield Anna E,Huot Ordom Brian,Martin Kathleen M,Kondo Hideki,Dietzgen Ralf G
Current opinion in virology
Classical plant rhabdoviruses infect monocot and dicot plants, have unsegmented negative-sense RNA genomes and have been taxonomically classified in the genera Cytorhabdovirus and Nucleorhabdovirus. These viruses replicate in their hemipteran vectors and are transmitted in a circulative-propagative mode and virus infection persists for the life of the insect. Based on the discovery of numerous novel rhabdoviruses in arthropods during metagenomic studies and extensive phylogenetic analyses of the family Rhabdoviridae, it is hypothesized that plant-infecting rhabdoviruses are derived from insect viruses. Analyses of viral gene function in plants and insects is beginning to reveal conserved and unique biology for these plant viruses in the two diverse hosts. New tools for insect molecular biology and infectious clones for plant rhabdoviruses are increasing our understanding of the lifestyles of these viruses.
10.1016/j.coviro.2018.11.002
A New Orbivirus Isolated from Mosquitoes in North-Western Australia Shows Antigenic and Genetic Similarity to Corriparta Virus but Does Not Replicate in Vertebrate Cells.
Harrison Jessica J,Warrilow David,McLean Breeanna J,Watterson Daniel,O'Brien Caitlin A,Colmant Agathe M G,Johansen Cheryl A,Barnard Ross T,Hall-Mendelin Sonja,Davis Steven S,Hall Roy A,Hobson-Peters Jody
Viruses
The discovery and characterisation of new mosquito-borne viruses provides valuable information on the biodiversity of vector-borne viruses and important insights into their evolution. In this study, a broad-spectrum virus screening system, based on the detection of long double-stranded RNA in inoculated cell cultures, was used to investigate the presence of novel viruses in mosquito populations of northern Australia. We detected and isolated a new virus (tentatively named Parry's Lagoon virus, PLV) from Culex annulirostris, Culex pullus, Mansonia uniformis and Aedes normanensis mosquitoes that shares genomic sequence similarities to Corriparta virus (CORV), a member of the Orbivirus genus of the family Reoviridae. Despite moderate to high (72.2% to 92.2%) amino acid identity across all proteins when compared to CORV, and demonstration of antigenic relatedness, PLV did not replicate in several vertebrate cell lines that were permissive to CORV. This striking phenotypic difference suggests that PLV has evolved to have a very restricted host range, indicative of a mosquito-only life cycle.
10.3390/v8050141
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster.
PLoS biology
Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs, we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2,000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont--which is known to be protective against virus infections in Drosophila--we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets, we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host-virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.
10.1371/journal.pbio.1002210
Discovery of associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family.
Virus evolution
In the global context of arboviral emergence, deep sequencing unlocks the discovery of new mosquito-borne viruses. Mosquitoes of the species , , and were sampled from 22 locations worldwide for transcriptomic analyses. A virus discovery pipeline was used to analyze the dataset of 0.7 billion reads comprising 22 individual transcriptomes. Two closely related 6.8 kb viral genomes were identified in and named as Culex pipiens associated tunisia virus (CpATV) strains Ayed and Jedaida. The CpATV genome contained four ORFs. ORF1 possessed helicase and RNA-dependent RNA polymerase (RdRp) domains related to new viral sequences recently found mainly in dipterans. ORF2 and 4 contained a capsid protein domain showing strong homology with plant viruses. ORF3 displayed similarities with eukaryotic Rhoptry domain and a merozoite surface protein (MSP7) domain only found in mosquito-transmitted , suggesting possible interactions between CpATV and vertebrate cells. Estimation of a strong purifying selection exerted on each ORFs and the presence of a polymorphism maintained in the coding region of ORF3 suggested that both CpATV sequences are genuine functional viruses. CpATV is part of an entirely new and highly diversified group of viruses recently found in insects, and that bears the genomic hallmarks of a new viral family.
10.1093/ve/vex040
Discovery and characterization of a novel picorna-like RNA virus in the cotton bollworm Helicoverpa armigera.
Yang Xianming,Xu Pengjun,Yuan He,Graham Robert I,Wilson Kenneth,Wu Kongming
Journal of invertebrate pathology
We characterize a novel picorna-like virus, named Helicoverpa armigera Nora virus (HaNV), with a genome length of 11,200 nts, the sequence of which was isolated from the lepidopteran host cotton bollworm Helicoverpa armigera, using RNA-Seq. Phylogenetic analysis, using the putative amino acid sequence of the conserved RNA-dependent RNA polymerase (RdRp) domain, indicated that HaNV clustered with Spodoptera exigua Nora virus, Drosophila Nora virus and Nasonia vitripennis virus-3 with a high bootstrap value (100%), which might indicate a new viral family within the order Picornavirales. HaNV was efficiently horizontally transmitted between hosts via contaminated food, and transmission was found to be dose-dependent (up to 100% efficiency with 10 viral copy number/µl). HaNV was also found to be transmitted vertically from parent to offspring, mainly through transovum transmission (virus contamination on the surface of the eggs), but having a lower transmission efficiency (around 43%). Infection distribution within the host was also investigated, with HaNV mainly found in only the gut of both adult moths and larvae (>90%). Moreover, our results showed that HaNV appears not to be an overtly pathogenic virus to its host.
10.1016/j.jip.2018.11.003
Insect-specific viruses and their potential impact on arbovirus transmission.
Vasilakis Nikos,Tesh Robert B
Current opinion in virology
Arthropod-borne viruses (arboviruses) are the causative agents of significant morbidity and mortality among humans and animals globally. In the past few years, the widespread adoption of next generation sequencing and metagenomics has led to a new era of virus discovery, where many novel viruses have been documented, exhibiting a restricted host-range in mosquitoes. They represent a wide-range of insect-specific viruses within the families of Bunyaviridae, Flaviviridae, Mesoniviridae, Reoviridae, Rhabdoviridae, Togaviridae, and the newly recognized taxon of Negeviruses. Collectively, their discovery has opened new vistas about the extent of viral diversity and evolution, their influence on vector competence and ability of their insect hosts to transmit human pathogens (e.g. arboviruses), and their potential development as biological control agents or novel vaccine platforms.
10.1016/j.coviro.2015.08.007
Insect-specific viruses: from discovery to potential translational applications.
Nouri Shahideh,Matsumura Emilyn E,Kuo Yen-Wen,Falk Bryce W
Current opinion in virology
Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.
10.1016/j.coviro.2018.07.006
Arbovirus and insect-specific virus discovery in Kenya by novel six genera multiplex high-resolution melting analysis.
Villinger Jandouwe,Mbaya Martin K,Ouso Daniel,Kipanga Purity N,Lutomiah Joel,Masiga Daniel K
Molecular ecology resources
A broad diversity of arthropod-borne viruses (arboviruses) of global health concern are endemic to East Africa, yet most surveillance efforts are limited to just a few key viral pathogens. Additionally, estimates of arbovirus diversity in the tropics are likely to be underestimated as their discovery has lagged significantly over past decades due to limitations in fast and sensitive arbovirus identification methods. Here, we developed a nearly pan-arbovirus detection assay that uses high-resolution melting (HRM) analysis of RT-PCR products from highly multiplexed assays to differentiate broad diversities of arboviruses. We differentiated 15 viral culture controls and seven additional synthetic viral DNA sequence controls, within Flavivirus, Alphavirus, Nairovirus, Phlebovirus, Orthobunyavirus and Thogotovirus genera. Among Bunyamwera, sindbis, dengue and Thogoto virus serial dilutions, detection by multiplex RT-PCR-HRM was comparable to the gold standard Vero cell plaque assays. We applied our low-cost method for enhanced broad-range pathogen surveillance from mosquito samples collected in Kenya and identified diverse insect-specific viruses, including a new clade in anopheline mosquitoes, and Wesselsbron virus, an arbovirus that can cause viral haemorrhagic fever in humans and has not previously been isolated in Kenya, in Culex spp. and Anopheles coustani mosquitoes. Our findings demonstrate how multiplex RT-PCR-HRM can identify novel viral diversities and potential disease threats that may not be included in pathogen detection panels of routine surveillance efforts. This approach can be adapted to other pathogens to enhance disease surveillance and pathogen discovery efforts, as well as the study of pathogen diversity and viral evolutionary ecology.
10.1111/1755-0998.12584
Insect-Specific Viruses: A Historical Overview and Recent Developments.
Roundy Christopher M,Azar Sasha R,Rossi Shannan L,Weaver Scott C,Vasilakis Nikos
Advances in virus research
Arthropod-borne viruses (arboviruses) have in recent years become a tremendous global health concern resulting in substantial human morbidity and mortality. With the widespread utilization of molecular technologies such as next-generation sequencing and the advancement of bioinformatics tools, a new age of viral discovery has commenced. Many of the novel agents being discovered in recent years have been isolated from mosquitoes and exhibit a highly restricted host range. Strikingly, these insect-specific viruses have been found to be members of viral families traditionally associated with human arboviral pathogens, including but not limited to the families Flaviviridae, Togaviridae, Reoviridae, and Bunyaviridae. These agents therefore present novel opportunities in the fields of viral evolution and viral/vector interaction and have tremendous potential as agents for biocontrol of vectors and or viruses of medical importance.
10.1016/bs.aivir.2016.10.001