scholarly journals Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 865 ◽  
Author(s):  
Sejal Modha ◽  
Joseph Hughes ◽  
Giovanni Bianco ◽  
Heather M. Ferguson ◽  
Barbara Helm ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Current Knowledge ◽  
Specific Protein ◽  
Disease Vectors ◽  
Viral Diversity ◽  
Biting Midges ◽  
Biting Midge ◽  
Virus Sequence ◽  
Novel Virus

Biting midges (Culicoides species) are vectors of arboviruses and were responsible for the emergence and spread of Schmallenberg virus (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from Culicoides impunctatus (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors.

scholarly journals A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV)

2021 ◽  
Vol 9 (5) ◽  
pp. 972
Author(s):  
Joana Abrantes ◽  
Ana M. Lopes
Keyword(s):  
Disease Virus ◽  
Diagnostic Tests ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
European Rabbit ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Hemorrhagic Disease ◽  
Rabbit Hemorrhagic Disease ◽  
Detection And Diagnosis

Since the early 1980s, the European rabbit (Oryctolagus cuniculus) has been threatened by the rabbit hemorrhagic disease (RHD). The disease is caused by a lagovirus of the family Caliciviridae, the rabbit hemorrhagic disease virus (RHDV). The need for detection, identification and further characterization of RHDV led to the development of several diagnostic tests. Owing to the lack of an appropriate cell culture system for in vitro propagation of the virus, much of the methods involved in these tests contributed to our current knowledge on RHD and RHDV and to the development of vaccines to contain the disease. Here, we provide a comprehensive review of the RHDV diagnostic tests used since the first RHD outbreak and that include molecular, histological and serological techniques, ranging from simpler tests initially used, such as the hemagglutination test, to the more recent and sophisticated high-throughput sequencing, along with an overview of their potential and their limitations.

scholarly journals Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 654
Author(s):  
Gianluca Marucci ◽  
Ilaria Zullino ◽  
Lucia Bertuccini ◽  
Serena Camerini ◽  
Serena Cecchetti ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Diarrheal Disease ◽  
Current Knowledge ◽  
Biological Significance ◽  
Giardia Duodenalis ◽  
Protozoan Parasite ◽  
Protein Translation ◽  
Mass Spectrometry Analysis ◽  
Animal Origin ◽  
Spectrometry Analysis

Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied; moreover, a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. Here we report high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin. We also report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with an RdRp domain homologous to Totiviridae and Botybirnaviridae. The result of our sequencing and proteomic analyses challenge the current knowledge on GLV and strongly suggest that viral capsid protein translation unusually starts with a proline and that translation of the RNA-dependent RNA polymerase (RdRp) occurs via a +1/−2 ribosomal frameshift mechanism. Nucleotide polymorphism, confirmed by mass-spectrometry analysis, was also observed among and between GLV strains. Phylogenetic analysis indicated the occurrence of at least two GLV subtypes which display different phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate.

scholarly journals Challenges and Opportunities in NUT Carcinoma Research

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 235
Author(s):  
Bin Gu ◽  
Maxwell C. Hakun
Keyword(s):  
Cell Biology ◽  
Current Knowledge ◽  
Short Review ◽  
Specific Protein ◽  
Cell Of Origin ◽  
Chromosome Translocations ◽  
Very Young Children ◽  
Aggressive Cancer ◽  
Challenges And Opportunities ◽  
Nut Carcinoma

NUT carcinoma (NC) is a type of aggressive cancer driven by chromosome translocations. Fusion genes between a DNA-binding protein, such as bromodomain and extraterminal domain (BET) proteins, and the testis-specific protein NUTM1 generated by these translocations drive the formation of NC. NC can develop in very young children without significant accumulation of somatic mutations, presenting a relatively clean model to study the genetic etiology of oncogenesis. However, after 20 years of research, a few challenging questions still remain for understanding the mechanism and developing therapeutics for NC. In this short review, we first briefly summarize the current knowledge regarding the molecular mechanism and targeted therapy development of NC. We then raise three challenging questions: (1) What is the cell of origin of NC? (2) How does the germline analogous epigenetic reprogramming process driven by the BET-NUTM1 fusion proteins cause NC? and (3) How will BET-NUTM1 targeted therapies be developed? We propose that with the unprecedented technological advancements in genome editing, animal models, stem cell biology, organoids, and chemical biology, we have unique opportunities to address these challenges.

scholarly journals TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1223
Author(s):  
Andres S. Espindola ◽  
Daniela Sempertegui-Bayas ◽  
Danny F. Bravo-Padilla ◽  
Viviana Freire-Zapata ◽  
Francisco Ochoa-Corona ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Bioinformatic Analysis ◽  
Metagenomic Sample ◽  
Rrna Depletion ◽  
Virus Diagnostics ◽  
Management Preparation ◽  
Reverse Transcript

High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.

Management of North American Culicoides Biting Midges: Current Knowledge and Research Needs

2015 ◽  
Vol 15 (6) ◽  
pp. 374-384 ◽  
Author(s):  
Robert S. Pfannenstiel ◽  
Bradley A. Mullens ◽  
Mark G. Ruder ◽  
Ludek Zurek ◽  
Lee W. Cohnstaedt ◽  
...  
Keyword(s):  
North American ◽  
Current Knowledge ◽  
Research Needs ◽  
Biting Midges ◽  
Culicoides Biting Midges

scholarly journals Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1593-1600 ◽  
Author(s):  
Jiaxing Wu ◽  
Song Zhang ◽  
Sagheer Atta ◽  
Caixia Yang ◽  
Yan Zhou ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Biological Data ◽  
High Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Punjab Province ◽  
Transmission Electron ◽  
Genome Features ◽  
Yellow Mottle ◽  
Novel Virus ◽  
Citrus Trees

During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.

scholarly journals Inhibitory and complementary therapeutic effect of sweet lime (Citrus limetta) against RNA-viruses

2021 ◽  
Vol 7 (1) ◽  
pp. 37-44
Author(s):  
Sulagna Ray Pal ◽  
Swapan Banerjee
Keyword(s):  
Therapeutic Effect ◽  
Rna Viruses ◽  
Current Knowledge ◽  
Western World ◽  
Therapeutic Effects ◽  
Neuroprotective Effects ◽  
Nutrient Contents ◽  
Therapeutic Benefits ◽  
Sweet Lime ◽  
Antiviral Activities

Sweet lime (), known as 'Mousambi' or 'Mosambi' in India, is one of the best citrus fruits regarding its nutrient contents. Its bioactive compounds (BAC) are exclusively used for multiple clinical applications considering many therapeutic benefits not only in Asian countries but also in the western world. The fruit pulp and juice are the best sources of ascorbic acid, B-vitamins, amino acids, and other secondary metabolites. Specifically, polyphenols such as flavanones, hesperetin, naringenin, and chlorogenic acid are highly rich in the fruit. The nutrients in sweet lime altogether provide significant anti-inflammatory, antioxidant, anti-cancer, and neuroprotective effects. The purpose of this study is to review and analyze the inhibitory and complementary therapeutic effects of sweet lime's pulp and juices to inhibit the virulence caused by RNA viruses, mainly SARS-CoV-2. This review study was designed based on extensive online searches of relevant open-access literature available in the best quality and reliable databases by using specific keywords and boolean operators. After a rigorous review, we found that flavanones in the fruit can alter or inhibit the polyproteins (pp1a and pp1b) responsible for viral replication. Therefore, sweet lime has potentialities to provide an inhibitory and a complementary therapeutic effect against RNA viruses, mainly SARS-CoV-2. About the antiviral activities, more clinical trials are needed to prove its efficacy; however, reviewing current knowledge, is one of the potent antioxidant, inflammatory fruits available and affordable almost worldwide.

scholarly journals Cuticular and Internal Chemical Composition of Biting Midges Culicoides spp. (Diptera: Ceratopogonidae), Potential Vectors of Viral Diseases

2014 ◽  
Vol 9 (8) ◽  
pp. 1934578X1400900
Author(s):  
Mikel González ◽  
Sergio López ◽  
Gloria Rosell ◽  
Arturo Goldarazena ◽  
Angel Guerrero
Keyword(s):  
Chemical Composition ◽  
Gas Chromatography Mass Spectrometry ◽  
Viral Diseases ◽  
Chemical Profile ◽  
Biting Midges ◽  
Biting Midge ◽  
Branched Hydrocarbons ◽  
Hexane Extracts ◽  
Major Chemical ◽  
First Time

The chemical profile of the cuticle and internal tissues of four species of Culicoides have been studied for the first time by gas chromatography-mass spectrometry. The chemical composition of females of C. obsoletus s.l. and C. lupicaris, vectors of diverse viral diseases, have been compared with that of other biting midges, such as C. kibunensis and C. fascipennis, and the non-biting midge Forcipomyia bipunctata. A total of 61 compounds belonging to 8 major chemical classes were identified in cuticular and internal tissues in n-hexane extracts. The compounds include carboxylic acids (CAs) (C6-C20), with C16:0, C16:1 and C18:1 being dominant, branched hydrocarbons (C29 to C38 mono/di/trimethylalkanes), linear hydrocarbons (C15 to C33, mainly odd chain carbons), terpenes (geranylacetone, geranylgeraniol acetate, squalene, terpenic alcohol), steroids (cholesterol), aldehydes (C9-C10 and even chain C20 to C30), and esters. The chemical profile depends on the species and whether the extracts are external (cuticle) or internal. The contents of linear and branched hydrocarbons and aldehydes was high in cuticular extracts but practically absent in internal tissues, which were, in contrast, rich in CAs, terpenes and steroids. The results are discussed and compared with other Culicoides midges and mosquito-related species.

scholarly journals Development and Application of a Quantitative PCR Detection Method to Quantify Venturia oleaginea in Asymptomatic Olive (Olea europaea) Leaves

2020 ◽  
Vol 110 (3) ◽  
pp. 547-555
Author(s):  
Silvia Scibetta ◽  
Giovanni E. Agosteo ◽  
Ahmed Abdelfattah ◽  
Maria G. Li Destri Nicosia ◽  
Santa O. Cacciola ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Leaf Growth ◽  
Its Region ◽  
Qpcr Assay ◽  
Detection Methods ◽  
Effective Control ◽  
Its2 Region

Olive leaf spot (OLS), caused by Venturia oleaginea, is one of the most common and serious diseases of olive trees in the Mediterranean region. Understanding the pathogen life cycle is important for the development of effective control strategies. Current knowledge is incomplete owing to a lack of effective detection methods. It is extremely difficult to culture V. oleaginea in vitro, so primers were designed to amplify and sequence the internal transcribed spacer ITS1-5.8S-ITS2 region of the fungus directly from infected olive leaves. Sanger sequencing indicated a unique ITS region present in the European strains screened, confirming the appropriateness of the target region for developing a quantitative PCR (qPCR) assay. Furthermore, high-throughput sequencing of the same region excluded the presence of other Venturia species in the olive phyllosphere. The qPCR assay proved very specific and sensitive, enabling the detection of approximately 26 copies of target DNA. The analysis of symptomless leaves during early stages of the epidemic from the end of winter through spring revealed a similar quantity of pathogen DNA regardless of the leaf growth stage. In contrast, the pathogen titer changed significantly during the season. Data indicated that leaf infections start earlier than expected over the season and very young leaves are as susceptible as adult leaves. These findings have important practical implications and suggest the need for improved scheduling of fungicide treatments. The qPCR assay represents a valuable tool providing quantitative results and enables detection of V. oleaginea in all olive organs, including those in which OLS cannot be studied using previously available methods.

scholarly journals Schmallenberg virus: a systematic international literature review (2011-2019) from an Irish perspective

2019 ◽  
Vol 72 (1) ◽  
Author(s):  
Áine B. Collins ◽  
Michael L. Doherty ◽  
Damien J. Barrett ◽  
John F. Mee
Keyword(s):  
Scientific Literature ◽  
Current Knowledge ◽  
Clinical Signs ◽  
Control Measures ◽  
Schmallenberg Virus ◽  
Transmission Risk ◽  
Surveillance Program ◽  
Emerging Viruses ◽  
Biting Midges ◽  
Irish Case

Abstract In Autumn 2011, nonspecific clinical signs of pyrexia, diarrhoea, and drop in milk yield were observed in dairy cattle near the German town of Schmallenberg at the Dutch/German border. Targeted veterinary diagnostic investigations for classical endemic and emerging viruses could not identify a causal agent. Blood samples were collected from animals with clinical signs and subjected to metagenomic analysis; a novel orthobunyavirus was identified and named Schmallenberg virus (SBV). In late 2011/early 2012, an epidemic of abortions and congenital malformations in calves, lambs and goat kids, characterised by arthrogryposis and hydranencephaly were reported in continental Europe. Subsequently, SBV RNA was confirmed in both aborted and congenitally malformed foetuses and also in Culicoides species biting midges. It soon became evident that SBV was an arthropod-borne teratogenic virus affecting domestic ruminants. SBV rapidly achieved a pan-European distribution with most countries confirming SBV infection within a year or two of the initial emergence. The first Irish case of SBV was confirmed in the south of the country in late 2012 in a bovine foetus. Since SBV was first identified in 2011, a considerable body of scientific research has been conducted internationally describing this novel emerging virus. The aim of this systematic review is to provide a comprehensive synopsis of the most up-to-date scientific literature regarding the origin of SBV and the spread of the Schmallenberg epidemic, in addition to describing the species affected, clinical signs, pathogenesis, transmission, risk factors, impact, diagnostics, surveillance methods and control measures. This review also highlights current knowledge gaps in the scientific literature regarding SBV, most notably the requirement for further research to determine if, and to what extent, SBV circulation occurred in Europe and internationally during 2017 and 2018. Moreover, recommendations are also made regarding future arbovirus surveillance in Europe, specifically the establishment of a European-wide sentinel herd surveillance program, which incorporates bovine serology and Culicoides entomology and virology studies, at national and international level to monitor for the emergence and re-emergence of arboviruses such as SBV, bluetongue virus and other novel Culicoides-borne arboviruses.

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