scholarly journals Identification and characterisation of common glow-worm RNA viruses

Virus Genes ◽  
2020 ◽  
Vol 56 (2) ◽  
pp. 236-248 ◽  
Author(s):  
Lumi Viljakainen ◽  
Anna-Maria Borshagovski ◽  
Sami Saarenpää ◽  
Arja Kaitala ◽  
Jaana Jurvansuu
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Green Light ◽  
Sexually Active ◽  
Sequencing Data ◽  
Double Stranded Rna ◽  
Dna And Rna ◽  
The Common ◽  
Viral Sequences

AbstractThe common glow-worms (Lampyris noctiluca) are best known for emission of green light by their larvae and sexually active adult females. However, both their DNA and RNA viruses remain unknown. Glow-worms are virologically interesting, as they are non-social and do not feed as adults, and hence their viral transmission may be limited. We identified viral sequences from 11 different virus taxa by the RNA-sequencing of two Finnish populations of adult glow-worms. The viruses represent nine different virus families and have negative, positive, or double-stranded RNA genomes. We also found a complete retroviral genome. Similar viral sequences were found from the sequencing data of common eastern firefly of North America, a species belonging to the same family (Lampyridae) as that of the common glow-worm. On average, an individual glow-worm had seven different RNA virus types and most of them appeared to establish a stable infection since they were found from glow-worms during two consecutive years. Here we present the characterization of load, prevalence, and interactions for each virus. Most of the glow-worm RNA viruses seem to be transmitted vertically, which may reflect the biology of glow-worms as non-social capital breeders, i.e., they invest stored resources in reproduction.

scholarly journals Lactoferrin affects rhinovirus B-14 entry into H1-HeLa cells

2021 ◽  
Vol 166 (4) ◽  
pp. 1203-1211
Author(s):  
Caio Bidueira Denani ◽  
Antonio Real-Hohn ◽  
Carlos Alberto Marques de Carvalho ◽  
Andre Marco de Oliveira Gomes ◽  
Rafael Braga Gonçalves
Keyword(s):  
Innate Immune System ◽  
Rna Viruses ◽  
Innate Immune ◽  
Bovine Lactoferrin ◽  
Respiratory Illnesses ◽  
Dna And Rna ◽  
Viral Particles ◽  
The Common ◽  
Additional Influence

AbstractLactoferrin is part of the innate immune system, with antiviral activity against numerous DNA and RNA viruses. Rhinoviruses, the leading cause of the common cold, are associated with exacerbation of respiratory illnesses such as asthma. Here, we explored the effect of bovine lactoferrin (BLf) on RV-B14 infectivity. Using different assays, we show that the effect of BLf is strongest during adhesion of the virus to the cell and entry. Tracking the internalisation of BLf and virus revealed a degree of colocalisation, although their interaction was only confirmed in vitro using empty viral particles, indicating a possible additional influence of BLf on other infection steps.

scholarly journals Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 830 ◽  
Author(s):  
Yuliya Kleschenko ◽  
Danyil Grybchuk ◽  
Nadezhda S. Matveeva ◽  
Diego H. Macedo ◽  
Evgeny N. Ponirovsky ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cutaneous Leishmaniasis ◽  
Molecular Characterization ◽  
Leishmania Major ◽  
Geographical Origin ◽  
Rna Virus ◽  
Viral Sequences

Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.

scholarly journals Late Male-Killing Viruses in Homona magnanima Identified as Osugoroshi Viruses, Novel Members of Partitiviridae

2021 ◽  
Vol 11 ◽  
Author(s):  
Ryosuke Fujita ◽  
Maki N. Inoue ◽  
Takumi Takamatsu ◽  
Hiroshi Arai ◽  
Mayu Nishino ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Rna Polymerase ◽  
Rna Viruses ◽  
Rna Virus ◽  
Horizontal Transmission ◽  
Rna Dependent Rna Polymerase ◽  
Double Stranded Rna ◽  
First Report ◽  
Male Killing ◽  
Male Specific

Late male-killing, a male-specific death after hatching, is a unique phenotype found in Homona magnanima, oriental tea tortrix. The male-killing agent was suspected to be an RNA virus, but details were unknown. We herein successfully isolated and identified the putative male-killing virus as Osugoroshi viruses (OGVs). The three RNA-dependent RNA polymerase genes detected were phylogenetically related to Partitiviridae, a group of segmented double-stranded RNA viruses. Purified dsRNA from a late male-killing strain of H. magnanima revealed 24 segments, in addition to the RdRps, with consensus terminal sequences. These segments included the previously found male-killing agents MK1068 (herein OGV-related RNA16) and MK1241 (OGV-related RNA7) RNAs. Ultramicroscopic observation of purified virions, which induced late male-killing in the progeny of injected moths, showed sizes typical of Partitiviridae. Mathematical modeling showed the importance of late male-killing in facilitating horizontal transmission of OGVs in an H. magnanima population. This study is the first report on the isolation of partiti-like virus from insects, and one thought to be associated with late male-killing, although the viral genomic contents and combinations in each virus are still unknown.

scholarly journals A Genotype-to-Phenotype Modeling Framework to Predict Human Pathogenicity of Novel Coronaviruses

2021 ◽  
Author(s):  
Phillip Davis ◽  
Joseph A Russell
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Human Pathogens ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Modeling Framework ◽  
Strong Argument ◽  
Genomic Epidemiology ◽  
Phenotype Model ◽  
Level Information

Leveraging prior viral genome sequencing data to make predictions on whether an unknown, emergent virus harbors a phenotype-of-concern has been a long-sought goal of genomic epidemiology. A predictive phenotype model built from nucleotide-level information alone has previously been considered un-tenable with respect to RNA viruses due to the ultra-high intra-sequence variance of their genomes, even within closely related clades. Building from our prior work developing a degenerate k-mer method to accommodate this high intra-sequence variation of RNA virus genomes for modeling frameworks, and leveraging a taxonomic group-shuffle-split paradigm on complete coronavirus assemblies from prior to October 2018, we trained multiple regularized logistic regression classifiers at the nucleotide k-mer level capable of accurately predicting withheld SARS-CoV-2 genome sequences as human pathogens and accurately predicting withheld Swine Acute Diarrhea Syndrome coronavirus (SADS-CoV) genome sequences as non-human pathogens. LASSO feature selection identified several degenerate nucleotide predictor motifs with high model coefficients for the human pathogen class that were present across widely disparate classes of coronaviruses. However, these motifs differed in which genes they were present in, what specific codons were used to encode them, and what the translated amino acid motif was. This emphasizes the importance of a phenetic view of emerging pathogenic RNA viruses, as opposed to the canonical phylogenetic interpretations most-commonly used to track and manage viral zoonoses. Applying our model to more recent Orthocoronavirinae genomes deposited since October 2018 yields a novel contextual view of pathogen-potential across bat-related, canine-related, porcine-related, and rodent-related coronaviruses and critical adaptations which may have contributed to the emergence of the pandemic SARS-CoV-2 virus. Finally, we discuss the utility of these predictive models (and their associated predictor motifs) to novel biosurveillance protocols that substantially increase the pound-for-pound information content of field-collected sequencing data and make a strong argument for the necessity of routine collection and sequencing of zoonotic viruses.

Characterization of proteins from putative human DNA and RNA viruses.

2021 ◽  
Vol 18 ◽  
Author(s):  
Carlos Polanco ◽  
Vladimir N. Uversky ◽  
Gilberto Vargas-Alarcón ◽  
Thomas Buhse ◽  
Alberto Huberman ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Protein Sequences ◽  
Intrinsic Disorder ◽  
Public Health Issue ◽  
Dna Viruses ◽  
Dna And Rna ◽  
Human Dna ◽  
Uniprot Database ◽  
Significant Public Health

Background: In the vast variety of viruses known, there is a particular interest in those transmitted to humans and whose ability to disseminate represents a significant public health issue. Objective: The present study’s objective is to bioinformatically characterize the proteins of the two main divisions of viruses, RNA-viruses and DNA-viruses. Methods: In this work, a set of in-house computational programs was used to calculate the polarity/charge profiles and intrinsic disorder predisposition profiles of the proteins of several groups of viruses representing both types extracted from UniProt database. The efficiency of these computational programs was statistically verified. Results: It was found that the polarity/charge profile of the proteins is, in most cases, an efficient discriminant that allows the re-creation of the taxonomy known for both viral groups. Additionally, the entire set of "reviewed" proteins in UniProt database was analyzed to find proteins with the polarity/charge profiles similar to those obtained for each viral group. This search revealed a substantial number of proteins with such polarity-charge profiles. Conclusion: Polarity/charge profile represents a physicochemical metric, which is easy to calculate, and which can be used to effectively identify viral groups from their protein sequences.

Identification and molecular characterization of a new nonsegmented double-stranded RNA virus isolated from Culex mosquitoes in Japan

2011 ◽  
Vol 155 (1) ◽  
pp. 147-155 ◽  
Author(s):  
Haruhiko Isawa ◽  
Ryusei Kuwata ◽  
Keita Hoshino ◽  
Yoshio Tsuda ◽  
Kouji Sakai ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Rna Virus ◽  
Double Stranded Rna ◽  
Culex Mosquitoes

scholarly journals Characterization of a segmented double-stranded RNA virus inDrosophilaKccells

1983 ◽  
Vol 11 (11) ◽  
pp. 3665-3678 ◽  
Author(s):  
Julia T. Hsu ◽  
Marilyn M. Sanders
Keyword(s):  
Rna Virus ◽  
Double Stranded Rna

scholarly journals Novel RNA Viruses from the Transcriptome of Pheromone Glands in the Pink Bollworm Moth, Pectinophora gossypiella

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 556
Author(s):  
Xiaoyi Dou ◽  
Sijun Liu ◽  
Victoria Soroker ◽  
Ally Harari ◽  
Russell Jurenka
Keyword(s):  
Rna Viruses ◽  
Management Strategies ◽  
Pink Bollworm ◽  
Pectinophora Gossypiella ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Field Samples ◽  
Viral Sequences ◽  
Negative Sense ◽  
Pink Bollworm Moth

In this study, we analyzed the transcriptome obtained from the pheromone gland isolated from two Israeli populations of the pink bollworm Pectinophora gossypiella to identify viral sequences. The lab population and the field samples carried the same viral sequences. We discovered four novel viruses: two positive-sense single-stranded RNA viruses, Pectinophora gossypiella virus 1 (PecgV1, a virus of Iflaviridae) and Pectinophora gossypiella virus 4 (PecgV4, unclassified), and two negative-sense single-stranded RNA viruses, Pectinophora gossypiella virus 2 (PecgV2, a virus of Phasmaviridae) and Pectinophora gossypiella virus 3 (PecgV3, a virus of Phenuiviridae). In addition, sequences derived from two negative-sense single-stranded RNA viruses that belong to Mononegavirales were found in the data. Analysis of previous transcriptome sequencing data derived from the midgut of pink bollworm larvae of a USA population only identified PecgV1, but no other viruses. High viral sequence coverages of PecgV1 and PecgV4 were observed in both field and lab populations. This is the first report of viral sequences discovered from the pink bollworm. Results from this investigation suggest that the pink bollworm harbors multiple viruses. Further investigation of the viral pathogens may help to develop novel pest management strategies for control of the pink bollworm.

scholarly journals Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow

2018 ◽  
Author(s):  
A. Bal ◽  
M. Pichon ◽  
C. Picard ◽  
JS. Casalegno ◽  
M. Valette ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Real Time ◽  
Real Time Pcr ◽  
Viral Genome ◽  
Viral Infections ◽  
Rna Viruses ◽  
Next Generation ◽  
Dna And Rna ◽  
Generation Sequencing

AbstractBackgroundIn recent years, metagenomic Next-Generation Sequencing (mNGS) has increasingly been used for an accurate assumption-free virological diagnosis. However, the systematic workflow evaluation on clinical respiratory samples and implementation of quality controls (QCs) is still lacking.MethodsA total of 3 QCs were implemented and processed through the whole mNGS workflow: a notemplate-control to evaluate contamination issues during the process; an internal and an external QC to check the integrity of the reagents, equipment, the presence of inhibitors, and to allow the validation of results for each sample. The workflow was then evaluated on 37 clinical respiratory samples from patients with acute respiratory infections previously tested for a broad panel of viruses using semi-quantitative real-time PCR assays (28 positive samples including 6 multiple viral infections; 9 negative samples). Selected specimens included nasopharyngeal swabs (n = 20), aspirates (n = 10), or sputums (n = 7).ResultsThe optimal spiking level of the internal QC was first determined in order to be sufficiently detected without overconsumption of sequencing reads. According to QC validation criteria, mNGS results were validated for 34/37 selected samples. For valid samples, viral genotypes were accurately determined for 36/36 viruses detected with PCR (viral genome coverage ranged from 0.6% to 100%, median = 67.7%). This mNGS workflow allowed the detection of DNA and RNA viruses up to a semi-quantitative PCR Ct value of 36. The six multiple viral infections involving 2 to 4 viruses were also fully characterized. A strong correlation between results of mNGS and real-time PCR was obtained for each type of viral genome (R2 ranged from 0.72 for linear single-stranded (ss) RNA viruses to 0.98 for linear ssDNA viruses).ConclusionsAlthough the potential of mNGS technology is very promising, further evaluation studies are urgently needed for its routine clinical use within a reasonable timeframe. The approach described herein is crucial to bring standardization and to ensure the quality of the generated sequences in clinical setting. We provide an easy-to-use single protocol successfully evaluated for the characterization of a broad and representative panel of DNA and RNA respiratory viruses in various types of clinical samples.

Sign in / Sign up

Export Citation Format

Share Document