scholarly journals Geographical and Tick-Dependent Distribution of Flavi-Like Alongshan and Yanggou Tick Viruses in Russia

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 458
Author(s):  
Ivan S. Kholodilov ◽  
Oxana A. Belova ◽  
Evgeny S. Morozkin ◽  
Alexander G. Litov ◽  
Anna Y. Ivannikova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytopathic Effect ◽  
Rna Helicase ◽  
Ixodes Persulcatus ◽  
Tick Cell ◽  
Rna Dependent Rna Polymerase ◽  
Dermacentor Marginatus ◽  
Virus Prevalence ◽  
Successful Replication ◽  
Regions Of Russia

The genus Flavivirus includes related, unclassified segmented flavi-like viruses, two segments of which have homology with flavivirus RNA-dependent RNA polymerase NS5 and RNA helicase-protease NS3. This group includes such viruses as Jingmen tick virus, Alongshan virus, Yanggou tick virus and others. We detected the Yanggou tick virus in Dermacentor nuttalli and Dermacentor marginatus ticks in two neighbouring regions of Russia. The virus prevalence ranged from 0.5% to 8.0%. We detected RNA of the Alongshan virus in 44 individuals or pools of various tick species in eight regions of Russia. The virus prevalence ranged from 0.6% to 7.8%. We demonstrated the successful replication of the Yanggou tick virus and Alongshan virus in IRE/CTVM19 and HAE/CTVM8 tick cell lines without a cytopathic effect. According to the phylogenetic analysis, we divided the Alongshan virus into two groups: an Ixodes persulcatus group and an Ixodes ricinus group. In addition, the I. persulcatus group can be divided into European and Asian subgroups. We found amino acid signatures specific to the I. ricinus and I. persulcatus groups and also distinguished between the European and Asian subgroups of the I. persulcatus group.

scholarly journals First isolation and characterisation of Alongshan virus in Russia

2019 ◽  
Author(s):  
Ivan S. Kholodilov ◽  
Alexander G. Litov ◽  
Alexander S. Klimentov ◽  
Oxana A. Belova ◽  
Alexandra E. Polienko ◽  
...  
Keyword(s):  
Cell Line ◽  
Cytopathic Effect ◽  
Virus Isolation ◽  
Open Reading Frames ◽  
Spherical Particles ◽  
Ixodes Persulcatus ◽  
Tick Cell ◽  
Tick Cell Line ◽  
Upstream Orf ◽  
Reading Frames

AbstractIn recent decades, many new flavi-like viruses have been discovered predominantly in different invertebrates and, as was recently shown, some of them may cause disease in humans. The Jingmen tick virus (JMTV) group holds a special place among flavi-like viruses because, in contrast to the “classic” flaviviruses and other flavi-like viruses, they have a segmented ssRNA(+) genome. Two segments of the JMTV genome have homology with regions of the flavivirus genome encoding polymerase and helicase-protease proteins. JMTVs have several open reading frames (ORF) in segments encoding glycoprotein(s) and capsid protein and these ORF are specific only to them. JMTVs greatly differ in virion size.We isolated three strains of Alongshan virus (ALSV), which is a representative of the JMTV group, from adult Ixodes persulcatus ticks collected in two geographically-separated Russian regions in the tick cell line IRE/CTVM19. One of the strains persisted in the IRE/CTVM19 cells without cytopathic effect for three years. Most virions purified from tick cells were spherical with a diameter of approximately 40.5 nm. In addition, we found smaller particles of approximately 13.1 nm in diameter. We obtained full genome sequences of all four segments of two of the isolated ALSV strains, and partial sequences of one segment from the third strain. Phylogenetic analysis on genome segment 2 of the JMTV group clustered our novel strains with other ALSV strains. We found evidence for the existence of a novel upstream ORF in the glycoprotein-coding segment of ALSV and other members of the JMTV group.Significance StatementWe isolated three strains of Alongshan virus (ALSV) from adult Ixodes persulcatus ticks from two geographically separate areas of Russia in the Ixodes ricinus tick cell line IRE/CTVM19. One of the strains persisted in the IRE/CTVM19 cells without cytopathic effect for three years. Our study confirmed the value of tick cell lines in virus isolation and maintenance of persistent infection. The majority of virions of the ALSV strain Miass527 were enveloped spherical particles with a diameter of 40.5±3.7 nm. We found evidence for the existence of a novel upstream ORF in the glycoprotein-coding segment of ALSV and other members of the Jingmen tick virus group.

scholarly journals Isolation and Characterisation of Alongshan Virus in Russia

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 362 ◽  
Author(s):  
Ivan S. Kholodilov ◽  
Alexander G. Litov ◽  
Alexander S. Klimentov ◽  
Oxana A. Belova ◽  
Alexandra E. Polienko ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
Genome Segment ◽  
Upstream Open Reading Frame ◽  
Ixodes Persulcatus ◽  
Full Genome ◽  
Russian Regions ◽  
Genome Sequences ◽  
Tick Cell ◽  
Reading Frame ◽  
The Third

In recent decades, many new flavi-like viruses have been discovered predominantly in different invertebrates and, as was recently shown, some of them may cause disease in humans. The Jingmenvirus (JMV) group holds a special place among flaviviruses and flavi-like viruses because they have a segmented ssRNA(+) genome. We detected Alongshan virus (ALSV), which is a representative of the JMV group, in ten pools of adult Ixodes persulcatus ticks collected in two geographically-separated Russian regions. Three of the ten strains were isolated in the tick cell line IRE/CTVM19. One of the strains persisted in the IRE/CTVM19 cells without cytopathic effect for three years. Most ALSV virions purified from tick cells were spherical with a diameter of approximately 40.5 nm. In addition, we found smaller particles of approximately 13.1 nm in diameter. We obtained full genome sequences of all four segments of two of the isolated ALSV strains, and partial sequences of one segment from the third strain. Phylogenetic analysis on genome segment 2 of the JMV group clustered our novel strains with other ALSV strains. We found evidence for the existence of a novel upstream open reading frame in the glycoprotein-coding segment of ALSV and other members of the JMV group.

scholarly journals Detection of Alpha- and Betacoronaviruses in Miniopterus fuliginosus and Rousettus leschenaultii, two species of Sri Lankan Bats

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 650
Author(s):  
Therese Muzeniek ◽  
Thejanee Perera ◽  
Sahan Siriwardana ◽  
Dilara Bas ◽  
Fatimanur Kaplan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sanger Sequencing ◽  
Rectal Swab ◽  
Sri Lankan ◽  
Rna Dependent Rna Polymerase ◽  
Fecal Samples ◽  
Natural Hosts ◽  
Pathogenic Viruses ◽  
Miniopterus Fuliginosus ◽  
Important Basis

Bats are known to be potential reservoirs of numerous human-pathogenic viruses. They have been identified as natural hosts for coronaviruses, causing Severe Acute Respiratory Syndrome (SARS) in humans. Since the emergence of SARS-CoV-2 in 2019 interest in the prevalence of coronaviruses in bats was newly raised. In this study we investigated different bat species living in a sympatric colony in the Wavul Galge cave (Koslanda, Sri Lanka). In three field sessions (in 2018 and 2019), 395 bats were captured (Miniopterus, Rousettus, Hipposideros and Rhinolophus spp.) and either rectal swabs or fecal samples were collected. From these overall 396 rectal swab and fecal samples, the screening for coronaviruses with nested PCR resulted in 33 positive samples, 31 of which originated from Miniopterus fuliginosus and two from Rousettus leschenaultii. Sanger sequencing and phylogenetic analysis of the obtained 384-nt fragment of the RNA-dependent RNA polymerase revealed that the examined M. fuliginosus bats excrete alphacoronaviruses and the examined R. leschenaultii bats excrete betacoronaviruses. Despite the sympatric roosting habitat, the coronaviruses showed host specificity and seemed to be limited to one species. Our results represent an important basis to better understand the prevalence of coronaviruses in Sri Lankan bats and may provide a basis for pursuing studies on particular bat species of interest.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals A Novel Partitivirus in the Hypovirulent Isolate QT5-19 of the Plant Pathogenic Fungus Botrytis cinerea

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 24 ◽  
Author(s):  
Md Kamaruzzaman ◽  
Guoyuan He ◽  
Mingde Wu ◽  
Jing Zhang ◽  
Long Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Botrytis Cinerea ◽  
Pathogenic Fungus ◽  
Amino Acid Sequences ◽  
Potato Dextrose Agar ◽  
Rna Dependent Rna Polymerase ◽  
Virus Particles ◽  
Genome Feature ◽  
Infected Tobacco ◽  
Hyphal Contact

A pink isolate (QT5-19) of Botrytis cinerea was compared with three gray isolates of B. cinerea for growth and morphogenesis on potato dextrose agar (PDA), and for pathogenicity on tobacco. A double-stranded (ds) RNA mycovirus infecting QT5-19 was identified based on its genome feature and morphology of the virus particles. The results showed that QT5-19 grew rapidly and established flourishing colonies as the gray isolates did. However, it is different from the gray isolates, as it failed to produce conidia and sclerotia asthe gray isolates did. QT5-19 hardly infected tobacco, whereas the gray isolates aggressively infected tobacco. Two dsRNAs were detected in QT5-19, dsRNA 1 and dsRNA 2, were deduced to encode two polypepetides with homology to viral RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. Phylogenetic analysis of the amino acid sequences of RdRp and CP indicated that the two dsRNAs represent the genome of a novel partitivirus in the genus Alphapartitivirus, designated here as Botrytis cinerea partitivirus 2 (BcPV2). BcPV2 in QT5-19 was successfully transmitted to the three gray isolates through hyphal contact. The resulting BcPV2-infected derivatives showed rapid growth on PDA with defects in conidiogenesis and sclerogenesis, and hypovirulence on tobacco. This study suggests that BcPV2 is closely associated with hypovirulence of B. cinerea.

scholarly journals Discovery of an orthoreovirus in the aborted fetus of a Steller sea lion (Eumetopias jubatus)

2011 ◽  
Vol 92 (11) ◽  
pp. 2558-2565 ◽  
Author(s):  
Gustavo Palacios ◽  
James F. X. Wellehan ◽  
Stephen Raverty ◽  
Ana V. Bussetti ◽  
Jeffrey Hui ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Complete Genome ◽  
Cytopathic Effect ◽  
Interspecies Transmission ◽  
Steller Sea Lion ◽  
Eumetopias Jubatus ◽  
Sea Lion ◽  
Microarray Experiments ◽  
Viral Culture

An aborted mid-gestational male Steller sea lion fetus with an attached placenta was recovered on the floor of an open floating capture trap located off Norris Rock near Denman Island, British Columbia. Viral culture of the placenta demonstrated cytopathic effect. Although no specific signal was obtained in microarray experiments using RNA obtained from viral culture, elution and sequence analysis revealed the presence of a reovirus. Complete genome pyrosequencing led to the identification of an orthoreovirus that we have tentatively named Steller sea lion reovirus (SSRV). Phylogenetic analysis revealed similarities between SSRV and orthoreoviruses of birds, bats and other mammals that suggests potential for interspecies transmission.

scholarly journals Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

2021 ◽  
Vol 7 (3) ◽  
Author(s):  
Denise S. Whitford ◽  
Brendan T. Whitman ◽  
George W. Owttrim
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Helicase ◽  
Evolutionary Divergence ◽  
Sequence Motif ◽  
Rna Helicases ◽  
Homologous Proteins ◽  
Content Type ◽  
Conserved Sequence ◽  
Link Type ◽  
Dead Box

Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

Etiopathogenetic Assessment of Tick Skin Injuries in Vacationers of Suburban Resorts and Tourists of Ukraine as a Component of a Complex Diagnostic Algorithm of Babesiosis

2021 ◽  
Vol 63 (1) ◽  
pp. 38-42
Author(s):  
Inna I. Torianyk
Keyword(s):  
Ixodes Ricinus ◽  
Soft Tissues ◽  
Diagnostic Algorithm ◽  
Skin Lesions ◽  
The Body ◽  
Temperate Climate ◽  
Forest Steppe ◽  
Ixodes Persulcatus ◽  
Negative Consequences ◽  
Dermacentor Marginatus

Aim: The aim of the study is to improve the complex diagnostic algorithm of babesiosis by etiopathogenetic assessment of tick skin lesions in vacationers of suburban resorts and tourists of Ukraine. Material and Methods: In order to objectify the etiopathogenetic assessment of tick skin lesions in vacationers of suburban resorts and tourists of Ukraine, animals affected by attacks of active stages of Ixodes, to determine their role as a component in a comprehensive diagnostic algorithm of babesiosis, we used a set of epidemic, epizootological, clinical and diagnostic measures. Skin lesions were considered acaroidal only in cases when ticks from the superfamily Ixodoidea of the family Ixodidea of the species Ixodes ricinus and Ixodes persulcatus (n=34), Dermacentor marginatus and Dermacentor pictus (n=128) were detected on it or on the clothes of the bitten person. Ticks of the species Ixodes ricinus, Ixodes persulcatus, Dermacentor marginatus and Dermacentor pictus were studied and photographed on an Olympus BX-41 microscope (Japan) using a digital camera. The surveyed 64 people of both sexes, aged 17 to 68, belonged to different categories of vacationers or tourists (organized, semi-organized, «savages»). The morphological material (skin with underlying soft tissues) was collected in cases of attacks of Ixodes on pets (dogs), accompanying the owners on vacation, when it was possible. Microspecimens stained with hematoxylin and eosin, picrofuxin according to van Gizon, according to Mallory were studied using an Olympus BX-41 microscope (Japan) with subsequent processing with the Olympus DP-soft version 3.1 software. Results: Climatotherapy is a popular treatment and prevention measure in the coordinate system «doctor-patient». This treatment method is characterized by both positive health effects and negative consequences, among which are the development of such dangerous parasitic disease as babesiosis. Etiopathogenetic assessment of tick skin lesions in vacationers of suburban resorts and tourists of Ukraine is an important component of a comprehensive diagnostic algorithm for babesiosis. Its objectification is based on the effective application of the data informative potential on the cycle and period of development of one generation of carriers (imago), the specifics of active stages (differentiation into three-host mites), habitat characteristics (shrubs, deciduous trees), seasonality (April-June, August-September), climatic zonation (temperate climate of the forest-steppe), their ability to inoculate babesiosis pathogens into the body of warm-blooded vertebrates. Macroscopic and microscopic features of the skin with underlying soft tissues at the sites of fixation and feeding of mites in susceptible to pathogens babesiosis humans and animals depend on the duration of this damaging factor exposure. Conclusions: Etiopathogenetic assessment of tick skin lesions in vacationers of suburban resorts and tourists of Ukraine is of great importance in the diagnosis of babesiosis.

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