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.

scholarly journals Identification and Sequence Analysis of a Novel Ilarvirus Infecting Sweet Cherry

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 514
Author(s):  
Chrysoula G. Orfanidou ◽  
Fei Xing ◽  
Jun Zhou ◽  
Shifang Li ◽  
Nikolaos I. Katis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Sanger Sequencing ◽  
Sweet Cherry ◽  
Novel Species ◽  
Peach Tree ◽  
Sweet Cherries ◽  
Blastn Analysis ◽  
Fruit Orchards ◽  
Prunus Spp

In the present study, we utilized high throughput and Sanger sequencing to determine the complete nucleotide sequence of a putative new ilarvirus species infecting sweet cherry, tentatively named prunus virus I (PrVI). The genome of PrVI is comprised of three RNA segments of 3474 nt (RNA1), 2911 nt (RNA2), and 2231 nt (RNA3) and features conserved motifs representative of the genus Ilarvirus. BlastN analysis revealed 68.1–71.9% nt identity of PrVI with strawberry necrotic shock virus (SNSV). In subsequent phylogenetic analysis, PrVI was grouped together with SNSV and blackberry chlorotic ringspot virus (BCRV), both members of subgroup 1 of ilarviruses. In addition, mini-scale surveys in stone fruit orchards revealed the presence of PrVI in a limited number of sweet cherries and in one peach tree. Overall, our data suggest that PrVI is a novel species of the genus Ilarvirus and it consists the fifth member of the genus that is currently known to infect Prunus spp.

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.

Clidicus minilankanus sp. n., with notes on remaining Sri Lankan Clidicus species (Coleoptera, Staphylinidae, Scydmaeninae)

Zootaxa ◽  
2020 ◽  
Vol 4718 (1) ◽  
pp. 87-94
Author(s):  
PAWEŁ JAŁOSZYŃSKI
Keyword(s):  
Phylogenetic Analysis ◽  
Sri Lanka ◽  
Junior Synonym ◽  
Monophyletic Group ◽  
Evolutionary Relationships ◽  
Sri Lankan

Until now, four species of Clidicus Laporte were found in Sri Lanka, three known from female specimens only. Clidicus minilankanus sp. n., is described, and compared to all remaining sympatric congeners. The Sri Lankan species may form a monophyletic group characterized by several morphological oddities: the head only slightly impressed posteromedially, with a large portion of vertex and frons not divided longitudinally; the pronotum quadrangular and flattened, with vestigial or absent posterior ‘collar’, and the transverse groove that demarcates it from the disc lacking pits or even entirely or partly obliterated; and the metaventrite strongly shortened, so that meso- and metacoxae are nearly adjacent. These characters may justify resurrecting Erineus Walker, a junior synonym of Clidicus (proposed for the first described Sri Lankan species, C. monstrosus (Walker)), as a valid name for a subgenus. This problem must be addressed by a phylogenetic analysis of all Clidicus species, to establish evolutionary relationships within this interesting genus. 

scholarly journals Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation

2020 ◽  
Vol 21 (10) ◽  
pp. 3426 ◽  
Author(s):  
Joyce Kelly R. da Silva ◽  
Pablo Luis Baia Figueiredo ◽  
Kendall G. Byler ◽  
William N. Setzer
Keyword(s):  
Essential Oil ◽  
Essential Oils ◽  
Antiviral Agents ◽  
Rna Dependent Rna Polymerase ◽  
Protein Targets ◽  
Docking Analysis ◽  
Main Protease ◽  
Pathogenic Viruses ◽  
Oil Components ◽  
Molecular Docking Analysis

Essential oils have shown promise as antiviral agents against several pathogenic viruses. In this work we hypothesized that essential oil components may interact with key protein targets of the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 Mpro), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). The compound with the best normalized docking score to SARS-CoV-2 Mpro was the sesquiterpene hydrocarbon (E)-β-farnesene. The best docking ligands for SARS−CoV Nsp15/NendoU were (E,E)-α-farnesene, (E)-β-farnesene, and (E,E)−farnesol. (E,E)−Farnesol showed the most exothermic docking to SARS-CoV-2 ADRP. Unfortunately, the docking energies of (E,E)−α-farnesene, (E)-β-farnesene, and (E,E)−farnesol with SARS-CoV-2 targets were relatively weak compared to docking energies with other proteins and are, therefore, unlikely to interact with the virus targets. However, essential oil components may act synergistically, essential oils may potentiate other antiviral agents, or they may provide some relief of COVID-19 symptoms.

Novel Drugs Targeting the SARS-CoV-2/COVID-19 Machinery

2020 ◽  
Vol 20 (16) ◽  
pp. 1423-1433 ◽  
Author(s):  
Ariane Sternberg ◽  
Dwight L. McKee ◽  
Cord Naujokat
Keyword(s):  
Host Cell ◽  
Protein Processing ◽  
Cell Entry ◽  
Genome Replication ◽  
Rna Dependent Rna Polymerase ◽  
Main Protease ◽  
Novel Drugs ◽  
Pathogenic Viruses ◽  
Repurposed Drugs ◽  
Host Cell Entry

Like other human pathogenic viruses, coronavirus SARS-CoV-2 employs sophisticated macromolecular machines for viral host cell entry, genome replication and protein processing. Such machinery encompasses SARS-CoV-2 envelope spike (S) glycoprotein required for host cell entry by binding to the ACE2 receptor, viral RNA-dependent RNA polymerase (RdRp) and 3-chymotrypsin-like main protease (3Clpro/Mpro). Under the pressure of the accelerating COVID-19 pandemic caused by the outbreak of SARS-CoV-2 in Wuhan, China in December 2019, novel and repurposed drugs were recently designed and identified for targeting the SARS-CoV-2 reproduction machinery, with the aim to limit the spread of SARS-CoV-2 and morbidity and mortality due to the COVID-19 pandemic.

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 Phylogenetic Analysis of Bean yellow mosaic virus Isolates from Four Continents: Relationship Between the Seven Groups Found and Their Hosts and Origins

Plant Disease ◽  
2008 ◽  
Vol 92 (12) ◽  
pp. 1596-1603 ◽  
Author(s):  
S. J. Wylie ◽  
B. A. Coutts ◽  
M. G. K. Jones ◽  
R. A. C. Jones
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Bean Yellow Mosaic Virus ◽  
Host Specialization ◽  
Yellow Mosaic Virus ◽  
Nucleotide Substitutions ◽  
Natural Hosts ◽  
Plant Families ◽  
Natural Host Range ◽  
Intragroup Diversity

Genetic diversity of Bean yellow mosaic virus (BYMV) was studied by comparing sequences from the coat protein (CP) and genome-linked viral protein (VPg) genes of isolates from four continents. CP sequences compared were those of 17 new isolates and 47 others already on the database, while the VPg sequences used were from four new isolates and 10 from the database. Phylogenetic analysis of the CP sequences revealed seven distinct groups, six polytypic and one monotypic. The largest and most genetically diverse polytypic group, which had intragroup diversity of 0.061 nucleotide substitutions per site, contained isolates from natural infections in eight host species. These original isolation hosts included both wild (four) and domesticated (four) species and were from monocotyledonous and dicotyledonous plant families, indicating a generalized natural host range strategy. Only one of the other five polytypic groups spanned both monocotyledons and dicotyledons, and all contained isolates from fewer species (one to four), all of which were domesticated and had lower intragroup diversity (0.019 to 0.045 nucleotide substitutions per site), indicating host specialization. Phylogenetic analysis of the fewer VPg sequences revealed three polytypic and two monotypic groupings. These groups also correlated with original natural isolation hosts, but the branch topologies were sometimes incongruous with those formed by CPs. Also, intragroup diversity was generally higher for VPgs than for CPs. A plausible explanation for the groups found when the 64 different CP sequences were compared is that the generalized group represents the original ancestral type from which the specialist host groups evolved in response to domestication of plants after the advent of agriculture. Data on the geographical origins of the isolates within each group did not reveal whether the specialized groups might have coevolved with their principal natural hosts where these were first domesticated, but this seems plausible.

scholarly journals Occurrence of a novel strain of Moroccan watermelon mosaic virus infecting pumpkins in Kenya

Plant Disease ◽  
2021 ◽  
Author(s):  
Naomi Mumo ◽  
Elijah Miinda Ateka ◽  
Edward Mamati ◽  
Fredah Karambu Rimberia ◽  
George Ochieng' Asudi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Sanger Sequencing ◽  
Cucurbita Pepo ◽  
Citrullus Lanatus ◽  
Watermelon Mosaic Virus ◽  
Cucurbita Moschata ◽  
Genome Sequences ◽  
Mediterranean Regions ◽  
Sequence Identities

The potyvirus Moroccan watermelon mosaic virus (MWMV) naturally infects and severely threatens production of cucurbits and papaya. In this study, we identified and characterized MWMV isolated from pumpkin (Cucurbita moschata) intercropped with MWMV-infected papaya plants through next generation and Sanger sequencing approaches. Complete MWMV genome sequences were obtained from two pumpkin samples through NGS and validated using Sanger sequencing. The isolates share 83.4-83.7 % nucleotide (nt) and 92.3-95.1 % amino acid (aa) sequence identities in the coat protein and 79.5-79.9 % nt and 89.2-89.7 % aa identities in the polyprotein with papaya isolates of MWMV. Phylogenetic analysis using complete polyprotein nt sequences revealed the clustering of both pumpkin isolates of MWMV with corresponding sequences of cucurbit isolates of the virus from other parts of Africa and the Mediterranean regions, distinct from a clade formed by papaya isolates. Through sap inoculation, a pumpkin isolate of MWMV was pathogenic on zucchini (Cucurbita pepo), watermelon (Citrullus lanatus), and cucumber (Cucumis sativus), but not on papaya. Conversely, the papaya isolate of MWMV was non-pathogenic on pumpkin, watermelon, and cucumber, but infected zucchini. The results suggest occurrence of two strains of MWMV in Kenya having different biological characteristics associated with the host specificity.

scholarly journals Betanodavirus infection in Kuhlia rupestris and Ambassis marianus and isolation of betanodavirus from infected pond water

2020 ◽  
Vol 142 ◽  
pp. 1-11
Author(s):  
K Agnihotri ◽  
R Chong ◽  
D Underwood ◽  
C Kistler ◽  
M Hutchison
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Cell Line ◽  
Environmental Samples ◽  
Sanger Sequencing ◽  
High Throughput Sequencing ◽  
Pond Water ◽  
Fish Cell ◽  
Nervous Necrosis Virus ◽  
Necrosis Virus

This is the first report of betanodavirus infection in 2 species of finfish, Kuhlia rupestris (jungle perch) and Ambassis marianus (estuary perchlet). This report also describes isolation of betanodavirus from infected pond water using the SSN-1 cell line. Histopathology of K. rupestris larvae revealed vacuolation in the eye and brain, which was confirmed using betanodavirus-specific immunohistochemistry. The eye and brain from A. marianus and betanodavirus isolated from pond water were confirmed using real-time PCR and Sanger sequencing. High throughput sequencing was used to obtain betanodavirus sequences from paraffin blocks containing infected K. rupestris. The phylogenetic analysis of betanodavirus RNA1 and RNA2 sequences from all 3 sources were associated with the red-spotted grouper nervous necrosis virus (RGNNV) genotype. The RNA1 nucleotide sequence from jungle perch showed 100% identity with the betanodavirus water isolate and 99.37% identity with A. marianus. Furthermore, we have demonstrated the usefulness of combining recovery of viable virus from environmental samples through fish cell line culture with PCR testing as a means of validating the efficacy of chlorination to eradicate betanodavirus from the pond environment.

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