scholarly journals Experimental Infection and Genetic Characterization of Two Different Capripox Virus Isolates in Small Ruminants

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1098 ◽  
Author(s):  
Janika Wolff ◽  
Jacqueline King ◽  
Tom Moritz ◽  
Anne Pohlmann ◽  
Donata Hoffmann ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Clinical Signs ◽  
Small Ruminants ◽  
Long Reads ◽  
Animal Trial ◽  
Severity Of The Disease ◽  
Production Animals ◽  
Inoculation Route ◽  
High Quality Genome

Capripox viruses, with their members “lumpy skin disease virus (LSDV)”, “goatpox virus (GTPV)” and “sheeppox virus (SPPV)”, are described as the most serious pox diseases of production animals. A GTPV isolate and a SPPV isolate were sequenced in a combined approach using nanopore MinION sequencing to obtain long reads and Illumina high throughput sequencing for short precise reads to gain full-length high-quality genome sequences. Concomitantly, sheep and goats were inoculated with SPPV and GTPV strains, respectively. During the animal trial, varying infection routes were compared: a combined intravenous and subcutaneous infection, an only intranasal infection, and the contact infection between naïve and inoculated animals. Sheep inoculated with SPPV showed no clinical signs, only a very small number of genome-positive samples and a low-level antibody reaction. In contrast, all GTPV inoculated or in-contact goats developed severe clinical signs with high viral genome loads observed in all tested matrices. Furthermore, seroconversion was detected in nearly all goats and no differences concerning the severity of the disease depending on the inoculation route were observed. Conclusively, the employed SPPV strain has the properties of an attenuated vaccine strain, consistent with the genetic data, whereas the GTPV strain represents a highly virulent field strain.

scholarly journals SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification

2017 ◽  
Author(s):  
Manuel Tardaguila ◽  
Lorena de la Fuente ◽  
Cristina Marti ◽  
Cécile Pereira ◽  
Francisco Jose Pardo-Palacios ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Full Length ◽  
The Novel ◽  
Extensive Evaluation ◽  
Long Reads ◽  
Long Read ◽  
Novel Transcripts ◽  
Mouse Transcriptome

ABSTRACTHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

scholarly journals Putative Novel Atypical BTV Serotype ‘36’ Identified in Small Ruminants in Switzerland

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 721
Author(s):  
Christina Ries ◽  
Andrea Vögtlin ◽  
Daniela Hüssy ◽  
Tabea Jandt ◽  
Hansjörg Gobet ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Clinical Symptoms ◽  
Clinical Signs ◽  
Virus Transmission ◽  
Small Ruminants ◽  
Facial Oedema ◽  
The Novel ◽  
Transmission Pathways ◽  
Goat Flock ◽  
Edta Blood

We identified a putative novel atypical BTV serotype ‘36’ in Swiss goat flocks. In the initial flock clinical signs consisting of multifocal purulent dermatitis, facial oedema and fever were observed. Following BTV detection by RT-qPCR, serotyping identified BTV-25 and also a putative novel BTV serotype in several of the affected goats. We successfully propagated the so-called “BTV-36-CH2019” strain in cell culture, developed a specific RT-qPCR targeting Segment 2, and generated the full genome by high-throughput sequencing. Furthermore, we experimentally infected goats with BTV-36-CH2019. Regularly, EDTA blood, serum and diverse swab samples were collected. Throughout the experiment, neither fever nor clinical disease was observed in any of the inoculated goats. Four goats developed BTV viremia, whereas one inoculated goat and the two contact animals remained negative. No viral RNA was detected in the swab samples collected from nose, mouth, eye, and rectum, and thus the experimental infection of goats using this novel BTV serotype delivered no indications for any clinical symptoms or vector-free virus transmission pathways. The subclinical infection of the four goats is in accordance with the reports for other atypical BTVs. However, the clinical signs of the initial goat flock did most likely not result from infection with the novel BTV-36-CH0219.

Alterations in Ruminal Fluid and Serum Biochemical Constituents in Goats Affected with Ruminal Acidosis

2018 ◽  
Vol 13 (03) ◽  
Author(s):  
P. R. Chavelikar ◽  
G. and Neha Rao C. Mandali ◽  
Neha Rao
Keyword(s):  
Rumen Fluid ◽  
Clinical Signs ◽  
Small Ruminants ◽  
Ruminal Fluid ◽  
Mean Values ◽  
Biochemical Constituents ◽  
Ruminal Acidosis ◽  
Methylene Blue Reduction ◽  
Serum Biochemical ◽  
The Mean

Ruminal acidosis is an important clinical emergency in small ruminants. In this study, eight healthy farm goats and 24 goats presented at TVCC of the college of Veterinary Sciences and A.H., Anand with clinical signs of ruminal acidosis and having rumen liquor pH below 6 were examined for alterations in the ruminal fluid and serum biochemical parameters. Among various rumen fluid parameters evaluated, the mean values of rumen fluid pH decreased significantly (4.71±0.11 vs. 6.90±0.10), while sediment activity time (46.67±1.20 vs. 24.50±0.78 min) and methylene blue reduction time (29.50±0.73 vs. 10.03±0.27 min) increased significantly in acidotic goats. The normal greenish, aromatic viscous color, odour and consistency of rumen fluid of healthy goats also changed to milky grey/creamy, sour/pungent watery in acidotic goats. The rumen protozoal activity decreased to nil in acidotic goats as compared to the healthy goats. Among various serum biochemical constituents, the mean values of glucose (92.43±1.37 vs. 74.13±1.83 mg/dl), BUN (26.49±0.47 vs. 22.63±1.19 mg/dl), serum creatinine (01.01±0.02 vs. 00.83±0.02 mg/dl) and albumin (03.22±0.03 vs. 03.05±0.05 g/dl), ALT (56.75±1.55 vs. 27.88±1.14 IU/L) and AST (93.25±1.82 vs. 54.00±1.75 IU/L), increased significantly, while there was significant decrease in serum calcium (09.09±0.14 vs. 10.29±0.08 mg/dl) in acidotic goats. The mean values of alkaline phosphatase (IU/L) in acidotic goats increased non-significantly from the base values of healthy goats.

Clinico-Haematological Alterations in Goats Affected with Ruminal Acidosis

2017 ◽  
Vol 13 (02) ◽  
Author(s):  
P. R. Chavelikar ◽  
G. C. Mandali ◽  
D. M. Patel
Keyword(s):  
Clinical Signs ◽  
Clinical Manifestations ◽  
Nasal Discharge ◽  
Mean Values ◽  
Ruminal Acidosis ◽  
Reduced Body ◽  
Muscle Twitching ◽  
Haematological Profile ◽  
The Mean ◽  
Severity Of The Disease

Ruminal acidosis is one of the most important clinical emergencies in sheep and goats resulting into high mortality rate. In the present study, eight healthy farm goats and 24 goats presented to the TVCC of the college with clinical signs of ruminal acidosis like anorexia, tympany, increased pulse and respiratory rate, reduced body temperature, doughy rumen, enteritis, oliguria, grinding of teeth, purulent nasal discharge, muscle twitching, arched back, dehydration and recumbency with rumen liquor pH below 6 were examined for haematological alterations using autohaematoanalyzer. Among various haematological parameters evaluated from acidotic goats, the mean values of Hb (12.21±0.17 vs. 10.86±0.15 g/dl), TEC (14.28±0.16 vs. 12.04±0.36 ×106/ μl), TLC (13.43±0.11 vs. 11.11±0.27 ×103/μl), PCV (36.91±0.53 vs. 29.88±0.55%), neutrophils (64.54±0.93 vs. 28.13±0.92%), MCV (23.38±0.37 vs. 19.38±1.34 fl) and MCH (7.03±0.08 vs. 6.31±0.25 pg) were found significantly increased, while the mean values of lymphocytes (28.00±0.82 vs. 65.38±0.80%) and MCHC (24.55 ±0.26 vs. 34.88±0.97 g/dl) were decreased significantly from the base values of healthy goats. It was concluded that ruminal acidosis induced due to accidental heavy ingestion of readily fermentable carbohydrate rich grains and food waste significantly altered the haematological profile concurrent with clinical manifestations in goats, and hence can be used to assess the severity of the disease.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huan Li ◽  
Siruo Zhang ◽  
Ruina Liu ◽  
Lu Yuan ◽  
Di Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Interval Estimation ◽  
The Body ◽  
Taxon Richness ◽  
Time Since Death ◽  
Sprague Dawley ◽  
Sprague Dawley Rats ◽  
Level Data ◽  
Species Taxon

AbstractOnce the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

scholarly journals The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

2021 ◽  
Vol 7 (3) ◽  
pp. 194
Author(s):  
Carmen Gómez-Lama Cabanás ◽  
Antonio J. Fernández-González ◽  
Martina Cardoni ◽  
Antonio Valverde-Corredor ◽  
Javier López-Cepero ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Canary Islands ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Phenological Stage ◽  
Mother Plants ◽  
Fusarium Wilt Of Banana ◽  
Identification And Characterization

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amy Gaye ◽  
Tolla Ndiaye ◽  
Mouhamad Sy ◽  
Awa B. Deme ◽  
Alphonse B. Thiaw ◽  
...  
Keyword(s):  
West Africa ◽  
Dengue Virus ◽  
Clinical Signs ◽  
Health Concern ◽  
Public Health Concern ◽  
Local Circulation ◽  
Viral Genomes ◽  
Genomic Characterization ◽  
The City

AbstractDengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

scholarly journals Spectral Decomposition of the Flow and Characterization of the Sound Signals through Stenoses with Different Levels of Severity

2021 ◽  
Vol 8 (3) ◽  
pp. 41
Author(s):  
Fardin Khalili ◽  
Peshala T. Gamage ◽  
Amirtahà Taebi ◽  
Mark E. Johnson ◽  
Randal B. Roberts ◽  
...  
Keyword(s):  
Pressure Fluctuations ◽  
High Energy ◽  
Sound Sources ◽  
Severity Level ◽  
Non Invasive ◽  
Flow Through ◽  
Severity Of The Disease ◽  
Proper Orthogonal ◽  
Different Levels

Treatments of atherosclerosis depend on the severity of the disease at the diagnosis time. Non-invasive diagnosis techniques, capable of detecting stenosis at early stages, are essential to reduce associated costs and mortality rates. We used computational fluid dynamics and acoustics analysis to extensively investigate the sound sources arising from high-turbulent fluctuating flow through stenosis. The frequency spectral analysis and proper orthogonal decomposition unveiled the frequency contents of the fluctuations for different severities and decomposed the flow into several frequency bandwidths. Results showed that high-intensity turbulent pressure fluctuations appeared inside the stenosis for severities above 70%, concentrated at plaque surface, and immediately in the post-stenotic region. Analysis of these fluctuations with the progression of the stenosis indicated that (a) there was a distinct break frequency for each severity level, ranging from 40 to 230 Hz, (b) acoustic spatial-frequency maps demonstrated the variation of the frequency content with respect to the distance from the stenosis, and (c) high-energy, high-frequency fluctuations existed inside the stenosis only for severe cases. This information can be essential for predicting the severity level of progressive stenosis, comprehending the nature of the sound sources, and determining the location of the stenosis with respect to the point of measurements.

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