scholarly journals Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus

2013 ◽  
Vol 94 (7) ◽  
pp. 1547-1553 ◽  
Author(s):  
M. L. Joffret ◽  
C. Bouchier ◽  
M. Grandadam ◽  
H. Zeller ◽  
C. Maufrais ◽  
...  
Keyword(s):  
Central African Republic ◽  
Novel Species ◽  
Genomic Features ◽  
Protein Motifs ◽  
Ljungan Virus ◽  
Candidate Species ◽  
Genomic Characterization ◽  
Bioinformatics Workflows

We determined the genomic features and the taxonomic classification of Sebokele virus 1 (SEBV1), a previously unclassified arbovirus isolated in 1972 from rodents collected in Botambi, Central African Republic. The complete genome sequence was obtained using a deep sequencing approach (Illumina technology) and dedicated bioinformatics workflows for data analysis. Molecular analysis identified SEBV1 as a picornavirus, most closely related to Ljungan viruses of the genus Parechovirus. The genome has a typical Ljungan virus-like organization, including the presence of two unrelated 2A protein motifs. Phylogenetic analysis confirmed that SEBV1 belongs to the parechovirus phylogroup and was most closely related to the Ljungan virus species. However, it appeared clearly distinct from all members of this phylogroup, suggesting that it represents a novel species of the genus Parechovirus.

scholarly journals Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 177 ◽  
Author(s):  
Yael Yagel ◽  
Stephanie Sestito ◽  
Yair Motro ◽  
Anat Shnaiderman-Torban ◽  
Boris Khalfin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Opportunistic Infections ◽  
Species Classification ◽  
Genome Phylogeny ◽  
Genomic Characterization ◽  
Specific Species ◽  
Lactamase Gene

Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.

scholarly journals Bladder Cancer in the Genomic Era

2019 ◽  
Vol 143 (6) ◽  
pp. 695-704 ◽  
Author(s):  
Charles C. Guo ◽  
Bogdan Czerniak
Keyword(s):  
Bladder Cancer ◽  
Molecular Mechanisms ◽  
Complex Disease ◽  
Human Cancer ◽  
Wide Spectrum ◽  
Clinicopathologic Features ◽  
Pathologic Features ◽  
Genomic Characterization

Context.— Bladder cancer is a heterogeneous disease that exhibits a wide spectrum of clinical and pathologic features. The classification of bladder cancer has been traditionally based on morphologic assessment with the aid of immunohistochemistry. However, recent genomic studies have revealed that distinct alterations of DNA and RNA in bladder cancer may underlie its diverse clinicopathologic features, leading to a novel molecular classification of this common human cancer. Objective.— To update recent developments in genomic characterization of bladder cancer, which may shed insights on the molecular mechanisms underlying the origin of bladder cancer, dual-track oncogenic pathways, intrinsic molecular subtyping, and development of histologic variants. Data Sources.— Peer-reviewed literature retrieved from PubMed search and authors' own research. Conclusions.— Bladder cancer is likely to arise from different uroprogenitor cells through papillary/luminal and nonpapillary/basal tracks. The intrinsic molecular subtypes of bladder cancer referred to as luminal and basal exhibit distinct expression signatures, clinicopathologic features, and sensitivities to standard chemotherapy. Genomic characterization of bladder cancer provides new insights to understanding the biological nature of this complex disease, which may lead to more effective treatment.

scholarly journals Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences

2010 ◽  
Vol 84 (21) ◽  
pp. 11336-11349 ◽  
Author(s):  
Jan Felix Drexler ◽  
Florian Gloza-Rausch ◽  
Jörg Glende ◽  
Victor Max Corman ◽  
Doreen Muth ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Surface Expression ◽  
Emerging Viruses ◽  
Reading Frame ◽  
High Frequencies ◽  
Nyctalus Leisleri ◽  
Genomic Characterization

ABSTRACT Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4 × 108 copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri. A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.

scholarly journals Identification and genomic characterization of a novel species of feline anellovirus

2016 ◽  
Vol 13 (1) ◽  
Author(s):  
Wen Zhang ◽  
Hua Wang ◽  
Yan Wang ◽  
Zhijian Liu ◽  
Jingjiao Li ◽  
...  
Keyword(s):  
Novel Species ◽  
Genomic Characterization

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

scholarly journals Novel enteric viruses in fatal enteritis of grey squirrels

2020 ◽  
Vol 101 (7) ◽  
pp. 746-750
Author(s):  
Akbar Dastjerdi ◽  
Camilla Benfield ◽  
David Everest ◽  
Mark F. Stidworthy ◽  
Roland Zell
Keyword(s):  
Phylogenetic Analysis ◽  
Recombination Event ◽  
Novel Species ◽  
Structural Proteins ◽  
Virus Particles ◽  
Orf2 Sequence ◽  
Genomic Characterization ◽  
Generation Sequencing ◽  
Grey Squirrels

Astro- and kobuviruses infect both humans and animals. Here, we report on the disease history, detection and genomic characterization of novel astro- and kobuviruses from fatal diarrhoea of two juvenile grey squirrels. The virus particles had enterovirus-like morphology and a diameter of 28–32 nm. Next-generation sequencing confirmed astro- and kobuviruses and sequence analysis revealed typical astrovirus and picornavirus genome organizations. The astrovirus ORF2 sequence clustered with a clade of unassigned astroviruses, with marmot and rodent mamastroviruses as closest relatives. For the kobuvirus, divergences greater than 49.4 % for P1 and 43.5 % in the non-structural proteins indicated a novel species. However, phylogenetic analysis of the 3D polymerase showed that it clustered with that of the newly classified ludopivirus A1, suggesting a previous recombination event in the evolution of the kobuvirus. Our data provide further insights into the diversity of astro- and kobuviruses and broaden the spectrum of viruses infecting grey squirrels.

scholarly journals Discovery and Genomic Characterization of a Novel Bat Sapovirus with Unusual Genomic Features and Phylogenetic Position

PLoS ONE ◽  
2012 ◽  
Vol 7 (4) ◽  
pp. e34987 ◽  
Author(s):  
Herman Tse ◽  
Wan-Mui Chan ◽  
Kenneth S. M. Li ◽  
Susanna K. P. Lau ◽  
Patrick C. Y. Woo ◽  
...  
Keyword(s):  
Phylogenetic Position ◽  
Genomic Features ◽  
Genomic Characterization

scholarly journals Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy

Diagnostics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 79
Author(s):  
Vittoria Mattioni Marchetti ◽  
Ibrahim Bitar ◽  
Mario Sarti ◽  
Elena Fogato ◽  
Erika Scaltriti ◽  
...  
Keyword(s):  
Enterobacter Cloacae ◽  
Sequencing Technology ◽  
Genomic Features ◽  
Long Reads ◽  
Clinical Resistance ◽  
Genomic Characterization ◽  
Enterobacteriaceae Infections ◽  
Enterobacter Cloacae Complex ◽  
Conjugation Experiment

Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the blaVIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.

scholarly journals Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child’s oropharynx

2021 ◽  
Author(s):  
He Qi ◽  
Defeng Liu ◽  
Yang Zou ◽  
Nan Wang ◽  
Han Tian ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Novel Species ◽  
Optimal Growth ◽  
Whole Genome Sequence ◽  
High Susceptibility ◽  
Base Pairs ◽  
Streptococcus Species ◽  
Main Fatty Acid ◽  
Genomic Characterization

AbstractUsing the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).

scholarly journals Identification and genome characterization of Heliothis armigera cypovirus types 5 and 14 and Heliothis assulta cypovirus type 14

2006 ◽  
Vol 87 (2) ◽  
pp. 387-394 ◽  
Author(s):  
Yang Li ◽  
Li Tan ◽  
Yanqiu Li ◽  
Wuguo Chen ◽  
Jiamin Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heliothis Armigera ◽  
Amino Acid Sequences ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Electrophoretic Patterns ◽  
The Family ◽  
Genomic Characterization

Genomic characterization of Heliothis armigera cypovirus (HaCPV) isolated from China showed that insects were co-infected with several cypoviruses (CPVs). One of the CPVs (HaCPV-5) could be separated from the others by changing the rearing conditions of the Heliothis armigera larvae. This finding was further confirmed by nucleotide sequencing analysis. Genomic sequences of segments S10–S7 from HaCPV-14, S10 and S7 from HaCPV-5, and S10 from Heliothis assulta CPV-14 were compared. Results from database searches showed that the nucleotide sequences and deduced amino acid sequences of the newly identified CPVs had high levels of identity with those of reported CPVs of the same type, but not with CPVs of different types. Putative amino acid sequences of HaCPV-5 S7 were similar to that of the protein from Rice ragged stunt virus (genus Oryzavirus, family Reoviridae), suggesting that CPVs and oryzaviruses are related more closely than other genera of the family Reoviridae. Conserved motifs were also identified at the ends of each RNA segment of the same virus type: type 14, 5′-AGAAUUU…CAGCU-3′; and type 5, 5′-AGUU…UUGC-3′. Our results are consistent with classification of CPV types based on the electrophoretic patterns of CPV double-stranded RNA.

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