scholarly journals Genome Sequences of the Novel Porcine Parvovirus 3, Identified in Guangxi Province, China

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Hui Zhong ◽  
Xiangmin Li ◽  
Zekai Zhao ◽  
Chunjing An ◽  
Peng Wan ◽  
...  
Keyword(s):  
Molecular Characteristics ◽  
Porcine Parvovirus ◽  
The Novel ◽  
Guangxi Province ◽  
Genome Sequences

Porcine parvovirus 3 is a novel parvovirus that infects pigs. Here, we report two genome sequences of porcine parvovirus 3 strains GX1 and GX2, which are highly prevalent in Guangxi province. It will help in understanding the epidemiology and molecular characteristics of the porcine parvovirus 3.

Use of a cohorting-unit and systematic surveillance cultures to control a Klebsiella pneumoniae carbapenemase (KPC)–producing Enterobacteriaceae outbreak

2019 ◽  
Vol 40 (7) ◽  
pp. 767-773 ◽  
Author(s):  
Allison E. Reeme ◽  
Sarah L. Bowler ◽  
Blake W. Buchan ◽  
Mary Beth Graham ◽  
Elizabeth Behrens ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Infection Control ◽  
Organ Transplant ◽  
Index Patient ◽  
Molecular Characteristics ◽  
Solid Organ ◽  
The Novel ◽  
Transplant Recipients ◽  
Klebsiella Pneumoniae Carbapenemase ◽  
Surveillance Cultures

AbstractObjective:Describe the epidemiological and molecular characteristics of an outbreak of Klebsiella pneumoniae carbapenemase (KPC)–producing organisms and the novel use of a cohorting unit for its control.Design:Observational study.Setting:A 566-room academic teaching facility in Milwaukee, Wisconsin.Patients:Solid-organ transplant recipients.Methods:Infection control bundles were used throughout the time of observation. All KPC cases were intermittently housed in a cohorting unit with dedicated nurses and nursing aids. The rooms used in the cohorting unit had anterooms where clean supplies and linens were placed. Spread of KPC-producing organisms was determined using rectal surveillance cultures on admission and weekly thereafter among all consecutive patients admitted to the involved units. KPC-positive strains underwent pulsed-field gel electrophoresis and whole-genome sequencing.Results:A total of 8 KPC cases (5 identified by surveillance) were identified from April 2016 to April 2017. After the index patient, 3 patients acquired KPC-producing organisms despite implementation of an infection control bundle. This prompted the use of a cohorting unit, which immediately halted transmission, and the single remaining KPC case was transferred out of the cohorting unit. However, additional KPC cases were identified within 2 months. Once the cohorting unit was reopened, no additional KPC cases occurred. The KPC-positive species identified during this outbreak included Klebsiella pneumoniae, Enterobacter cloacae complex, and Escherichia coli. blaKPC was identified on at least 2 plasmid backbones.Conclusions:A complex KPC outbreak involving both clonal and plasmid-mediated dissemination was controlled using weekly surveillances and a cohorting unit.

scholarly journals Genome Sequences of Vibrio maerlii sp. nov. and Vibrio rhodolitus sp. nov., Isolated from Rhodoliths

2018 ◽  
Vol 7 (19) ◽  
Author(s):  
Camila S. F. Silva ◽  
Juline M. Walter ◽  
Maria S. Nobrega ◽  
Gabriela Calegario ◽  
Luciana R. Appolinario ◽  
...  
Keyword(s):  
The Novel ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Complete Genomes

We report here the genome sequences of the novel isolates G62T and G98T from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62T and 4.5 Mbp (4,085 CDS) for G98T.

scholarly journals Molecular Characteristics of the Novel Intermediate Filament Protein Paranemin

1997 ◽  
Vol 272 (51) ◽  
pp. 32489-32499 ◽  
Author(s):  
Philip M. Hemken ◽  
Robert M. Bellin ◽  
Suzanne W. Sernett ◽  
Bruno Becker ◽  
Ted W. Huiatt ◽  
...  
Keyword(s):  
Intermediate Filament ◽  
Molecular Characteristics ◽  
Intermediate Filament Protein ◽  
The Novel ◽  
Filament Protein

scholarly journals Specific capture and whole-genome phylogeography of Dolphin morbillivirus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Francesco Cerutti ◽  
Federica Giorda ◽  
Carla Grattarola ◽  
Walter Mignone ◽  
Chiara Beltramo ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Whole Genome ◽  
The Novel ◽  
Target Enrichment ◽  
Genome Sequences ◽  
Tissue Samples ◽  
Dolphin Morbillivirus ◽  
Field Samples ◽  
The Mediterranean ◽  
Phylodynamic Analysis

AbstractDolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. Only few DMV genomes are publicly available. Here, we report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. RNA from 15 tissue samples of cetaceans stranded along the Italian and French coasts (2008–2017) was purified and processed using custom probes (by bait hybridization) for target enrichment and sequenced on Illumina MiSeq. Data were mapped against the reference genome, and the novel sequences were aligned to the available genome sequences. The alignment was then used for phylogenetic and phylogeographic analysis using MrBayes and BEAST. We herein report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples. By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. The phylogenetic tree well discriminated the Mediterranean and the NE-Atlantic strains, circulating in the Mediterranean Sea and causing two different epidemics (2008–2015 and 2014–2017, respectively), with a limited time overlap of the two strains, sharing a common ancestor approximately in 1998.

scholarly journals High-Quality Draft Genome Sequences of Three Cyanobacteria Isolated from the Limestone Walls of the Old Cathedral of Coimbra, Portugal

2020 ◽  
Vol 9 (26) ◽  
Author(s):  
Fabiana Soares ◽  
João Trovão ◽  
Catarina Coelho ◽  
Inês Costa ◽  
Nuno Mesquita ◽  
...  
Keyword(s):  
Draft Genome ◽  
World Heritage Site ◽  
The Novel ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Heritage Site ◽  
Unesco World Heritage Site ◽  
Novel Taxa ◽  
High Quality Genome

ABSTRACT The recently described species Myxacorys almedinensis and two other cyanobacteria were isolated from the limestone walls of the Old Cathedral of Coimbra, Portugal (UNESCO World Heritage Site). The high-quality genome sequences presented here will be essential for characterization purposes and description of the novel taxa.

Genome sequences of porcine parvovirus 2 from the lung tissue of aborted pig fetuses in the Republic of Korea

2020 ◽  
Vol 44 (3) ◽  
pp. 140-141
Author(s):  
In-Ohk Ouh ◽  
Ju-Yeon Lee ◽  
Min-Soo Cho ◽  
Seyeon Park ◽  
Hyeonhae Choi ◽  
...  
Keyword(s):  
Lung Tissue ◽  
Republic Of Korea ◽  
Porcine Parvovirus ◽  
Genome Sequences ◽  
The Republic

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals Analysis of Whole Genome Sequences and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein of the Novel Coronavirus COVID-19 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

2020 ◽  
Author(s):  
Arun Shanker ◽  
Divya Bhanu ◽  
Anajani Alluri
Keyword(s):  
Binding Sites ◽  
Tertiary Structure ◽  
Vaccine Development ◽  
Homology Modelling ◽  
Whole Genome ◽  
The Novel ◽  
Structural Protein ◽  
Genome Sequences ◽  
Ligand Interaction ◽  
Percent Identity

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the Novel COVID-19 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and possible antiviral properties of these protein ligand complexes. Any information emerging from these protein models can be used for vaccine development. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the Novel COVID-19 whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible vaccine development. Our results showed that the tertiary structure of the polyprotein isolate COVID-19 _HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. Our results indicate that a part of the viral genome (residues 254 to 13480 in Frame 2 with 4409 amino acids) of the Novel COVID-19 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) when modelled with template 2a5i of the PDB database had 96 percent identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase. The part of the genome when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. It is possible that these viral inhibiters can be used for vaccine development for the Novel COVID-19.

scholarly journals A Review of the Clinical Characteristics and Novel Molecular Subtypes of Endometrioid Ovarian Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Shuangfeng Chen ◽  
Yuebo Li ◽  
Lili Qian ◽  
Sisi Deng ◽  
Luwen Liu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Reproductive Tract ◽  
Molecular Subtypes ◽  
Female Reproductive Tract ◽  
Molecular Characteristics ◽  
The Novel ◽  
Endometrioid Ovarian Carcinoma ◽  
Endometrioid Ovarian Cancer ◽  
Prediction Of Prognosis ◽  
Novel Therapeutic Strategies

Ovarian cancer is one of the most common gynecologic cancers that has the highest mortality rate. Endometrioid ovarian cancer, a distinct subtype of epithelial ovarian cancer, is associated with endometriosis and Lynch syndrome, and is often accompanied by synchronous endometrial carcinoma. In recent years, dysbiosis of the microbiota within the female reproductive tract has been suggested to be involved in the pathogenesis of endometrial cancer and ovarian cancer, with some specific pathogens exhibiting oncogenic having been found to contribute to cancer development. It has been shown that dysregulation of the microenvironment and accumulation of mutations are stimulatory factors in the progression of endometrioid ovarian carcinoma. This would be a potential therapeutic target in the future. Simultaneously, multiple studies have demonstrated the role of four molecular subtypes of endometrioid ovarian cancer, which are of particular importance in the prediction of prognosis. This literature review aims to compile the potential mechanisms of endometrioid ovarian cancer, molecular characteristics, and molecular pathological types that could potentially play a role in the prediction of prognosis, and the novel therapeutic strategies, providing some guidance for the stratified management of ovarian cancer.

scholarly journals Complete Genome Sequences of Four Foot-and-Mouth Disease Viruses of Serotype South African Territories 1 (SAT 1), Topotype X, Isolated from Cattle in Nigeria in 2015

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Frank Vandenbussche ◽  
Elisabeth Mathijs ◽  
Hussaini G. Ularamu ◽  
David O. Ehizibolo ◽  
Andy Haegeman ◽  
...  
Keyword(s):  
South African ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
The Novel ◽  
Genome Sequences ◽  
The West ◽  
Foot And Mouth ◽  
Sat 1

ABSTRACT The complete genome sequences of four foot-and-mouth disease viruses of South African territories 1 (SAT 1) serotype are reported. These viruses originate from an outbreak in Nigeria in 2015 and belong to the novel SAT 1 topotype X from the west and central African virus pool.

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