scholarly journals Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Mostafa Y. Abdel-Glil ◽  
Uwe Fischer ◽  
Dieter Steinhagen ◽  
Una McCarthy ◽  
Heinrich Neubauer ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Genetic Relatedness ◽  
Critical Role ◽  
Genome Structure ◽  
The United States ◽  
Genomic Islands ◽  
Stable Set ◽  
Whole Genome ◽  
Yersinia Ruckeri

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.

scholarly journals Genetic Diversity of the Ordinary Strain of Potato virus Y (PVY) and Origin of Recombinant PVY Strains

2011 ◽  
Vol 101 (7) ◽  
pp. 778-785 ◽  
Author(s):  
Alexander V. Karasev ◽  
Xiaojun Hu ◽  
Celeste J. Brown ◽  
Camille Kerlan ◽  
Olga V. Nikolaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Molecular Study ◽  
The United States ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Severe Stunting ◽  
Ordinary Strain

The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVYO was recently reported, PVYO-O5, which is spreading in the United States and is distinguished from other PVYO isolates serologically (i.e., reacting to the otherwise PVYN-specific monoclonal antibody 1F5). To characterize this new PVYO-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVYO and PVYO-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVYO isolates were sequenced, including 31 from the previously defined PVYO-O5 group, and subjected to whole-genome analysis. PVYO-O5 isolates formed a separate lineage within the PVYO genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVYO sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVYO genomes was conducted. The analysis revealed that PVYN:O and PVYN-Wi recombinants acquired their PVYO segments from two separate PVYO lineages, whereas the PVYNTN recombinant acquired its PVYO segment from the same lineage as PVYN:O. These data suggest that PVYN:O and PVYN-Wi recombinants originated from two separate recombination events involving two different PVYO parental genomes, whereas the PVYNTN recombinants likely originated from the PVYN:O genome via additional recombination events.

scholarly journals Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

BMJ Open ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. e030913 ◽  
Author(s):  
Adrian Egli ◽  
Claudia Saalfrank ◽  
Nina Goldman ◽  
Myrta Brunner ◽  
Yvonne Hollenstein ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Relatedness ◽  
Critical Role ◽  
Herd Immunity ◽  
Influenza Viruses ◽  
University Hospital ◽  
Whole Genome Sequencing Data ◽  
Whole Genome

IntroductionUrban transmission patterns of influenza viruses are complex and poorly understood, and multiple factors may play a critical role in modifying transmission. Whole genome sequencing (WGS) allows the description of patient-to-patient transmissions at highest resolution. The aim of this study is to explore urban transmission patterns of influenza viruses in high detail by combining geographical, epidemiological and immunological data with WGS data.Methods and analysisThe study is performed at the University Hospital Basel, University Children’s Hospital Basel and a network of paediatricians and family doctors in the Canton of Basel-City, Switzerland. The retrospective study part includes an analysis of PCR-confirmed influenza cases from 2013 to 2018. The prospective study parts include (1) a household survey regarding influenza-like illness (ILI) and vaccination against influenza during the 2015/2016 season; (2) an analysis of influenza viruses collected during the 2016/2017 season using WGS—viral genomic sequences are compared with determine genetic relatedness and transmissions; and (3) measurement of influenza-specific antibody titres against all vaccinated and circulated strains during the 2016/2017 season from healthy individuals, allowing to monitor herd immunity across urban quarters. Survey data and PCR-confirmed cases are linked to data from the Statistics Office of the Canton Basel-City and visualised using geo-information system mapping. WGS data will be analysed in the context of patient epidemiological data using phylodynamic analyses, and the obtained herd immunity for each quarter. Profound knowledge on the key geographical, epidemiological and immunological factors influencing urban influenza transmission will help to develop effective counter measurements.Ethics and disseminationThe study is registered and approved by the regional ethics committee as an observational study (EKNZ project ID 2015–363 and 2016–01735). It is planned to present the results at conferences and publish the data in scientific journals.Trial registration numberNCT03010007.

Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

2008 ◽  
Vol 51 (1) ◽  
pp. 21-26 ◽  
Author(s):  
ZhaoHui Xiong ◽  
CanDong Wei ◽  
Jian Yang ◽  
JunPing Peng ◽  
XingYe Xu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Structure ◽  
Streptococcus Suis ◽  
Whole Genome

scholarly journals Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

2021 ◽  
Author(s):  
Ahmed M. Moustafa ◽  
Colleen Bianco ◽  
Lidiya Denu ◽  
Azad Ahmed ◽  
Brandy Neide ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Comparative Genomics ◽  
Neutralizing Antibodies ◽  
Whole Genome ◽  
High Coverage ◽  
The Us ◽  
The Uk ◽  
Induced Immunity

AbstractRapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote “escape” from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

scholarly journals First Complete Genome Sequence of a Feline Morbillivirus Isolate from Germany

2018 ◽  
Vol 6 (16) ◽  
pp. e00244-18 ◽  
Author(s):  
Michael Sieg ◽  
Annett Vahlenkamp ◽  
Christoph Georg Baums ◽  
Thomas Wilhelm Vahlenkamp
Keyword(s):  
United States ◽  
Cell Culture ◽  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Cell Culture Isolation

ABSTRACT The first cell culture isolation and whole-genome sequence of a feline morbillivirus from Germany are described here. Phylogenetic analysis revealed highest similarity to isolates from Japan and a more distant relationship to strains from Italy, Hong Kong, and the United States. Therefore, feline morbilliviruses should be divided into two different genotypes.

scholarly journals A tightly clustered hepatitis E virus genotype 1a is associated with endemic and outbreak infections in Bangladesh

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255054
Author(s):  
Trang Nguyen Hoa ◽  
Saif Ullah Munshi ◽  
Khanh Nguyen Ngoc ◽  
Chau Le Ngoc ◽  
Thanh Tran Thi Thanh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
T Cell ◽  
Hepatitis E Virus ◽  
Genetic Relatedness ◽  
Hepatitis E ◽  
Immunoglobulin M ◽  
Whole Genome Sequence ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Genotype 1A

Background Hepatitis E virus (HEV) infection is endemic in Bangladesh and there are occasional outbreaks. The molecular characteristics and pathogenesis of endemic and outbreak HEV strains are poorly understood. We compared the genetic relatedness and virulence associated mutations of endemic HEV strains with outbreak strains. Methods We analyzed systematically collected serum samples from HEV immunoglobulin M (IgM) positive patients attended at Bangabandhu Sheikh Mujib Medical University, Dhaka from August 2013 to June 2015. HEV RNA positive samples were subjected to whole genome sequencing. Genotype and subtype of the strains were determined by phylogenetic analysis. Virulence associated mutations e.g. acute viral hepatitis (AVH), fulminant hepatic failure (FHF), chronic hepatitis, ribavirin treatment failure (RTF), B and T cell neutralization epitopes were determined. Results 92 HEV immunoglobulin M (IgM) antibody positive plasma samples (43 in 2013–2014 and 49 in 2014–2015) were studied. 77.1% (70/92) of the samples were HEV RNA positive. A 279 bp open reading frame (ORF) 2 and ORF 3 sequence was obtained from 54.2% (38/70) of the strains. Of these 38 strains, whole genome sequence (WGS) was obtained from 21 strains. In phylogenetic analysis of 38 (279 bp) sequence all HEV sequences belonged to genotype 1 and subtype 1a. Further phylogenetic analysis of 21 HEV WGS, Bangladeshi HEV sequences clustered with genotype 1a sequences from neighboring countries. Within genotype 1a cluster, Bangladesh HEV strains formed a separate cluster with the 2010 HEV outbreak strains from northern Bangladesh. 80.9 to 100% of the strains had A317T, T735I, L1120I, L1110F, P259S, V1479I, G1634K mutations associates AVH, FHF and RTF. Mutations in T cell recognition epitope T3, T5, T7 was observed in 76.1%, 100% and 100% of the strains respectively. Conclusion Strains of HEV genotype 1a are dominant in Bangladesh and are associated with endemic and outbreak of HEV infection. HEV isolates in Bangladesh have high prevalence of virulence associated mutations and mutation which alters antigenicity to B and T cell epitopes.

scholarly journals Phylogenetic analysis of perfect repeats in the genomes of unicellular cyanobacteria

2005 ◽  
Vol 3 (2) ◽  
pp. 15-21
Author(s):  
Lidia E Mikheeva ◽  
Yuri L Orlov ◽  
Nikolay A Kolchanov ◽  
Sergey V Shestakov
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Molecular Phylogeny ◽  
Genome Organization ◽  
Whole Genome ◽  
Ecological Genomics ◽  
Close Phylogenetic Relationship ◽  
Complete Genomes ◽  
Relationship Of ◽  
Close Genetic Relationship

We have fulfilled in silico research of number, structure, distribution and location of direct and inverted repeated sequences in eight complete genomes of unicellular cyanobacteria. Analysis of whole genome repeats has shown utility of this approach for purposes of molecular phylogeny and ecological genomics. Comparative analysis of nonrandom repeats patterns has allowed: 1) to confirm the close genetic relationship of two Prochlorococcus marinus strains (MED4 and SS120) that have reduced genomes and inhabit the econiches with different light intensities; 2) to suggest the close phylogenetic relationship of genomes Prochlorococcus marinus MIT9313 and Synechococcus WH8102 that significantly differ by sets of lightharvesting photosystem; 3) to  reveal specific differences in genome organization between marine and freshwater cyanobacteria.

Bilingual and Monolingual Students' Perceptions of the CSD Major: A Qualitative Study

2015 ◽  
Vol 18 (1) ◽  
pp. 16-31 ◽  
Author(s):  
Flora Keshishian ◽  
Rebecca Wiseheart
Keyword(s):  
Qualitative Study ◽  
Undergraduate Students ◽  
Critical Role ◽  
School Setting ◽  
The United States ◽  
Bilingual Students ◽  
Speech Language Pathology ◽  
Diverse Environment ◽  
Language Pathology ◽  
Areas Of Interest

There is a growing demand for bilingual services in speech-language pathology and audiology. To meet this growing demand, and given their critical role in the recruitment of more bilingual professionals, higher education institutions need to know more about bilingual students' impression of Communication Sciences and Disorders (CSD) as a major. The purpose of this qualitative study was to investigate bilingual and monolingual undergraduate students' perceptions of the CSD major. One hundred and twenty-two students from a large university located in a highly multicultural metropolitan area responded to four open-ended questions aimed at discovering students' major areas of interest (and disinterest) as well as their motivations for pursuing a degree in CSD. Consistent with similar reports conducted outside the United States, students from this culturally diverse environment indicated choosing the major for altruistic reasons. A large percentage of participants were motivated by a desire to work with children, but not in a school setting. Although 42% of the participants were bilingual, few indicated an interest in taking an additional course in bilingual studies. Implications of these findings as well as practical suggestions for the recruitment of bilingual students are discussed.

Comparative analysis of the trade policy of Barack Obama and Donald Trump

2020 ◽  
pp. 59-71
Author(s):  
V. Iordanova ◽  
A. Ananev
Keyword(s):  
United States ◽  
Economic Development ◽  
Comparative Analysis ◽  
Trade Policy ◽  
World Economy ◽  
The United States ◽  
Barack Obama ◽  
Scientific Article ◽  
Donald Trump ◽  
Entire World

The authors of this scientific article conducted a comparative analysis of the trade policy of US presidents Barack Obama and Donald Trump. The article states that the tightening of trade policy by the current President is counterproductive and has a serious impact not only on the economic development of the United States, but also on the entire world economy as a whole.

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