scholarly journals Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus

2012 ◽  
Vol 93 (5) ◽  
pp. 1103-1119 ◽  
Author(s):  
Daisy Stainton ◽  
Simona Kraberger ◽  
Matthew Walters ◽  
Elizabeth J. Wiltshire ◽  
Karyna Rosario ◽  
...  
Keyword(s):  
Protein Gene ◽  
Full Genome ◽  
Genome Sequences ◽  
Tropical Africa ◽  
Common Region ◽  
Banana Bunchy Top Virus ◽  
Recombination Hotspot ◽  
Recombination Hotspots ◽  
The Common ◽  
Ssdna Viruses

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5′ side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.

scholarly journals Active and inactive transplacement of the M26 recombination hotspot in Schizosaccharomyces pombe.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 33-48
Author(s):  
J B Virgin ◽  
J Metzger ◽  
G R Smith
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Meiotic Recombination ◽  
Plasmid Dna ◽  
Context Effect ◽  
Intragenic Recombination ◽  
Multicopy Plasmid ◽  
Chromosomal Locus ◽  
Sequence Element ◽  
Recombination Hotspot ◽  
Recombination Hotspots

Abstract The ade6-M26 mutation of the fission yeast Schizosaccharomyces pombe creates a meiotic recombination hotspot that elevates ade6 intragenic recombination approximately 10-15-fold. A heptanucleotide sequence including the M26 point mutation is required but not sufficient for hotspot activity. We studied the effects of plasmid and chromosomal context on M26 hotspot activity. The M26 hotspot was inactive on a multicopy plasmid containing M26 embedded within 3.0 or 5.9 kb of ade6 DNA. Random S. pombe genomic fragments totaling approximately 7 Mb did not activate the M26 hotspot on a plasmid. M26 hotspot activity was maintained when 3.0-, 4.4-, and 5.9-kb ade6-M26 DNA fragments, with various amounts of non-S. pombe plasmid DNA, were integrated at the ura4 chromosomal locus, but only in certain configurations relative to the ura4 gene and the cointegrated plasmid DNA. Several integrations created new M26-independent recombination hotspots. In all cases the non-ade6 DNA was located > 1 kb from the M26 site, and in some cases > 2 kb. Because the chromosomal context effect was transmitted over large distances, and did not appear to be mediated by a single discrete DNA sequence element, we infer that the local chromatin structure has a pronounced effect on M26 hotspot activity.

scholarly journals Genetic and Antigenic Characterization of Avian Avulavirus Type 6 (AAvV-6) Circulating in Canadian Wild Birds (2005–2017)

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 543
Author(s):  
Tamiko Hisanaga ◽  
Catherine Soos ◽  
Nicola Lewis ◽  
Oliver Lung ◽  
Matthew Suderman ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Fusion Gene ◽  
Full Genome ◽  
Genome Sequences ◽  
Viral Shedding ◽  
Genetic Groups ◽  
Antigenic Characterization ◽  
Specific Pathogen ◽  
First Time

We describe for the first time the genetic and antigenic characterization of 18 avian avulavirus type-6 viruses (AAvV-6) that were isolated from wild waterfowl in the Americas over the span of 12 years. Only one of the AAvV-6 viruses isolated failed to hemagglutinate chicken red blood cells. We were able to obtain full genome sequences of 16 and 2 fusion gene sequences from the remaining 2 isolates. This is more than double the number of full genome sequences available at the NCBI database. These AAvV-6 viruses phylogenetically grouped into the 2 existing AAvV-6 genotype subgroups indicating the existence of an intercontinental epidemiological link with other AAvV-6 viruses isolated from migratory waterfowl from different Eurasian countries. Antigenic maps made using HI assay data for these isolates showed that the two genetic groups were also antigenically distinct. An isolate representing each genotype was inoculated in specific pathogen free (SPF) chickens, however, no clinical symptoms were observed. A duplex fusion gene based real-time assay for the detection and genotyping of AAvV-6 to genotype 1 and 2 was developed. Using the developed assay, the viral shedding pattern in the infected chickens was examined. The chickens infected with both genotypes were able to shed the virus orally for about a week, however, no significant cloacal shedding was detected in chickens of both groups. Chickens in both groups developed detectable levels of anti-hemagglutinin antibodies 7 days after infection.

scholarly journals Full-Genome Sequences of Influenza A(H1N1)pdm09 Viruses Isolated from Finnish Patients from 2009 to 2013

2014 ◽  
Vol 2 (1) ◽  
Author(s):  
T. Lakspere ◽  
J. Tynell ◽  
M. Kaloinen ◽  
M. Vanlede ◽  
A. Parsons ◽  
...  
Keyword(s):  
Influenza A ◽  
Full Genome ◽  
Genome Sequences ◽  
Influenza A H1n1

scholarly journals Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Steven Van Borm ◽  
Toon Rosseel ◽  
Andy Haegeman ◽  
Mpolokang Elliot Fana ◽  
Latoa Seoke ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Clinical Samples ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Genome Sequences ◽  
Foot And Mouth

The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

scholarly journals Characterization of a Novel Plasmid-Mediated Cephalosporinase (CMY-9) and Its Genetic Environment in an Escherichia coli Clinical Isolate

2002 ◽  
Vol 46 (8) ◽  
pp. 2427-2434 ◽  
Author(s):  
Yohei Doi ◽  
Naohiro Shibata ◽  
Keigo Shibayama ◽  
Kazunari Kamachi ◽  
Hiroshi Kurokawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Gene Cassette ◽  
Single Amino Acid ◽  
Common Region ◽  
Class 1 Integron ◽  
Class 1 ◽  
The Common ◽  
High Level

ABSTRACT An Escherichia coli strain, HKYM68, which showed resistance to broad-spectrum cephalosporins was isolated from a sputum specimen in Japan. The high-level resistance of the strain to ceftazidime, cefpirome, and moxalactam was carried by a self-transferable plasmid. The β-lactamase gene responsible for the resistance was cloned and sequenced. The deduced amino acid sequence of this gene product, CMY-9, had a single amino acid substitution (E85D), the residue reported to be part of the recognition site for the R1 side chain of β-lactams, compared with the amino acid sequence of CMY-8 and also had 78% identity with the amino acid sequence of CepH, a chromosomal cephalosporinase of Aeromonas hydrophila. A sul1-type class 1 integron containing an aacA1-orfG gene cassette was identified upstream of bla CMY-9 and ended with a truncated 3′ conserved segment. The following 2.1 kb was almost identical to the common region of integrons In6 and In7 and the integron of pSAL-1, except that orf513 encoding a putative transposase was identified instead of orf341 due to addition of a single nucleotide. bla CMY-9 was closely located downstream of the end of the common region. These observations are indicative of the exogenous derivation of bla CMY-9 from some environmental microorganisms such as aeromonads.

scholarly journals Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 28
Author(s):  
Nabil Abid ◽  
Giovanni Chillemi ◽  
Marco Salemi
Keyword(s):  
Statistical Approach ◽  
Viral Proteins ◽  
Viral Fitness ◽  
Interaction Networks ◽  
Full Genome ◽  
Genome Sequences ◽  
Potential Effectiveness ◽  
Genome Wide ◽  
Coevolution Analysis ◽  
Infants And Young Children

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.

Full genome sequences and molecular characterization of tick-borne encephalitis virus strains isolated from human patients

2015 ◽  
Vol 6 (1) ◽  
pp. 38-46 ◽  
Author(s):  
Petra Formanová ◽  
Jiří Černý ◽  
Barbora Černá Bolfíková ◽  
James J. Valdés ◽  
Irina Kozlova ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Encephalitis Virus ◽  
Full Genome ◽  
Genome Sequences ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus ◽  
Virus Strains

scholarly journals Genome Sequences of Nine Vesicular Stomatitis Virus Isolates from South America

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Veronica L. Fowler ◽  
David J. King ◽  
Emma L. A. Howson ◽  
Mikidache Madi ◽  
Steven J. Pauszek ◽  
...  
Keyword(s):  
Cell Culture ◽  
Next Generation Sequencing ◽  
Vesicular Stomatitis Virus ◽  
Full Genome ◽  
Genome Sequences ◽  
Viral Genomes ◽  
Vesicular Stomatitis ◽  
Culture Supernatants ◽  
Virus Isolates ◽  
Generation Sequencing

We report nine full-genome sequences of vesicular stomatitis virus obtained by Illumina next-generation sequencing of RNA, isolated from either cattle epithelial suspensions or cell culture supernatants. Seven of these viral genomes belonged to the New Jersey serotype/species (clade III), while two isolates belonged to the Indiana serotype/species.

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