Phylogenetic and molecular evolutionary analysis of SENV DNA isolated from Iraqi Hepatitis Patients

SEN Virus (SENV) is a newly discovered group of transmissible, hepatotropic, single-stranded, circular, non-enveloped DNA viruses that are distantly linked to the widely distributed Torque Teno Virus (TTV) family. This research aimed to use nucleotide sequencing to identify the genetic alterations of SEN-V and to investigate the similarities between isolates. Seven DNA samples of SENV, which were previously extracted from blood of post transfusion hepatitis, were used to identify the genetic variation of SEN-V by nucleotide sequencing. According to the current analysis results, specific primer pairs were used to detect SENV DNA sequences isolated from Iraqi patients with hepatitis; however, those specific primers can also detect two new variants of SENV that are closely related to the Torque Teno Virus. In addition, four SENV isolates showed several substitution mutations, and one of them revealed the replacement of Proline (P) at position 11 with Serine (S). Only one local isolate of SENV was 100% identical to the Iranian isolate (GenBank acc. no. GQ452051.1) from thalassemia.

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Is the Rate of Insertion and Deletion Mutation Male Biased?: Molecular Evolutionary Analysis of Avian and Primate Sex Chromosome Sequences

Genetics ◽

10.1093/genetics/164.1.259 ◽

2003 ◽

Vol 164 (1) ◽

pp. 259-268

Author(s):

Hannah Sundström ◽

Matthew T Webster ◽

Hans Ellegren

Keyword(s):

Dna Sequences ◽

Large Scale ◽

Sex Chromosome ◽

Z Chromosome ◽

Crossing Over ◽

Evolutionary Analysis ◽

W Chromosome ◽

Insertion And Deletion ◽

Indel Mutation ◽

Molecular Evolutionary Analysis

Abstract The rate of mutation for nucleotide substitution is generally higher among males than among females, likely owing to the larger number of DNA replications in spermatogenesis than in oogenesis. For insertion and deletion (indel) mutations, data from a few human genetic disease loci indicate that the two sexes may mutate at similar rates, possibly because such mutations arise in connection with meiotic crossing over. To address origin- and sex-specific rates of indel mutation we have conducted the first large-scale molecular evolutionary analysis of indels in noncoding DNA sequences from sex chromosomes. The rates are similar on the X and Y chromosomes of primates but about twice as high on the avian Z chromosome as on the W chromosome. The fact that indels are not uncommon on the nonrecombining Y and W chromosomes excludes meiotic crossing over as the main cause of indel mutation. On the other hand, the similar rates on X and Y indicate that the number of DNA replications (higher for Y than for X) is also not the main factor. Our observations are therefore consistent with a role of both DNA replication and recombination in the generation of short insertion and deletion mutations. A significant excess of deletion compared to insertion events is observed on the avian W chromosome, consistent with gradual DNA loss on a nonrecombining chromosome.

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Significance of SEN virus in post-transfusion hepatitis. Bedeutung von SEN-Viren für die Posttransfusionshepatitis

LaboratoriumsMedizin ◽

10.1515/jlm.2005.017 ◽

2005 ◽

Vol 29 (2) ◽

Author(s):

Abdurrahman Sagir ◽

Dieter Häussinger

Keyword(s):

Acute Hepatitis ◽

Viral Hepatitis ◽

Hepatitis Viruses ◽

Dna Viruses ◽

Hepatitis G Virus ◽

Tt Virus ◽

Post Transfusion Hepatitis ◽

Causative Agents ◽

Sen Virus ◽

Different Strains

AbstractFive hepatitis viruses (A-E) cause more than 80% of cases of viral hepatitis. However, the fact that nearly 20% of individuals with acute hepatitis test negative for all known hepatitis viruses, as do up to 10% of patients with transfusion-associated hepatitis, suggests the existence of other viral hepatitis agents. Hepatitis G virus (HGV) and TT virus (TTV) were originally proposed as potential causative agents. The SEN virus (SENV) belongs to a recently discovered group of DNA viruses whose members (SENV D and SENV H) are associated with post-transfusion hepatitis. Eight different strains of SENV have been identified and provisionally classified as members of the

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Genomic and Molecular Evolutionary Analysis of a Newly Identified Infectious Agent (SEN Virus) and Its Relationship to the TT Virus Family

The Journal of Infectious Diseases ◽

10.1086/318091 ◽

2001 ◽

Vol 183 (3) ◽

pp. 359-367 ◽

Cited By ~ 116

Author(s):

Yasuhito Tanaka ◽

Daniele Primi ◽

Richard Y. H. Wang ◽

Takeji Umemura ◽

Anthony E. T. Yeo ◽

...

Keyword(s):

Infectious Agent ◽

Evolutionary Analysis ◽

Virus Family ◽

Tt Virus ◽

Sen Virus ◽

Molecular Evolutionary Analysis

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satDNA Analyzer 1.2 as a Valuable Computing Tool for Evolutionary Analysis of Satellite-DNA Families: Revisiting Y-Linked Satellite-DNA Sequences of Rumex (Polygonaceae)

Bioinformatics Research and Development - Lecture Notes in Computer Science ◽

10.1007/978-3-540-71233-6_11 ◽

2007 ◽

pp. 131-139

Author(s):

Rafael Navajas-Pérez ◽

Manuel Ruiz Rejón ◽

Manuel Garrido-Ramos ◽

José Luis Aznarte ◽

Cristina Rubio-Escudero

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Evolutionary Analysis

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The Location of Substitutions and Bacterial Genome Arrangements

Genome Biology and Evolution ◽

10.1093/gbe/evaa260 ◽

2020 ◽

Author(s):

Daniella F Lato ◽

G Brian Golding

Keyword(s):

Sinorhizobium Meliloti ◽

Bacterial Genome ◽

Evolutionary Analysis ◽

Origin Of Replication ◽

Ancestral Reconstruction ◽

Molecular Change ◽

E Coli ◽

A Genome ◽

The Impact ◽

Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

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