scholarly journals Mutagenesis-Induced, Large Fitness Variations with an Invariant Arenavirus Consensus Genomic Nucleotide Sequence

2005 ◽  
Vol 79 (16) ◽  
pp. 10451-10459 ◽  
Author(s):  
Ana Grande-Pérez ◽  
Gema Gómez-Mariano ◽  
Pedro R. Lowenstein ◽  
Esteban Domingo
Keyword(s):  
Nucleotide Sequence ◽  
Genomic Sequence ◽  
Rna Virus ◽  
Molecular Genetic ◽  
Lymphocytic Choriomeningitis ◽  
Molecular Genetic Analysis ◽  
Viral Population ◽  
Molecular Events ◽  
Induced Mutagenesis ◽  
Genomic Nucleotide Sequence

ABSTRACT Enhanced mutagenesis may result in RNA virus extinction, but the molecular events underlying this process are not well understood. Here we show that 5-fluorouracil (FU)-induced mutagenesis of the arenavirus lymphocytic choriomeningitis virus (LCMV) resulted in preextinction populations whose consensus genomic nucleotide sequence remained unaltered. Furthermore, fitness recovery passages in the absence of FU, or alternate virus passages in the presence and absence of FU, led to profound differences in the capacity of LCMV to produce progeny, without modification of the consensus genomic sequence. Molecular genetic analysis failed to produce evidence of hypermutated LCMV genomes. The results suggest that low-level mutagenesis to enrich the viral population with defector, interfering genomes harboring limited numbers of mutations may mediate the loss of infectivity that accompanies viral extinction.

scholarly journals Molecular Genetic Analysis of the Complete Genome of Tick-Borne Encephalitis Virus (Siberia Subtype): Modern Kolarovo-2008 Isolate

2011 ◽  
pp. 44-48 ◽  
Author(s):  
E. V. Chausov ◽  
V. A. Ternovoy ◽  
E. V. Protopopova ◽  
S. N. Konovalova ◽  
Yu. V. Kononova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Genome ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Encephalitis Virus ◽  
Nucleotide Sequence Analysis ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus ◽  
Siberian Subtype

Determined is the complete genome sequence of Kolarovo-2008 strain (Siberia subtype) of Tick-borne encephalitis virus (TBEV), isolated from a tick in the suburbs of the Tomsk city. Nucleotide sequence analysis testifies of the fact that the level of genetic differences within the Siberian subtype of TBEV amounts to 10 % of the nucleotide sequence and to 7 % of amino-acid sequence for certain virus genes. 3'-HTO of the genome of Siberian subtype has the highest rate of variability and the homology level ranging from 65 to 97 %. Kolarovo-2008 and Vasilchenko (isolated in Novosibirsk in 1969) strains have the highest level of genome homology. The level of dissimilarity between the two Tomsk strains is substantially higher: the total number of amino-acid substitutions in Tomsk Zausaev and Kolarovo-2008 strains equals to 124, and 3'HTO level of homology is 79 %. Identified genetic variability of the Siberian subtype of TBEV is of a great importance for further development and enhancement of tick-borne encephalitis virus diagnostics.

scholarly journals Hidden Virulence Determinants in a Viral Quasispecies In Vivo

2008 ◽  
Vol 82 (21) ◽  
pp. 10465-10476 ◽  
Author(s):  
Marta Sanz-Ramos ◽  
Fayna Díaz-San Segundo ◽  
Cristina Escarmís ◽  
Esteban Domingo ◽  
Noemí Sevilla
Keyword(s):  
Genomic Sequence ◽  
Rna Virus ◽  
Consensus Sequence ◽  
Nucleotide Sequences ◽  
Intermediate Phenotype ◽  
Viral Population ◽  
Virulence Determinants ◽  
Mouth Disease Virus ◽  
Mutant Spectrum

ABSTRACT The characterization of virulence determinants of pathogenic agents is of utmost relevance for the design of disease control strategies. So far, two classes of virulence determinants have been characterized for viral populations: those imprinted in the nucleotide sequence of some specific genomic regions and those that depend on the complexity of the viral population as such. Here we provide evidence of a virulence determinant that depends neither on a genomic sequence nor on detectable differences in population complexity. Foot-and-mouth disease virus is lethal for C57BL/6 mice showing the highest viral load in pancreas. Virus isolated from pancreas after one passage in mice showed an attenuated phenotype, with no lethality even at the highest dose tested. By contrast, virus from sera of the same mice displayed a virulence similar to that of the parental wild-type clone and virus isolated from spleen displayed an intermediate phenotype. However, viral populations from pancreas, spleen, and serum showed indistinguishable consensus genomic nucleotide sequences and mutant spectrum complexities, as quantified according to the mutation frequencies of both entire genomic nucleotide sequences of biological clones. The results show that the populations with differing virulences cannot be distinguished either by the consensus sequence or by the average complexity of the mutant spectrum. Differential harvesting of virus generated by cell transfection of RNA from serum and pancreas failed to reveal genetic differences between subpopulations endowed with differing virulences. In addition to providing evidence of hidden virulence determinants, this study underlines the capacity of a clone of an RNA virus to rapidly diversify phenotypically in vivo.

scholarly journals Use of the method of phylogenetic analysis in an epidemiological investigation in case of HIV infection in pediatric practice

2021 ◽  
Vol 13 (1) ◽  
pp. 106-114
Author(s):  
S. P. Kruglyak ◽  
V. O. Kotova ◽  
E. I. Miroshnichenko ◽  
O. A. Skaly ◽  
E. S. Makhno ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Hiv Infection ◽  
Phylogenetic Trees ◽  
Comparison Group ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Epidemiological Investigation

The aim of the study is to study the main pathways and risk factors for HIV infection in a child, to establish a probable source of infection for a child, as well as to exclude the possibility of criminal or nosocomial infection.Materials and methods. At the first stage, an epidemiological investigation was conducted. Next, a molecular genetic analysis of two blood plasma samples studied (child and mother) and a comparison group were used, in which 18 nucleotide sequences of HIV-1 variants were used, obtained from patients living in the Primorsky Region, and 8 characterized nucleotide sequences additionally taken from GenBank international database. Distance calculation and phylogenetic analysis were performed by constructing phylogenetic trees using the Maximum Likelihood method using the GTR evolution model.Research results. The data obtained indicate that the nucleotide sequence from the child is most similar to the nucleotide sequence from the mother (potential source) and reliably grouped on the phylogenetic tree, forming a common cluster that is different from the samples of the comparison group. This indicates the likelihood of an epidemiological link between HIV infections in the mother and her child.Conclusion. According to the results of this study, we can conclude that the child is infected from an HIV-infected mother, approximately at the age of a child older than 4 years old, when he received the last negative test result for HIV markers.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

Diagnosis and Management of Cardiomyopathies – A Focus on Genetics, Cardiac Magnetic Resonance and Clinical Features

2011 ◽  
Vol 7 (3) ◽  
pp. 225
Author(s):  
Gianfranco Sinagra ◽  
Michele Moretti ◽  
Giancarlo Vitrella ◽  
Marco Merlo ◽  
Rossana Bussani ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Cardiac Magnetic Resonance ◽  
Magnetic Resonance ◽  
Imaging Techniques ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Routine Clinical Practice ◽  
Clinical Approach ◽  
Diagnosis And Management ◽  
Made In

In recent years, outstanding progress has been made in the diagnosis and treatment of cardiomyopathies. Genetics is emerging as a primary point in the diagnosis and management of these diseases. However, molecular genetic analyses are not yet included in routine clinical practice, mainly because of their elevated costs and execution time. A patient-based and patient-oriented clinical approach, coupled with new imaging techniques such as cardiac magnetic resonance, can be of great help in selecting patients for molecular genetic analysis and is crucial for a better characterisation of these diseases. This article will specifically address clinical, magnetic resonance and genetic aspects of the diagnosis and management of cardiomyopathies.

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