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At least 469 records · Page 26Linked to original sources
PubMed1997

Sequence determination and phylogenetic analysis of the Akabane bunyavirus S RNA genome segment.

The nucleotide sequence of the small (S) RNA segment of Akabane (AKA) bunyavirus was determined. The segment is 858 nucleotides long and contains two overlapping open reading frames (ORFs), which encode the nucleocapsid (N) and nonstructural (NSs) proteins, consistent with other bunyaviruses. Comparisons with the Aino virus S RNA sequence indicated that there is 73.5% identity in nucleotide sequence. However, the sequence identity of the 5' non-coding region of the genomic RNA between these two viruses is only 55%. The N ORFs from 20 Japanese and 2 Australian isolates of AKA virus were sequenced and subjected to phylogenetic analysis. This suggested that AKA virus has evolved in multiple lineages. Twenty-three isolates were grouped into three major clusters, and the cluster which includes recent isolates was subdivided into two branches. Thus, phylogenetic analysis of the AKA virus N protein gene gives a greater insight into bunyavirus evolution.

Genome, Viral↗
PubMed2005

Genetic diversity and evolution of hepatitis C virus in the Latin American region.

Hepatitis C virus (HCV) has been the subject of intense research and clinical investigations, as a consequence of the recognition of its major role in human disease. HCV evolution is a highly dynamic process. HCV exploits all known mechanisms of genetic variation, such as recombination and mutation, to ensure its survival. Like most RNA viruses, HCV circulates in vivo as a complex population of different but closely related variants, commonly referred to as a quasi species. This work describes the genetic variability of HCV in Latin America, with special emphasis on its diversification and recombination in this area of the world, and discusses how our knowledge of these issues can contribute to its control.

Comorbidity↗
PubMed1998

Evolution of hypervariable region 1 of hepatitis C virus in primary infection.

The hypervariable region 1 (HVR-1) of the putative envelope encoding E2 region of hepatitis C virus (HCV) RNA was analyzed in sequential samples from three patients with acute type C hepatitis infected from different sources to address (i) the dynamics of intrahost HCV variability during the primary infection and (ii) the role of host selective pressure in driving viral genetic evolution. HVR-1 sequences from 20 clones per each point in time were analyzed after amplification, cloning, and purification of plasmid DNA from single colonies of transformed cells. The intrasample evolutionary analysis (nonsynonymous mutations per nonsynonymous site [Ka], synonymous mutations per synonymous site [Ks], Ka/Ks ratio, and genetic distances [gd]) documented low gd in early samples (ranging from 2. 11 to 7.79%) and a further decrease after seroconversion (from 0 to 4.80%), suggesting that primary HCV infection is an oligoclonal event, and found different levels and dynamics of host pressure in the three cases. The intersample analysis (pairwise comparisons of intrapatient sequences; rKa, rKs, rKa/rKs ratio, and gd) confirmed the individual features of HCV genetic evolution in the three subjects and pointed to the relative contribution of either neutral evolution or selective forces in driving viral variability, documenting that adaptation of HCV for persistence in vivo follows different routes, probably representing the molecular counterpart of the viral fitness for individual environments.

Adolescent↗
PubMed1986

Fixation of mutations in the viral genome during an outbreak of foot-and-mouth disease: heterogeneity and rate variations.

Rates of fixation of mutations during the evolution of the foot-and-mouth disease virus (FMDV) C1 in nature have been estimated by hybridization of viral RNA to cloned cDNAs representing defined FMDV genome segments, and comparison of the selected RNAs by T1 RNase oligonucleotide fingerprinting. Values ranged from less than 0.04 X 10(-2) to 4.5 X 10(-2) substitutions per nucleotide per year (s/nt/yr), depending on the time period and the genomic segment considered. Rates for viral structural protein genes were up to sixfold higher than for nonstructural protein genes. Values in excess of 10(-2) s/nt/yr have been measured for the RNA region that encodes VP1-VP3. The nucleotide sequences of the major immunogenic region of capsid protein VP1 have been determined for six new FMDV C1 isolates, and they are compared with the two previously known sequences of FMDV C1 (C-S8 and C1-O). Both oligonucleotide fingerprinting of selected RNA fragments and direct nucleotide sequencing demonstrate that genetic heterogeneity exists among three viruses isolated on the same day, introducing a significant indetermination in the evaluation of fixation rates of mutations. During the FMDV C1 outbreak, amino acid substitutions did occur that are known to affect the immunological properties of the virus. The proportion of mutations between two viral RNAs does not increase significantly with the time elapsed between the two isolations, suggesting a cocirculation of multiple, related, nonidentical FMDVs ('evolving quasispecies') as the mode of evolution of this agent.

Amino Acid Sequence↗
PubMed1989

Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 1.

The nucleotide sequence of RNA 1 of the Fny strain (Subgroup I) of cucumber mosaic virus (CMV) was determined and compared at both the nucleic acid and protein levels with the corresponding sequence of RNA 1 of the Q strain (Subgroup II) of CMV. Fny-CMV RNA 1 consisted of 3357 nucleotides and contained a single long open reading frame (ORF) of 2979 nucleotides, whereas Q-CMV RNA 1 consists of 3389 nucleotides and contains a single ORF of 2973 nucleotides. The levels of sequence homology between the two RNAs were 76% at the nucleotide level and 85% at the protein level. These homologies were distributed widely over the molecules, with 45% of the non-conservative differences in amino acid sequence located between amino acids 503 and 705, and another 15% of the differences located between amino acids 224 and 298. While the C-terminal 141 amino acids contain more basic than acidic amino acids, the region of greatest amino acid sequence heterogeneity, amino acids 503 to 600, contained a preponderance of acidic amino acids in the putative translation products of RNAs 1 of both Q-CMV and Fny-CMV. The last 180 nucleotides of the 3'-terminal non-coding region of Fny-CMV RNAs 1 and 2 were 96% homologous, whereas the sequence homology between Fny-CMV RNA 1 and Q-CMV RNA 1 was 64% in this region. Furthermore, the tRNA-like secondary structures formed by the 3'-terminal non-coding regions of Fny-CMV RNAs 1 and 2 were virtually identical. By contrast, there was only 84% sequence homology between the 5'-terminal non-coding regions of these two RNAs and 81% sequence homology between the 5'-terminal non-coding regions of Q-CMV RNA 1 and Fny-CMV RNA 1. The non-equivalent divergence in the non-coding regions of these RNAs, as well as possible functions for the translation product of RNA 1, are discussed.

Amino Acid Sequence↗
PubMed1994

Emergence of a replicating species from an in vitro RNA evolution reaction.

The technique of self-sustained sequence replication allows isothermal amplification of DNA and RNA molecules in vitro. This method relies on the activities of a reverse transcriptase and a DNA-dependent RNA polymerase to amplify specific nucleic acid sequences. We have modified this protocol to allow selective amplification of RNAs that catalyze a particular chemical reaction. During an in vitro RNA evolution experiment employing this modified system, a unique class of "selfish" RNAs emerged and replicated to the exclusion of the intended RNAs. Members of this class of selfish molecules, termed RNA Z, amplify efficiently despite their inability to catalyze the target chemical reaction. Their amplification requires the action of both reverse transcriptase and RNA polymerase and involves the synthesis of both DNA and RNA replication intermediates. The proposed amplification mechanism for RNA Z involves the formation of a DNA hairpin that functions as a template for transcription by RNA polymerase. This arrangement links the two strands of the DNA, resulting in the production of RNA transcripts that contain an embedded RNA polymerase promoter sequence.

Avian Myeloblastosis Virus↗
PubMed1990

The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro- and coronaviruses are evolutionarily related.

Sequence analysis of the 3' part (8 kb) of the polymerase gene of the torovirus prototype Berne virus (BEV) revealed that this area contains at least two open reading frames (provisionally designated ORF1a and ORF1b) which overlap by 12 nucleotides. The complete sequence of ORF1b (6873 nucleotides) was determined. Like the coronaviruses, BEV was shown to express its ORF1b by ribosomal frameshifting during translation of the genomic RNA. The predicted tertiary RNA structure (a pseudoknot) in the toro- and coronaviral frameshift-directing region is similar. Analysis of the amino acid sequence of the predicted BEV ORF1b translation product revealed homology with the ORF1b product of coronaviruses. Four conserved domains were identified: the putative polymerase domain, an area containing conserved cysteine and histidine residues, a putative helicase motif, and a domain which seems to be unique for toro- and coronaviruses. The data on the 3' part of the polymerase gene of BEV supplement previously observed similarities between toro- and coronaviruses at the level of genome organization and expression. The two virus families are more closely related to each other than to other families of positive-stranded RNA viruses.

Amino Acid Sequence↗
PubMed2004

An evolutionary model for protein-coding regions with conserved RNA structure.

Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume evolutionary independence between short nucleotide tuples. In our model we address this by replacing context dependencies within codons by annotation-specific heterogeneity in the substitution process. Through a general procedure, we fragment the alignment into sets of short nucleotide tuples based on both the protein coding and the structural annotation. These individual tuples are assumed to evolve independently, and the different tuple sets are assigned different annotation-specific substitution models shared between their members. This allows us to build a composite model of the substitution process from components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses concerning the relation of these effects. Of particular interest, we found evidence of a functional role of loop and bulge regions, as these were shown to evolve according to a different and more constrained selective regime than the nonpairing regions outside the RNA structures. Other potential applications of the model include comparative RNA structure prediction in coding regions and RNA virus phylogenetics.

Base Sequence↗
PubMed1991

Small cysteine-rich proteins of different groups of plant RNA viruses are related to different families of nucleic acid-binding proteins.

The 3'-terminal genes in genomic RNAs of four groups of plant positive strand RNA viruses (hordei-, furo-, tobra-, and carlaviruses) encode small proteins enriched in Cys residues. The arrangement of Cys and in some cases also His residues in these proteins is compatible with finger formation. A computer-assisted sequence comparison of viral Cys-rich proteins reveals no significant similarity between them. It is shown that the hordeivirus Cys-rich protein (17K) is related to a group of chloroplast tRNA intron-encoded proteins, whereas the respective furovirus protein (14K) is similar to E6 proteins of papillomaviruses. Somewhat less significant similarity, marked, however, by conservation of a number of positively charged residues, was observed between the sequences of tobravirus Cys-rich proteins and the basic domains of high mobility group chromatin proteins. It can be speculated that plant RNA virus Cys-rich proteins bind RNA and/or DNA and might be involved in regulation of virus and/or host genome expression. In the course of evolution these virus proteins may have originated from different nucleic acid-binding proteins.

Amino Acid Sequence↗
PubMed1992

Coat protein phylogeny and systematics of potyviruses.

The feasibility of applying molecular phylogenetic methods of analysis to aligned coat-protein sequences and other molecular data derived from coat proteins or genomic sequences of members of the proposed taxonomic family of Potyviridae, is discussed. We show that comparative sequence analysis of whole coat-protein sequences may be used reliably to differentiate between sequences of closely related strains, and to show groupings of more distantly related viruses; that coat proteins of putative Potyviridae cluster according to the proposed generic divisions, and, even if some are only very distantly related, the members of the family form a cluster distinct from coat proteins of other filamentous and rod-shaped viruses. Taxonomic revisions based on perceived evolutionary relationships, and the lack of feasibility of erecting higher taxa for these viruses, are discussed.

Amino Acid Sequence↗
PubMed2002

Strand transfer occurs in retroviruses by a pause-initiated two-step mechanism.

Recombination promotes retrovirus evolution. It involves transferring a growing DNA primer from one genomic RNA template in the virus to the other. Strand transfer results in vitro suggested that pausing of the reverse transcriptase during synthesis allows enhanced RNase H cleavage of the initial, or donor, RNA template that facilitates primer interaction with the acceptor template. Hairpins are common structures in retrovirus RNAs that induce pausing. Analyzing primer transfers in hairpins by base substitution markers showed transfer sites well beyond the site of pausing. We developed methods to distinguish the initial site of primer-acceptor template interaction from the site of primer terminus transfer. The strand transfer mechanism was confirmed to involve two steps. In the first, the acceptor template invades the primer-donor complex. However, the primer terminus continues elongation on the donor RNA. The interacting primer and acceptor strands then propagate by branch migration to catch the advancing primer terminus. Some distance downstream of the invasion site the primer terminus transfers, marking the genetic shift from donor to acceptor. Nucleocapsid protein (NC) is known to influence primer elongation and strand exchange. The presence of NC increased the efficiency of transfers but did not appear to alter the fundamental transfer mechanism.

Base Sequence↗