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PubMed1994

Reinfection with influenza B virus in children: analysis of the reinfection influenza B viruses.

Influenza B virus reinfection in Japanese children was studied epidemiologically during 1979-91 and virologically during 1985-91. During this investigation, there were four epidemics caused by influenza B viruses, each of which accompanied antigenic drift. Between the epidemics in 1987/88 and 1989/90, the viruses changed drastically, both genetically and antigenically. The minimum rate of reinfection with influenza B virus during the whole period was 3-25% depending on the influenza seasons. The antigens of primary and reinfection strains of influenza B virus isolated from 18 children during 1985-90, which covered three epidemic periods, were studied by haemagglutination inhibition tests. The results showed that the viruses isolated in the 1984/85 and 1987/88 influenza seasons, which belonged to the same lineage, were antigenically close, and reinfection occurred with these viruses. The results of amino-acid analysis of the HA1 polypeptide of these viruses corresponded with those of antigenic analysis. There were no specific amino-acid changes shared by the primary infection and reinfection influenza B viruses; the patients were infected with the viruses epidemic at that time.

Adolescent↗
PubMed1996

Targeting sites within HIV-1 cDNA with a DNA-cleaving ribozyme.

A variant of the Tetrahymena ribozyme that efficiently cleaves single-stranded DNA under simulated physiological conditions [Tsang, J., & Joyce, G. F. (1994) Biochemistry 33, 5966-5973] was evaluated as a potential therapeutic agent on the basis of its ability to cleave synthetic oligonucleotide substrates corresponding to conserved target sites within HIV-I cDNA. In order to increase the sequence selectivity of the ribozyme, its substrate recognition domain was extended from 6 to 12 nucleotides, allowing base pairing with substrate nucleotides that lie both upstream and downstream of the cleavage site. The sequence of the extended recognition domain could be changed to allow cleavage of a variety of different DNA targets. The ribozyme exhibited a high degree of sequence specificity, discriminating by a factor of 10(2) to more than 10(4) against substrates that form a single-base mismatch with the ribozyme's recognition domain. Mismatches that occurred close to the cleavage site led to a greater decrease in activity compared to those that occurred farther away.

Animals↗
PubMed1997

30 years later--a new approach to Sol Spiegelman's and Leslie Orgel's in vitro evolutionary studies. Dedicated to Leslie Orgel on the occasion of his 70th birthday.

The conditions necessary for evolution are amplification, mutagenesis and selection. Here we describe the evolutionary response of an in vitro replicating system to the selection pressure for fast growth and show what happens to the amplified molecules within this replication system. Our emphasis is on methodology, on the monitoring and the automation of experiments in molecular evolution. In order to perform in vitro studies on the evolution of RNA molecules, a modified self-sustained sequence replication (3SR) method was used. In the first step of the 3SR reaction, the RNA template is reversely transcribed by HIV-1 reverse transcriptase, followed by a second strand synthesis and the transcription of the resulting dsDNA by T7 RNA polymerase. The selection pressure (fast growth) was achieved by applying the principle of serial transfer pioneered in the laboratories of Sol Spiegelman and Leslie Orgel. At the end of the exponential growth phase of the 3SR reaction, an aliquot of the reaction mixture is transferred into a new sample containing only buffer, nucleotides and enzymes while RNA template molecules are provided by the transfer. The conditions in the exponential growth phase allow the RNA molecules to be amplified in a constant environment; all enzymes (HIV-1 reverse transcriptase and T7 RNA polymerase) and nucleotides are present in large excess. Therefore, transferring reproducibly within the exponential growth phase is equivalent to selecting for fast growth; those molecules which can replicate faster will displace others after several transfers. The experiments were performed using a serial transfer apparatus (STA) which allows the nucleic acid concentration to be monitored on-line by measuring the laser-induced fluorescence caused by intercalation of thiazole orange monomers into the RNA/DNA amplification products. The serial transfer experiments were carried out with an RNA template (220b RNA) that represents a 220-base segment of the HIV-1 genome and comprises the in vivo primer binding site (PBS) for the HIV-1 reverse transcriptase. It could be shown that after only two serial transfers two RNA species (EP1 and EP2) emerged that were much shorter. EP1 (48b) and EP2 (54b) were formed by deletion mutations within the original 220b RNA template in the very beginning of the serial transfer experiment; due to their higher replication rate (calculated from the growth curves derived on-line) these two deletion mutants displaced the original 220b RNA template in the course of the following thirty transfers. We assume that these two RNA species evolved independently of each other. Their formation was probably induced by a strand-transfer reaction of HIV-1 reverse transcriptase. Sequence analyses of these two evolution products seem to confirm such a presented pathway. 30 years after Spiegelman's experiment, the study described here is another answer to the question he posed: 'How do molecules evolve if the only demand is the biblical injunction: multiply?'. The answer, derived from a modified 3SR amplification system (mimicking a part of the HIV-1 replication cycle in vitro), is the same as thirty years ago: The RNA molecules adapt to the new conditions by throwing away any ballast not needed for fast replication. Clearly, this is only one aspect of molecular evolution; however, it shows that we should be careful in designating unidentified genetic material as 'junk DNA'.

Bacteriophage T7↗
PubMed1997

Evolutionary analysis of influenza C virus M genes.

The previous study of the 25 hemagglutinin-esterase (HE) glycoprotein genes of influenza C viruses identified four discrete lineages represented by C/Yamagata/26/81, C/Aichi/1/81, C/Aomori/74 and C/Mississippi/80, respectively. Here we compared the M gene sequence among the 24 viruses isolated between 1964 and 1991. A phylogenetic analysis showed that these genes have evolved into three distinct lineages. Lineage I included most of viruses with the HE genes of C/Yamagata/26/81-related lineage. The predominant members of lineage II were viruses having the HE genes of either C/Aichi/1/81- or C/Mississippi/80-related lineage. Lineage III contained only C/Aomori/74. Phylogenetic positions of several strains (C/Yamagata/64, C/Kanagawa/1/76, C/Miyagi/77 and C/Nara/1/85) were different between the M and HE gene trees, suggesting that they are reassortants. Furthermore, phylogenetic relationships between C/Mississippi/80-like and C/Aichi/1/81-like viruses were much closer for the M gene than the HE gene, raising the possibility that these two virus groups are genetically related by a reassortment event. Nucleotide changes in the M genes occurred at about 7% positions with a uniform distribution throughout the molecules. However, the predicted amino acid sequence of the matrix protein (M1) was conserved almost completely among the isolates analyzed. The amino acid sequence of the second protein (CM2) encoded by M gene was also highly conserved, but was more divergent than the M1 protein sequence, suggesting that the two M gene products are evolving differently in response to selective pressures or structural and functional constraints.

Amino Acid Sequence↗
PubMed1998

Arenavirus phylogeny: a new insight.

Arenaviridae is a worldwide distributed family, of enveloped, single stranded, RNA viruses. The arenaviruses were divided in two major groups (Old World and New World), based on serological properties and genetic data, as well as the geographic distribution. In this study the phylogenetic relationship among the members of the Arenaviridae was examined, using the reported genomic sequences. The comparison of the aligned nucleotide sequences of the S RNA and the predicted amino acid sequences of the GPC and N proteins, together with the phylogenetic analysis, strongly suggest a possible kinship of Pichindé and Oliveros viruses, with the Old World arenavirus group. This analysis points at the evolutive relationships between the arenaviruses of the Americas and can be used to evaluate the different hypotheses about their origin.

Arenavirus↗
PubMed2001

Spike gene analysis of the DE072 strain of infectious bronchitis virus: origin and evolution.

The entire S2 gene of the DE072 strain of infectious bronchitis virus (IBV) was sequenced. The nucleotide and amino acid sequence was most similar to the D1466 strain and was 84.8% and 89.9% identity, respectively. The nucleotide and amino acid sequence similarity among the DE072 strain and other IBV strains was less than 71.9% and 76.6%, respectively. Phylogenetic analysis, based on both nucleotide and amino acid sequence, showed that IBV isolates were divided into two distinct groups. The DE072 strain clustered only with the D1466 strain, and all of the other strains were distinct from those two viruses. Further the nucleotide sequence analysis of the entire spike glycoprotein gene of the DE072 strain demonstrated that most of the gene contained a D1466-like sequence, and five putative cross-over sites were identified. Based on cross-over site, phylogenetic trees were constructed for different regions of the spike gene, and a difference in topology between these trees was observed. Considering the difference in S2 gene sequence identity and tree topology, we assume that DE072 and D1466 viruses share a different origin from other isolates of IBV. Furthermore, entire spike gene analysis indicates that the DE072 strain has undergone recombination event as well as extensive antigenic variation.

Amino Acid Sequence↗
PubMed2001

Satsuma dwarf and related viruses belong to a new lineage of plant picorna-like viruses.

Satsuma dwarf virus (SDV) and two closely related viruses, Citrus mosaic (CiMV), and Naval orange infectious mottling (NIMV), seriously affect citrus varieties grown in Japan and East Asia. All three viruses have icosahedral particles built of two proteins encapsidating two single-stranded genomic RNAs. The natural mode of transmission of these SDV-like viruses is unknown, and they were previously placed among tentative members of the family Comoviridae. Recently, a complete genome of SDV was sequenced, and its replication-related proteins were found only distantly related to those of viruses from the family Comoviridae (Iwanami T., Kondo Y., and Karasev A.V. J Gen Virol 80, 793-797, 1999). Here we present a partial genome sequence for another SDV-like virus, NIMV, and a thorough phylogenetic analysis of the gene products encoded by SDV, CiMV, and NIMV to assess their relationships with picorna-like viruses infecting plants, insects, and vertebrates. The RdRp's of SDV-like viruses form a new lineage, separate from members of Como- and Sequiviridae families. Phylogenetic analysis suggests that SDV-like viruses may represent a new family of plant picorna-like viruses. Sequence analysis of the capsid proteins (CPs) encoded by the SDV-like viruses revealed a region of similarity to CPs of animal calici- and picornaviruses that encompasses the structural core of the eight-strand beta-barrel characteristic of picornaviral CPs. These data suggest that SDV and related bipartite viruses evolved separately from the viruses in the family Comoviridae and that the split of an ancestor, monopartite picorna-like virus genome might have occurred more than once.

Amino Acid Sequence↗
PubMed2001

Complete genome sequence of transmissible gastroenteritis coronavirus PUR46-MAD clone and evolution of the purdue virus cluster.

The complete sequence (28580 nt) of the PUR46-MAD clone of the Purdue cluster of transmissible gastroenteritis coronavirus (TGEV) has been determined and compared with members of this cluster and other coronaviruses. The computing distances among their S gene sequences resulted in the grouping of these coronaviruses into four clusters, one of them exclusively formed by the Purdue viruses. Three new potential sequence motifs with homology to the alpha-subunit of the polymerase-associated nucleocapsid phosphoprotein of rinderpest virus, the Bowman-Birk type of proteinase inhibitors, and the metallothionein superfamily of cysteine rich chelating proteins have been identified. Comparison of the TGEV polymerase sequence with that of other RNA viruses revealed high sequence homology with the A-E domains of the palm subdomain of nucleic acid polymerases.

Amino Acid Sequence↗
PubMed2002

Sequence similarities and evolutionary relationships of influenza virus A hemagglutinins.

This study brings the analysis of amino acid sequences of hemagglutinin (HA) from the influenza virus A that can infect a wide variety of birds and mammals. 191 sequences belonging to all known 15 HA subtypes were compared. The emphasis was given on functional sites (receptor-binding cavity with its right and left edges) and degree of their conservation in each subtype. Three evolutionary trees of 15 avian HA representatives were constructed: one tree based on the alignment of the entire HA sequences and two trees based on the alignment of HA1 and HA2 chains, respectively. The results have shown that, despite low degree of sequence similarity among the 191 sequences of HA1 subunit, the active site is well conserved, and that there are only marginal differences in the clustering of the individual HA subtypes between the two subunit trees. In this respect, the subtype H9 seems to be the most fluctuating example. The proposals of the probable avian HAs that could be the closest relatives to human (mammalian) HAs were also provided for several HA subtypes.

Amino Acid Sequence↗
PubMedDate not supplied

[A new KIAA1245 gene family with or without HERV-K LTRs in their introns].

A transcript containing the long terminal repeat (LTR) and the sequence homologous to the KIAA1245 mRNA fragment were revealed among the transcribed LTRs of human endogenous viruses of the K family in normal and tumor tissues. Ten other sequences with a high level of homology to the KIAA1245 mRNA were found in the GenBank. The intron-exon structures were determined for all the sequences, and their exon sequences were compared. The comparison showed that they differ both in the extent of the exon homology and in the presence or absence of the HERV-K LTR in the third intron. The revealed sequences form a new gene family that comprises at least four subfamilies. Two of these subfamilies have the LTR, and the other two do not. We showed by PCR that the LTR was integrated into the introns after the divergence of the orangutan evolutionary branch from other hominoids but before the divergence of the gorilla branch, i.e., 8-13 million years ago. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.

Animals↗
PubMed2002

Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains.

A total of 199 serum samples from patients with measles collected in Denmark, Greenland and the Faroe Islands from 1964 to 1983 were analysed by PCR. Measles virus (MV) RNA could be detected in 38 (19%) of the samples and a total of 18 strains were subjected to partial sequence analysis of the hemagglutinin gene. The strains exhibited a considerable genomic diversity, which is at odds with the assumption that one genome type prevailed among globally circulating MV strains prior to the advent of live-attenuated vaccines. Our data indicate that the similarity of the various vaccine strains is attributed to their having originated from the same primary isolate. Consequently, it is implied that a small number of clinical manifestations of MV worldwide from which strains similar to the vaccine strain were identified were vaccine related rather than being caused by members of a persistently circulating ancient genome type. The Danish pre- and early-vaccination era MV strains seem to change the evolutionary spectrum of genome types A, C2 and E into one coherent group, suggesting that the genome types of MV strains circulating in the world at present do not represent far ranging evolutionary lineages but merely members of an evolutionary continuum of pre-vaccination era MV strains which by chance or due to an improved capability survived the worldwide partial herd immunity accomplished through vaccination.

Child↗
PubMedDate not supplied

Mode of proviral activation of a putative mammary oncogene (int-1) on mouse chromosome 15.

Most mammary carcinomas induced in C3H mice by the mouse mammary tumour virus (MMTV) bear a new proviral insertion within a highly conserved locus on chromosome 15 called int-1. A transcriptional unit within this locus is inactive in all tested normal tissues but expressed at low levels in mammary tumours with proviral insertions positioned on either the 5' and 3' sides of the gene. Transcription of the proviruses proceeds away from int-1; thus an indirect mechanism appears to activate expression of this putative oncogene.

Animals↗
PubMedDate not supplied

Nucleotide sequence evidence for relationship of AIDS retrovirus to lentiviruses.

Lentiviruses are a subfamily of retroviruses which have been aetiologically linked to the induction of arthritis, encephalitis, progressive pneumonia and slow neurological diseases in certain species. Relatively little is known about their genome structure, mechanisms of pathogenesis or evolutionary relationships with other retroviral subfamilies. In an effort to understand better the mechanisms by which these viruses induce such a variety of chronic diseases, we have molecularly cloned and physically characterized the genomes of caprine arthritis-encephalitis virus (CAEV) and equine infectious anaemia virus (EIAV) (A.Y. et al., in preparation). The latter, which bears some morphological similarity to the lentiviruses, has yet to be classified definitively as one. Here, we have determined the nucleotide sequence of a highly conserved region within the CAEV and EIAV pol genes. We demonstrate a much closer relationship of their predicted pol gene products to that of the presumed aetiological agent of human acquired immune deficiency syndrome (AIDS) than to those of other retroviruses. Additional pairwise comparisons allowed us to generate an evolutionary tree showing that the pol genes of lentiviruses and oncoviruses have evolved from a common progenitor.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

CpG-rich islands and the function of DNA methylation.

It is likely that most vertebrate genes are associated with 'HTF islands'--DNA sequences in which CpG is abundant and non-methylated. Highly tissue-specific genes, though, usually lack islands. The contrast between islands and the remainder of the genome may identify sequences that are to be constantly available in the nucleus. DNA methylation appears to be involved in this function, rather than with activation of tissue specific genes.

Animals↗