PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “genome segmentation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
PubMed2001

Direct evidence for genome segment reassortment between concurrently-circulating human rotavirus strains.

Extensive heterogeneity in electropherotypes observed among group A human rotaviruses has been considered as a result of two major mechanisms; i.e., the accumulation of point mutations and genetic reassortment between concurrently-circulating strains. However, no evidence was reported thus far indicating that any one of field isolates of rotavirus was formed by direct reassortment of concurrently circulating two parental strains. Comparison of the genome of human rotavirus specimens collected over a six year period by electropherotyping and by the sequencing of selected gene segments identified two reassortants that were generated in nature between strains circulating co-dominantly in the same epidemic season. This is the first report directly showing that at least some part of electrophoretic diversity observed among rotavirus strains was explained by genetic reassortment between strains concurrently circulating in the human population. This supports the hypothesis that genetic reassortment among co-circulating strains operates as a key mechanism for the genetic variability of rotaviruses in nature.

Base Sequence↗
PubMed1996

Coding sequences of both genome segments of a European 'very virulent' infectious bursal disease virus.

The sequences of segment A (encoding the VP2-VP4-VP3 polyprotein and VP5) and segment B (encoding VP1) of a recent, 'very virulent' (VV) European isolate (UK661) of infectious bursal disease virus (IBDV), a birnavirus, have been determined. There are 26 to 36 amino acid substitutions compared to any other type I IBDV within the segment A polyprotein (of these, 15 are unique) and about 50 substitutions within VP1 (of which 16 are unique). There is more variation compared to classical and antigenic variant viruses, of both virulent and attenuated phenotype, in VP1, VP3 and VP4 than in VP2, even though the latter has previously been identified as the most variable protein between different strains of type I IBDV. In VP3 and VP4, UK661 is the most diverged type I IBDV. Thus the origin of the virus is unclear. It is possible that strong functional constraints have preferentially maintained the primary structure of VP2, though the possibility of recombination cannot be excluded. There are no clear candidate mutations to account for the enhanced virulence of the VV IBDV. Polymerase motifs are well conserved in VP1 but there is an amino acid substitution next to the predicted active-site serine of the viral protease (VP4). In addition, there is a conservative substitution close to the postulated VP2-VP4 cleavage site. It is also now apparent that sequences of IBDV segment B (the segment encoding the RNA polymerase) do not group according to serotype (specified by the capsid proteins encoded on segment A), indicating that segment reassortment has occurred.

Amino Acid Sequence↗
PubMed1987

Mapping of the large RNA genome segment of infectious pancreatic necrosis virus by hybrid arrested translation.

Segment A, the larger dsRNA segment of IPNV which encodes three of the four virus-coded polypeptides (preVP2, VP3, and NS) was cloned and physically mapped. The plus and minus RNA strands of the virus genome were separated and the A+ and B+ RNA strands were identified. A nested set of cDNA subclones, coterminal with the 5' end of A+ RNA, were used in hybrid arrested translation experiments. Hybrid arrest conditions which blocked the 5' two-thirds of A+ RNA allowed the in vitro synthesis of only VP3, while hybridization of the RNA to cDNA representing the 5' half of A+ RNA allowed the synthesis of both NS and VP3 but not of preVP2. In vitro translation of A+ RNA yielded all three polypeptides. It is, therefore, concluded that the order of the three polypeptides on A+ RNA is 5'-preVP2-NS-VP3-3'. These results imply that internal initiation of translation could take place on the RNA at least in vitro at sites located hundreds of nucleotides downstream from the first in-phase AUG codon near the 5' end.

Animals↗
PubMed1996

Defective RNAs inhibit the assembly of influenza virus genome segments in a segment-specific manner.

Four avian influenza viruses have been generated, each containing a single extra defective RNA segment in addition to the eight standard segments. Three of the extra RNAs were derived from segment 1 and the fourth from segment 2. Chick embryo fibroblast cells were infected with each virus, and a wild-type virus. Virus RNA was quantified in extracts of virus-infected cells and in virus released by 10 hr postinfection using reverse transcription and by Northern blot analysis. In the case of two of the viruses the presence of the defective RNA did not markedly affect the accumulation of virus RNA within the infected cell, but significantly and selectively reduced the amount of the "parent" segment in released virus. This effect was reduced in a third virus. In a fourth virus, defective RNA was found to be present at a low-input multiplicity and results were varied. Mixed infections of one of the viruses with a closely related wild-type virus resulted in reduction of the corresponding vRNA segment of the nondefective virus. We conclude that assembly of influenza virus segments is not a purely random process.

Animals↗
PubMed1990

Diagnostic complementary DNA probes for genome segments 2 and 3 of epizootic hemorrhagic disease virus serotype 1.

Potential diagnostic complementary DNA (cDNA) clones of gene segments 2 and 3 from epizootic hemorrhagic disease virus serotype 1 (EHDV-1) have been produced. Individual segments of EHDV-1 were isolated, denatured with methylmercury hydroxide, and polyadenylated. The polyadenylated RNA was reverse-transcribed and self-hybridized into duplex structures, and the incomplete ends were repaired. The resulting product was then cloned into the plasmid vector pBR322, using the complementary tailing method. Two clones, 1 from segment 2 (E1-2-10) and 1 from segment 3 (E1-3-16) were isolated, colony-purified, and characterized by cDNA/RNA blot hybridization and endonuclease restriction analysis. The cDNA clones of RNA segment 3 of EHDV-1 cross hybridized with the corresponding segment of EHDV serotype 2 by results of cDNA/RNA blot hybridization, but not with RNA of bluetongue virus serotypes isolated in the United States. After cDNA/RNA dot-blot hybridization analysis of 17 EHDV field strains, the segment-2 clone was found to be serotype-specific, whereas the segment-3 clone was serogroup-specific.

Animals↗
PubMed2003

Sequence analysis of both genome segments of two very virulent infectious bursal disease virus field isolates with distinct pathogenicity.

The deduced amino acid sequences of segment A and B of two very virulent Infectious bursal disease virus (vvIBDV) isolates, UPM94/273 and UPM97/61 were compared with 25 other IBDV strains. Twenty amino acid residues (8 in VP1, 5 in VP2, 2 in VP3, 4 in VP4, 1 in VP5) that were common to vvIBDV strains were detected. However, UPM94/273 is an exceptional vvIBDV with usual amino acid substitutions. The differences in the divergence of segment A and B indicated that the vvIBDV strains may have been derived from genetic reassortment of a single ancestral virus or both segments have different ability to undergo genetic variation due to their different functional constraints.

Amino Acid Sequence↗
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↗
PubMed1997

Completion of molecular characterization of Toscana phlebovirus genome: nucleotide sequence, coding strategy of M genomic segment and its amino acid sequence comparison to other phleboviruses.

The M RNA segment of Toscana (TOS) phlebovirus was cloned and the complete nucleotide sequence determined. The M RNA segment is 4215 nucleotides in length, and it contains a single major open reading frame (ORF) in the viral-complementary sequence, between nucleotides 18 and 4034, which can encode for a polyprotein of 1339 amino acids (Mr 149 kDa). The viral segment is expressed via a unique mRNA containing 10-14 non-templated nucleotides at the 5' end and it is truncated at the 3' end by about 140 nucleotides in a purine-rich region. In M predicted amino acid sequences, several hydrophobic regions have been identified. They could function as a signal sequence or a transmembrane region for the different proteins. Comparison of the deduced amino acid sequence of M precursor product revealed 38, 36, and 25% identity and 58, 56, and 47% similarity with those of Rift Valley fever (RVF), Punta Toro (PT) and Unkuniemi (UUK) viruses, respectively. Residues conserved among the proteins are mainly located at the COOH-portion of the precursor, while the major divergence is in the NSm coding regions. Based on sequence comparison and similarity of hydropathic pattern of TOS M segment with other phleboviruses the N-termini of TOS GN and GC glycoproteins were placed at residues 297 and 936 of the precursor.

Amino Acid Sequence↗
PubMedDate not supplied

[Production of full length DNA copies of genomic segments of influenza virus using DNA recombination in the process of polymerase chain reaction].

The case study comprises a description of a method used for producing the full-length cDNA complementary to influenza virus segments made through the recombination of homologous DNA fragments in the process of polymerase chain reaction (PCR). The detailed protocol of the method is presented alongside with a discussion of the advantages of the suggested approach.

Base Sequence↗
PubMed2004

DNM1DN: a new class of paralogous genomic segments (duplicons) with highly conserved copies on chromosomes Y and 15.

Screening a testis cDNA selection library for Y-linked genes yielded 79 cDNAs. Of these, 9 matched the 3' region of the dynamin 1 gene (DNM1) on chromosome 9q34 with >90% identity. Fluoresence in situ hybridisation and PCR amplification were used to localise a large number of DNM1-like sequences to human chromosomes 15 and Y. PCR amplification of overlapping Y-linked YACs allowed a more accurate mapping of the Y-linked DNM1-like cDNAs to a euchromatic locus in close proximity to heterochromatin at Yq11.23. A search of the genome database identified 64 highly homologous copies of the DNM1 fragment. Most of these copies were localised to chromosomes 15 and Y, but others mapped to chromosomes 5, 8, 10, 12, 19 and 22. These sequences exhibit all the major features of a duplicon and have been designated DNM1DN (DNM1 duplicon). Evolutionary studies using fluorescence in situ hybridisation indicate that transposition of the DNM1DN sequence to chromosome 15 took place earlier in primate evolution than the transposition to the Y chromosome. The translocation to the Y took place at a time following the divergence of a common ancestor from gorilla, approximately 4-7 million years ago.

Animals↗
PubMed2003

Unique properties of the inner core of bacteriophage phi8, a virus with a segmented dsRNA genome.

The inner core of bacteriophage phi8 is capable of packaging and replicating the plus strands of the RNA genomic segments of the virus in vitro. The particles composed of proteins P1, P2, P4, and P7 can be assembled in cells of E. coli that carry plasmids with cDNA copies of genomic segment L. The gene arrangement on segment L was found to differ from that of other cystoviruses in that the gene for the ortholog of protein P7 is located at the 3' end of the plus strand rather than near the 5' end. In place of the normal location of gene 7 is gene H, whose product is necessary for normal phage development, but not necessary for in vitro genomic packaging and replication. Genomic packaging is dependent upon the activity of an NTPase motor protein, P4. P4 was purified from cell extracts and was found to form hexamers with little NTPase activity until associated with inner core particles. Labeling studies of in vitro packaging of phi8 RNA do not show serial dependence; however, studies involving in vitro packaging for the formation of live virus indicate that packaging is stringent. Studies with the acquisition of chimeric segments in live virus indicate that phi8 does package RNA in the order s/m/l. The inner core of bacteriophage phi8 differs from that of its relatives in the Cystoviridae in that the major structural protein P1 is able to interact with the host cell membrane to effect penetration of the inner core into the cell.

Adenosine Triphosphatases↗
PubMed1997

Organization of the M genomic segment of Toscana phlebovirus.

The nucleotide sequence of the Toscana (TOS) virus M RNA segment contains a single major open reading frame in the viral-complementary sequence, which can encode a polyprotein of 1339 amino acids. To map the TOS M segment product(s), different regions of the putative M polypeptide were expressed as glutathione S-transferase fusion proteins, which were purified and inoculated into mice to produce hyperimmune sera. By Western blot analysis, a protein of approximately 30 kDa and two glycoproteins, G1 and G2, with the same molecular mass (approximately 65 kDa) were identified in TOS virus-infected cells. The 30 kDa protein, which reacted with antibodies raised to the NH2-terminal, was found to be a non-structural protein (designated NSm). By immunoprecipitation analysis of TOS virus-infected cell lysates, both treated or untreated with tunicamycin, the relative positions of glycoproteins G1 and G2 were determined. The gene order, with respect to the genomic M RNA, was found to be 3' NSm-G1 -G2 5'

Animals↗
PubMed1999

Deletion of a large genomic segment in tobacco varieties that are resistant to potato virus Y (PVY).

Recessive alleles (va, va1, va2, etc) of the tobacco Va locus confer resistance to potato virus Y (PVY). To elucidate the mechanism underlying this resistance, we attempted to identify randomly amplified polymorphic (RAPD) markers that reveal polymorphism between two nearly isogenic lines (NILs) that differ in their susceptibility to PVY. Using each of 500 primers and 800 pairs of primers, we identified over 100 RAPD fragments that differed between the NILs. We applied these RAPD primers or primer combinations to an F2 population obtained from a cross between the susceptible line BY4 and the resistant va2-bearing NIL, F55. It was found that only 10 RAPD markers were polymorphic between resistant and susceptible plants. Unexpectedly, these markers were all linked to Va. All 10 RAPD markers were present in all 8 susceptible varieties tested. At least one RAPD marker was not detected in 8 out of 10 resistant varieties. Southern analysis revealed that the sequences of markers were not present in the genomes of resistant varieties, and the markers were found in individually distinct positions on the chromosomes of susceptible tobacco varieties. These results strongly suggest that the resistance conferred by va is due to deletions at the Va locus governing susceptibility to PVY.

Base Sequence↗
PubMed2001

The avian reovirus genome segment S1 is a functionally tricistronic gene that expresses one structural and two nonstructural proteins in infected cells.

The avian reovirus S1 gene contains three partially overlapping, out-of-phase open reading frames (ORFs) that the highly conserved in all avian reovirus strains examined to date. The three S1 ORFs of the avian reovirus strain S1133 were individually expressed in bacterial cells, and their purified translation products used as antigens to raise specific polyclonal antibodies. With these antibodies we were able to demonstrate that all three S1 ORFs from different avian reovirus strains are translatable in infected cells. Proteins p10 and p17, which are specified by ORF1 and ORF2, respectively, are nonstructural proteins which associate with cell membranes, whereas ORF3 directs the synthesis of protein sigma C, a structural oligomeric protein responsible for cell attachment. While intracellular synthesis of protein sigma C was demonstrated a long time ago and that of protein p10 was reported recently, this is the first time that expression of the S1 ORF2 has been demonstrated experimentally. Thus, the previously reported coding capacity of the avian reovirus genome is now expanded to 14 proteins, of which ten are structural (lambda A, lambda B, lambda C, microA, microB, microBC, microBN, sigma A, sigma B, and sigma C) and four are nonstructural (microNS, sigma NS, p17, and p10). Finally, protein p10, but not p17 or sigma C, induces cell-cell fusion when transiently expressed in mammalian cells, supporting a previously published observation that the polypeptide encoded by the S1 ORF1 plays an important role in the syncytial phenotype displayed by avian reoviruses.

Animals↗
PubMed1993

Nucleotide and deduced amino acid sequences of the M and S genome segments of two Puumala virus isolates from Russia.

Hemorrhagic fever with renal syndrome (HFRS) is caused by viruses in the Hantavirus genus, family Bunyaviridae. Three serologically distinct hantaviruses, Hantaan, Seoul and Puumala viruses, are known to cause HFRS. We report here, for the first time, gene sequences of two human Puumala virus isolates, P360 and K27, obtained in an HFRS endemic region of the former Soviet Union. We compared the nucleotide sequences and the derived amino acid sequences of their gene products to a Puumala virus isolate from rodents.

Amino Acid Sequence↗
PubMed1992

Sequence of genome segment 9 of bluetongue virus (serotype 1, South Africa) and expression analysis demonstrating that different forms of VP6 are derived from initiation of protein synthesis at two distinct sites.

Bluetongue virus (BTV) VP6 is often resolved into two closely migrating bands by SDS-PAGE (VP6 and VP6a). RNA segment 9 of BTV-serotype 1 South Africa (encoding VP6) has been cloned as cDNA, and the complete sequence has been determined. Expression of this clone both in vitro and in tissue culture produced the same polypeptide doublet as seen previously in extracts from BTV-infected cells. Modification of the cDNA, including the removal of the first initiation codon, demonstrated that the two forms of VP6 are derived from initiation of protein synthesis at two distinct sites and not by post-translational modification.

Amino Acid Sequence↗
PubMed1993

Generation of reovirus core-like particles in cells infected with hybrid vaccinia viruses that express genome segments L1, L2, L3, and S2.

When mouse L fibroblasts are infected with various combinations of recombinant vaccinia viruses possessing thymidine kinase (TK) genes with inserted reovirus genes that encode core components, particles are formed that closely resemble reovirus cores. In cells infected with vaccinia viruses that express reovirus proteins lambda 1 and sigma 2, particles are formed that are very similar to reovirus core shells; if, in addition, the cells are also infected with vaccinia virus that expresses protein lambda 2, particles are formed that also possess the characteristic icosahedrally located projections/spikes that are present on reovirus cores. If, in either case, the cells are also infected with vaccinia virus that expresses the reovirus RNA polymerase, protein lambda 3, the resultant particles are morphologically identical with those formed in its absence, but also contain protein lambda 3.

Animals↗