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 19 recordsLinked to original sources
PubMed1976

A provisional classification of cytoplasmic polyhedrosis viruses based on the sizes of the RNA genome segments.

The RNA genome segments of thirty-three isolates of cytoplasmic polyhedrosis viruses (CPVs) were examined by polyacrylamide gel electrophoresis. Major differences were observed in the gel profiles of the RNA segments from many of the viruses; differences which were reinforced by polyacrylamide gel electrophoresis of the virus structural proteins. As a result of these studies, a provisional classification scheme for CPVs is proposed, where viruses with similar RNA gel profiles are included within the same 'type', while isolates differing in the molecular weights of most, or all of the RNA segments are assigned to different types. Using this system, eleven distinct CPV types were recognized. All eleven CPV types, like reoviruses, probably contain ten segments of RNA with a toatl mol. wt. of approx. 15 X 10(6).

Electrophoresis, Polyacrylamide Gel↗
PubMed2025

Combinatorial genome engineering of pseudorabies virus Bartha by developing a reverse genetic system based on three overlapping genomic segments.

INTRODUCTION: The 138-kilobase genome of pseudorabies virus vaccine strain Bartha K61 harbors many nonessential genes for replication and exhibits remarkable capacity for incorporating foreign genes for therapeutic applications. However, the large size of the Bartha genome complicates its efficient engineering. OBJECTIVES: Development of a reverse genetic system for pseudorabies virus Bartha based on three overlapping genomic segments to facilitate multiplex genome engineering. METHODS: The 138-kb genome of Bartha was split into three overlapping segments (42 kb, 43 kb, and 53 kb), each cloned in a bacterial artificial chromosome (BAC) to facilitate genome engineering. The infectious virus was reconstituted by transfecting the 3 genomic fragments released from the BACs into Vero cells in which a complete virus genome was assembled using 2-kb overlaps between adjacent pieces. RESULTS: Employing the reverse genetic system, we individually deleted 15 candidate nonessential genes and confirmed that 10 were dispensable for viral growth in cell culture. Deletion of 7 nonessential genes had no impact on viral growth, whereas UL47 deletion reduced viral growth rate and deletions of UL44, UL47, or US3 resulted in smaller viral plaques. A total of 45 viral genomes with double deletions of nonessential genes were constructed, among which 22 were successfully rescued into infectious virions. Fifteen double-deletion mutant viruses had a viral titer comparable with the wild-type Bartha, while the remaining 7 showed a lower titer. Additionally, expressions of the mNeonGreen reporter gene at nonessential gene loci were evaluated. Cells infected with recombinant viruses carrying mNeonGreen at 8 loci showed strong green fluorescence, whereas those with mNeonGreen at 2 loci exhibited very weak fluorescence. CONCLUSION: The reverse genetic system developed in this study enables rapid and combinatorial engineering of viruses with the large DNA genome, and will accelerate development of large DNA virus-based therapeutics including live-attenuated vaccines, vector vaccines, and oncolytic herpesviruses.

Herpesvirus 1, Suid↗
PubMed1979

A new method for the size estimation of the RNA genome segments of influenza virus.

Previous estimates of the size of the RNA genome segments of influenza virus have been unreliable because of a lack of suitable RNA species as size markers. We have attempted to overcome this problem by utilising the ability of AMV reverse transcriptase to synthesise full length DNA copies of RNA molecules in the presence of a suitable primer. By comparing such DNA copies of the RNA segments of the influenza virus genome with sequenced restriction fragments from the E. coli plasmid pBR322, we have made more reliable estimates of the sizes of the eight genome segments from influenza virus A/NT/60/68.

Avian Myeloblastosis Virus↗
PubMed2025

Orthobunyavirus neurovirulence is a complex trait involving all three genome segments.

La Crosse orthobunyavirus (LACV) is a tri-segmented negative sense RNA virus and is the leading cause of pediatric arboviral encephalitis in the USA. The viral factors that mediate LACV's ability to replicate and cause damage and disease in the brain (neurovirulence) are not fully understood. We previously characterized the neurovirulence of LACV and closely related Inkoo virus (INKV) and discovered they have opposing neurovirulence phenotypes in mice and human neuronal cells: LACV has high neurovirulence and INKV has low neurovirulence. We therefore generated reassortant viruses between LACV and INKV to map the genome segments that mediate LACV's high neurovirulence phenotype. We recovered all six possible reassortant viruses of the L, M, and S genome segments using coinfection and reverse genetics approaches. We evaluated the neurovirulence of these reassortant viruses in mice in vivo and in human neuronal cells in vitro. Our results show that no single LACV genome segment alone was sufficient to cause wildtype LACV-like neurological disease in mice, and in fact all six reassortant viruses were attenuated from wildtype LACV. We found that the LACV M and S segments together were the primary drivers of neurological disease in mice, whereas the LACV L segment played a minor role. Our in vitro results indicate that the LACV M segment is crucial for efficient replication in neurons, but the LACV L segment appears to mediate slightly more efficient neuronal replication than the INKV L segment. The LACV M and S segments together induced wildtype LACV-like levels of neuronal death, indicating the LACV M and S are the primary mediators of neuronal death, and the L segment is not required. Together, these results indicate that LACV neurovirulence is a complex trait mediated by viral proteins on all three genome segments.

Journal Article↗
PubMed1979

Polymorphism of the migration of double-stranded RNA genome segments of reovirus isolates from humans, cattle, and mice.

A series of 94 isolates of reovirus from humans, cattle, and mice, showed extensive variability in the patterns of migration of the ten double-stranded RNA genome segments. This variation was found in all three serotypes, and involved all ten genome segments, including the segment responsible for serological specificity. Although a single pattern was present among several samples isolated from individuals and collected at a single time and place, there were often multiple genetic variants of a single serotype present in a population. Samples isolated from widely different geographic origins or different mammalian hosts showed different patterns; samples from a single species from the same area over a period of time showed more limited variations. Among most isolates, the migration of the slowest S segment, the segment that encodes the hemagglutinin and is responsible for serological specificity in laboratory strains, was similar to reference strains for type 1 and type 3 isolates. However, the type 2 isolates showed considerable variation in this segment.

Anal Canal↗
PubMed1979

5' and 3' terminal nucleotide sequences of the RNA genome segments of influenza virus.

EXtensive nucleotide sequence analysis of the 5' and the 3' terminal of the RNA segments of the genome of fowl plague virus, an avian strain of influenza virus, confirms the presence of a common sequence at the 5' terminus of each segment and a common sequence at the 3' terminus of each segment. Between the ends of each individual segment there is a complementary sequence which may be important in the control of transcription and replication of the genome. In addition, the probable sites of initiation of translation of fowl plague virus mRNA are indicated along with the corresponding NH2-terminal amino acid sequences of the virus polypeptides.

Base Sequence↗
PubMed2025

ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.

MOTIVATION: Tumor viruses account for ∼10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as viral oncogene dose may impact the disease course. To our knowledge, no tool has been proposed to assess the intra-viral copy number alterations that define the gene dose of viral oncogenes and associated suppressive pathways native to the pathogen's normal life cycle. RESULTS: We propose an R package, "ELViS," that analyzes viral copy number changes from DNA sequencing of whole viral genomes. The method adjusts for viral load with 2D transformation and segmentation to offer the relative viral gene doses. AVAILABILITY AND IMPLEMENTATION: The ELViS R package is available from https://bioconductor.org/packages/ELViS. This article used controlled access data from dbGaP (phs001713.v1.p1).

Software↗
PubMed2026

Ramu stunt virus genome reveals previously unreported segments and nucleocapsid domain duplication in Mechlorovirus.

Ramu stunt virus (RmSV), a member of the genus Mechlorovirus within the family Phenuiviridae, was previously described as a six-segmented RNA virus infecting sugarcane. In this study, we re-examined type material and additional isolates using high-throughput sequencing and RT-PCR validation, revealing that RmSV possesses a nine-segmented genome, making it the largest reported in the Phenuiviridae. This expanded architecture includes duplicated RNA segments (RNA 2a and RNA 2b) encoding nucleocapsid-like proteins and two novel segments (RNA 7 and RNA 8). Comparative analysis showed that RNA 2a and 2b share about 84% amino acid identity, while RNA 5 encodes a third nucleocapsid homolog, indicating unprecedented domain redundancy. Structural modeling confirmed that all three nucleocapsid proteins maintain a conserved fold despite low sequence identity, with electrostatic mapping suggesting differential RNA-binding potential. Additionally, RNA 6 encodes a hypothetical protein structurally similar to the rice stripe virus disease-specific S-protein, implicating a role in symptom development. Transcript abundance analysis revealed RNA 6 as the most highly expressed segment across isolates. These findings revise the genomic composition of RmSV, highlight mechanisms of genome plasticity and adaptive evolution in plant-infecting bunyaviruses, and underscore practical implications for diagnostic assay design, resistance breeding, and biosecurity surveillance.

Genome, Viral↗
PubMed1979

The smallest genome RNA segment of influenza virus contains two genes that may overlap.

The genome of influenza virus consists of eight segments of single-stranded RNA, each of which encodes a different polypeptide. In addition to the eight recognized gene products, the virus specifies a distinct smaller nonstructural polypeptide (NS2), which is translated from a separate species of virus-specific mRNA. The location on the virus genome of the gene encoding this polypeptide was investigated by hybridization of the NS2 mRNA with isolated subgenomic RNA species, and by correlation of the inheritance of a strain-specific NS2 with inheritance of particular genome RNA segments during recombination between two different virus strains. The genetic information for NS2 was found to reside in the smallest genome RNA segment of the virion, which also encodes the NS1 polypeptide. Considering the sizes of the molecules involved, it is likely that the coding sequences for the two polypeptides overlap.

Genes, Viral↗
PubMed1977

Molecular basis of reovirus virulence: role of the S1 gene.

A genetic approach has been used to define the molecular basis for the different patterns of virulence and central nervous system cell tropism exhibited by reovirus types 1 and 3. Intracerebral inoculation of reovirus type 3 into newborn mice causes a necrotizing encephalitis (without ependymal damage) that is uniformly fatal. Animal inoculated with reovirus type 1 generally survive and may develop epedymal cell damage (without neuronal necrosis) and hydrocephalus. Using recombinant clones derived from crosses between reovirus types 1 and 3, we have been able to determine that the S1 genome segment is responsible for the differing cell tropism of reovirus serotypes and is the major determinant of neurovirulence. The type 1 S1 genome segment is responsible for ependymal damage with subsequent hydrocephalus; the type 3 S1 genome segment is responsible for neuronal necrosis and neurovirulence. We postulate that these differences are due to the specific interaction of the sigma1 outer capsid polypeptide (the protein coded for by the S1 genome segment) with receptors on the surface of either ependymal cells or neuronal cells.

Animals↗
PubMed1978

Common sequence at the 5' ends of the segmented RNA genomes of influenza A and B viruses.

Guanylyl- and methyltransferases, isolated from purified vaccinia virus, were used to specifically label the 5' ends of the genome RNAs of influenza A and B viruses. All eight segments were labeled with [alpha-(32)P]guanosine 5'-triphosphate or S-adenosyl[methyl-(3)H]methionine to form "cap" structures of the type m(7)G(5')pppN(m)-, of which unmethylated (p)ppN- represents the original 5' end. Further analyses indicated that m(7)G(5')pppA(m), m(7)G(5')pppA(m)pGp, and m(7)G(5')pppA(m)pGpUp were released from total and individual labeled RNA segments by digestion with nuclease P1, RNase T1, and RNase A, respectively. Consequently, the 5'-terminal sequences of most or all individual genome RNAs of influenza A and B viruses were deduced to be (p)ppApGpUp. The presence of identical sequences at the ends of RNA segments of both types of influenza viruses indicates that they have been specifically conserved during evolution.

Base Sequence↗
PubMed1979

Segment 8 of the influenza virus genome is unique in coding for two polypeptides.

In previous studies we showed that a ninth polypeptide with a molecular weight of approximately 11,000 (NS2) found in influenza virus-infected cells was unique, that it could be synthesized in vitro, and that its expression in vivo required early protein synthesis. On the basis of these results we suggested that one of the eight genome RNA segments of influenza virus codes for two polypeptides [Lamb, R.A., Etkind, P.R. & Choppin, P.W. (1978) Virology 91, 60-78]. We describe here differences in the electrophoretic mobility of the NS2 polypeptides of different strains of influenza A virus. These results provided further evidence that NS2 is virus coded and also made possible genetic studies using recombinants between two virus strains (HK and PR8) whose NS2 polypeptides differ. These studies showed that the gene for NS2 reassorts with that of the nonstructural polypeptide NS1, which is coded by genome segment 8. A mRNA for NS2 has been separated from that of NS1 and the other viral polypeptides by centrifugation and has been translated in vitro. Hybridization of genome segment 8 to the total mRNAs from infected cells specifically prevented the synthesis of NS2 and NS1. These results indicate that influenza virus genome segment 8 is transcribed into two separate mRNAs that code for two polypeptides, NS1 and NS2. Possible mechanisms for the transcription of the two mRNAs from either contiguous or overlapping genes are discussed.

DNA, Viral↗
PubMed2025

Borrelia burgdorferi loses essential genetic elements and cell proliferative potential during stationary phase in culture but not in the tick vector.

The Lyme disease agent Borrelia burgdorferi is a polyploid bacterium with a segmented genome in which both the chromosome and over 20 distinct plasmids are present in multiple copies per cell. This pathogen can survive for at least 9 months in its tick vector in an apparent dormant state between blood meals, without losing cell proliferative capability when re-exposed to nutrients. Cultivated B. burgdorferi cells grown to stationary phase or resuspended in nutrient-limited media are often used to study the effects of nutrient deprivation. However, a thorough assessment of the spirochete's ability to recover from nutrient depletion has been lacking. Our study shows that starved B. burgdorferi cultures rapidly lose cell proliferative ability. Loss of genetic elements essential for cell proliferation contributes to the observed proliferative defect in stationary phase. The gradual decline in copies of genetic elements is not perfectly synchronized between chromosomes and plasmids, generating cells that harbor one or more copies of the essential chromosome but lack all copies of one or more non-essential plasmids. This phenomenon likely contributes to the well-documented issue of plasmid loss during in vitro cultivation of B. burgdorferi. In contrast, B. burgdorferi cells from ticks starved for 14 months showed no evidence of reduced cell proliferative ability or plasmid loss. Beyond their practical implications for studying B. burgdorferi, these findings suggest that the midgut of the tick vector offers a unique environment that supports the maintenance of B. burgdorferi's segmented genome and cell proliferative potential during periods of tick fasting.IMPORTANCEBorrelia burgdorferi causes Lyme disease, a prevalent tick-borne illness. B. burgdorferi must survive long periods (months to a year) of apparent dormancy in the midgut of the tick vector between blood meals. Resilience to starvation is a common trait among bacteria. However, this study reveals that, in laboratory cultures, B. burgdorferi poorly endures starvation and rapidly loses viability. This decline is linked to a gradual loss of genetic elements required for cell proliferation. These results suggest that the persistence of B. burgdorferi in nature is likely shaped more by unique environmental conditions in the midgut of the tick vector than by an innate ability of this bacterium to endure nutrient deprivation.

Borrelia burgdorferi↗