scholarly journals Distinct Viral Populations Differentiate and Evolve Independently in a Single Perennial Host Plant

2006 ◽  
Vol 80 (5) ◽  
pp. 2349-2357 ◽  
Author(s):  
Chiraz Jridi ◽  
Jean-François Martin ◽  
Véronique Marie-Jeanne ◽  
Gérard Labonne ◽  
Stéphane Blanc
Keyword(s):  
Complex Structure ◽  
Plum Pox Virus ◽  
Virus Population ◽  
Intensive Study ◽  
Heterogeneous Distribution ◽  
Nested Clade Analysis ◽  
Viral Genomes ◽  
Immunodeficiency Virus ◽  
Single Host ◽  
Exhaustive Study

ABSTRACT The complex structure of virus populations has been the object of intensive study in bacteria, animals, and plants for over a decade. While it is clear that tremendous genetic diversity is rapidly generated during viral replication, the distribution of this diversity within a single host remains an obscure area in this field of science. Among animal viruses, only Human immunodeficiency virus and Hepatitis C virus populations have recently been thoroughly investigated at an intrahost level, where they are structured as metapopulations, demonstrating that the host cannot be considered simply as a “bag” containing a homogeneous or unstructured swarm of mutant viral genomes. In plants, a few reports suggested a possible heterogeneous distribution of virus variants at different locations within the host but provided no clues as to how this heterogeneity is structured. Here, we report the most exhaustive study of the structure and evolution of a virus population ever reported at the intrahost level through the analysis of a Prunus tree infected by Plum pox virus for over 13 years following a single inoculation event and by using analysis of molecular variance at different hierarchical levels combined with nested clade analysis. We demonstrate that, following systemic invasion of the host, the virus population differentiates into several distinct populations that are isolated in different branches, where they evolve independently through contiguous range expansion while colonizing newly formed organs. Moreover, we present and discuss evidence that the tree harbors a huge “bank” of viral clones, each isolated in one of the myriad leaves.

scholarly journals Development of a homology model for clade A human immunodeficiency virus type 1 gp120 to localize temporal substitutions arising in recently infected women

2004 ◽  
Vol 85 (6) ◽  
pp. 1479-1484
Author(s):  
Mary Poss ◽  
David C. Holley ◽  
Roman Biek ◽  
Harold Cox ◽  
John Gerdes
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Envelope Gene ◽  
Virus Population ◽  
Gene Sequences ◽  
Virus Diversity ◽  
Immunodeficiency Virus ◽  
Hiv 1

The virus population transmitted by a human immunodeficiency virus type 1 (HIV-1) infected individual undergoes restriction and subsequent diversification in the new host. However, in contrast to men, who have limited virus diversity at seroconversion, there is measurable diversity in viral envelope gene sequences in women infected with clade A HIV-1. In this study, virus sequence diversity in three unrelated, clade A infected women preceding and shortly after seroconversion was evaluated. It was demonstrated that there is measurable evolution of envelope gene sequences over this time interval. Furthermore, in each of the three individuals, amino acid substitutions arose at five or six positions in sequences derived at or shortly after seroconversion relative to sequences obtained from the seronegative sample. Presented here is a model of clade A gp120 to determine the location of substitutions that appeared as the virus population became established in three clade A HIV-1 infected women.

scholarly journals Human Immunodeficiency Virus Types 1 and 2 Differ in the Predominant Mechanism Used for Selection of Genomic RNA for Encapsidation

1999 ◽  
Vol 73 (4) ◽  
pp. 3023-3031 ◽  
Author(s):  
Jane F. Kaye ◽  
Andrew M. L. Lever
Keyword(s):  
Human Immunodeficiency Virus ◽  
Genomic Rna ◽  
Rna Packaging ◽  
Packaging Signal ◽  
Initiation Mechanism ◽  
Gag Protein ◽  
Gag Proteins ◽  
Viral Genomes ◽  
Immunodeficiency Virus

ABSTRACT Retroviral RNA encapsidation is a highly selective process mediated through recognition by the viral Gag proteins of cis-acting RNA packaging signals in genomic RNA. This RNA species is also translated, producing the viral gag gene products. The relationship between these processes is poorly understood. Unlike that of human immunodeficiency virus type 1 (HIV-1), the dominant packaging signal of HIV-2 is upstream of the major splice donor and present in both unspliced and spliced viral RNAs, necessitating additional mechanisms for preferential packaging of unspliced genomic RNA. Encapsidation studies of a series of HIV-2-based vectors showed efficient packaging of viral genomes only if the unspliced, encapsidated RNA expressed full-length Gag protein, including functional nucleocapsid. We propose a novel encapsidation initiation mechanism, providing selectivity, in which unspliced HIV-2 RNA is captured in cis by the Gag protein. This has implications for the use of HIV-2 and other lentiviruses as vectors.

scholarly journals A Dominant Role for CD8+-T-Lymphocyte Selection in Simian Immunodeficiency Virus Sequence Variation

2004 ◽  
Vol 78 (24) ◽  
pp. 14012-14022 ◽  
Author(s):  
David H. O'Connor ◽  
Adrian B. McDermott ◽  
Kendall C. Krebs ◽  
Elizabeth J. Dodds ◽  
Jacqueline E. Miller ◽  
...  
Keyword(s):  
Positive Selection ◽  
Simian Immunodeficiency Virus ◽  
Dominant Role ◽  
Viral Envelope ◽  
Viral Escape ◽  
Viral Genomes ◽  
Cd8 T Lymphocyte ◽  
Immunodeficiency Virus ◽  
Variable Loops ◽  
Virus Sequence

ABSTRACT CD8+ T lymphocytes (CD8-TL) select viral escape variants in both human immunodeficiency virus and simian immunodeficiency virus (SIV) infections. The frequency of CD8-TL viral escape as well as the contribution of escape to overall virus diversification has not been assessed. We quantified CD8-TL selection in SIV infections by sequencing viral genomes from 35 SIVmac239-infected animals at the time of euthanasia. Here we show that positive selection for sequences encoding 46 known CD8-TL epitopes is comparable to the positive selection observed for the variable loops of env. We also found that >60% of viral variation outside of the viral envelope occurs within recognized CD8-TL epitopes. Therefore, we conclude that CD8-TL selection is the dominant cause of SIV diversification outside of the envelope.

scholarly journals Evolution of CCR5 Use before and during Coreceptor Switching

2008 ◽  
Vol 82 (23) ◽  
pp. 11758-11766 ◽  
Author(s):  
Mia Coetzer ◽  
Rebecca Nedellec ◽  
Janelle Salkowitz ◽  
Sherry McLaughlin ◽  
Yi Liu ◽  
...  
Keyword(s):  
Envelope Gene ◽  
Virus Population ◽  
Ccr5 Expression ◽  
Immunodeficiency Virus ◽  
Coreceptor Switch ◽  
Transmitted Sequence ◽  
Rapid Divergence ◽  
Selective Forces ◽  
Hiv 1

ABSTRACT The envelope gene (env) of human immunodeficiency virus type 1 (HIV-1) undergoes rapid divergence from the transmitted sequence and increasing diversification during the prolonged course of chronic infection in humans. In about half of infected individuals or more, env evolution leads to expansion of the use of entry coreceptor from CCR5 alone to CCR5 and CXCR4. The stochastic nature of this coreceptor switch is not well explained by host selective forces that should be relatively constant between infected individuals. Moreover, differences in the incidence of coreceptor switching among different HIV-1 subtypes suggest that properties of the evolving virus population drive the switch. We evaluated the functional properties of sequential env clones from a patient with evidence of coreceptor switching at 5.67 years of infection. We found an abrupt decline in the ability of viruses to use CCR5 for entry at this time, manifested by a 1- to 2-log increase in susceptibility to CCR5 inhibitors and a reduced ability to infect cell lines with low CCR5 expression. There was an abnormally rapid 5.4% divergence in env sequences from 4.10 to 5.76 years of infection, with the V3 and V4/V5 regions showing the greatest divergence and evidence of positive selection. These observations suggest that a decline in the fitness of R5 virus populations may be one driving force that permits the emergence of R5X4 variants.

scholarly journals Coreceptor Specificity of Temporal Variants of Simian Immunodeficiency Virus Mne

1999 ◽  
Vol 73 (2) ◽  
pp. 1655-1660 ◽  
Author(s):  
Jason T. Kimata ◽  
John J. Gosink ◽  
Vineet N. KewalRamani ◽  
Lyle M. Rudensey ◽  
Dan R. Littman ◽  
...  
Keyword(s):  
T Cell ◽  
Simian Immunodeficiency Virus ◽  
Coreceptor Usage ◽  
Virus Population ◽  
Genetic Changes ◽  
Course Of Disease ◽  
Antigenic Properties ◽  
Immunodeficiency Virus ◽  
Variant Virus ◽  
Late Stages

ABSTRACT The simian immunodeficiency virus (SIV) Mne envelope undergoes genetic changes that alter tropism, syncytium-inducing capacity, and antigenic properties of the emerging variant virus population during the course of an infection. Here we investigated whether the mutations in envelope of SIVMne also influence coreceptor usage. The data demonstrate that the infecting macrophage-tropic SIVMne clone as well as the envelope variants that are selected during the course of disease progression all recognize both CCR5 and Bob (GPR15) but not Bonzo (STRL33), CXCR4, or CCR3. Although it remains to be determined if there are other coreceptors specific for dualtropic or T-cell-tropic variants of SIVMne that emerge during late stages of infection, these data suggest that such SIV variants that evolve in pathogenic infections do not lose the ability to recognize CCR5 or Bob/GPR15.

scholarly journals The Therapeutic Potential of Ribozymes

Blood ◽  
1998 ◽  
Vol 91 (2) ◽  
pp. 371-382 ◽  
Author(s):  
Helen A. James ◽  
Ian Gibson
Keyword(s):  
Therapeutic Potential ◽  
New Developments ◽  
Rna Molecules ◽  
Viral Genomes ◽  
Chromosome Translocations ◽  
Immunodeficiency Virus ◽  
Deleterious Gene ◽  
Target Rna ◽  
Hiv 1

Ribozymes are catalytic RNA molecules that recognize their target RNA in a highly sequence-specific manner. They can therefore be used to inhibit deleterious gene expression (by cleavage of the target mRNA) or even repair mutant cellular RNAs. Targets such as the mRNAs of oncogenes (resulting from base mutations or chromosome translocations, eg, ras or bcr-abl) and viral genomes and transcripts (human immunodeficiency virus–type 1 [HIV-1]) are ideal targets for such sequence-specific agents. The aim of this review is therefore to introduce the different classes of ribozymes, highlighting some of the chemistry of the reactions they catalyze, to address the specific inhibition of genes by ribozymes, the problems yet to be resolved, and how new developments in the field give hope to the future for ribozymes in the therapeutic field.

scholarly journals Species and Genotypic Diversities and Similarities of Pathogenic Yeasts Colonizing Women †

1999 ◽  
Vol 37 (12) ◽  
pp. 3835-3843 ◽  
Author(s):  
Jianping Xu ◽  
Cynthia M. Boyd ◽  
Elizabeth Livingston ◽  
Wieland Meyer ◽  
John F. Madden ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Similar Species ◽  
Yeast Strains ◽  
Significant Difference ◽  
Immunodeficiency Virus ◽  
Single Host ◽  
Candida Lusitaniae ◽  
Multiple Species ◽  
Three Body

We examined the patterns of strain relatedness among pathogenic yeasts from within and among groups of women to determine whether there were significant associations between genotype and host condition or body site. A total of 80 yeast strains were isolated, identified, and genotyped from 49 female volunteers, who were placed in three groups: (i) 19 women with AIDS, (ii) 11 pregnant women without human immunodeficiency virus (HIV) infection, and (iii) 19 women who were neither pregnant nor infected with HIV. Seven yeast species were recovered, including 59 isolates of Candida albicans, 9 isolates of Candida parapsilosis, 5 isolates ofCandida krusei, 3 isolates of Candida glabrata, 2 isolates of Saccharomyces cerevisiae, and 1 isolate each of Candida tropicalis and Candida lusitaniae. Seventy unique genotypes were identified by PCR fingerprinting with the M13 core sequence and by random amplified polymorphic DNA analysis. Of the nine shared genotypes, isolates from three different hosts were of one genotype and pairs of strains from different body sites of the same host shared each of the other eight genotypes. Genetic similarities among groups of strains were calculated and compared. We found no significant difference in the patterns of relatedness of strains from the three body sites (oral cavity, vagina, and rectum), regardless of host conditions. The yeast microflora of all three host groups had similar species and genotypic diversities. Furthermore, a single host can be colonized with multiple species or multiple genotypes of the same species at the same or different body sites, indicating dynamic processes of yeast colonization on women.

scholarly journals Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms

Diversity ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 225
Author(s):  
Yuji Tomaru ◽  
Kei Kimura
Keyword(s):  
Culture Method ◽  
Host Cells ◽  
Natural Sediment ◽  
Viral Genomes ◽  
Planktonic Diatoms ◽  
Ecological Relationships ◽  
Ssrna Virus ◽  
Single Host ◽  
Complete Lysis ◽  
Ssdna Viruses

Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.

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