Defective viral particles in caprine arthritis encephalitis virus infection

Defective deletion mutant amplification

Defective deletion mutants can be replicated in superinfected cells by parasitism of the intact virus' replication machinery, and through replication with the host cell. We show by analysis of a mathematical model that dynamic stability of superinfected cell growth is crucial in determining the frequency of deletion mutant infected cells, i.e. there is a critical infectivity threshold rho(sc)below which the density of proliferative virus is significantly reduced by the presence of defective deletion mutants. Above rho(sc), proliferative virus principally occurs as superinfected cells (wild type with defective deletion mutant). The threshold rho(sc), and the interference effects of the deletion mutant, increase with deletion mutant parasitism of the wild-type replication machinery in superinfected cells. The interaction of virally infected cells with host homeostasis determines whether immune escape by deletion mutant infected cells is necessary for the interference window to exist. Only when the deletion mutant has a detrimental effect on infected host cell replication did we observe periodic behaviour.

Accumulation of defective viral genomes in peripheral blood mononuclear cells of human immunodeficiency virus type 1-infected individuals

Human immunodeficiency virus type 1 (HIV-1) genomes present in peripheral blood mononuclear cells (PBMCs) of infected persons or in lymphocytes infected in vitro were studied by long-distance PCR (LD-PCR) using primers localized in the HIV-1 long terminal repeats. The full-length 9-kb DNA was the only LD-PCR product obtained in peripheral and cord blood lymphocytes from seronegative donors infected in vitro. However, a high proportion (27% to 66%) of distinct populations of extensively deleted HIV-1 genomes of variable size was detected in PBMCs of 15 of 16 HIV-1-infected persons. Physical mapping of defective genomes showed that the frequency of deletions is proportional to their proximity to the central part of HIV-1 genome, which is consistent with a deletion mechanism involving a single polymerase jump during reverse transcription. Sequencing of deletion junctions revealed the presence of short direct repeats of three or four nucleotides. The number of defective HIV-1 genomes decreased after in vitro activation of PBMCs. Persistence of full-length and deleted genomes in in vitro activated PBMCs correlated with isolation of an infectious virus. Our results represent the first quantitative assessment of intragenomic rearrangements in HIV-1 genomes in PBMCs of infected persons and demonstrate that, in contrast to in vitro infection, defective genomes accumulate in PBMCs of infected persons.

PCR and reverse dot hybridization for the detection of endogenous retroviral transcripts

Two degenerated oligonucleotide primers, known to amplify a fragment of the pol gene in all retroviruses tested so far have been used to amplify pol related sequences from human genomic DNA. Cloning and sequencing these fragments confirm a retroviral relationship for most of them and define 96 groups on the basis of their internal similarity. 96 pol fragments were probed with PCR amplified cDNA in reverse dot hybridization to investigate pol related transcripts. PCR amplified genomic DNA served as a control for contamination of genomic DNA in the RNA preparations. Isopycnic centrifugation in cesium trifluoroacetate yielded RNA with the lowest possible amounts of contaminating DNA. This technique is a powerful and a well-controlled tool for the detection of endogenous retroviral transcripts and may be helpful for investigating the involvement of endogenous retroviruses in various diseases.