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.

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In this paper, we investigate the dynamics behavior of DS-I-A epidemic model with multiple stochastic perturbations. Sufficient conditions for extinction of disease are established. Especially, we conclude that there is a stationary distribution for the stochastic system and it has ergodicity under appropriate conditions. At last, some examples and simulations are provided to illustrate our results.KEYWORDS ergodicity, extinction, infectious disease models, multiple stochastic perturbations, stationary Markov process 6024

We investigate degenerate stochastic SIR epidemic model with saturated incidence. For the constant coefficients case, we achieve a threshold which determines the extinction and persistence of the epidemic by utilizing Markov semigroup theory. Furthermore, we conclude that environmental white noise plays a positive effect in the control of infectious disease in some sense comparing to the corresponding deterministic system. For the stochastic non-autonomous system, we prove the existence of periodic solution.