第9回千葉県胆膵研究会 11.

Additional file 13: Table S5. Statistical analysis of all experiments separated for transmission pairs with high and low diversity transmitters and for transmission pairs where recipient is closer to ancestral genotype, respectively

HIV-1 dynamics during cART.

<p>Circles denote measured data of patient 112 and lines represent the best fit of the default model. Model fits to data of the four other patients are given in <i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi.1003871.s001" target="_blank">Text S1</a></i>.</p

Decay kinetics of subclasses of HIV-1-infected cells during cART.

<p>The five subclasses of PBMCs are: DNA (containing HIV-1 DNA, black circles), Low (containing solely HIV-1 UsRNA, red diamonds), Mid (containing only HIV-1 MsRNA-tatrev or MsRNA-nef, green crosses), High (containing elevated levels of both HIV-1 MsRNA-tatrev and MsRNA-nef, blue triangles) and Extra (carrying virion-enclosed HIV-1 RNA, chocolate squares). Thick lines and symbols represent the geometric means of the five patients from the study by Fischer et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi.1003871-Fischer3" target="_blank">[12]</a>. Thin transparent lines for each color represent the original data for each subclass of cells of each individual patient. The dashed line represents the limit of detection that was set at 50% of the lowest measured cell count. Measurements below this threshold were assumed to be at 50% of the detection limit to include them in the mean.</p

Development of the latently infected cell pool during acute and chronic of HIV-1 infection.

<p>The pool of latently infected cells (+) is shown as a red line, the number of HIV-1 DNA positive cells as a blue dash-dotted line and the plasma HIV-1 RNA as a black dashed line. The average parameter estimates from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi-1003871-t001" target="_blank">Table 1</a> were used for the model simulation. The gray areas represent two standard deviations around the mean of the number of HIV-1 DNA positive cells in patients that initiated cART during acute and chronic infection <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi.1003871-Schmid1" target="_blank">[33]</a> (for details, see <i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi.1003871.s001" target="_blank">Text S1</a></i>).</p

Dynamics of HIV-1-infected subpopulations during cART.

<p>The 12 different cellular subpopulations from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi-1003871-g003" target="_blank">Figure 3</a> (patient 112) are shown together with the virus. CD4 target cells (): black dashed line; actively infected cells during the intracellular eclipse phase ( to ): blue dashed lines; activated, virus-producing cells (): blue solid line; defectively infected cells (): chocolate line; latently infected cells ( and ): red dashed and solid line, respectively; persistently infected cells ( and ): green dashed and solid line, respectively; virus particles (): black solid line. The dynamics of the cellular subpopulations for all other patients are given in <i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003871#pcbi.1003871.s001" target="_blank">Text S1</a></i>.</p

Model of HIV-1 dynamics.

<p>Actively infected cells move through an intracellular eclipse phase ( to ) before they start to produce virus particles (). Some of the cells during the intracellular eclipse phase become either defectively infected (), latently infected () or persistently infected (). Both latently ( and ) and persistently ( and ) can move between two transcriptional states. Persistently infected cells that are in a high transcriptional state () also contribute to virus production. The different subpopulations of infected cells can be stratified according to their HIV-1 DNA and RNA content (shown on top).</p

Baseline characteristics of 290 patients with primary HIV-1 infection.

<p>Abbreviations: MSM: men who have sex with men; IVDU, intravenous drug users; STIs, sexually transmitted infections; HIV-1, human immunodeficiency virus type 1; TDR, transmitted drug resistance.</p>a<p>Other subtypes: CRF01_AE, C, A, F1, G, CRF02_AG, CRF14_BG, A1D, CR 12_BF, D</p>b<p>One case from a needle stick.</p>c<p>Concomitant STIs: syphilis and/or chlamydia and/or gonorrhoea and/or genital herpes</p>d<p>Non infectious disease specialist or other institutions (e.g. dermatologist, gynaecologist, blood donation center etc.).</p>e<p>In 21 patients a Fiebig stage could not be assigned due to missing p24-antigen values.</p><p>Baseline characteristics of 290 patients with primary HIV-1 infection.</p

Clusters of host genes correlated with viral progression.

<p>Temporal expression patterns of 7,991 genes modulated in concordance with key steps of viral replication (panel <b>A</b>) were grouped into 18 clusters with differential expression profiles at three phases of the viral life cycle, namely reverse transcription, integration, and late phase. The cluster code characters ‘+’ and ‘−’ mark significant (<i>p</i><10⁻²) upregulation and downregulation, respectively, while ‘o’ indicates no significant deviation from zero. For example, the cluster ‘−+o’ contains 373 genes downregulated during reverse transcription, upregulated during integration, and unregulated during the late phase. In total, six upregulated clusters (<b>B</b>), four clusters with mixed patterns of regulation (<b>C</b>), and eight downregulated clusters (<b>D</b>) were found. Details of clusters are available at the dedicated web resource <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003161#ppat.1003161-Bartha1" target="_blank">[6]</a>.</p

Symptoms of acute retroviral syndrome reported in eleven retrospective studies or review articles.

<p>Symptoms of acute retroviral syndrome reported in eleven retrospective studies or review articles.</p

Acute Retroviral Syndrome Severity Score (ARSSS).

a<p>e.g. encephalitis, aseptic meningitis, paresis, facial nerve paresis</p><p>Acute Retroviral Syndrome Severity Score (ARSSS).</p