Diagnostic results of patients with dual HIV-1/HIV-2 infection (n = 9).

<p>Diagnostic results of patients with dual HIV-1/HIV-2 infection (n = 9).</p

Line immunoassay of patient 1 showing seropositivity for both HIV-1 and HIV-2.

<p>Patient sample: specific HIV-1 envelope antibodies (sgp120 and gp41) and specific HIV-2 envelope antibodies (gp36 and sgp105) are present. Positive and negative strip controls are shown.</p

Alignment of PI-2 pilus islets, adapted from [22].

<p>Genes are represented by colored arrows pointing in the direction of transcription. Gene names are indicated. % of identity are indicated for homologs found in <i>S</i>. <i>tigurinus</i> AZ_14 and <i>S</i>. <i>oralis</i> Uo5 (strains highlighted in red). % identity highlighted in red is those for the genes included in the PI-2 islet. Similarly as in all strains listed, the <i>S</i>. <i>tigurinus</i> PI-2 islets are inserted intergenically between <i>pepT</i> and <i>hemH</i>. Shaded areas indicate pseudogenes (one asterisk indicates a mutation in the start codon and two asterisks indicate the position of a stop-codon).</p

Phylogenetic rooted tree based on 1'331 single copy core genes.

<p>Both HV strains cluster together (AZ_3a^T and AZ_14, red branches) far from the LV strain (AZ_8, green branch). <i>S</i>. <i>oralis</i> Uo5 was chosen as outgroup.</p

Pairwise comparison based on 1'331 ORFs belonging to the core proteome.

<p>Pairwise comparison based on 1'331 ORFs belonging to the core proteome.</p

Presence and absence of the identified relevant gene clusters in the genomes of all strains investigated in this study.

<p>A black box means a homolog to the corresponding gene found in AZ_3a^T is present on the genome of the considered strain; a white box means no homolog to the corresponding gene found in AZ_3a^T is present on the genome of the considered strain.</p

General features of genomes investigated in this study.

<p>General features of genomes investigated in this study.</p

EBV persistence without its EBNA3A and 3C oncogenes in vivo

<div><p>The oncogenic Epstein Barr virus (EBV) infects the majority of the human population and usually persists within its host for life without symptoms. The EBV oncoproteins nuclear antigen 3A (EBNA3A) and 3C (EBNA3C) are required for B cell transformation in vitro and are expressed in EBV associated immunoblastic lymphomas in vivo. In order to address the necessity of EBNA3A and EBNA3C for persistent EBV infection in vivo, we infected NOD-<i>scid</i> γ_c^null mice with reconstituted human immune system components (huNSG mice) with recombinant EBV mutants devoid of EBNA3A or EBNA3C expression. These EBV mutants established latent infection in secondary lymphoid organs of infected huNSG mice for at least 3 months, but did not cause tumor formation. Low level viral persistence in the absence of EBNA3A or EBNA3C seemed to be supported primarily by proliferation with the expression of early latent EBV gene products transitioning into absent viral protein expression without elevated lytic replication. In vitro, EBNA3A and EBNA3C deficient EBV infected B cells could be rescued from apoptosis through CD40 stimulation, mimicking T cell help in secondary lymphoid tissues. Thus, even in the absence of the oncogenes EBNA3A and 3C, EBV can access a latent gene expression pattern that is reminiscent of EBV persistence in healthy virus carriers without prior expression of its whole growth transforming program.</p></div

EBNA3A or EBNA3C deficient EBV infection causes CD8⁺ T cell expansion.

<p><b>(A)</b> The number of splenic CD8⁺ T cells and <b>(B)</b> splenic CD4⁺ T cells of huNSG mice infected with either 10⁵ RIU of wt, 3AKO or 3CKO 5 weeks p.i. (n = 14-21/group) or 10⁶ RIU of 3AKO or 3CKO 6 weeks p.i. (n = 7-13/group) or non-infected control (mock) huNSG mice was determined by flow cytometry, applying the determined frequency to the spleen cell count. <b>(C)</b> The ratio of spleen to body weight (BW) of individual huNSG mice infected with either 10⁵ RIU of wt, 3AKO or 3CKO 5 weeks p.i. (n = 14-21/group) or 10⁶ RIU of 3AKO or 3CKO 6 weeks p.i. (n = 7-13/group) or non-infected control (mock) huNSG mice is depicted. <b>(A-C)</b> Pooled data from 4 low and 2 high infectious dose experiments with mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001, Mann-Whitney U test.</p

EBV persists without EBNA3A or EBNA3C in vivo.

<p><b>(A)</b> Splenic endpoint viral DNA load and <b>(B)</b> viral DNA load per gram lymph node tissue determined by qPCR of huNSG mice infected with either 10⁵ RIU of wt, 3AKO or 3CKO for 5 weeks (spleen: n = 18-21/group, lymph node: n = 8-11/group) or 10⁶ RIU of 3AKO or 3CKO for 6 weeks (spleen: n = 13-14/group, lymph node: n = 12-13/group). Values for mice in which no viral DNA was detected are plotted on the X-axis. <b>(C)</b> Blood DNA viral load over time determined by qPCR of huNSG mice infected with either 10⁵ RIU of wt, 3AKO or 3CKO 5 weeks p.i. (n = 18-21/group) or 10⁶ RIU of 3AKO or 3CKO 6 weeks p.i. (n = 13-14/group). Horizontal dashed line indicates the viral load of 3 times the lower limit of quantification (LLOQ). Horizontal dotted line indicates the LLOQ. <b>(D)</b> Frequency of huNSG mice infected with 10⁵ RIU of 3AKO, 3CKO or wt 5 weeks p.i. or 10⁶ RIU of 3AKO or 3CKO 6 weeks p.i. with EBV DNA copies above (≥200) or below (<200) 3 times the LLOQ in either the blood, the spleen or lymph nodes (n = 10-13/group) as determined by qPCR. Pooled data from 4 low and 2 high infectious dose experiments. *P < 0.05, **P < 0.01, Fisher’s exact test. <b>(E)</b> EBER-ISH (original magnification, 400x) of splenic sections from huNSG mice infected with 10⁶ RIU of 3AKO or 3CKO 6 weeks p.i.. <b>(G)</b> EBER-ISH (original magnification, 200x) of splenic sections from huNSG mice infected with 10⁵ RIU of 3AKO or 3CKO 12 weeks p.i.. <b>(F, H)</b> Quantification of EBER⁺ cells/mm² of <b>E</b> (n = 10-13/group) and <b>G</b> (n = 3-5/group) respectively and of huNSG mice infected with 10⁵ RIU of wt 5 weeks p.i. (n = 4/group) or mock (n = 3-8/group). <b>(I)</b> Frequency of huNSG mice infected with 10⁵ RIU of 3AKO or 3CKO 12 weeks p.i., with EBV DNA copies above (≥200) or below (<200) 3 times the LLOQ in either the blood, the spleen or lymph nodes (n = 3-5/group) as determined by qPCR. Pooled data from 2 experiments. <b>(A-C)</b> Pooled data from 4 low and 2 high infectious dose experiments are displayed with mean ± SEM. **P < 0.01, ***P < 0.001, two-way ANOVA with Bonferroni correction for blood viral load and Mann-Whitney U test for splenic viral load, lymph node viral load and EBER-ISH.</p