The genome of the human immunodeficiency virus is highly prone to recombination^1,2,3, although it is not obvious whether recombinants arise infrequently or whether they are constantly being spawned but escape identification because of the massive and rapid turnover of virus particles^4,5. Here we use fluorescence in situ hybridization to estimate the number of proviruses harboured by individual splenocytes from two HIV patients, and determine the extent of recombination by sequencing amplified DNA from these cells. We find an average of three or four proviruses per cell and evidence for huge numbers of recombinants and extensive genetic variation. Although this creates problems for phylogenetic analyses, which ignore recombination effects, the intracellular variation may help to broaden immune recognition.

Fibroblastic reticular cells (FRCs) form the cellular scaffold of lymph nodes (LNs) and establish distinct microenvironmental niches to provide key molecules that drive innate and adaptive immune responses and control immune regulatory processes. Here, we have used a graph theory-based systems biology approach to determine topological properties and robustness of the LN FRC network in mice. We found that the FRC network exhibits an imprinted small-world topology that is fully regenerated within 4 wk after complete FRC ablation. Moreover, in silico perturbation analysis and in vivo validation revealed that LNs can tolerate a loss of approximately 50% of their FRCs without substantial impairment of immune cell recruitment, intranodal T cell migration, and dendritic cell-mediated activation of antiviral CD8⁺ T cells. Overall, our study reveals the high topological robustness of the FRC network and the critical role of the network integrity for the activation of adaptive immune responses. Fibroblastic reticular cells (FRCs) in lymph nodes are organized in a highly connected cellular network that not only acts as a scaffold for lymphocyte migration but also provides key factors for induction and maintenance of immune responses. By utilizing high-resolution microscopy coupled with computational approaches to complex network analysis, we determined the topological properties and robustness of the FRC network. The underlying structure of the FRC network has been identified as a small-world network analogous to many other biological networks. Moreover, we demonstrate that this distinct structural organization is an imprinted trait of the FRC network, which is capable of fully regenerating after complete FRC ablation. In silico perturbation analysis of the FRC network confirmed that lymph nodes are able to tolerate FRC loss of approximately 50%. In vivo experiments corroborated these findings by demonstrating substantial impairment of immune cell recruitment, migration, and dendritic cell-mediated activation of antiviral CD8⁺ T cells, after critical loss of FRCs. In conclusion, the present study reveals the extraordinary topological robustness of the FRC network, crucial for establishing effective immunity.

The speed of virus replication has typically been seen as an advantage for a virus in overcoming the ability of the immune system to control its population growth. Under some circumstances, the converse may also be true: more slowly replicating viruses may evoke weaker cellular immune responses and therefore enhance their likelihood of persistence. Using the model of lymphocytic choriomeningitis virus (LCMV) infection in mice, we provide evidence that slowly replicating strains induce weaker cytotoxic-T-lymphocyte (CTL) responses than a more rapidly replicating strain. Conceptually, we show a “bell-shaped” relationship between the LCMV growth rate and the peak CTL response. Quantitative analysis of human hepatitis C virus infections suggests that a reduction in virus growth rate between patients during the incubation period is associated with a spectrum of disease outcomes, from fulminant hepatitis at the highest rate of viral replication through acute resolving to chronic persistence at the lowest rate. A mathematical model for virus-CTL population dynamics (analogous to predator [CTL]-prey [virus] interactions) is applied in the clinical data-driven analysis of acute hepatitis B virus infection. The speed of viral replication, through its stimulus of host CTL responses, represents an important factor influencing the pathogenesis and duration of virus persistence within the human host. Viruses with lower growth rates may persist in the host because they “sneak through” immune surveillance.