The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes

The relative contributions of infectious and mitotic spread to HTLV-1 persistence

Human T-lymphotropic virus type-1 (HTLV-1) persists within hosts via infectious spread (de novo infection) and mitotic spread (infected cell proliferation), creating a population structure of multiple clones (infected cell populations with identical genomic proviral integration sites). The relative contributions of infectious and mitotic spread to HTLV-1 persistence are unknown, and will determine the efficacy of different approaches to treatment. The prevailing view is that infectious spread is negligible in HTLV-1 persistence beyond early infection. However, in light of recent high-throughput data on the abundance of HTLV-1 clones, and recent estimates of HTLV-1 clonal diversity that are substantially higher than previously thought (typically between 10⁴ and 10⁵ HTLV-1⁺ T cell clones in the body of an asymptomatic carrier or patient with HTLV-1-associated myelopathy/tropical spastic paraparesis), ongoing infectious spread during chronic infection remains possible. We estimate the ratio of infectious to mitotic spread using a hybrid model of deterministic and stochastic processes, fitted to previously published HTLV-1 clonal diversity estimates. We investigate the robustness of our estimates using three alternative estimators. We find that, contrary to previous belief, infectious spread persists during chronic infection, even after HTLV-1 proviral load has reached its set point, and we estimate that between 100 and 200 new HTLV-1 clones are created and killed every day. We find broad agreement between all estimators. The risk of HTLV-1-associated malignancy and inflammatory disease is strongly correlated with proviral load, which in turn is correlated with the number of HTLV-1-infected clones, which are created by de novo infection. Our results therefore imply that suppression of de novo infection may reduce the risk of malignant transformation.

There is no effective antiretroviral treatment for infection with Human T-lymphotropic virus type-1 (HTLV-1), which causes a range of inflammatory diseases and the aggressive malignancy Adult T-cell Leukaemia/Lymphoma (ATL) in approximately 10% of infected people. Within hosts the virus spreads via infectious spread (de novo infection) and mitotic spread (infected cell division). The relative contributions of each mechanism are unknown, and have major implications for drug development and clinical management of infection. We estimate the ratio of infectious to mitotic spread during the infection’s chronic phase using three methods. Each method indicates infectious spread at low but persistent levels after proviral load has reached set point, contrary to the prevailing view that infectious spread features in early infection only. Risk of disease in HTLV-1 infection is known to increase with proviral load, via mutations accrued from repeated infected cell division. Our analyses suggest that ongoing infectious spread may provide an additional mechanism whereby chronic infection becomes malignant. Further, because antiretroviral drugs against Human Immunodeficiency Virus (HIV) inhibit HTLV-1 infectious spread, they may reduce the risk of HTLV-1 malignancy.

Inferring the immune response from repertoire sequencing

High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between repertoires is confounded by variability in the read count of each receptor clonotype due to sampling, library preparation, and expression noise. Here, we present a general Bayesian approach to disentangle repertoire variations from these stochastic effects. Using replicate experiments, we first show how to learn the natural variability of read counts by inferring the distributions of clone sizes as well as an explicit noise model relating true frequencies of clones to their read count. We then use that null model as a baseline to infer a model of clonal expansion from two repertoire time points taken before and after an immune challenge. Applying our approach to yellow fever vaccination as a model of acute infection in humans, we identify candidate clones participating in the response.

Selected before selection: A case for inherent antigen bias in the T cell receptor repertoire

T cell receptor recombination is frequently described as a random or semi-random process that belies the now well-established principle that recombination is extremely biased towards the generation of particular receptor chains. Here we describe the experimental and theoretical work arising from new TCR repertoire sequencing approaches, including the recognition of high rates of public receptors across individuals, estimates of the size and distribution of receptors in the naive repertoire, and the roles of evolutionary, thymic, and peripheral selection in generating public, pathogen-specific responses. Molecular studies of recombination that have identified epigenetic, transcriptional, and topological contributions to variable segment usage are presented as examples of possible mechanisms shaped by natural selection to bias the TCR repertoire. Lastly, we suggest experimental approaches that might contribute to resolving some of the controversies in these areas.