Estimation of clonal diversity in HTLV-1 infection

Within hosts, Human T-Lymphotropic Virus Type-1 (HTLV-1) is spread through de novo infection and infected cell proliferation, producing multiple T cell clones (infected cells with the same genomic proviral integration site). Between hosts, the number of clones observed from a 10μg sample of DNA varies by up to three orders of magnitude. The question arises: what is the total number of clones in the host from which that sample was drawn? Considering each clone as a “species”, the question becomes analogous to the “unseen species problem” in population ecology. We tested four species richness (number of species) estimators, and a novel approach, “DivE”, using three independent datasets: (i) viral populations from patients infected with HTLV-1, (ii) T cell antigen receptor clonotype repertoires, and (iii) microbial data from infant faecal samples. In all datasets, DivE was substantially more accurate than the ecological estimators, which were strongly biased by sample size when applied to datasets where the majority of species was not already present. DivE can also be used to estimate with accuracy the population clone structure from small samples. Previous estimates of HTLV-1 clone diversity in vivo were in the order of 102, and have increased in line with method sensitivity. In contrast, the mean estimated number of clones in the circulation of a single host (asymptomatic carriers and patients with chronic inflammation) by DivE was more than two logs higher than previously estimated. These estimates will inform our understanding of the dynamics and pathogenesis of HTLV-1 infection.