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  • Oral presentation
  • Open Access

Estimation of clonal diversity in HTLV-1 infection

  • 1Email author,
  • 1,
  • 2,
  • 1, 3,
  • 4,
  • 5,
  • 4,
  • 5,
  • 5, 6,
  • 1 and
  • 1
Retrovirology201411 (Suppl 1) :O50

  • Published:


  • Infected Cell
  • Integration Site
  • Asymptomatic Carrier
  • Clonal Diversity
  • Viral Population

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.

Authors’ Affiliations

Section of Immunology, Wright-Fleming Institute, Imperial College School of Medicine, London, UK
Centre for Integrative Systems Biology and Bioinformatics, South Kensington Campus, Imperial College, London, UK
Department of Molecular and Cellular Epigenetics, University of Liège, Liège, Belgium
Section of Paediatrics, Wright-Fleming Institute, Imperial College School of Medicine, London, UK
Vaccine Research Center, National Institutes of Health, Bethesda, USA
Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK


© Laydon et al; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.