On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy

Abstract

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, were-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Is HIV-1 evolving to a less virulent form in humans?

“…There are four classified retroviruses that infect humans and cause symptomatic disease. Human T-cell lymphotropic virus (HTLV) types 1 and 2 are members of the Deltaretrovirus genus in the subfamily Orthoretrovirinae, show a low rate of evolution in the human population, and probably originated from a non-human primate millions of years ago [1][2][3][4] . The high frequency of HTLV-1 infections was localized in specific endemic areas (for example, southern Japan) until recent times, indicating a relatively slow spread in the human population compared with another human retrovirus, HIV-1.…”

In contrast to HIV, KIR3DS1 does not influence outcome in HTLV-1 retroviral infection

“…In light of the recent emergence of HIV, specific activation of KIR3DS1 during HIV infection cannot have been the driving force behind the evolution of this KIR. In contrast, HTLV-1 has been present in the human population for a much longer period of time [30, 31]. It is tempting to speculate that KIR3DS1 may have arisen to recognize changes induced upon infection with HTLV-1 (e.g.…”

E box motifs as mediators of proviral latency of human retroviruses

“…HTLV-1a, often referred to as the Cosmopolitan clade, represents by far the most widely distributed strain in HTLV-1 infected persons. It is striking to observe that an overwhelming majority (97%) of HTLV-1a isolates harbour this putative E box (as deduced from the analysis of alignments [ 22 ]), suggesting a selection for this motif during evolution (Figure 2 ). Such an observation might suggest that the presence of an E box might have contributed to the spread of the retrovirus, possibly by favouring the transcriptional repression of viral genes and thus facilitating virus- escape from the host immune system.…”

“…This tree has been obtained through the analysis of a dataset derived from Coulthart et al . [ 22 ].…”