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, we re-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.

Fig. 1

Cladogram of 168 strains belonging to the Cosmopolitan clade of HTLV-1, estimated using statistical parsimony (Templeton et al., 1992) as implemented in the program TCS, version 1.13 (Clement et al., 2000) and a multiple-sequence alignment of 521 bp from the LTR region. Branch tips and internal nodes occupied by extant viral sequences are labelled by the strain name, empty internal nodes by zeroes. Nodes co-occupied by more than one strain with the same genotype are indicated by ellipses, labelled with a single representative strain name from the co-occupying set. Numbers of co-occupant strains at such a node are shown in circles adjacent to each such node. Each line segment, regardless of length as drawn, represents one inferred mutational step as defined by a 95% confidence limit of nine steps. Closed cells in the network result from multiple, equally parsimonious connections between subnetworks at a particular step during execution of the TCS algorithm. For visual clarity locations of five strain clusters are symbolized schematically: (a) South American cluster; (b) Central Asian cluster; (c–e) miscellaneous strains. Two equally parsimonious attachment points of an outgroup composed of 24 non-Cosmopolitan (African and Melanesian) strains to the main network are labelled. Subclades A–E are demarcated in boxes. Predominant nucleotide states found within each subclade at five phylogenetically informative positions (268, 323, 328, 335 and 353) are indicated. Where the genotype of an individual strain differs from the predominant state within a subclade, only the states of divergent sites are given. Occurrence of mummy-associated LTR genotype I (Li et al., 1999) throughout subclade B is indicated by gray shading and the Roman numeral “I”. Possible phylogenetic placements of mummy-associated LTR sequences belonging to genotype III (Li et al., 1999) are marked by asterisks and labelled IIIa–IIId. Note that points of attachment IIIb and IIId of mummy genotype III on the unoccupied branches leading to strains HCT, MW2R and L195 cannot be specified exactly; one possibility was therefore chosen arbitrarily in each case. Nucleotide positions are numbered according to reference strain ATK (GenBank J02029).