Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology731210489-502 pubmed

Correction

The equation in the sentence:

Under a neutral model of evolution, sa0 is one randomly selected sequence, and E[d(sa0,s1)]  = E[d(s0x, s0y)] where the right-hand term...
(p. 10490, right column, second paragraph)

should be:

E[d(sa0,s0)] = E[d(s0x,s0y)].

We are grateful to Anders Kvist of Lund University for bringing this error to our attention.

Sequences

Genbank Accession numbers AF137629-AF138163, AF138166-AF138263, and AF138305-AF138703 correspond to sequences for this study. Each sequence record contains the subject ID, whether the sequence was sampled from peripheral blood mononuclear cells (PBMC) or from plasma, and time following seroconversion. This is illustrated below for two sequences:

LOCUS       AF137716                 597 bp    RNA     linear   VRL 08-FEB-2000
DEFINITION  HIV-1 p1p080-326 from USA envelope glycoprotein (env) gene, partial
            cds.
							
LOCUS       AF137715                 597 bp    DNA     linear   VRL 08-FEB-2000
DEFINITION  HIV-1 p1c077-317 from USA envelope glycoprotein (env) gene, partial
            cds.

Both of these are from subject #1 (p1). AF137716, clone number 326, was sampled from plasma (p for plasma) collected 80 months post seroconversion. Similarly, the AF137715, clone number 317, was from PBMC (c for cellular) sampled 77 months post seroconversion.

Nucleotide alignments from this study are available in fasta or nexus format.

Appendix Materials

Fig1-GlobalTree-2-sm.gif

Appendix Figure 1(gif pdf) Phylogenetic characterization of 1300 sequences sampled from the 9 participants described in this study and six selected sequences from GenBank. A neighbor-joining tree was constructed using maximum-likelihood distances in Phylip v3.5 (1) after regions that could not be unambiguously aligned were removed. Sequences sampled from each study participant formed monophyletic clusters separate from the other participants as well as from the six unrelated sequences included in this illustration. No viral sequence from this study was found to be closely related to prototypic HIV-1 sequences or to other known strains present or sequences determined in the laboratory. These observations are consistent with an absence of sample contamination or mix-up (3).

Fig2sm.gif

Appendix Figure 2 (pdf, single-page gif: 1 2 3 4 5 6 7) Pairwise comparisons of virus population divergence from the founder population (panels on the left side of the figure) and diversity within each sample (panels on the right) in each of the nine participants. Pairwise distances were estimated using the Kimura 2-parameter model of viral evolution (2). These distances were plotted on the y-axis at the corresponding times following seroconversion. The lines within each panel connect the mean values for each time point.  Comparisons of sequences from PBMC are shown with a red open circle for each data point, those from plasma are shown with a blue vertical line for each data point. The first 5 panels show the estimates of viral diversification for participants in which sequences were sampled from both PBMC and plasma. Subsequent panels show these estimates sequences sampled from PBMC DNA or from plasma RNA (but not both at any time point).

Fig3sm.gif

Appendix Figure 3 (pdf, single-page gif: 1 2 3) Phylogenetic analysis of HIV-1 env C2-V5 sequences from each of the nine participants. Sequences were aligned and visually adjusted using GDE (4). The phylograms were estimated by the method of neighbor-joining from a matrix of pairwise maximum likelihood sequence distances (transition/transversion ratio = 1.4) using programs from version 3.5 of the PHYLIP package (1). Trees were rooted to one of the sequences sampled at the first time point using Treeview (from R. Page). The legend for each phylogram shows the time of sampling in months following seroconversion and is depicted in an arbitrary color gradient. DNA sequences from PBMC are depicted as squares and plasma RNA sequences as triangles. Sequence changes expected to confer an X4 phenotype (SI phenotype on MT-2 cells and CXCR4 co-receptor specificity) based on basic amino acid substitution at any of the three positions (#306, 319, 320 of gp120) are indicated by a red asterisk.

Fig4sm.gif

Appendix Figure 4 (pdf, gif) Comparison of DNA distance estimations in nine participants using Kimura 2-parameter (K2P) model of evolution with a transition to transversion ratio of 2 (2) vs. a General Time Reversible (GTR) model with a site-to-site variation in substitution rates (discrete approximation of a γ distribution with a shape parameter,α=0.5) (5). DNA distance estimates are shown for sequences from PBMC only in all participants except for Participant1, where plasma data is shown for the time points when PBMC samples were not available, and Participant 11 for whom insufficient amounts of viral DNA was found in PBMC. K2P distances are plotted as blue circles and GTR DNA distances are plotted as red triangles. Intra-time point DNA diversity is depicted by open symbols and the DNA distance as compared to founder sequences is shown by filled symbols. These comparisons show similar trends using either K2P or the GTR distances, and as expected, at high levels of DNA differences, GTR model yields a comparatively higher DNA distances.

Appendix References

  1. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c, Seattle, WA.
  2. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
  3. Learn, G. H., B. T. M. Korber, B. Foley, B. H. Hahn, S. M. Wolinsky, and J. I. Mullins. 1996. Maintaining the integrity of HIV sequence databases. J. Virol. 70:5720-5730.
  4. Smith, S. W., R. Overbeek, C. R. Woese, W. Gilbert, and P. M. Gillevet. 1994. The Genetic Data Environment: An expandable GUI for multiple sequence analysis. CABIOS. 10:671-675.
  5. Swofford, D. L. 1999. PAUP 4.0: Phylogenetic Analysis Using Parsimony (And Other Methods), version 4.0. Sinauer Associates, Inc.
Department of Microbiology
School of Medicine
University of Washington
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