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Sequence Alignments for Keele et al. 2008
Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection

Data Download all alignments.


  • The zip file contains individual alignments of full-length Env sequences for 102 subjects. For each patient, there are between 12 and 63 sequences, plus a consensus sequence generated for each patient's sequences.
  • The file "all_acute_patients.fasta" is an alignment of all sequences from the individual patient sets.
  • The file "n102_acute_within_patient_consensuses.fasta" is an alignment of just the consensus sequences from all patients.
  • All subjects were sampled at precisely-known stages of early infection, defined by Fiebig stage.
  • These alignments were provided by the authors. Fasta format is used.
  • Each clonal sequence is named according to the following format:
  • Each consensus sequence is labeled as:
  • Click here for the file, which contains 30 separate files, each an alignment from 1 of 10 patients with longitudinal sampling, for a total of 1,043 sequences. (Added on 2 November, 2009)
  • These sequences can be viewed in GenBank or the LANL HIV Database under accession numbers EU574937-EU579293.
Primary Reference

Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM.
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection.
Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7.
PMID 18490657

Additional studies that used these data

Wood et al., PLoS Computational Biology, in press.

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last modified: Tue Apr 20 12:36 2010

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