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Sequence Alignments for Salazar et al.
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification


Set of 129 full-length genome sequences from 12 patients in early infection, plus longitudinal sequences from 3 patients.


  • Patient Alignments (click here)
    • This zip archive contains a fasta-formatted file of aligned sequences from 12 patients, a consensus sequence for each patient, and 8 reference sequences (4 from subtype B and 4 from subtype C).
    • The 12 patient codes are CH40, CH58, CH77, 226_2, 396_0, SUMA, TRJO, WEAU, WITO, ZM246F, ZM247F, and ZM249M
    • Sequence names are formatted as follows: PatientCode_SequenceNumber.
    • Consensus sequences are labeled as PatientCode_con, e.g. CH40_con.
    • Because patient ZM247F was infected by 2 variants, 2 consensus sequences (ZM247FB_con and ZM247FA_con) were made accordingly.
    • Transmitted sequences are labeled CH58_transmitted and CH77_transmitted.
    • The qualifier _fl indicates a full-length sequence.

  • Longitudinal Alignments (click here)
    • This zip archive contains 3 fasta-formatted files of within-patient sequence alignments from CH40, CH58, and CH77. A consensus sequence or the transmitted isolate is included for each patient.
    • For sequences in longitudinal samples, time when sample was drawn is labeled as dN_, where N is the number of days elapsed since screening.
Primary Reference

Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM.

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection.

J Exp Med. 2009 Jun 8;206(6):1273-89.
PMID 19487424

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last modified: Tue Apr 20 12:36 2010

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