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Sequence Alignments for Keele et al. 2009
Low Dose Rectal Inoculation of Rhesus Macaques by SIVsmE660 or SIVmac251 Recapitulates Human Mucosal Infection by HIV-1


Full-length env sequences from 18 experimentally infected Indian rhesus macaques (986 sequences) and 2 challenge stocks (SIVsmE660 and SIVmac251, 104 sequences). Animals were inoculated intrarectally or intravenously with either SIVmac251 or SIVsmE660. Sequences are from two post-infection samples, early in acute infection and at peak viremia.

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  • The zip file contains one codon-aligned set of 1090 full-length env sequences from 18 Indian Rhesus macaques and 2 challenge stocks (SIVsmE660 and SIVmac251), in fasta format.
  • Sequence identifiers from challenge stock are formatted as follows: StockID.SequenceName.GenbankAccession, where StockID is either E660 or 251.
  • Sequence identifiers from infected Macaques have the following format: AnimalID.TimePoint.SequenceName.GenbankAccession
  • Macaques were sampled at 2 time-points, early in acute infection ("ramp-up" viral load, designated RU) and at peak viremia (PK). One animal (CP23) was sampled only once, 2 weeks after peak viremia (2PP).
  • The following 8 animals were infected with SIVsmE660: AK9F, CG7G, CG7V, CG87, CP23, CP37, CP3C, and CR54.
  • The following 10 animals were infected with SIVmac251: AH4X, AV66, AV74, CG5G, CG71, CP1W, CR2A, CR53, CT76, and PBE.
  • Information about mode of infection and viral load levels are available in the paper referenced below.
  • These sequences can be viewed in GenBank or the LANL HIV Database under accession numbers FJ578007-FJ579096.
Primary Reference

Brandon F. Keele, Hui Li, Gerald H. Learn, Peter Hraber, Elena E. Giorgi, Truman Grayson, Chuanxi Sun, Yalu Chen, Wendy W. Yeh, Norman L. Letvin, Gary J. Nabel, Barton F. Haynes, Tanmoy Bhattacharya, Alan S. Perelson, Bette T. Korber, Beatrice H. Hahn and George M. Shaw.

Low Dose Rectal Inoculation of Rhesus Macaques by SIVsmE660 or SIVmac251 Recapitulates Human Mucosal Infection by HIV-1. J Exp Med, 2009 May 4.
PMID 19414559

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last modified: Mon Dec 20 13:31 2010

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