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HIV sequence database

Special Interest Data Set 5
Acute infection sequences: subtype C env


Set of 1505 full-length env sequences from 69 patients in early stages of infection with HIV-1 subtype C. For each patient, there are approximately 22 sequences plus a consensus sequence.


→ Data (.zip)

The zip file contains 4 files:

  • n1505_acuteC_env.fasta (all sequences, including consensus for each patient)
  • n69_patientConsensuses.fasta (just the consensus sequence for each patient)
  • n1505_acuteC_env.csv

Sequences correspond to accession numbers FJ443128-FJ444632.

Additional details are explained in the README file.

Primary reference

Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium.
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants.
J Virol. 2009 Apr;83(8):3556-67.
PMID 19193811

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last modified: Thu Dec 12 10:57 2013

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