Special Interest Alignments
Purpose: To provide easy access to published HIV and SIV sequence alignments and accompanying data. For each set of data, we provide aligned DNA sequences and any other accompanying data that are available. Sets are selected for inclusion based on the availability of data and the likelihood that other researchers will have an interest in using them.
How to Cite: When using these data, please cite the primary reference(s) listed for the specific set of data.
Note: We consider these data to be a community effort that supports research in many fields. In order to provide these data, we need your help. Please contact us if:
- Your data are presented here, and you are able to provide more or better data than what is currently offered.
- You find any errors or inconsistencies.
- You know of any additional published studies that used or re-analyzed these data.
- You have an alignment that would be useful to include here.
Longitudinal Studies
Env evolution| Description | Env evolution was studied in 11 subjects infected with B-clade HIV-1 sampled over a period of approximately 6-12 years. Includes over 1900 clonal env C2-V5 sequences with associated clinical data. |
| References |
Shankarappa et al. J Virol. 1999 Dec;73(12):10489-502.
PMID 10559367
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| Data | Information and data... |
Transmission Chains
Swedish transmission chain| Description | Study of 11 Swedish patients with a known transmission chain. Includes alignments of 13 env V3 sequences and 13 gag p17 sequences plus associated clinical data and tree file. |
| Reference | Leitner et al. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10864-9. PMID 8855273 |
| Data | Information and data... |
| Description | Study of 9 patients with known transmission chain and treatment histories. Includes alignments of env and pol sequences. |
| Reference | Lemey et al. J Virol 2005 79(18): 11981-11989. PMID 16140774 |
| Data | Information and data... |
Acute Infection Studies
Pre-seroconversion sequences, subtype B env| Description | Set of 567 subtype B env sequences from 37 subjects prior to seroconversion. |
| Reference | Gottlieb et al. J Infect Dis. 2008 Apr 1;197(7):1011-5. PMID 18419538 |
| Data | Information and data... |
| Description | Set of 3449 subtype B env sequences from 102 subjects during early infection. A CHAVI study. |
| Reference | Keele et al. Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7. PMID 18490657 |
| Data | Information and data... |
| Description | Set of 1407 subtype B env sequences from 30 subjects during early infection. |
| Reference | Li et al. PLOS Pathogens 2010 May 13;6(5):e1000890. PMID 20485520 |
| Data | Information and data... |
| Description | Set of 1505 subtype C env sequences from 69 patients in early infection. A CHAVI study. |
| Reference | Abrahams et al. J Virol. 2009 Apr;83(8):3556-67. PMID 19193811 |
| Data | Information and data... |
| Description | Set of 129 full-length genome sequences from 12 patients in early infection, plus longitudinal sequences from 3 patients. A CHAVI study. |
| Reference | Salazar-Gonzalez et al. J Exp Med. 2009 Jun 8;206(6):1273-89. PMID 19487424 |
| Data | Information and data... |
| Description | Set of 393 subtype B env sequences from 10 intravenous drug users during early infection. |
| Reference | Bar et al. J Virol. 2010 Jun;84(12):6241-7. PMID 20375173 |
| Data | Information and data... |
SIV Sequences
SIV acute infection sequences| Description | Full-length env sequences from 18 experimentally infected Indian rhesus macaques (986 sequences) and 2 challenge stocks (SIVsmE660 and SIVmac251, 104 sequences). A CHAVI study. |
| Reference | Keele et al. J Exp Med. 2009 May 4. PMID 19414559 |
| Data | Information and data... |
Immunological Reagent Sequences
Standardized assessments of neutralizing antibodies| Description | A reference panel of Env-pseudotyped viruses to facilitate standardized assessments of neutralizing antibodies. The alignment includes 36 clade B and C gp120 sequences with reference sequences. |
| References | Li et al. J Virol. 2005 Aug;79(16):10108-25
PMID 16051804
Mascola et al. J Virol. 2005 Aug;79(16):10103-7. PMID 16051803 Montefiori et al. 2008 Registry (PDF) |
| Data | Information and data... |