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:
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
PMID 10559367
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Description | In-depth longitudinal sequences from a single subject, together with clinical and antibody neutralization data. |
References |
Liao et al. Nature 2013 PMID 23552890 |
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Description | Longitudinal study of viral genetic changes and T-cell immunity in one subject at 17 time points during the first 3 years of infection. |
References |
Liu et al. J Virol 2006 PMID 16973556
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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 USA PMID 8855273 |
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Description | Data from two studies of Belgian patients with a known transmission chain. |
References | Lemey et al. J Virol 2005
PMID 16140774
Vrancken et al. PLoS Comput Biol. 2014 PMID 24699231 |
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Description | Set of 567 subtype B env sequences from 37 subjects prior to seroconversion. |
Reference | Gottlieb et al. J Infect Dis. 2008 PMID 18419538 |
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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 PMID 18490657 |
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Description | Set of 1407 subtype B env sequences from 30 subjects during early infection. |
Reference | Li et al. PLOS Pathogens 2010 PMID 20485520 |
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Description | Set of 1505 subtype C env sequences from 69 patients in early infection. A CHAVI study. |
Reference | Abrahams et al. J Virol. 2009 PMID 19193811 |
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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 PMID 19487424 |
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Description | Set of 393 subtype B env sequences from 10 intravenous drug users during early infection. |
Reference | Bar et al. J Virol. 2010 PMID 20375173 |
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Description | Half-genome and full-genome alignments from 12 patients. |
Reference | Baalwa et al. Virology. 2013 PMID 23123038 |
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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 PMID 19414559 |
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Description | A large panel of Env-pseudotyped viruses assayed against plasmas from chronic infection. Both were selected to represent M-group diversity. |
References | Hraber et al. J Virol. 2014
PMID 25142591
deCamp et al. J Virol. 2014 PMID 24352443 Hraber et al. AIDS. 2014 PMID 24361678 |
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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
PMID 16051804
Mascola et al. J Virol. 2005 PMID 16051803 Montefiori et al. 2008 Registry (PDF) |
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Description | A preventative vaccine trial with sequences from 68 newly-infected participants. |
Reference | Rolland et al. 2011 Nature Medicine PMID 21358627 |
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Description | A preventative vaccine trial with sequences from 121 participants. |
Reference | Rolland et al. 2012 Nature PMID 22960785 |
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