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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:


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 PMID 10559367
Jensen et al. J Virol. 2003 PMID 14645592
Shriner et al. Genetics. 2004 PMID 15082537

Data Details...
Env/Antibody co-evolution
Description In-depth longitudinal sequences from a single subject, together with clinical and antibody neutralization data.
References

Liao et al. Nature 2013 PMID 23552890

Data Details...
Longitudinal CTL Responses
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
Liu et al. J Virol 2007 PMID 17728222
Liu et al. PLoS One 2011 PMID 21283794

Data Details...

 

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 USA PMID 8855273
Data Details...
Belgian transmission chain
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
Data Details...

 

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 PMID 18419538
Data Details...
Acute infection sequences, subtype B env
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
Data Details...
Acute infection sequences, subtype B env
Description Set of 1407 subtype B env sequences from 30 subjects during early infection.
Reference Li et al. PLOS Pathogens 2010 PMID 20485520
Data Details...
Acute infection sequences, subtype C env
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
Data Details...
Acute infection sequences, full-length genomes
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

Data Details...
Acute infection sequences, subtype B, 3' half-genomes
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
Data Details...
Transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones
Description Half-genome and full-genome alignments from 12 patients.
Reference Baalwa et al. Virology. 2013 PMID 23123038
Data Details...

 

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 PMID 19414559
Data Details...

 

Immunological Reagent Sequences

Neutralization Serotype Discovery Panel
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
Data Details...
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 PMID 16051804
Mascola et al. J Virol. 2005 PMID 16051803
Montefiori et al. 2008 Registry (PDF)
Data Details...

 

 

 

 

last modified: Mon Jul 20 12:03 2015


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