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Special Interest Data Set 1:
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.

Data

All alignments are env C2-V5 DNA sequences in Fasta format.

Sequence names (Mullins lab): patient | visit | clone | cell/plasma | clone

for example: 3V11X08 is patient 3, visit 11, cellular, clone 8
for example: 8V15P13 is patient 8, visit 15, plasma, clone 13

Alignment 1

1300 sequences associated with Shankarappa et al. 1999.
MACS pts 1, 2, 3, 5, 6, 7, 8, 9, 11.
Accession numbers AF137629-AF138703 & AF204402-AF204670.
Original alignment provided by the Mullins lab.
 

Alignment 2

212 sequences associated with Shriner et al. 2004.
MACS pts 2, 3, 7, 8, 9.
Accession numbers AY348333-AY348544.
Alignment prepared by the LANL HIV Database.
 

Alignment 3

250 sequences associated with Jensen et al. 2003.
MACS pt 4.
Accession numbers AY449806 - AY450055.
Original alignment provided by the Mullins lab.
 

Alignment 4

202 sequences associated with Jensen et al. 2003.
MACS pt 10.
Accession numbers AY450056 - AY450257.
Original alignment provided by the Mullins lab.
 

Alignment 5

5 unpublished sequences.
Additional unpublished sequences from MACS pt 11.
Original alignment provided by the Mullins lab.
 

Clinical Data

Viral load, CD3, CD4, CD8 and time post-seroconversion.
MACS pts 1 through 11.
Data provided by the Mullins lab.
Primary references

Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection.
J Virol. 1999 Dec;73(12):10489-502.
PMID 10559367
Supplemental information

Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI. Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.
J Virol. 2003 Dec;77(24):13376-88.
PMID 14645592

Shriner D, Shankarappa R, Jensen MA, Nickle DC, Mittler JE, Margolick JB, Mullins JI. Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection.
Genetics. 2004 Mar;166(3):1155-64.
PMID 15082537

Additional studies that used these data

Seo, TK, Thorne, JL. Hasegawa, M; Kishino, H. Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach.
Genetics. 2002 Apr;160(4):1283-93.
PMID 11973287

Guindon, S; Rodrigo, AG; Dyer, KA; Huelsenbeck, JP. Modeling the site-specific variation of selection patterns along lineages.
Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12957-62.
PMID 15326304

Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, Kelly JK. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients.
Mol Biol Evol. 2005 Apr;22(4):1157. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1157.
PMID 15509726

Huson, DH, Bryant, D. Application of phylogenetic networks in evolutionary studies.
Mol Biol Evol. 2006 Feb;23(2):254-67.
PMID 16221896

Carvajal-Rodriguez, A, Crandall, KA, Posada, D. Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method.
Mol Biol Evol. 2006 Apr;23(4):817-27.
PMID 16452117

Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, Rambaut A. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.
PLoS Comput Biol. 2007 Feb 16;3(2):e29.
PMID 17305421

Lee HY, Perelson AS, Park SC, Leitner T. Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression.
PLoS Comput Biol. 2008 Dec;4(12):e1000240.s
PMID 19079613

Neher RA, Leitner T. Recombination rate and selection strength in HIV intra-patient evolution.
PLoS Comput Biol. 2010 Jan 29;6(1):e1000660.
PMID 20126527

Skar H, Gutenkunst RN, Wilbe K, Alaeus A, Albert J, Leitner T. 2011. Persistence of multiple env subpopulations is consistent with neutrality during high-frequency sampling of a chronic HIV-1 patient.
PLoS One 6(8): e21747.
PMID 21829600

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last modified: Wed Sep 19 12:28 2012


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