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Title: Molecular clock of HIV-1 envelope genes under early immune selection

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Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; Work for Others (WFO)
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1321764
Report Number(s):
Journal ID: ISSN 1742-4690; 38; PII: 269
Grant/Contract Number:  
Resource Type:
Published Article
Journal Name:
Additional Journal Information:
Journal Name: Retrovirology Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 1742-4690
Springer Science + Business Media
Country of Publication:
United Kingdom
59 BASIC BIOLOGICAL SCIENCES; biological science; HIV-1; envelope gene; molecular clock; mathematical model

Citation Formats

Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., and Lee, Ha Youn. Molecular clock of HIV-1 envelope genes under early immune selection. United Kingdom: N. p., 2016. Web. doi:10.1186/s12977-016-0269-6.
Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., & Lee, Ha Youn. Molecular clock of HIV-1 envelope genes under early immune selection. United Kingdom. doi:10.1186/s12977-016-0269-6.
Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., and Lee, Ha Youn. Wed . "Molecular clock of HIV-1 envelope genes under early immune selection". United Kingdom. doi:10.1186/s12977-016-0269-6.
title = {Molecular clock of HIV-1 envelope genes under early immune selection},
author = {Park, Sung Yong and Love, Tanzy M. T. and Perelson, Alan S. and Mack, Wendy J. and Lee, Ha Youn},
abstractNote = {},
doi = {10.1186/s12977-016-0269-6},
journal = {Retrovirology},
number = 1,
volume = 13,
place = {United Kingdom},
year = {2016},
month = {6}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s12977-016-0269-6

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Cited by: 2 works
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Works referenced in this record:

Dating the common ancestor of SIVcpz and HIV‐1 group M and the origin of HIV‐1 subtypes by using a new method to uncover clock‐like molecular evolution
journal, December 2000

  • Salemi, Marco; Strimmer, Korbinian; Hall, William W.
  • The FASEB Journal, Vol. 15, Issue 2
  • DOI: 10.1096/fj.00-0449fje

Unveiling the Molecular Clock in the Presence of Recombination
journal, October 2001

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
journal, June 2009

  • Goonetilleke, Nilu; Liu, Michael K. P.; Salazar-Gonzalez, Jesus F.
  • The Journal of Experimental Medicine, Vol. 206, Issue 6
  • DOI: 10.1084/jem.20090365

Primary Structure and Evolution of Cytochrome c
journal, October 1963

  • Margoliash, E.
  • Proceedings of the National Academy of Sciences, Vol. 50, Issue 4
  • DOI: 10.1073/pnas.50.4.672

Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1)
journal, June 2001

SPMM: estimating infection duration of multivariant HIV-1 infections
journal, December 2015

Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution
journal, January 2015

Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition
journal, December 1991

  • Phillips, Rodney E.; Rowland-Jones, Sarah; Nixon, Douglas F.
  • Nature, Vol. 354, Issue 6353
  • DOI: 10.1038/354453a0

Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform
journal, December 2013

  • Park, S. Y.; Goeken, N.; Lee, H. J.
  • Journal of Virology, Vol. 88, Issue 5
  • DOI: 10.1128/JVI.03128-13

Molecular clock of viral evolution, and the neutral theory.
journal, December 1990

  • Gojobori, T.; Moriyama, E. N.; Kimura, M.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 24
  • DOI: 10.1073/pnas.87.24.10015

A molecular timescale for vertebrate evolution
journal, April 1998

  • Kumar, Sudhir; Hedges, S. Blair
  • Nature, Vol. 392, Issue 6679
  • DOI: 10.1038/31927

The immune response during acute HIV-1 infection: clues for vaccine development
journal, December 2009

  • McMichael, Andrew J.; Borrow, Persephone; Tomaras, Georgia D.
  • Nature Reviews Immunology, Vol. 10, Issue 1
  • DOI: 10.1038/nri2674

Mutation rates in mammalian genomes
journal, January 2002

  • Kumar, S.; Subramanian, S.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 2
  • DOI: 10.1073/pnas.022629899

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
journal, June 2009

  • Salazar-Gonzalez, Jesus F.; Salazar, Maria G.; Keele, Brandon F.
  • The Journal of Experimental Medicine, Vol. 206, Issue 6
  • DOI: 10.1084/jem.20090378

Decay characteristics of HIV-1-infected compartments during combination therapy
journal, May 1997

  • Perelson, Alan S.; Essunger, Paulina; Cao, Yunzhen
  • Nature, Vol. 387, Issue 6629
  • DOI: 10.1038/387188a0

Molecular clocks: four decades of evolution
journal, August 2005

  • Kumar, Sudhir
  • Nature Reviews Genetics, Vol. 6, Issue 8
  • DOI: 10.1038/nrg1659

Quantitative Image Analysis of HIV-1 Infection in Lymphoid Tissue
journal, November 1996

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
journal, March 2010

Intra-host evolutionary rates in HIV-1C env and gag during primary infection
journal, October 2013

Timing the Ancestor of the HIV-1 Pandemic Strains
journal, June 2000

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
journal, April 2013

  • Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing
  • Nature, Vol. 496, Issue 7446
  • DOI: 10.1038/nature12053

Rate of HIV-1 decline following antiretroviral therapy is related to viral load at baseline and drug regimen
journal, January 1998

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
journal, May 2008

  • Keele, B. F.; Giorgi, E. E.; Salazar-Gonzalez, J. F.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 21
  • DOI: 10.1073/pnas.0802203105

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics
journal, January 2007

  • Lemey, Philippe; Kosakovsky Pond, Sergei L.; Drummond, Alexei J.
  • PLoS Computational Biology, Vol. 3, Issue 2
  • DOI: 10.1371/journal.pcbi.0030029

Amino-Acid Sequence Investigations of Fibrinopeptides from Various Mammals: Evolutionary Implications
journal, April 1964

  • Doolittle, Russell F.; BlombÄCk, Birger
  • Nature, Vol. 202, Issue 4928
  • DOI: 10.1038/202147a0

Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection
journal, August 2011

  • Ganusov, V. V.; Goonetilleke, N.; Liu, M. K. P.
  • Journal of Virology, Vol. 85, Issue 20
  • DOI: 10.1128/JVI.00655-11

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
journal, January 2014

Treatment response in acute/early infection versus advanced AIDS: equivalent first and second phases of HIV RNA decline
journal, January 2008

HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes
journal, January 2013

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
journal, October 2008

  • Worobey, Michael; Gemmel, Marlea; Teuwen, Dirk E.
  • Nature, Vol. 455, Issue 7213
  • DOI: 10.1038/nature07390

CD4 binding site broadly neutralizing antibody selection of HIV-1 escape mutants
journal, July 2015

  • Pade, Corinna; Dreja, Hanna; Chen, Lei
  • Journal of General Virology, Vol. 96, Issue 7
  • DOI: 10.1099/vir.0.000120

Rapid evolution of the neutralizing antibody response to HIV type 1 infection
journal, March 2003

  • Richman, D. D.; Wrin, T.; Little, S. J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
  • DOI: 10.1073/pnas.0630530100

Escape from highly effective public CD8+ T-cell clonotypes by HIV
journal, August 2011

Natural Variation in Vif: Differential Impact on APOBEC3G/3F and a Potential Role in HIV-1 Diversification
journal, January 2005

The molecular clock of HIV-1 unveiled through analysis of a known transmission history
journal, September 1999

  • Leitner, T.; Albert, J.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 19
  • DOI: 10.1073/pnas.96.19.10752

The early spread and epidemic ignition of HIV-1 in human populations
journal, October 2014

Modeling sequence evolution in acute HIV-1 infection
journal, November 2009

  • Lee, Ha Youn; Giorgi, Elena E.; Keele, Brandon F.
  • Journal of Theoretical Biology, Vol. 261, Issue 2
  • DOI: 10.1016/j.jtbi.2009.07.038

Designing a genome-based HIV incidence assay with high sensitivity and specificity
journal, January 2011

Immune Selection for Altered Antigen Processing Leads to Cytotoxic T Lymphocyte Escape in Chronic HIV-1 Infection
journal, April 2004

  • Draenert, Rika; Le Gall, Sylvie; Pfafferott, Katja J.
  • The Journal of Experimental Medicine, Vol. 199, Issue 7
  • DOI: 10.1084/jem.20031982

HIV-1 adaptation to HLA: a window into virus–host immune interactions
journal, April 2015

Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis
journal, February 2002

  • Jenkins, Gareth M.; Rambaut, Andrew; Pybus, Oliver G.
  • Journal of Molecular Evolution, Vol. 54, Issue 2
  • DOI: 10.1007/s00239-001-0064-3

Molecular clock-like evolution of human immunodeficiency virus type 1
journal, November 2004