Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission
Abstract
Some previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have been transmitted. Such forms may have advantages later in infection, and may thus be detected in follow-up samples. Furthermore, because HIV-1 frequently recombines, phylogenetic analyses that ignore recombination may miss transmission of multiple forms if they recombine after transmission. Moreover, recombination may facilitate adaptation, thus providing an advantage in establishing infection. The effect of recombination on viral evolution in HIV-1 infected children has not been well defined.
- Authors:
-
- Univ. of Massachusetts, Worcester, MA (United States). Dept. of Chemistry
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1236028
- Report Number(s):
- LA-UR-15-26872
Journal ID: ISSN 1742-4690; PII: 222
- Grant/Contract Number:
- R01AI097265; F32-AI108414; AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Retrovirology
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1742-4690
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; HV-1; MTCT; transmitted/founder virus; recombination; adaptation; evolutionary rate
Citation Formats
Sanborn, Keri B., Somasundaran, Mohan, Luzuriaga, Katherine, and Leitner, Thomas K. Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. United States: N. p., 2015.
Web. doi:10.1186/s12977-015-0222-0.
Sanborn, Keri B., Somasundaran, Mohan, Luzuriaga, Katherine, & Leitner, Thomas K. Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. United States. https://doi.org/10.1186/s12977-015-0222-0
Sanborn, Keri B., Somasundaran, Mohan, Luzuriaga, Katherine, and Leitner, Thomas K. Mon .
"Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission". United States. https://doi.org/10.1186/s12977-015-0222-0. https://www.osti.gov/servlets/purl/1236028.
@article{osti_1236028,
title = {Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission},
author = {Sanborn, Keri B. and Somasundaran, Mohan and Luzuriaga, Katherine and Leitner, Thomas K.},
abstractNote = {Some previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have been transmitted. Such forms may have advantages later in infection, and may thus be detected in follow-up samples. Furthermore, because HIV-1 frequently recombines, phylogenetic analyses that ignore recombination may miss transmission of multiple forms if they recombine after transmission. Moreover, recombination may facilitate adaptation, thus providing an advantage in establishing infection. The effect of recombination on viral evolution in HIV-1 infected children has not been well defined.},
doi = {10.1186/s12977-015-0222-0},
journal = {Retrovirology},
number = 1,
volume = 12,
place = {United States},
year = {Mon Nov 16 00:00:00 EST 2015},
month = {Mon Nov 16 00:00:00 EST 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 2 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1.
journal, October 1992
- Shioda, T.; Levy, J. A.; Cheng-Mayer, C.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 20
HIV/AIDS in Women: An Expanding Epidemic
journal, June 2005
- Quinn, T. C.
- Science, Vol. 308, Issue 5728
An exploratory algorithm to identify intra-host recombinant viral sequences
journal, November 2008
- Salemi, Marco; Gray, Rebecca R.; Goodenow, Maureen M.
- Molecular Phylogenetics and Evolution, Vol. 49, Issue 2
Correlation between HIV sequence evolution, specific immune response and clinical outcome in vertically infected infants
journal, January 1997
- Halapi, Eva; Leitner, Thomas; Jansson, Marianne
- AIDS, Vol. 11, Issue 14
Possible involvement of cell fusion and viral recombination in generation of human immunodeficiency virus variants that display dual resistance to AZT and 3TC
journal, October 1995
- Gu, Z.; Gao, Q.; Faust, E. A.
- Journal of General Virology, Vol. 76, Issue 10
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
journal, August 2006
- Anisimova, Maria; Gascuel, Olivier
- Systematic Biology, Vol. 55, Issue 4
The role of recombination in the emergence of a complex and dynamic HIV epidemic
journal, March 2010
- Zhang, Ming; Foley, Brian; Schultz, Anne-Kathrin
- Retrovirology, Vol. 7, Issue 1
Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny
journal, May 2014
- Romero-Severson, Ethan; Skar, Helena; Bulla, Ingo
- Molecular Biology and Evolution, Vol. 31, Issue 9
Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response
journal, April 2009
- Troyer, Ryan M.; McNevin, John; Liu, Yi
- PLoS Pathogens, Vol. 5, Issue 4
Rates of amino acid change in the envelope protein correlate with pathogenicity of primate lentiviruses
journal, July 1993
- Shpaer, EugeneG.; Mullins, JamesI.
- Journal of Molecular Evolution, Vol. 37, Issue 1
Genotypic and functional properties of early infant HIV-1 envelopes
journal, January 2011
- Kishko, Michael; Somasundaran, Mohan; Brewster, Frank
- Retrovirology, Vol. 8, Issue 1
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
journal, February 2006
- Bruen, Trevor C.; Philippe, Hervé; Bryant, David
- Genetics, Vol. 172, Issue 4
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
journal, January 2010
- Neher, Richard A.; Leitner, Thomas
- PLoS Computational Biology, Vol. 6, Issue 1
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
journal, January 2010
- Neher, Richard A.; Leitner, Thomas
- PLoS Computational Biology, Vol. 6, Issue 1
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
Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS
journal, October 1997
- Delwart, E. L.; Pan, H.; Sheppard, H. W.
- Journal of Virology, Vol. 71, Issue 10
Recent developments in the MAFFT multiple sequence alignment program
journal, March 2008
- Katoh, K.; Toh, H.
- Briefings in Bioinformatics, Vol. 9, Issue 4
Reduced evolutionary rates in HIV-1 reveal extensive latency periods among replicating lineages
journal, October 2014
- Immonen, Taina T.; Leitner, Thomas
- Retrovirology, Vol. 11, Issue 1
Evolution in Sexual and Asexual Populations
journal, November 1965
- Crow, James F.; Kimura, Motoo
- The American Naturalist, Vol. 99, Issue 909
Human immunodeficiency viruses
journal, May 1986
- Coffin, J.; Haase, A.; Levy, J.
- Science, Vol. 232, Issue 4751
Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers.
journal, March 1993
- Scarlatti, G.; Leitner, T.; Halapi, E.
- Proceedings of the National Academy of Sciences, Vol. 90, Issue 5
Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection
journal, December 1999
- Shankarappa, Raj; Margolick, Joseph B.; Gange, Stephen J.
- Journal of Virology, Vol. 73, Issue 12
Genotypic and functional properties of early infant HIV-1 envelopes
journal, January 2011
- Kishko, Michael; Somasundaran, Mohan; Brewster, Frank
- Retrovirology, Vol. 8, Issue 1
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
journal, October 2009
- Gouy, M.; Guindon, S.; Gascuel, O.
- Molecular Biology and Evolution, Vol. 27, Issue 2
Adaptive Evolution of Human Immunodeficiency Virus-Type 1 During the Natural Course of Infection
journal, April 1996
- Wolinsky, S. M.; Korber, B. T. M.; Neumann, A. U.
- Science, Vol. 272, Issue 5261
Recombination in HIV-1
journal, March 1995
- Robertson, David L.; Sharp, Paul M.; McCutchan, Francine E.
- Nature, Vol. 374, Issue 6518, p. 124-126
Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1
text, January 2014
- Moradigaravand, Danesh; Kouyos, Roger; Hinkley, Trevor
- Public Library of Science (PLoS)
A Statistical Characterization of Consistent Patterns of Human Immunodeficiency Virus Evolution Within Infected Patients
journal, October 2004
- Williamson, Scott; Perry, Steven M.; Bustamante, Carlos D.
- Molecular Biology and Evolution, Vol. 22, Issue 3
Why do RNA viruses recombine?
journal, July 2011
- Simon-Loriere, Etienne; Holmes, Edward C.
- Nature Reviews Microbiology, Vol. 9, Issue 8
Pervasive Genomic Recombination of HIV-1 in Vivo
journal, August 2004
- Shriner, Daniel; Rodrigo, Allen G.; Nickle, David C.
- Genetics, Vol. 167, Issue 4
Hypermutation of HIV-1 DNA in the Absence of the Vif Protein
journal, May 2003
- Lecossier, D.
- Science, Vol. 300, Issue 5622
Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality
journal, August 2011
- Skar, Helena; Gutenkunst, Ryan N.; Wilbe Ramsay, Karin
- PLoS ONE, Vol. 6, Issue 8
Biological and Molecular Characterization of Subtype D, G, and A/D Recombinant HIV-1 Transmissions in Sweden
journal, May 1995
- Leitner, Thomas; Escanilla, David; Marquina, Silvia
- Virology, Vol. 209, Issue 1
Genotypic and phenotypic characterization of HIV-1 patients with primary infection
journal, August 1993
- Zhu, T.; Mo, H.; Wang, N.
- Science, Vol. 261, Issue 5125
Pervasive Genomic Recombination of HIV-1 in Vivo
journal, August 2004
- Shriner, Daniel; Rodrigo, Allen G.; Nickle, David C.
- Genetics, Vol. 167, Issue 4
Dynamics of HIV-1 recombination in its natural target cells
journal, March 2004
- Levy, D. N.; Aldrovandi, G. M.; Kutsch, O.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 12
Intercompartmental Recombination of HIV-1 Contributes to env Intrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors
journal, April 2011
- Brown, R. J. P.; Peters, P. J.; Caron, C.
- Journal of Virology, Vol. 85, Issue 12
Evolution in Sexual and Asexual Populations
book, July 2017
- Crow, James F.; Kimura, Motoo
- Group Selection
Recombination in HIV-1
journal, March 1995
- Robertson, David L.; Sharp, Paul M.; McCutchan, Francine E.
- Nature, Vol. 374, Issue 6518, p. 124-126
Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission
journal, March 2004
- Derdeyn, C. A.
- Science, Vol. 303, Issue 5666
Transmission of HIV-1 in the Face of Neutralizing Antibodies
journal, November 2007
- Blish, Catherine; Blay, Wendy; Haigwood, Nancy
- Current HIV Research, Vol. 5, Issue 6
A Computer Program Designed to Screen Rapidly for HIV Type 1 Intersubtype Recombinant Sequences
journal, November 1995
- Siepel, Adam C.; Halpern, Aaron L.; Macken, Catherine
- AIDS Research and Human Retroviruses, Vol. 11, Issue 11
Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure.
journal, June 1996
- Moutouh, L.; Corbeil, J.; Richman, D. D.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 12
Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants
journal, February 1992
- Wolinsky, S.; Wike, C.; Korber, B.
- Science, Vol. 255, Issue 5048
Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
journal, December 2008
- Lee, Ha Youn; Perelson, Alan S.; Park, Su-Chan
- PLoS Computational Biology, Vol. 4, Issue 12
Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
journal, December 2008
- Lee, Ha Youn; Perelson, Alan S.; Park, Su-Chan
- PLoS Computational Biology, Vol. 4, Issue 12
Antibody neutralization and escape by HIV-1
journal, March 2003
- Wei, Xiping; Decker, Julie M.; Wang, Shuyi
- Nature, Vol. 422, Issue 6929
Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance
journal, February 1995
- Kellam, P.; Larder, B. A.
- Journal of Virology, Vol. 69, Issue 2
Recombination rate and selection strength in HIV intra-patient evolution
text, January 2010
- Neher, Richard A.; Leitner, Thomas
- Library of Science
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
text, January 2009
- S., Perelson, Alan; Christina, Ochsenbauer-Jambor,; C., Kappas, John
- The University of North Carolina at Chapel Hill University Libraries
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
Human Immunodeficiency Viruses
book, January 2015
- Reitz, Marvin S.; Gallo, Robert C.
- Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases
Selection for recombination in a polygenic model – the mechanism
journal, February 1988
- Smith, J. Maynard
- Genetical Research, Vol. 51, Issue 1
Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response
journal, April 2009
- Troyer, Ryan M.; McNevin, John; Liu, Yi
- PLoS Pathogens, Vol. 5, Issue 4
The Evolutionary Advantage of Recombination
journal, October 1974
- Felsenstein, Joseph
- Genetics, Vol. 78, Issue 2
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
journal, July 2005
- Guindon, S.; Lethiec, F.; Duroux, P.
- Nucleic Acids Research, Vol. 33, Issue Web Server
Human immunodeficiency viruses
journal, May 1986
- Coffin, J.; Haase, A.; Levy, J.
- Science, Vol. 232, Issue 4751
SplitsTree: analyzing and visualizing evolutionary data
journal, February 1998
- Huson, D. H.
- Bioinformatics, Vol. 14, Issue 1
Classification of Hypotheses on the Advantage of Amphimixis
journal, September 1993
- Kondrashov, A. S.
- Journal of Heredity, Vol. 84, Issue 5
Some Genetic Aspects of Sex
journal, March 1932
- Muller, H. J.
- The American Naturalist, Vol. 66, Issue 703
Adaptive value of sex in microbial pathogens
journal, May 2008
- Michod, Richard E.; Bernstein, Harris; Nedelcu, Aurora M.
- Infection, Genetics and Evolution, Vol. 8, Issue 3
Multidimensional epistasis and the disadvantage of sex
journal, October 2001
- Kondrashov, F. A.; Kondrashov, A. S.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 21
Recombination Accelerates Adaptation on a Large-Scale Empirical Fitness Landscape in HIV-1
journal, June 2014
- Moradigaravand, Danesh; Kouyos, Roger; Hinkley, Trevor
- PLoS Genetics, Vol. 10, Issue 6
APOBEC3F Properties and Hypermutation Preferences Indicate Activity against HIV-1 In Vivo
journal, August 2004
- Liddament, Mark T.; Brown, William L.; Schumacher, April J.
- Current Biology, Vol. 14, Issue 15
An exploratory algorithm to identify intra-host recombinant viral sequences
journal, November 2008
- Salemi, Marco; Gray, Rebecca R.; Goodenow, Maureen M.
- Molecular Phylogenetics and Evolution, Vol. 49, Issue 2
Transmission of HIV-1 in the Face of Neutralizing Antibodies
journal, November 2007
- Blish, Catherine; Blay, Wendy; Haigwood, Nancy
- Current HIV Research, Vol. 5, Issue 6
The genetical theory of natural selection.
book, January 1930
- Fisher, Ronald Aylmer
- Oxford, Clarendon Press, 1930
The Evolutionary Advantage of Recombination
journal, October 1974
- Felsenstein, Joseph
- Genetics, Vol. 78, Issue 2
Works referencing / citing this record:
Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation
journal, September 2017
- Romero-Severson, Ethan O.; Bulla, Ingo; Hengartner, Nick
- Genetics, Vol. 207, Issue 3