Within-host and between-host evolutionary rates across the HIV-1 genome

Retrovirology

Volumn 10, Issue 1, 2013, Pages

  Alizon, Samuel ^a   Fraser, Christophe ^b  

^a University de Montpellier   (France)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ENVELOPE GENE; EVOLUTIONARY ADAPTATION; EVOLUTIONARY RATE; GENE LOCATION; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; STRAIN DIFFERENCE; STRUCTURAL GENE; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS TRANSMISSION;

EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; MUTATION RATE; PHYLOGENY; RNA, VIRAL;

HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84876878971     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-10-49     Document Type: Article

References (34)

1. 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, 73(12):10489-10502. 113104, 10559367.
2. Rambaut A, Posada D, Crandall KA, Holmes EC. The causes and consequences of HIV evolution. Nat Rev Genet 2004, 5:52-61. 10.1038/nrg1246, 14708016.
3. Levin BR, Bull JJ. Short-sighted evolution and the virulence of pathogenic microorganisms. Trends Microbiol 1994, 2(3):76-81. 10.1016/0966-842X(94)90538-X, 8156275.
4. Lemey P, Rambaut A, Pybus OG. HIV evolutionary dynamics within and among hosts. AIDS Rev 2006, 8(3):125-140.
5. Alizon S, Luciani F, Regoes RR. Epidemiological and clinical consequences of within-host evolution. Trends Microbiol 2011, 19:24-32. 10.1016/j.tim.2010.09.005, 21055948.
6. Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet 2009, 10(8):540-550. 10.1038/nrg2583, 19564871.
7. Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol Biol 2011, 11:131. 10.1186/1471-2148-11-131, 3112090, 21595904.
8. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. Measurably evolving populations. Trends Ecol Evol 2003, 18(9):481-488.
9. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006, 4(5):e88. 10.1371/journal.pbio.0040088, 1395354, 16683862.
10. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214, 2247476, 17996036.
11. Cao J, McNevin J, Malhotra U, McElrath MJ. Evolution of CD8+ T cell immunity and viral escape following acute HIV-1 infection. J Immunol 2003, 171(7):3837-3846.
12. Liu Y, McNevin J, Cao J, Zhao H, Genowati I, Wong K, McLaughlin S, McSweyn MD, Diem K, Stevens CE, Maenza J, He H, Nickle DC, Shriner D, Holte SE, Collier AC, Corey L, McElrath MJ, Mullins JI. Selection on the human immunodeficiency virus type 1 proteome following primary infection. J Virol 2006, 80(19):9519-9529. 10.1128/JVI.00575-06, 1617227, 16973556.
13. Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol 2011, 85(15):7523-7534. 10.1128/JVI.02697-10, 3147913, 21593162.
14. Wang YE, Li B, Carlson JM, Streeck H, Gladden AD, Goodman R, Schneidewind A, Power KA, Toth I, Frahm N, Alter G, Brander C, Carrington M, Walker BD, Altfeld M, Heckerman D, Allen TM. Protective HLA class I alleles that restrict acute-phase CD8+ T-cell responses are associated with viral escape mutations located in highly conserved regions of human immunodeficiency virus type 1. J Virol 2009, 83(4):1845-1855. 10.1128/JVI.01061-08, 2643763, 19036810.
15. 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, 3(2):e29. 10.1371/journal.pcbi.0030029, 1797821, 17305421.
16. Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, Vandamme AM. The molecular population genetics of HIV-1 group O. Genetics 2004, 167(3):1059-1068. 10.1534/genetics.104.026666, 1470933, 15280223.
17. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 2012, 8(3):e1002529. 10.1371/journal.ppat.1002529, 3297584, 22412369.
18. Lythgoe K, Fraser C. New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels. Proc R Soc Lond B 2012, 279(1741):3367-3375.
19. Sharp PM. What can AIDS virus codon usage tell us?. Nature 1986, 324(6093):114. 10.1038/324114a0, 3641061.
20. Seo TK, Thorne JL, Hasegawa M, Kishino H. A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics 2002, 18:115-123. 10.1093/bioinformatics/18.1.115, 11836219.
21. Kemal KS, Beattie T, Dong T, Weiser B, Kaul R, Kuiken C, Sutton J, Lang D, Yang H, Peng YC, Collman R, Philpott S, Rowland-Jones S, Burger H. Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune control. J Acquir Immune Defic Syndr 2008, 48(2):119-126. 10.1097/QAI.0b013e31816b6abd, 18520675.
22. Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S. Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol 2009, 83(6):2715-2727. 10.1128/JVI.01960-08, 2648286, 19116249.
23. Fang G, Burger H, Chappey C, Rowland-Jones S, Visosky A, Chen CH, Moran T, Townsend L, Murray M, Weiser B. Analysis of transition from long-term nonprogressive to progressive infection identifies sequences that may attenuate HIV type 1. AIDS Res Hum Retroviruses 2001, 17(15):1395-1404. 10.1089/088922201753197060, 11679152.
24. Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova NL, Nowak MA, Hahn BH, Kwong PD, Shaw GM. Antibody neutralization and escape by HIV-1. Nature 2003, 422(6929):307-312. 10.1038/nature01470, 12646921.
25. Blankson JN, Bailey JR, Thayil S, Yang HC, Lassen K, Lai J, Gandhi SK, Siliciano JD, Williams TM, Siliciano RF. Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. J Virol 2007, 81(5):2508-2518. 10.1128/JVI.02165-06, 1865922, 17151109.
26. Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010, 27(2):221-224. 10.1093/molbev/msp259, 19854763.
27. Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20(2):289-290. 10.1093/bioinformatics/btg412, 14734327.
28. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26(19):2462-2463. 10.1093/bioinformatics/btq467, 2944210, 20798170.
29. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
30. Drummond A, Pybus OG, Rambaut A. Inference of viral evolutionary rates from molecular sequences. Adv Parasitol 2003, 54:331-358.
31. Ramsden C, Holmes EC, Charleston MA. Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol 2009, 26:143-153.
32. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol 2008, 25(7):1253-1256. 10.1093/molbev/msn083, 18397919.
33. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005, 22(5):1185-1192. 10.1093/molbev/msi103, 15703244.
34. Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 2001, 18(6):1001-1013. 10.1093/oxfordjournals.molbev.a003872, 11371589.