Intra-host evolutionary rates in HIV-1C env and gag during primary infection.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

Volumn 19, Issue , 2013, Pages 361-368

  Novitsky, Vlad ^a   Wang, Rui ^b   Rossenkhan, Raabya ^b   Moyo, Sikhulile ^b   Essex, M ^b  

^a Harvard AIDS Institute   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; CODON; GAG PROTEIN; GLYCOPROTEIN GP 120;

ADULT; CLASSIFICATION; CODON; COHORT ANALYSIS; DRUG EFFECTS; FEMALE; GENETICS; HIV INFECTIONS; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MALE; MIDDLE AGED; MOLECULAR EVOLUTION; MUTATION; NONPARAMETRIC TEST; VIROLOGY; VIRUS LOAD; YOUNG ADULT;

ADULT; ANTI-RETROVIRAL AGENTS; CODON; COHORT STUDIES; EVOLUTION, MOLECULAR; FEMALE; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HOST-PATHOGEN INTERACTIONS; HUMANS; MALE; MIDDLE AGED; MUTATION; STATISTICS, NONPARAMETRIC; VIRAL LOAD; YOUNG ADULT;

EID: 84900179100     PISSN: None     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2013.02.023     Document Type: Article

References (54)

1. A.B. Abecasis A.-M. Vandamme P. Lemey Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution J. Virol. 83 2009 12917 12924
2. J.M. Coffin S.H. Hughes H.E. Varmus Retroviruses 1997 Cold Spring Laboratory Press Cold Spring Harbor, NY
3. A.J. Drummond S.Y. Ho M.J. Phillips A. Rambaut Relaxed phylogenetics and dating with confidence PLoS Biol. 4 2006 e88
4. A.J. Drummond A. Rambaut BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol. Biol. 7 2007 214
5. S. Duffy L.A. Shackelton E.C. Holmes Rates of evolutionary change in viruses: patterns and determinants Nat. Rev. Genet. 9 2008 267 276
6. K.A. Dugan H.S. Lawrence D.R. Hares C.L. Fisher B. Budowle An improved method for post-PCR purification for mtDNA sequence analysis J. Forensic Sci. 47 2002 811 818
7. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
8. D. Edo-Matas P. Lemey J.A. Tom C. Serna-Bolea A.E. van den Blink A.B. van ‘t Wout H. Schuitemaker M.A. Suchard Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models Mol. Biol. Evol. 28 2011 1605 1616
9. C.T.T. Edwards E.C. Holmes O.G. Pybus D.J. Wilson R.P. Viscidi E.J. Abrams R.E. Phillips A.J. Drummond Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection Genetics 174 2006 1441 1453
10. T.C. Friedrich E.J. Dodds L.J. Yant L. Vojnov R. Rudersdorf C. Cullen D.T. Evans R.C. Desrosiers B.R. Mothe J. Sidney A. Sette K. Kunstman S. Wolinsky M. Piatak J. Lifson A.L. Hughes N. Wilson D.H. O’Connor D.I. Watkins Reversion of CTL escape-variant immunodeficiency viruses in vivo Nat. Med. 10 2004 275 281
11. T. Gojobori E.N. Moriyama M. Kimura Molecular clock of viral evolution, and the neutral theory Proc. Natl. Acad. Sci. USA 87 1990 10015 10018
12. J. Goudsmit V.V. Lukashov Dating the origin of HIV-1 subtypes Nature 400 1999 325 326
13. R.R. Gray J. Parker P. Lemey M. Salemi A. Katzourakis O.G. Pybus The mode and tempo of hepatitis C virus evolution within and among hosts BMC Evol. Biol. 11 2011 131
14. S. Guindon F. Delsuc J.F. Dufayard O. Gascuel Estimating maximum likelihood phylogenies with PhyML Methods Mol. Biol. 537 2009 113 137
15. S. Guindon J.F. Dufayard V. Lefort M. Anisimova W. Hordijk O. Gascuel New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Syst. Biol. 59 2010 307 321
16. T.A. Hall BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl. Acids. Symp. Ser. 41 1999 95 98
17. G.M. Jenkins A. Rambaut O.G. Pybus E.C. Holmes Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis J. Mol. Evol. 54 2002 156 165
18. B. Korber M. Muldoon J. Theiler F. Gao R. Gupta A. Lapedes B.H. Hahn S. Wolinsky T. Bhattacharya Timing the ancestor of the HIV-1 pandemic strains Science 288 2000 1789 1796
19. B. Korber J. Theiler S. Wolinsky Limitations of a molecular clock applied to considerations of the origin of HIV-1 Science 280 1998 1868 1871
20. H.Y. Lee A.S. Perelson S.C. Park T. Leitner Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression PLoS Comput. Biol. 4 2008 e1000240
21. T. Leitner J. Albert The molecular clock of HIV-1 unveiled through analysis of a known transmission history Proc. Natl. Acad. Sci. USA 96 1999 10752 10757
22. P. Lemey S.L. Kosakovsky Pond A.J. Drummond O.G. Pybus B. Shapiro H. Barroso N. Taveira A. Rambaut Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics PLoS Comput. Biol. 3 2007 e29
23. P. Lemey A. Rambaut O.G. Pybus HIV evolutionary dynamics within and among hosts AIDS Rev. 8 2006 125 140
24. A.J. Leslie K.J. Pfafferott P. Chetty R. Draenert M.M. Addo M. Feeney Y. Tang E.C. Holmes T. Allen J.G. Prado M. Altfeld C. Brander C. Dixon D. Ramduth P. Jeena S.A. Thomas A. St John T.A. Roach B. Kupfer G. Luzzi A. Edwards G. Taylor H. Lyall G. Tudor-Williams V. Novelli J. Martinez-Picado P. Kiepiela B.D. Walker P.J. Goulder HIV evolution: CTL escape mutation and reversion after transmission Nat. Med. 10 2004 282 289
25. B. Li A.D. Gladden M. Altfeld J.M. Kaldor D.A. Cooper A.D. Kelleher T.M. Allen Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution J. Virol. 81 2007 193 201
26. W.H. Li M. Tanimura P.M. Sharp Rates and dates of divergence between AIDS virus nucleotide sequences Mol. Biol. Evol. 5 1988 313 330
27. S.-L. Liu A.G. Rodrigo R. Shankarappa G.H. Learn L. Hsu O. Davidov L.P. Zhao J.I. Mullins B.F. Haynes G. Pantaleo A.S. Fauci HIV quasispecies and resampling Science 273 1996 413c 417
28. I. Maljkovic Berry R. Ribeiro M. Kothari G. Athreya M. Daniels H.Y. Lee W. Bruno T. Leitner Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases J. Virol. 81 2007 10625 10635
29. V. Novitsky E. Woldegabriel C. Wester E. McDonald R. Rossenkhan M. Ketunuti J. Makhema G.R. Seage 3rd M. Essex Identification of primary HIV-1C infection in Botswana. NIHMSID # 79283 AIDS Care 20 2008 806 811
30. V. Novitsky S. Lagakos M. Herzig C. Bonney L. Kebaabetswe R. Rossenkhan D. Nkwe L. Margolin R. Musonda S. Moyo E. Woldegabriel E. van Widenfelt J. Makhema M. Essex Evolution of proviral gp120 over the first year of HIV-1 subtype C infection. NIHMSID # 79286 Virology 383 2009 47 59
31. V. Novitsky R. Wang L. Margolin J. Baca L. Kebaabetswe R. Rossenkhan C. Bonney M. Herzig D. Nkwe S. Moyo R. Musonda E. Woldegabriel E. van Widenfelt J. Makhema S. Lagakos M. Essex Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection PLoS One 4 2009 e7727
32. V. Novitsky E. Woldegabriel L. Kebaabetswe R. Rossenkhan B. Mlotshwa C. Bonney M. Finucane R. Musonda S. Moyo C. Wester E. van Widenfelt J. Makhema S. Lagakos M. Essex Viral Load and CD4+ T cell dynamics in primary HIV-1 subtype C infection J. Acquir. Immune Defic. Syndr. 50 2009 65 76
33. V. Novitsky R. Wang H. Bussmann S. Lockman M. Baum R. Shapiro I. Thior C. Wester C.W. Wester A. Ogwu A. Asmelash R. Musonda A. Campa S. Moyo E. van Widenfelt M. Mine C. Moffat M. Mmalane J. Makhema R. Marlink P. Gilbert G.R. Seage 3rd V. DeGruttola M. Essex HIV-1 subtype C-infected individuals maintaining high viral load as potential targets for the “test-and-treat” approach to reduce HIV transmission PLoS One 5 2010 e10148
34. V. Novitsky R. Wang L. Margolin J. Baca S. Moyo R. Musonda M. Essex Dynamics and timing of in vivo mutations at Gag residue 242 during primary HIV-1 subtype C infection Virology 403 2010 37 46
35. V. Novitsky T. Ndung’u R. Wang H. Bussmann F. Chonco J. Makhema V. De Gruttola B.D. Walker M. Essex Extended high viremics: a substantial fraction of individuals maintain high plasma viral RNA levels after acute HIV-1 subtype C infection AIDS 25 2011 1515 1522
36. V. Novitsky R. Wang J. Baca L. Margolin M.F. McLane S. Moyo E. van Widenfelt J. Makhema M. Essex Evolutionary gamut of in vivo Gag substitutions during early HIV-1 subtype C infection Virology 421 2011 119 128
37. V. Novitsky R. Wang L. Margolin J. Baca R. Rossenkhan S. Moyo E. van Widenfelt M. Essex Transmission of single and multiple viral variants in primary HIV-1 subtype C infection PLoS One 6 2011 e16714
38. S. Palmer M. Kearney F. Maldarelli E.K. Halvas C.J. Bixby H. Bazmi D. Rock J. Falloon R.T. Davey Jr. R.L. Dewar J.A. Metcalf S. Hammer J.W. Mellors J.M. Coffin Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis J. Clin. Microbiol. 43 2005 406 413
39. A.S. Perelson A.U. Neumann M. Markowitz J.M. Leonard D.D. Ho HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time Science 271 1996 1582 1587
40. D. Posada JModelTest: phylogenetic model averaging Mol. Biol. Evol. 25 2008 1253 1256
41. B.D. Preston B.J. Poiesz L.A. Loeb Fidelity of HIV-1 reverse transciptase Science 242 1988 1168 1171
42. O.G. Pybus A. Rambaut Evolutionary analysis of the dynamics of viral infectious disease Nat. Rev. Genet. 10 2009 540 550
43. A. Rambaut D. Posada K.A. Crandall E.C. Holmes The causes and consequences of HIV evolution Nat. Rev. Genet. 5 2004 52 61
44. P.P. Rose B.T. Korber Detecting hypermutations in viral sequences with an emphasis on G → A hypermutation Bioinformatics 16 2000 400 401
45. M. Salemi K. Strimmer W.W. Hall M. Duffy E. Delaporte S. Mboup M. Peeters A.M. Vandamme Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution FASEB J. 15 2001 276 278
46. R. Shankarappa J.B. Margolick S.J. Gange A.G. Rodrigo D. Upchurch H. Farzadegan P. Gupta C.R. Rinaldo G.H. Learn X. He X.L. Huang J.I. Mullins Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection J. Virol. 73 1999 10489 10502
47. D. Shriner R. Shankarappa M.A. Jensen D.C. Nickle J.E. Mittler J.B. Margolick J.I. Mullins Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection Genetics 166 2004 1155 1164
48. T. Stadler R. Kouyos V. von Wyl S. Yerly J. Boni P. Burgisser T. Klimkait B. Joos P. Rieder D. Xie H.F. Gunthard A.J. Drummond S. Bonhoeffer Estimating the basic reproductive number from viral sequence data Mol. Biol. Evol. 29 2012 347 357
49. Y. Suzuki Y. Yamaguchi-Kabata T. Gojobori Nucleotide substitution rates of HIV-1 AIDS Rev. 2 2000 39 47
50. P.R. Walker O.G. Pybus A. Rambaut E.C. Holmes Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth Infect. Genet. Evol. 5 2005 199 208
51. S. Williamson Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression Mol. Biol. Evol. 20 2003 1318 1325
52. S.M. Wolinsky B.T. Korber A.U. Neumann M. Daniels K.J. Kunstman A.J. Whetsell M.R. Furtado Y. Cao D.D. Ho J.T. Safrit Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection Science 272 1996 537 542 [see comments]
53. Z. Yang A.D. Yoder Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species Syst. Biol. 52 2003 705 716
54. K. Yusim M. Peeters O.G. Pybus T. Bhattacharya E. Delaporte C. Mulanga M. Muldoon J. Theiler B. Korber Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution. Philosophical transactions of the Royal Society of London, Series B, Biol. Sci. 356 2001 855 866