New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels

Proceedings of the Royal Society B: Biological Sciences

Volumn 279, Issue 1741, 2012, Pages 3367-3375

  Lythgoe, Katrina A ^a   Fraser, Christophe ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

HIV; Mathematical model; Rate of evolution; Viral latency

Indexed keywords

DISEASE TRANSMISSION; DIVERGENCE; DRUG RESISTANCE; EPIDEMIC; EPIDEMIOLOGY; HUMAN IMMUNODEFICIENCY VIRUS; IMMUNE SYSTEM; MUTATION; NUMERICAL MODEL; PHYLOGENETICS; TEMPORAL VARIATION; VACCINE; VIRULENCE; VIRUS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84863863242     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2012.0595     Document Type: Article

References (52)

1. Shankarappa, R. et al. 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73, 10489-10502.
2. Wei, X. et al. 1995 Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373, 117-122. (doi:10.1038/373117a0)
3. Abecasis, A. B., Vandamme, A.-M. & Lemey, P. 2009 Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution. J. Virol. 83, 12917-12924. (doi:10.1128/JVI.01022-09)
4. Lemey, P., Kosakovsky Pond, S. L., Drummond, A. J., Pybus, O. G., Shapiro, B., Barroso, H., Taveira, N. & Rambaut, A. 2007 Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput. Biol. 3, e29. (doi:10.1371/journal.pcbi.0030029)
5. Lemey, P., Rambaut, A. & Pybus, O. G. 2006 HIV evolutionary dynamics within and among hosts. AIDS Rev. 8, 125-140.
6. Pybus, O. G. & Rambaut, A. 2009 Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540-550. (doi:10.1038/nrg2583)
7. Herbeck, J.T., Nickle, D. C., Learn, G. H., Gottlieb, G. S., Curlin, M. E., Heath, L. & Mullins, J. I. 2006 Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. J. Virol. 80, 1637-1644. (doi:10.1128/JVI.80.4.1637)
8. Herbeck, J. T. et al. 2011 Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J. Virol. 85, 7523-7534. (doi:10.1128/JVI.02697-10)
9. Redd, A. et al. 2011 Previously transmitted HIV-1 viral strains are preferentially selected for during subsequent sexual transmissions. 18th Conference on Retroviruses and Opportunistic Infections, 27 February-2 March 2011, Boston, MA.
10. Maljkovic Berry, I., Ribeiro, R., Kothari, M., Athreya, G., Daniels, M., Lee, H. Y., Bruno, W. & Leitner, T. 2007 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, 10625-10635. (doi:10.1128/JVI.00985-07)
11. Keele, B. F. et al. 2008 Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl Acad. Sci. USA 105, 7552-7557. (doi:10.1073/pnas.0802203105)
12. Salazar-Gonzalez, J. F. et al. 2009 Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206, 1273-1289. (doi:10.1084/jem.20090378)
13. Fischer, W. et al. 2010 Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS ONE 5, e12303. (doi:10.1371/journal.pone.0012303)
14. Henn, M. R. et al. 2012 Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 8, e1002529. (doi:10.1371/journal.ppat.1002529)
15. Neher, R. A. & Leitner, T. 2010 Recombination rate and selection strength in HIV intra-patient evolution. PLoS Comput. Biol. 6, e1000660. (doi:10.1371/journal.pcbi.1000660)
16. Cuevas, J. M., Domingo-Calap, P. & Sanjuán, R. 2011 The fitness effects of synonymous mutations in DNA and RNA viruses. Mol. Biol. Evol. 29, 17-20. (doi:10.1093/molbev/msr179)
17. Sanjuán, R. & Bordería, A. V. 2011 Interplay between RNA structure and protein evolution in HIV-1. Mol. Biol. Evol. 28, 1333-1338. (doi:10.1093/molbev/msq329)
18. Le, S.-Y, Chen, J.-H, Braun, M. J., Gonda, M. A. & Maizel, J. V. 1988 Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-1). Nucleic Acids Res. 16, 5153-5168. (doi:10.1093/nar/16.11.5153)
19. Matthews, P. C. et al. 2008 Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J. Virol. 82, 8548-8559. (doi:10.1128/JVI.00580-08)
20. Little, S. J., Frost, S. D. W., Wong, J. K., Smith, D. M., Pond, S. L. K., Ignacio, C. C., Parkin, N. T., Petropoulos, C. J. & Richman, D. D. 2008 Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J. Virol. 82, 5510-5518. (doi:10.1128/JVI.02579-07)
21. Leslie, A. J. et al. 2004 HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10, 282-289. (doi:10.1038/nm992)
22. Fryer, H. R., McLean, A. R., Frater, J., Duda, A., Roberts, M. G. & Phillips, R. E. 2010 Modelling the spread of HIV immune escape mutants in a vaccinated population. PLoS Pathog. 6, e1001196. (doi:10.1371/journal.ppat.1001196)
23. Kelly, J. K. 1996 Replication rate and evolution in the human immunodeficiency virus. J. Theor. Biol. 180, 359-364. (doi:10.1006/jtbi.1996.0108)
24. Kelly, J. K., Williamson, S., Orive, M. E., Smith, M. S. & Holt, R. D. 2003 Linking dynamical and population genetic models of persistent viral infection. Am. Nat. 162, 14-28. (doi:10.1086/375543)
25. Stevenson, M., Stanwick, T. L., Dempsey, M. P. & Lamonica, C. A. 1990 HIV-1 replication is controlled at the level of T cell activation and proviral integration. EMBO J. 9, 1551-1560.
26. Ho, D. D., Neumann, A. U., Perelson, A. S., Chen, W., Leonard, J. M. & Markowitz, M. 1995 Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373, 123-126. (doi:10.1038/373123a0)
27. Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M. & Ho, D. D. 1996 HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271, 1582-1586. (doi:10.1126/science.271.5255.1582)
28. Finzi, D. et al. 1997 Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278, 1295-1300. (doi:10.1126/science.278.5341.1295)
29. + T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5, 512-517. (doi:10.1038/8394)
30. Dinoso, J. B. et al. 2009 Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc. Natl Acad. Sci. USA 106, 9403-9408. (doi:10.1073/pnas.0903107106)
31. Gandhi, R. T. et al. 2010 No evidence for decay of the latent reservoir in HIV-1-infected patients receiving intensive enfuvirtide-containing antiretroviral therapy. J. Infect. Dis. 201, 293-296. (doi:10.1086/649569)
32. + T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J. Virol. 83, 8470-8481. (doi:10.1128/JVI.02568-08)
33. Sagar, M. et al. 2009 Selection of HIV variants with signature genotypic characteristics during heterosexual transmission. J. Infect. Dis. 199, 580-589. (doi:10.1086/596557)
34. Li, H. et al. 2010 High multiplicity infection by HIV-1 in men who have sex with men. PLoS Pathog. 6, e1000890. (doi:10.1371/journal.ppat.1000890)
35. Boeras, D. I. et al. 2011 Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc. Natl Acad. Sci. USA 108, E1156-E1163. (doi:10.1073/pnas.1103764108)
36. Keele, B. F. et al. 2009 Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J. Exp. Med. 206, 1117-1134. (doi:10.1084/jem.20082831)
37. Haase, A. T. 2010 Targeting early infection to prevent HIV-1 mucosal transmission. Nature 464, 217. (doi:10.1038/nature08757)
38. Goepfert, P. A. et al. 2008 Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J. Exp. Med. 205, 1009-1017. (doi:10.1084/jem.20072457)
39. Miura, T. et al. 2010 Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J. Virol. 84, 7581-7591. (doi:10.1128/JVI.00286-10)
40. Go, E. P., Hewawasam, G., Liao, H.-X., Chen, H., Ping, L.-H., Anderson, J. A., Hua, D. C., Haynes, B. F. & Desaire, H. 2011 Characterization of glycosylation profiles of HIV-1 transmitted/founder envelopes by mass spectrometry. J. Virol. 85, 8270-8284. (doi:10.1128/JVI.05053-11)
41. Gnanakaran, S. et al. 2011 Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog. 7, e1002209. (doi:10.1371/journal.ppat.1002209)
42. + T cells as key targets in mucosal transmission. PLoS Pathog. 7, e1001301. (doi:10.1371/journal.ppat.1001301)
43. Scarlatti, G. et al. 1997 In vivo evolution of HIV-1 coreceptor usage and sensitivity to chemokine-mediated suppression. Nat. Med. 3, 1259-1265. (doi:10.1038/nm1197-1259)
44. Raymond, S. et al. 2011 Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing. AIDS 25, 1668-1670. (doi:10.1097/QAD.0b013e3283498305)
45. Chalmet, K. et al. 2011 Presence of CXCR4-using HIV-1 in patients with recently diagnosed infection: correlates and evidence for transmission. J. Infect. Dis. 205, 174-184. (doi:10.1093/infdis/jir714)
46. Nowak, M. & May, R. M. 2000 Virus dynamics: mathematical principles of immunology and virology. Oxford, UK: Oxford University Press.
47. Kimura, M. 1985 The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press.
48. Hollingsworth, T. D., Anderson, R. M. & Fraser, C. 2008 HIV-1 transmission, by stage of infection. J. Infect. Dis. 198, 687-693. (doi:10.1086/590501)
49. Wawer, M. J. et al. 2005 Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda. J. Infect. Dis. 191, 1403-1409. (doi:10.1086/429411)
50. Wensing, M. J., van de Vijver, D. A., Angarano, G., Al, E., Asjo, B., Balotta, C. & Boeri, E. 2005 Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J. Infect. Dis. 192, 958-966. (doi:10.1086/432916)
51. Yerly, S., Junier, T., Gayet-Ageron, A., Amari, E. B. E., von Wyl, V., Gunthard, H. F., Hirschel, B., Zdobnov, E. & Kaiser, L. 2009 The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS 23, 1415-1423. (doi:10.1097/QAD. 0b013e32832d40ad)
52. Abbas, U. L., Hood, G., Wetzel, A. W. & Mellors, J. W. 2011 Factors influencing the emergence and spread of HIV drug resistance arising from rollout of antiretroviral pre-exposure prophylaxis (PrEP). PLoS ONE 6, e18165. (doi:10.1371/journal.pone.0018165)