A novel methodology for large-scale phylogeny partition

Nature Communications

Volumn 2, Issue 1, 2011, Pages

  Prosperi, Mattia C F ^a,b,c   Ciccozzi, Massimo ^d   Fanti, Iuri ^a   Saladini, Francesco ^e   Pecorari, Monica ^f   Borghi, Vanni ^f   Di Giambenedetto, Simona ^a   Bruzzone, Bianca ^g   Capetti, Amedeo ^h   Vivarelli, Angela ⁱ   Rusconi, Stefano ^h   Re, Maria Carla ^j   Gismondo, Maria Rita ^h   Sighinolfi, Laura ^k   Gray, Rebecca R ^b,c   Salemi, Marco ^b,c   Zazzi, Maurizio ^e   De Luca, Andrea ^a,l  

^a CATHOLIC UNIVERSITY   (Italy)

^b UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF FLORIDA   (United States)

^d ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^e UNIVERSITY OF SIENA   (Italy)

^f Modena Hospital   (Italy)

^g UNIVERSITY OF GENOA   (Italy)

^h UNIVERSITY OF MILAN   (Italy)

ⁱ PISTOIA HOSPITAL   (Italy)

^j UNIVERSITY OF BOLOGNA   (Italy)

^k S ANNA HOSPITAL   (Italy)

^l UNIVERSITY HOSPITAL OF SIENA   (Italy)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CONJUGATE; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; LARGE SCALE PRODUCTION; MALE; METHODOLOGY; NONHUMAN; PHYLOGENY; RELIABILITY; VALIDATION STUDY; CLASSIFICATION; DISEASE TRANSMISSION; EVALUATION; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; ISOLATION AND PURIFICATION; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

POL PROTEIN;

ALGORITHMS; CLASSIFICATION; FEMALE; GENE PRODUCTS, POL; HIV INFECTIONS; HIV-1; HUMANS; MALE; PHYLOGENY;

EID: 79957564900     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms1325     Document Type: Article

References (41)

1. Perrin, L., Kaiser, L. & Yerly, S. Travel and the spread of HIV-1 genetic variants. Lancet Infect. Dis. 3, 22-27 (2003).
2. Gray, R. R. et al. Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 23, F9-F17 (2009).
3. Resik, S. et al. Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. AIDS Res. Hum. Retroviruses 23, 347-356 (2007).
4. Brown, A. E. et al. Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions. J. Infect. Dis. 199, 427-431 (2009).
5. Hué, S., Clewley, J. P., Cane, P. A. & Pillay, D. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 18, 719-728 (2004).
6. Wilson, D. P., Law, M. G., Grulich, A. E., Cooper, D. A. & Kaldor, J. M. Relation between HIV viral load and infectiousness: a model-based analysis. Lancet 372, 314-320 (2008).
7. Marcelin, A. G. et al. Detection of HIV-1 RNA in seminal plasma samples from treated patients with undetectable HIV-1 RNA in blood plasma. AIDS 22, 1677-1679 (2008).
8. Attia, S., Egger, M., Mueller, M., Zwahlen, M. & Low, N. Sexual transmission of HIV according to viral load and antiretroviral therapy: systematic review and meta-analysis. AIDS 23, 1397-1404 (2009).
9. Wensing, A. M. et al. Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J. Infect. Dis. 192, 958-966 (2005).
10. Pillay, D. et al. The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS 20, 21-28 (2006).
11. Di Giambenedetto, S. et al. Declining prevalence of HIV-1 drug resistance in treatment-failing patients: a clinical cohort study. Antivir. Ther. 12, 835-839 (2007).
12. Marks, A. J., Pillay, D. & McLean, A. R. The effect of intrinsic stochasticity on transmitted HIV drug resistance patterns. J. Theor. Biol. 262, 1-13 (2010).
13. Brenner, B. G. et al. Transmission networks of drug resistance acquired in primary/early stage HIV infection. AIDS 22, 2509-2515 (2008).
14. Recordon-Pinson, P. et al. HIV type-1 transmission dynamics in recent seroconverters: relationship with transmission of drug resistance and viral diversity. Antivir. Ther. 14, 551-556 (2009).
15. Lewis, F., Hughes, G. J., Rambaut, A., Pozniak, A. & Leigh Brown, A. J. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 5, e50 (2008).
16. Hué, S., Gifford, R. J., Dunn, D., Fernhill, E. & Pillay, D. Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naïve individuals. J. Virol. 83, 2645-2654 (2009).
17. Hughes, G. J. et al. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog. 5, e1000590 (2009).
18. Fisher, M. et al. Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach. AIDS 24, 1739-1747 (2010).
19. Yerly, S. et al. The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS 23, 1415-1423 (2009).
20. Kouyos, R. D. et al. Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J. Infect. Dis. 201, 1488-1497 (2010).
21. Ragonnet-Cronin, M. et al. Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics. J. Acquir. Immune. Defic. Syndr. 55, 102-108 (2010).
22. Bezemer, D. et al. Transmission networks of HIV-1 among men having sex with men in the Netherlands. AIDS 24, 271-282 (2010).
23. Wicker, N., Perrin, G. R., Thierry, J. C. & Poch, O. Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol. Biol. Evol. 18, 1435-1441 (2001).
24. Archer, J. & Robertson, D. L. CTree: comparison of clusters between phylogenetic trees made easy. Bioinformatics 23, 2952-2953 (2007).
25. Razzolini, F. et al. Three-class-resistant human immunodeficiency virus type 1 variant in a drug-naive heterosexual couple. J. Clin. Microbiol. 46, 3856-3859 (2008).
26. Romano, L., Venturi, G., Vivarelli, A., Galli, L. & Zazzi, M. Detection of a drug-resistant human immunodeficiency virus variant in a newly infected heterosexual couple. Clin. Infect. Dis. 34, 116-117 (2002).
27. Salemi, M. et al. Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes. Proc. Natl Acad. Sci. USA 96, 13253-13258 (1999).
28. Goodreau, S. M. Assessing the effects of human mixing patterns on HIV-1 interhost phylogenetics through social network simulation. Genetics 142, 2033-2045 (2006).
29. Sloot, P. M. A., Ivanov, S. V., Boukhanovsky, A. V., Van De Vijver, D.A.M.C. & Boucher, C. A. B. Stochastic simulation of HIV population dynamics through complex network modelling. Int. J. Comput. Math. 85, 1175-1187 (2008).
30. Drumright, L. N. & Frost, S. D. Sexual networks and the transmission of drug-resistant HIV. Curr. Opin. Infect. Dis. 21, 644-652 (2008).
31. Smith, R. J., Okano, J. T., Kahn, J. S., Bodine, E. N. & Blower, S. Evolutionary dynamics of complex networks of HIV drug-resistant strains: the case of San Francisco. Science 327, 697-701 (2010).
32. Lai, A. et al. Changing patterns in HIV-1 non-B clade prevalence and diversity in Italy over three decades. HIV Med. 11, 593-602 (2010).
33. Nickle, D. C., Shriner, D., Mittler, J. E., Frenkel, L. M. & Mullins, J. I. Importance and detection of virus reservoirs and compartments of HIV infection. Curr. Opin. Microbiol. 6, 410-416 (2003).
34. Salemi, M. et al. Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J. Virol. 79, 11343-11352 (2005).
35. Salemi, M. et al. Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies. PLoS One 2, e950 (2007).
36. Gray, R. R. et al. Multiple independent lineages of HIV-1 persist in breast milk and plasma. AIDS 25, 143-152 (2011).
37. Keele, B. F. et al. Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J. Exp. Med. 206, 1117-1134 (2009).
38. Li, K. B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19, 1585-1586 (2003).
39. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS ONE. 5, e9490 (2010).
40. Knuth, D. E. The Art of Computer Programming 3rd edn, Vol 1 (Addison-Wesley, 1997).
41. Hubert, L. & Arabie, P. Comparing partitions. J. Classif. 2, 193-218 (1985).