메뉴 건너뛰기




Volumn 77, Issue 13, 2003, Pages 7202-7213

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EVOLUTION; GENETIC DISTANCE; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; LENTIVIRINAE; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIMATE; PRIORITY JOURNAL; SIMIAN IMMUNODEFICIENCY VIRUS; VIRUS GENOME; VIRUS RECOMBINATION;

EID: 0037663940     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.77.13.7202-7213.2003     Document Type: Article
Times cited : (34)

References (51)
  • 1
    • 34047267637 scopus 로고
    • A canonical decomposition theory for metrics on a finite set
    • Bandelt, H.-J., and A. Dress. 1992. A canonical decomposition theory for metrics on a finite set. Adv. Mathematics 9:47-105.
    • (1992) Adv. Mathematics , vol.9 , pp. 47-105
    • Bandelt, H.-J.1    Dress, A.2
  • 5
    • 0023228920 scopus 로고
    • Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses
    • Chakrabarti, L., M. Guyader, M. Alizon, M. D. Daniel, R. C. Desrosiers, P. Tiollais, and P. Sonigo. 1987. Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses. Nature 328:543-547.
    • (1987) Nature , vol.328 , pp. 543-547
    • Chakrabarti, L.1    Guyader, M.2    Alizon, M.3    Daniel, M.D.4    Desrosiers, R.C.5    Tiollais, P.6    Sonigo, P.7
  • 6
    • 0036623490 scopus 로고    scopus 로고
    • Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny
    • Charleston, M. A., and D. L. Robertson. 2002. Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Syst. Biol. 51:528-535.
    • (2002) Syst. Biol. , vol.51 , pp. 528-535
    • Charleston, M.A.1    Robertson, D.L.2
  • 7
    • 0029938478 scopus 로고    scopus 로고
    • Genetic characterization of new West African simian immunodeficiency virus SIVsm: Geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty mangabey troop
    • Chen, Z., P. Telfer, A. Gettie, P. Reed, L. Zhang, D. D. Ho, and P. A. Marx. 1996. Genetic characterization of new West African simian immunodeficiency virus SIVsm: geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty mangabey troop. J. Virol. 70:3617-3627.
    • (1996) J. Virol. , vol.70 , pp. 3617-3627
    • Chen, Z.1    Telfer, P.2    Gettie, A.3    Reed, P.4    Zhang, L.5    Ho, D.D.6    Marx, P.A.7
  • 8
    • 0031001926 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 2 (HIV-2) seroprevalence and characterization of a distinct HIV-2 genetic subtype from the natural range of simian immunodeficiency virus-infected sooty mangabeys
    • Chen, Z., A. Luckay, D. L. Sodora, P. Telfer, P. Reed, A. Gettie, J. M. Kanu, R. F. Sadek, J. Yee, D. D. Ho, L. Zhang, and P. A. Marx. 1997. Human immunodeficiency virus type 2 (HIV-2) seroprevalence and characterization of a distinct HIV-2 genetic subtype from the natural range of simian immunodeficiency virus-infected sooty mangabeys. J. Virol. 71:3953-3960.
    • (1997) J. Virol. , vol.71 , pp. 3953-3960
    • Chen, Z.1    Luckay, A.2    Sodora, D.L.3    Telfer, P.4    Reed, P.5    Gettie, A.6    Kanu, J.M.7    Sadek, R.F.8    Yee, J.9    Ho, D.D.10    Zhang, L.11    Marx, P.A.12
  • 9
    • 0035169607 scopus 로고    scopus 로고
    • Characterization of a novel simian immunodeficiency virus from guereza colobus monkeys (Colobus guereza) in Cameroon: A new lineage in the nonhuman primate lentivirus family
    • Courgnaud, V., X. Pourrut, F. Bibollet-Ruche, E. Mpoudi-Ngole, A. Bourgeois, E. Delaporte, and M. Peeters. 2001. Characterization of a novel simian immunodeficiency virus from guereza colobus monkeys (Colobus guereza) in Cameroon: a new lineage in the nonhuman primate lentivirus family. J. Virol. 75:857-866.
    • (2001) J. Virol. , vol.75 , pp. 857-866
    • Courgnaud, V.1    Pourrut, X.2    Bibollet-Ruche, F.3    Mpoudi-Ngole, E.4    Bourgeois, A.5    Delaporte, E.6    Peeters, M.7
  • 10
    • 0036319292 scopus 로고    scopus 로고
    • Characterization of a novel simian imunodeficiency virus with a vpu gene from greater spot-nosed monkeys (Cercopithecus nictitans) provides new insights into the simian/human immunodeficiency virus phylogeny
    • Courgnaud, V., M. Salemi, X. Pourrut, E. Mpoudi-Ngole, B. Abela, P. Auzel, F. Bibollet-Ruche, B. Hahn, A.-M. Vandamme, E. Delaporte, and M. Peeters. 2002. Characterization of a novel simian imunodeficiency virus with a vpu gene from greater spot-nosed monkeys (Cercopithecus nictitans) provides new insights into the simian/human immunodeficiency virus phylogeny. J. Virol. 76:8298-8309.
    • (2002) J. Virol. , vol.76 , pp. 8298-8309
    • Courgnaud, V.1    Salemi, M.2    Pourrut, X.3    Mpoudi-Ngole, E.4    Abela, B.5    Auzel, P.6    Bibollet-Ruche, F.7    Hahn, B.8    Vandamme, A.-M.9    Delaporte, E.10    Peeters, M.11
  • 11
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 12
    • 0023820579 scopus 로고
    • Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group
    • Fukasawa, M., T. Miura, A. Hasegawa, S. Morikawa, H. Tsujimoto, K. Miki, T. Kitamura, and M. Hayami. 1988. Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group. Nature 333:457-461.
    • (1988) Nature , vol.333 , pp. 457-461
    • Fukasawa, M.1    Miura, T.2    Hasegawa, A.3    Morikawa, S.4    Tsujimoto, H.5    Miki, K.6    Kitamura, T.7    Hayami, M.8
  • 15
    • 0028063444 scopus 로고
    • Genetic diversity of human immunodeficiency virus type 2: Evidence for distinct sequence subtypes with differences in virus biology
    • Gao, F., L. Yue, D. L. Robertson, S. C. Hill, H. Hui, R. J. Biggar, A. E. Neequaye, T. M. Whelan, D. D. Ho, and G. M. Shaw. 1994. Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. J. Virol. 68:7433-7447.
    • (1994) J. Virol. , vol.68 , pp. 7433-7447
    • Gao, F.1    Yue, L.2    Robertson, D.L.3    Hill, S.C.4    Hui, H.5    Biggar, R.J.6    Neequaye, A.E.7    Whelan, T.M.8    Ho, D.D.9    Shaw, G.M.10
  • 18
    • 0034723385 scopus 로고    scopus 로고
    • AIDS as a zoonosis: Scientific and public health implications
    • Hahn, B. H., G. M. Shaw, K. M. De Cock, and P. M. Sharp. 2000. AIDS as a zoonosis: scientific and public health implications. Science 287:607-614.
    • (2000) Science , vol.287 , pp. 607-614
    • Hahn, B.H.1    Shaw, G.M.2    De Cock, K.M.3    Sharp, P.M.4
  • 20
    • 0032935029 scopus 로고    scopus 로고
    • Characterization of a novel simian immunodeficiency virus (SIV) from L'Hoest monkeys (Cercopithecus l'hoesti): Implications for the origins of SIVmnd and other primate lentiviruses
    • Hirsch, V. M., B. J. Campbell, E. Bailes, R. Goeken, C. Brown, W. R. Elkins, M. Axthelm, M. Murphey-Corb, and P. M. Sharp. 1999. Characterization of a novel simian immunodeficiency virus (SIV) from L'Hoest monkeys (Cercopithecus l'hoesti): implications for the origins of SIVmnd and other primate lentiviruses. J. Virol. 73:1036-1045.
    • (1999) J. Virol. , vol.73 , pp. 1036-1045
    • Hirsch, V.M.1    Campbell, B.J.2    Bailes, E.3    Goeken, R.4    Brown, C.5    Elkins, W.R.6    Axthelm, M.7    Murphey-Corb, M.8    Sharp, P.M.9
  • 23
    • 0032546809 scopus 로고    scopus 로고
    • Limitations of a molecular clock applied to considerations of the origin of HIV-1
    • Korber, B. T. M., J. Theiler, and S. Wolinsky. 1998. Limitations of a molecular clock applied to considerations of the origin of HIV-1. Science 280:1868-1871.
    • (1998) Science , vol.280 , pp. 1868-1871
    • Korber, B.T.M.1    Theiler, J.2    Wolinsky, S.3
  • 24
    • 0031010764 scopus 로고    scopus 로고
    • Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history
    • Leitner, T., S. Kumar, and J. Albert. 1997. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71:4761-4770.
    • (1997) J. Virol. , vol.71 , pp. 4761-4770
    • Leitner, T.1    Kumar, S.2    Albert, J.3
  • 26
    • 0023074036 scopus 로고
    • An evaluation of the molecular clock hypothesis using mammalian DNA sequences
    • Li, W.-H., M. Tanimura, and P. M. Sharp. 1987. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25:330-342.
    • (1987) J. Mol. Evol. , vol.25 , pp. 330-342
    • Li, W.-H.1    Tanimura, M.2    Sharp, P.M.3
  • 27
    • 0023740248 scopus 로고
    • Rates and dates of divergence between AIDS virus nucleotide sequences
    • Li, W.-H., M. Tanimura, and P. M. Sharp. 1988. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5:313-330.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 313-330
    • Li, W.-H.1    Tanimura, M.2    Sharp, P.M.3
  • 31
    • 0034814736 scopus 로고    scopus 로고
    • Unveiling the molecular clock in the presence of recombination
    • Posada, D. 2001. Unveiling the molecular clock in the presence of recombination. Mol. Biol. Evol. 18:1976-1978.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1976-1978
    • Posada, D.1
  • 32
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 33
    • 0035923699 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
    • Posada, D., and K. A. Crandall. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 98:13757-13762.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 13757-13762
    • Posada, D.1    Crandall, K.A.2
  • 34
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 37
    • 0035261070 scopus 로고    scopus 로고
    • 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
    • Salemi, M., K. Strimmer, W. W. Hall, M. Duffy, E. Delaporte, S. Mboup, M. Peeters, and A.-M. Vandamme. 2001. 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. 15:276-278.
    • (2001) FASEB J. , vol.15 , pp. 276-278
    • Salemi, M.1    Strimmer, K.2    Hall, W.W.3    Duffy, M.4    Delaporte, E.5    Mboup, S.6    Peeters, M.7    Vandamme, A.-M.8
  • 39
    • 0033793521 scopus 로고    scopus 로고
    • Consequences of recombination on traditional phylogenetic analysis
    • Schierup, M. H., and J. Hein. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879-891.
    • (2000) Genetics , vol.156 , pp. 879-891
    • Schierup, M.H.1    Hein, J.2
  • 40
    • 0033805038 scopus 로고    scopus 로고
    • Recombination and the molecular clock
    • Schierup, M. H., and J. Hein. 2000. Recombination and the molecular clock. Mol. Biol. Evol. 17:1578-1579.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1578-1579
    • Schierup, M.H.1    Hein, J.2
  • 42
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of loglikelihoods with applications to phylogenetic inference
    • Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 44
    • 0029880314 scopus 로고    scopus 로고
    • The effect of topology on estimates of among-site rate variation
    • Sullivan, J., K. E. Holsinger, and C. Simon. 1996. The effect of topology on estimates of among-site rate variation. J. Mol. Evol. 42:308-312.
    • (1996) J. Mol. Evol. , vol.42 , pp. 308-312
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 46
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. Hillis, C. Moritz, and B. K. Mable (ed.), Sinauer Associates Inc., Sunderland, Mass.
    • Swofford, D. L., G. J. Olsen, P. J. Waddel, and D. M. Hillis. 1996. Phylogenetic inference, p. 407-514. In D. M. Hillis, C. Moritz, and B. K. Mable (ed.), Molecular systematics, 2nd ed. Sinauer Associates Inc., Sunderland, Mass.
    • (1996) Molecular Systematics, 2nd Ed. , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddel, P.J.3    Hillis, D.M.4
  • 47
    • 0346952694 scopus 로고    scopus 로고
    • Phylogeny. Inference based on parsimony and other methods using PAUP*
    • M. Salemi and A.-M. Vandamme (ed.), in press. Cambridge University Press, New York, N.Y.
    • Swofford, D. L., and J. Sullivan. Phylogeny. Inference based on parsimony and other methods using PAUP*. In M. Salemi and A.-M. Vandamme (ed.), The phylogenetic handbook: a practical approach to DNA and protein phylogeny, in press. Cambridge University Press, New York, N.Y.
    • The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
    • Swofford, D.L.1    Sullivan, J.2
  • 48
    • 0028947661 scopus 로고
    • Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences
    • van der Kuyl, A. C., C. L. Kuiken, J. T. Dekker, and J. Goudsmit. 1995. Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences. J. Mol. Evol. 40:173-180.
    • (1995) J. Mol. Evol. , vol.40 , pp. 173-180
    • Van der Kuyl, A.C.1    Kuiken, C.L.2    Dekker, J.T.3    Goudsmit, J.4
  • 51
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.