Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host

Retrovirology

Volumn 3, Issue , 2006, Pages

  Demma, L J ^a,b   Vanderford, T H ^a   Logsdon Jr , John M ^a,e   Feinberg, Mark B ^c,d   Staprans, S I ^a,c  

^a EMORY UNIVERSITY   (United States)

^b CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^c EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d MERCK RESEARCH LABORATORIES   (United States)

^e UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; PROTEIN P27; VIRUS ENVELOPE PROTEIN; PRIMER DNA; VIRUS DNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANTIBODY RESPONSE; ARTICLE; CONTROLLED STUDY; FREQUENCY ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LENTIVIRINAE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN GLYCOSYLATION; RETROVIRUS; SEQUENCE ANALYSIS; SIMIAN VIRUS; SPECIES DIFFERENCE; UNINDEXED SEQUENCE; VIRUS CELL INTERACTION; VIRUS ENVELOPE; VIRUS TRANSMISSION; VIRUS VIRULENCE; ANIMAL; CLASSIFICATION; DISEASE TRANSMISSION; GENETIC VARIABILITY; GENETICS; HUMAN; IMMUNOLOGY; ISOLATION AND PURIFICATION; MOLECULAR CLONING; PHYLOGENY; PRIMATE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; VIROLOGY; ZOONOSIS;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; LENTIVIRUS; SIMIAN IMMUNODEFICIENCY VIRUS; SIMIAN VIRUS;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; DNA PRIMERS; DNA, VIRAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; HIV-1; HUMANS; PHYLOGENY; PRIMATES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; VIRAL ENVELOPE PROTEINS; ZOONOSES;

EID: 33645552001     PISSN: 17424690     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-3-19     Document Type: Article

References (97)

1. Woolhouse MEJ: Population biology of emerging and reemerging pathogens. Trends Microbiol 2002, 10:S3-S7.
2. Mahy BWJ: Human viral infections: an expanding frontier. Antivir Res 1997, 36:75-80.
3. Domingo E: Viruses at the edge of adaptation. Virology 2000, 270:251-253.
4. Domingo E, Holland JJ: Mutation rates and rapid evolution of RNA viruses. In Evolutionary Biology of Viruses Edited by: Morse SS. New York, Raven Press; 1994:161-184.
5. Lucas M, Karrer U, Lucas A, Klenerman P: Viral escape mechanisms-escapology taught by viruses. Int J Exp Path 2001, 82:269-286.
6. Matrosovich M, Krauss S, Webster RG: H9N2 influenza A viruses from poultry in Asia have human virus-like receptor specificity. Virology 2001, 281:156-162.
7. Webby RJ, Webster RG: Emergence of influenza A viruses. Phil Trans R Soc Land B 2001, 356:1817-1828.
8. Skehel JJ, Wiley DC: Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Ann Rev Biochem 2000, 69:531-569.
9. Morzunov SP, Rowe JE, Ksiazek TG, Peters CJ, St. Jeor SC, Nichol ST: Genetic analysis of the diversity and origin of hantaviruses in Persomyscus luecopus mice in North America. J Virol 1998, 72:57-64.
10. Hughes AL, Friedman R: Evolutionary diversification of protein-coding genes of hantaviruses. Mol Biol Evol 2000, 17:1558-1568.
11. Feuer R, Boone JD, Netski D, Morzunov SP, Jeor SCS: Temporal and spatial analysis of sin nombre virus quasispecies in naturally infected rodents. J Virol 1999, 73(11):9544-9554.
12. Hughes JM, Peters CJ, Cohen ML, Mahy BWJ: Hantavirus pulmonary syndrome: an emerging infectious disease. Science 1993, 262:850-851.
13. Childs JE, Ksiazek TG, Spiropoulou CF, Krebs JW, Morzunov S, Maupin GO, Gage KL, Rollin PE, Sarisky J, Enscore RE: Serologic and genetic identification of Peromyscus maniculatus as the primary rodent reservoir for a new hantavirus in the southwestern United States. J Infect Dis 1994, 169:1271-1280.
14. Parrish CR, Kawaoka Y: The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses. Ann Rev Microbial 2005, 59(1):553-586.
15. De Cock KM: Epidemiology and the emergence of human immunodeficiency virus and acquired immune deficiency syndrome. Phil Trans R Soc Land B 2001, 356:795-798.
16. Sharp PM, Bailes E, Gao F, Beer BE, Hirsch VM, Hahn BH: Origins and evolution of AIDS viruses: estimating the time-scale. Biochem Soc Trans 2000, 28:275-282.
17. Sharp PM, Bailes E, Robertson DL, Gao F, Hahn BH: Origins and evolution of AIDS viruses. Biol Bull 1999, 196:338-342.
18. Lemey P, Pybus OG, Wang B, Saksena NK, Salemi M, Vandamme AM: Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci USA 2003, 100:6588-6592.
19. Apetrei C, Kaur A, Lerche NW, Metzger M, Pandrea I, Hardcastle J, Falkenstein S, Bohm R, Koehler J, Traina-Dorge V, Williams T, Staprans S, Plauche G, Veazey RS, McClure H, Lackner AA, Gormus B, Robertson DL, Marx PA: Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm. J Virol 2005, 79(14):8991-9005.
20. Apetrei C, Robertson DL, Marx P: The history of SIVs and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Front Biosci 2004, 9:225-254.
21. Hahn BH, Shaw GM, Cock KMD, Sharp PM: AIDS as a zoonosis: scientific and public health implications. Science 2000, 287:607-614.
22. Silvestri G, Fedanov A, Germon S, Kozyr N, Kaiser W, Garber D, McClure H, Feinberg MB, Staprans SI: Divergent host responses during primary SIVsmm infection of natural mangabey and non-natural rhesus macaque hosts. J Virol 2005, 79:4043-4054.
23. Silvestri G, Sodora DL, Koup RA, Paiardini M, O'Neil SP, McClure HM, Staprans SI, Feinberg MB: Non-pathogenic simian immunodeficiency virus infection of sooty mangabey mokeys is characterized by limited bystander immunopathology despite chronic high-level viremia. Immunity 2003, 18:441-452.
24. Demma LJ, Logsdon JMJ, Vanderford TH, Feinberg MB, Staprans SI: SIV quasispecies adaptation to a simian new host. PLoS Path 2005, 1(1):e3.
25. Ilyushina N, Rudneva I, Gambaryan A, Bovin N, Kaverin N: Monoclonal antibodies differentially affect the interaction between the hemagglutinin of H9 influenza virus escape mutants and sialic receptors. Virology 2004, 329(1):33-39.
26. Suzuki Y. Sialobioloogy of influenza: molecular mechanism of host range variation of influenza viruses. Biol Pharm Bull 2005, 28(3):399-408.
27. Qu XX Hao P, Song XJ, Jiang SM, Liu YX, Wang PG, Rao X, Song HD, Wang SY, Zuo Y, Zheng AH, Luo M, Wang HL, Deng F, Wang HZ, Hu ZH, Ding MX, Zhao GP, Deng HK: Identification of two critical amino acid residues of the severe acute respiratory syndrome coronavirus spike protein for its variation in zoonotic tropism transition via a double substitution strategy. J Biol Chem 2005, 280(33):29588-29595.
28. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken CL, Korber B: Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology 2004, 14:1229-1246.
29. Chackerian B, Rudensey LM, Overbaugh J: Specific N-linked and O-linked glycosylation modifications in the envelope VI domain of simian immunodeficiency virus variants that evolve in the host alter recognition by neutralizing antibodies. J Virol 1997, 71(10):7719-7727.
30. Reiter JN, Means RE, Desrosiers RC: A role for carbohydrates in immune evasion in AIDS. Nat Med 1998, 4:679-684.
31. Quinones-Kochs MI, Buonocore L, Rose JK: Role of N-linked glycans in a human immunodeficiency virus envelope glycoprotein: effects on protein function and the neutralizing antibody response. J Virol 2002, 76:4199-4211.
32. Ohgimoto S, Shioda T, Mori K, Nakayama EE, Hu H, Nagai Y: Location-specific, unequal contribution of the N glycans in simian immunodeficiency virus gp120 to viral infectivity and removal of multiple glycans without disturbing infectivity. J Virol 1998, 72:8365-8370.
33. Kinsey NE, Anderson MG, Unangst TJ, Joag SV, Narayan O, Zink MC, Clements JE: Antigenic variation of SIV: mutations in V4 alter the neutralization profile. Virology 1996, 231:14-21.
34. Kwong PD, Doyle ML, Casper DJ, Cicala C, Leavitt: SA, Majeed S, Steenbeke TD, Venturi M, Chaiken I, Fung M, Katinger H, Parren PWIH, Robinson J, Van Ryk D, Wang L, Burton DR, Freire E, Wyatt R, Sodroski J, Hendrickson WA, Arthos J: HIV-I evades antibodymediated neutralization through conformational masking of receptor-binding sites. Nature 2002, 420:678-682.
35. Cheng-Mayer C, Brown A, Harouse JM, Luciw PA, Mayer AJ: Selection for neutralization resistance of the simian/human immunodeficiency virus SHIVsf33a variant in vivo by virtue of sequence changes in the extracellular envelope glycoprotein that modify N-linked glycosylation. J Virol 1999, 73(7):5294-5300.
36. Holmes KV: Structural biology. Adaptation of SARS coronavirus to humans. Science 2005, 309(5742):1822-1823.
37. Antia R, Regoes RR, Koella JC, Bergstrom CT: The role of evolution in the emergence of infectious diseases. Nature 2003, 426(6967):658-661.
38. Frost SDW, Wrin T, Smith DM, Pond SLK, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD: Neutralizing antibody responses drive the evolution of human immunodeficiency virus type I envelope during recent HIV infection. Proc Natl Acad Sci USA 2005, 102(51):18514-18519.
39. Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT: Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) reveal imprints of immune evasion on HIV-I global variation. Journal of Virology 2002, 76:8757-8768.
40. Beer BE, Bailes E, Dapolito G, Campbell BJ, Goeken R, Axthelm MK, Markham PD, Bernard J, Zagury D, Franchini G, Sharp PM, Hirsch V: Patterns of genomic sequence diversity among their simian immunodeficiency viruses suggest that L'Hoest monkeys (Cercopithecus Ihoesti) are a natural lentivirus reservoir. J Virol 2000, 74(8):3892-3898.
41. Beer BE, Bailes E, Goeken R, Dapolito G, Coulibaly C, Norley SG, Kurth R, Gautier JP, Gautier-Hion A, Vallet D, Sharp PM, Hirsch V: Simian immunodeficiency virus (SIV) from sun-tailed monkeys (Ceropithecus solatus): evidence for host-dependent evolution of SIV within the C. I'hoesti superspecies. J Virol 1999, 73(9):7734-7744.
42. Peeters M, Janssens W, Fransen K, Brandful J, Heyndrickx L, Koffi K, Delaporte E, Piot P, Gershy-Damet GM, Van Der Groen G: Isolation of simian immunodeficiency viruses from two sooty mangabeys in Cote d'Ivoire: virological and genetic characterization and relationship to other HIV type 2 and SIVsm/mac strains. AIDS Res Hum Retrov 1994, 10:1289-1294.
43. Allan JS, Kanda P, Kennedy RC, Cobb EK, Anthony M, Eichberg JW: Isolation and characterization of simian immunodeficiency viruses from two subspecies of African green monkeys. AIDS Res Hum Retrov 1990, 6:275-284.
44. Nowak MA, Anderson RM, McLean AR, Wolfs TFW, Goudsmit J, May RM: Antigenic diversity thresholds and the development of AIDS. Science 1991, 254:963-969.
45. Nowak MA, May RM: Mathematical biology of HIV infections: antigenic variation and diversity threshold. Mathematical Bioscience 1991, 106:1-21.
46. McDonald RA, Mayers DL, Chung RCY, Wagner KF, Ratto-Kim S, Birx DL, Michael NL: Evolution of human immunodeficiency virus type 1 env sequence variation in patients with diverse rates of disease progression and T-cell function. J Virol 1997, 71:1871-1879.
47. Shankarappa R, Margolick J, Gange S, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CRJ, Learn G, He X, Huang XL, Mullins JI: Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999, 73:10489-10502.
48. Lambotte O, Chaix ML, Gubler B, Nasreddine N, Wallon C, Goujard C, Rouzioux C, Taoufik Y, Delfraissy JF: The lymphocyte HIV reservoir in patients on long-term HAART is a memory of virus evolution. AIDS 2004, 18:1147-1158.
49. Schnittman SS, Psallidopoulos MC, Lane HC, Thompson L, M B, F M, C.H. F, N.P. S, A.S. F: The reservoir for HIV-I in human peripheral blood is a T cell that maintains expression of CD4. Science 1989, 245:305-308.
50. Puffer BA, Altamura LA, Pierson TC, Doms RW: Determinants within gp 120 and gp41 contribute to CD4 independence of SIV Envs. Virology 2004,327:16-25.
51. Vodros D, Thorstensson R, Doms RW, Fenyo EM, Reeves JD: Evolution of coreceptor use and CD4-independence in envelope clones derived from SIVsm-infected macaques. J Virol 2003, 316:17-28.
52. Richman DD, Wrin T, Little SJ, Petropoulos CJ: Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci USA 2003, 100:4144-4149.
53. Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova N, Nowak MA, Hahn BH, Kwong PD, Shaw GM: Antibody neutralization and escape by HIV-I. Nature 2003, 422:307-311.
54. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, Shaw GM, Korber BT, Allen S, Hunter E: Envelope-constrained neutralization-sensitive HIV-I after heterosexual transmission. Science 2004, 303(5666):2019-2022.
55. Kalish ML, Korber BT, Robbins KE, Leo YS, Saekhou A, Verghese I, Gerrish P, Goh CL, Lupo D, Tan BH, Brown TM, Chan R: The sequential introduction of HIV-I subtype B and CRF0 IÆ in Singapore by sexual transmission: accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology 2002, 304:311-329.
56. Muller-Trutwin MC, Corbet S, Tavares MD, Herve VMA, Nerrienet E, Georges-Courbot MC, Saurin W, Sonigo P, Barre-Sinoussi F: The evolutionary rate of nonpathogenic simian immunodeficiency virus (SIVagm) is in agreement with a rapid and continuous replication in vivo. Virology 1996, 223:89-102.
57. Rey-Cuille MA, Berthier JL, Bomsel-Demontoy MC, Chaduc Y, Montagnier L, Hovanessian AG, Chakrabarti LA: Simian immunodeficiency virus replicates to high levels in sooty mangabeys without inducing disease. J Virol 1998, 72(5):3872-3886.
58. Baier M, Dittmar MT, Cichutek K, Kurth R: Development in vivo of genetic variability of simian immunodeficiency virus. Proc Natl Acad Sci USA 1991, 88:8126-8130.
59. Johnson PR, Fomsgaard A, Allan JS, Gravell M, London WT, Olmsted RA, Hirsch V: Simian immunodeficiency viruses from African green monkeys display unusual genetic diversity. J Virol 1990, 64:1086-1092.
60. Norley SG: SIVagm infection of its natural African geen monkey host. Immunol Lett 1996, 51:53-58.
61. Kurth R, Norley S: Simian immunodeficiency viruses of African green monkeys. Curr Top Microbiol Immunol 1994, 188:21-33.
62. Goldstein S, Ourmanov I, Brown CR, Beer BE, Elkins WR, Plishka R, Buckler-White A, Hirsch V: Wide range of viral load in healthy African green monkeys naturally infected with simian immunodeficiency virus. J Virol 2000, 74:11744-11753.
63. Broussard SR, Staprans SI, White R, Whitehead EM, Feinberg MB, Allan JS: Simian immunodeficiency virus replicates to high levels in naturally infected african green monkeys without inducing immunologic or neurologic disease. J Virol 2001, 75:2262-2275.
64. Masciotra S, Owen SM, Rudolph D, Yang C, Wang B, Saksena NK, Spira T, Dhawan S, Lal RB: Temporal relationship between VIV2 variation, macrophage replication, and coreceptor adaptation during HIV-I disease progression. AIDS 2002, 16:1887-1898.
65. Palmer C, Balfe P, Fox D, May JC, Frederiksson R, Fenyo EM, McKeating JA: Functional characterization of the V1V2 region of human immunodeficiency virus type I. Virology 1996, 220:436-449.
66. Valli PJS, Lukashov VV, Heeney JL, Goudsmit J: Shortening of the symptom-free period in rhesus macaques is associated with decreasing nonsynonymous variation in the env variable regions of simian immunodeficiency viurs SIVsm during passage. J Virol 1998, 72(9):7494-7500.
67. Poss M, Rodrigo AG, Gosink JJ, Learn GH, De Vange Fateleeff D, Martin HLJ, Bwayo J, Kreiss JK, Overbaugh J: Evolution of envelope sequences from the genital tract peripheral blood of women infected with clade A human immunodeficiency virus type I. J Virol 1998, 72(10):8240-8251.
68. Shankarappa R, Gupta P, Learn GHJ, Rodrigo AG, Rinaldo CRJ, Gorry MC, Mullins JI, Nara PL, Ehrlich GD: Evolution of human immunodeficiency virus type I sequences in infected individuals with differing disease progression profiles. Virology 1998, 241:251-259.
69. Courgnaud V, Laure F, Fultz PN, Montagnier L, Brechot C, Sonigo P: Genetic differences accounting for evolution and pathogenicity of simian immunodeficiency virus from a sooty mangabey monkey after cross-species transmission to a pig-tailed macaque. J Virol 1992, 66:414-419.
70. Fomsgaard A, Johnson PR, London WT, Hirsch V: Genetic variation of the SIVagm transmembrane glycoprotein in naturally and experimentally infected primates. AIDS 1993, 7:1041-1047.
71. Ondoa P, Davis D, Willems B, Heyndrickx L, Kestens L, van der Berg I, Coppens S, Janssens W, Heeney J, Van Der Groen G: Genetic variability of the V1 and V2 env domains of SIVcpz-ant and neutralization pattern of plasma viruses in a, chimpanzee infected naturally. J Med Virol 2001, 65:765-776.
72. Silvestri G, Feinberg MB: Turnover of lymphocytes and conceptual paradigms in HIV infection. J Clin Invest 2003, 112(6):821-824.
73. Rodrigo A, Felsenstein J: Coalescent Approaches to HIV Population Genetics. In The Evolution of HIV Edited by: Crandall KA. Baltimore, MD, The Johns Hopkins University Press; 1999:233-274.
74. Silvestri G: Naturally SIV-infected sooty mangabeys: are we closer to understanding why they do not develop AIDS? J Med Primatol 2005, 34(5-6):243-252.
75. Kantor R, Shafer RW, Follansbee S, Taylor J, Shilane D, Hurley L, Nguyen DP, Katzenstein D, Fessel WJ: Evolution of resistance to drugs in HIV-I-infected patients failing antiretroviral therapy. AIDS 2004, 18:1503-1511.
76. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA, Sodroski J: The antigenic structure of the HlVgp120 envelope glycoprotein. Nature 1998, 393:705-711.
77. Kunstman KJ, Puffer B, Korber BT, Kuiken C, Smith UR, Kunstman J, Stanton J, Agy M, Shibata R, Yoder AD, Pillai S, Dorns RW, Marx P, Wolinsky SM: Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea. J Virol 2003, 77(22):12310-12318.
78. Fomsgaard A, Hirsch VM, Johnson PR: Cloning and sequences of primate CD4 molecules: diversity of the cellular receptor for simian immunodeficiency virus/human immunodeficiency virus. Eur J Immunol 1992, 22:2973-2981.
79. Farci P, Strazzera R, Alter HJ, Farci S, Degioannis D, Coiana A, Peddis G, Usai F, Serra G, Chessa L, Diaz G, Balestrieri A, Purcell RH: Early changes in hepatitis C viral quasispecies during interferon therapy predict the therapeutic outcome. Proc Natl Acad Sci USA 2002, 99(5):3081-3086.
80. Bowen DG, Walker CM: The origin of quasispecies: cause or consequence of chronic hepatitis C viral infection? Journal of Hepatology 2005, 42:408-417.
81. Los Alamos HIV Databases, http://www.hiv.lanl.gov/.
82. Rodrigo AG, Hanley EW, Goracke PC, Learn GHJ: Sampling and processing HIV molecular sequences: a computational evolutionary biologist's perspective. In Computational and evolutionary analysis of HIV molecular sequences Edited by: Rodrigo AG, Learn GH. Boston, Kluwer Academic Publishers; 2001:1-18.
83. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 1994, 22:4673-4680.
84. Maddison WP, Maddison DR: Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol 1989, 53(1-4):190-202.
85. Hall HT: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98.
86. McAllister J, Casino C, Davidson F, Power J, Lawlor E, Yap PL, Simmonds P, Smith DB: Long-term evolution of the hypervariable region of hepatitis C in a common-source-infected cohort. J Virol 1998, 72(6):4893-4905.
87. Posada D, Crandall KA. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14(9):817-818.
88. Jobb G: Treefinder. Munich, Germany, www.treefinder.de; 2002.
89. Gu X, Li WH: A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc Natl Acad Sci USA 1996, 93:4671-4676.
90. Gu X, Li WH: Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution. Proc Natl Acad Sci USA 1998, 95:5899-5905.
91. Yang Z: Estimating the pattern of nucleotide substitution. J Mol Evol 1994, 39(1):105-111.
92. Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleoticle substitutions. Mol Biol Evol 1986, 3(5):418-426.
93. Ota T, Nei M: Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Molecular Biology and Evolution 1994, 11(4):613-619.
94. Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993, 10:512-526.
95. Kumar S, Tamura K, Nei M: Molecular Evolutionary Genetic Analysis. 2.0th edition. University Park, Pennsylvania; 2000.
96. Kumar S, Tamura K, Jakobsen I, Nei M: MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 2001, 17:1244-1245.
97. Ihaka R, Gentleman R: R: A language for data analysis and graphics. J Comput Graph Stat 1996, 5:299-314.