Rapid adversarial co-evolution of viruses and cellular restriction factors

Current Topics in Microbiology and Immunology

Volumn 371, Issue , 2013, Pages 123-151

  Johnson, Welkin E ^a  

^a BOSTON COLLEGE   (United States)

Author keywords

Cross species transmission; Emergence; Endogenous retrovirus; Paleovirology; Positive selection

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3G; CAPSID PROTEIN; CELL PROTEIN; RESTRICTION FACTOR; TRIPARTITE MOTIF PROTEIN 5; UNCLASSIFIED DRUG; VIRUS ENVELOPE PROTEIN; VIRUS PROTEIN;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL SURFACE; DNA POLYMORPHISM; DNA VIRUS; ENDEMIC DISEASE; FLAVIVIRUS; GENE; GENE AMPLIFICATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOTYPE; HOST CELL; HUMAN; HUMAN GENOME; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MICROBIAL ACTIVITY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RESTRICTION FACTOR GENE; RETROVIRUS; RNA VIRUS; VIRAL GENETICS; VIRAL TROPISM; VIRUS CAPSID; VIRUS CELL INTERACTION; VIRUS ENTRY; VIRUS GENE; VIRUS GENOME; VIRUS INFECTION; VIRUS INHIBITION; VIRUS MUTATION; VIRUS REPLICATION; VIRUS STRAIN; VIRUS TRANSMISSION; ANIMAL; EVOLUTION; PHYSIOLOGY; REVIEW; VIRUS;

MAMMALIA; PRIMATES;

ANIMALS; BIOLOGICAL EVOLUTION; HUMANS; VIRAL TROPISM; VIRUSES;

EID: 84882322810     PISSN: 0070217X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-37765-5_5     Document Type: Article

References (123)

1. Ambrose Z, KewalRamani VN, Bieniasz PD, Hatziioannou T (2007) HIV/AIDS: in search of an animal model. Trends Biotechnol 25:333-337 . doi:10.1016/j.tibtech.2007.05.004 (Pubitemid 47042916)
2. An P, Bleiber G, Duggal P et al (2004) APOBEC3G genetic variants and their influence on the progression to AIDS. J Virol 78:11070-11076. doi:10.1128/JVI.78.20.11070-11076 .2004 (Pubitemid 39299647)
3. Andersen KG, Shylakhter I, Tabrizi S et al (2012) Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever. Philos Trans R Soc Lond B Biol Sci 367:868-877. doi:10.1098/rstb.2011.0299
4. Antia R, Regoes RR, Koella JC, Bergstrom CT (2003) The role of evolution in the emergence of infectious diseases. Nature 426:658-661. doi:10.1038/nature02104 (Pubitemid 38009372)
5. Apetrei C, Robertson DL, Marx PA (2004) The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Front Biosci 9:225-254 (Pubitemid 38925456)
6. Arnaud F, Varela M, Spencer TE, Palmarini M (2008) Endogenous retroviruses. Cell Mol Life Sci 65:3422-3432. doi:10.1007/s00018-008-8500-9
7. Battivelli E, Migraine J, Lecossier D et al (2011) Gag cytotoxic T lymphocyte escape mutations can increase sensitivity of HIV-1 to human TRIM5alpha, linking intrinsic and acquired immunity. J Virol 85:11846-11854. doi:10.1128/JVI.05201-11
8. Belyi VA, Levine AJ, Skalka AM (2010) Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in Vertebrate genomes. PLoS Pathog 6:e1001030. doi:10.1371/journal.ppat.1001030. t006
9. Best S, Tissier PL, Towers G, Stoye JP (1996) Positional cloning of the mouse retrovirus restriction gene Fvl. Nature 382:826-829. doi:10.1038/382826a0 (Pubitemid 26299569)
10. Bishop KN, Bock M, Towers G, Stoye JP (2001) Identification of the regions of Fv1 necessary for murine leukemia virus restriction. J Virol 75:5182-5188doi: 10.1128/JVI.75.IL518296-5188 (Pubitemid 32448540)
11. Brennan G, Kozyrev Y, Hu SL (2008) From the cover: TRIMCyp expression in old world primates Macaca nemestrina and Macaca fascicularis. Proc Natl Acad Sci 105:3569-3574. doi:10.1073/pnas.0709511105 (Pubitemid 351723593)
12. Brennan G, Kozyrev Y, Kodama T, Hu S-L (2007) Novel TRIM5 isoforms expressed by Macaca nemestrina. J Virol 81:12210-12217 (Pubitemid 350085836)
13. Charlesworth D (2006) Balancing selection and its effects on sequences in nearby genome regions. PLoS Genet 2:e64
14. Coffin JM (1997) Retroviruses. CSHL Press, New York.
15. Collinge J, Palmer MS, Dryden AJ (1991) Genetic predisposition to iatrogenic Creutzfeldt-Jakob disease. Lancet 337:1441-1442
16. Compton AA, Emerman M (2013) Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses. PLoS Pathog 9:e1003135. doi:10.1371/journal.ppat. 1003135
17. Dandekar S, Rossitto P, Pickett S et al (1987) Molecular characterization of the Akvr-1 restriction gene: a defective endogenous retrovirus-borne gene identical to Fv-4r. J Virol 61:308-314 (Pubitemid 17001726)
18. Desrosiers R (1990) The simian immunodeficiency viruses. Annu Rev Immunol 8:557-578 (Pubitemid 20135639)
19. Dewannieux M, Harper F, Richaud A et al (2006) Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res 16:1548-1556 . doi:10.1101/gr.5565706 (Pubitemid 44878493)
20. Diehl WE, Johnson WE, Hunter E (2013) Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation. PLoS One 8(3):e58532
21. Domingo E, Holland JJ (2008) Origin and evolution of viruses. Academic Press, New York.
22. Domingo E, Sheldon J, Perales C (2012) Viral quasispecies evolution. Microbiol Mol Biol Rev 76:159-216 . doi:10.1128/MMBR.05023-11
23. Elde NC, Child SJ, Eickbush MT et al (2012) Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 150:831-841. doi:10.1016/j.cell.2012.05.049
24. Elde NC, Child SJ, Geballe AP, Malik HS (2008) Protein kinase R reveals an evolutionary model for defeating viral mimicry. Nature 457:485-489. doi:10.1038/nature07529
25. Emerman M, Malik HS (2010) Paleovirology-modern consequences of ancient viruses. PLoS Biol 8:e1000301. doi:10.1371/journal.pbio.1000301
26. Evans DT, Serra-Moreno R, Singh RK, Guatelli JC (2010) BST-2/tetherin: a new component of the innate immune response to enveloped viruses. Trends Microbiol 18:388-396 . doi:10.1016/j.tim.2010.06.010
27. Feschotte C, Gilbert C (2012) Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 13:283-296. doi:10.1038/nrg3199
28. Gardner MB, Kozak CA, O'Brien SJ (1991) The Lake Casitas wild mouse: evolving genetic resistance to retroviral disease. Trends Genet 7:22-27 (Pubitemid 121001897)
29. Gifford R, Tristem M (2003) The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315
30. Gilbert C, Feschotte C (2010) Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol. doi:10.1371/journal.pbio.1000495
31. Goldschmidt V, Bleiber G, May M et al (2006) Role of common human TRIM5alpha variants in HIV-1 disease progression. Retrovirology 3:54
32. Grossman SR, Shlyakhter I, Shylakhter I et al (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883-886 . doi:10.1126/science.1183863
33. Hauser H, Lopez LA, Yang SJ et al (2011) HIV-1 Vpu and HIV-2 Env counteract BST-2/tetherin by sequestration in a perinuclear compartment. Retrovirology 8:85. doi:10.1186/1742-4690-8-85
34. Haygood R, Babbitt CC, Fedrigo O, Wray GA (2010) Contrasts between adaptive coding and noncoding changes during human evolution. Proc Natl Acad Sci 107:7853-7857. doi:10.10 73/pnas.0911249107
35. Heffernan JM, Smith RJ, Wahl LM (2005) Perspectives on the basic reproductive ratio. J R Soc Interface 2:281-293. doi:10.1098/rsif.2005.0042
36. Holmes EC, Drummond AJ (2007) The evolutionary genetics of viral emergence. Curr Top Microbiol Immunol 315:51-66
37. Horie M, Honda T, Suzuki Y et al (2010) Endogenous non-retroviral RNA virus elements in Mammalian genomes. Nature 463:84-87. doi:10.1038/nature08695
38. Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet 18:486
39. Ikeda H, Sugimura H (1989) Fv-4 resistance gene: a truncated endogenous Murine leukemia virus with ecotropic interference properties. J Virol 63:5405-5412 (Pubitemid 19278781)
40. Javanbakht H, An P, Gold B et al (2006) Effects of human TRIM5alpha polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection. Virology 354:15-27 (Pubitemid 44468115)
41. Jern P, Coffin JM (2008) Effects of retroviruses on host genome function. Annu Rev Genet 42:709-732. doi:10.1146/annurev.genet.42.110807.091501
42. Jern P, Stoye JP, Coffin JM (2007) Role of APOBEC3 in genetic diversity among endogenous Murine leukemia viruses. PLoS Genet 3:2014-2022. doi:10.1371/journal.pgen.0030183 (Pubitemid 350072064)
43. Johnson WE (2010) Endless forms most viral. PLoS Genet 6:e1001210. doi:10.1371/journal.pgen.1001210
44. Johnson WE, Coffin JM (1999) Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci USA 96:10254-10260 (Pubitemid 29422545)
45. Johnson WE, Lifson JD, Lang SM et al (2003) Importance of B-cell responses for immunological control of variant strains of simian immunodeficiency virus. J Virol 77:375-381 (Pubitemid 36004977)
46. Johnson WE, Sawyer SL (2009) Molecular evolution of the antiretroviral TRIM5 gene. Immunogenetics 61:163-176. doi:10.1007/s00251-009-0358-y
47. Kaiser SM, Malik HS, Emerman M (2007) Restriction of an extinct retrovirus by the human TRIM5 antiviral protein. Science 316:1756-1758. doi:10.1126/science.1140579 (Pubitemid 46988552)
48. Katzourakis A, Gifford RJ (2010) Endogenous viral elements in animal genomes. PLoS Genet 6:e1001191. doi:10.1371/journal.pgen.1001191
49. Kidd JM, Newman TL, Tuzun E et al (2007) Population stratification of a common APOBEC gene deletion polymorphism. PLoS Genet 3:e63. doi:10.1371/journal. pgen.0030063 (Pubitemid 46683474)
50. Kirmaier A, Wu F, Newman RM et al (2010) TRIM5 suppresses cross-species transmission of a primate immunodeficiency virus and selects for emergence of resistant variants in the new species. PLoS Biol. doi:10.1371/journal.pbio. 1000462
51. Kobayashi Y, Horie M, Tomonaga K, Suzuki Y (2011) No evidence for natural selection on endogenous borna-like nucleoprotein elements after the divergence of old world and new world monkeys. PLoS ONE 6:e24403. doi:10.1371/journal.pone. 0024403
52. Laguette N, Rahm N, Sobhian B et al (2012) Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 11:205-217. doi:10.1016/j.chom. 2012.01.007
53. Le Tortorec A, Neil SJD (2009) Antagonism to and intracellular sequestration of human tetherin by the human immunodeficiency virus type 2 envelope glycoprotein. J Virol 83:11966-11978. doi:10.1128/JVI.01515-09
54. Lee Y, Bieniasz PD (2007) Reconstitution of an infectious human endogenous retrovirus. PLoS Pathog 3:e10. doi:10.1371/journal.ppat.0030010 (Pubitemid 46168849)
55. Liao C, Kuang Y, Liu HL et al (2007) A novel fusion gene mnTRIMCyp in pig-tailed macaques determines its susceptibility to HIV-1 infection. Unpublished
56. Lim ES, Fregoso OI, McCoy CO et al (2012a) The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe 11:194-204. doi:10.1016/j.chom.2012.01.004
57. Lim ES, Malik HS, Emerman M (2010a) Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J Virol 84:7124-7134. doi:10.1128/JVI.00468-10
58. Lim ES, Wu LI, Malik HS, Emerman M (2012b) The function and evolution of the restriction factor viperin in primates was not driven by lentiviruses. Retrovirology 9:55. doi:10.1186/1742-4690-9-55
59. Lim S-Y, Rogers T, Chan T et al (2010b) TRIM5α modulates immunodeficiency virus control in Rhesus monkeys. PLoS Pathog 6:e1000738. doi:10.1371/journal.ppat.1000738.t002
60. Liu H, Fu Y, Li B et al (2011) Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol Biol 11:276. doi:10.1186/1471-2148-11-276
61. Lock LF, Keshet E, Gilbert DJ et al (1988) Studies of the mechanism of spontaneous germline ecotropic provirus acquisition in mice. EMBO J 7:4169-4177
62. Malfavon-Borja R, Wu LI, Emerman M, Malik HS (2013) Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci. doi:10.1073/pnas.1216542110
63. Malim MH (2009) APOBEC proteins and intrinsic resistance to HIV-1infection. Philos Trans R Soc Lond B Biol Sci 364:675-687. doi:10.1098/rstb.2008.0185
64. Marx PA, Apetrei C, Drucker E (2004) AIDS as a zoonosis? Confusion over the origin of the virus and the origin of the epidemics. J Med Primatol 33:220-226. doi:10.1111/j.1600-0684.2004.00078.x (Pubitemid 39378009)
65. McEwan WA, Schaller T, Ylinen LM et al (2009) Truncation of TRIM5 in the Feliformia explains the absence of retroviral restriction in cells of the domestic cat. J Virol 83:8270-8275. doi:10.1128/JVI.00670-09
66. McNatt MW, Zang T, Hatziioannou T et al (2009) Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants. PLoS Pathog 5:e1000300. doi:10.1371/journal.ppat.1000300
67. Mead S, Whitfield J, Poulter M et al (2008) Genetic susceptibility, evolution and the kuru epidemic. Philos Trans R Soc Lond B Biol Sci 363:3741-3746. doi:10.1098/rstb.2008.0087
68. Meyerson NR, Sawyer SL (2011) Two-stepping through time: mammals and viruses. Trends Microbiol 19:286-294. doi:10.1016/j.tim.2011.03.006
69. Mitchell PS, Patzina C, Emerman M et al (2012) Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA. Cell Host Microbe 12:598-604. doi:10.1016/j.chom.2012.09.005
70. Mura M, Murcia P, Caporale M et al (2004) Late viral interference induced by transdominant gag of an endogenous retrovirus. Proc Natl Acad Sci USA 101:11117-11122 . doi:10.1073/pnas.0402877101 (Pubitemid 38989593)
71. Murcia PR, Arnaud F, Palmarini M (2007) The transdominant endogenous retrovirus enJS56A1 associates with and blocks intracellular trafficking of Jaagsiekte sheep retrovirus gag. J Virol 81:1762-1772. doi:10.1128/JVI.01859-06 (Pubitemid 46214450)
72. Münk C, Willemsen A, Bravo IG (2012) An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals. BMC Evol Biol 12:71. doi:10.1186/1471-2148-12-71
73. Neil S, Bieniasz P (2009) Human immunodeficiency virus, restriction factors, and interferon. J Interferon Cytokine Res 29:569-580. doi:10.1089/jir.2009.0077
74. Neil SJD, Zang T, Bieniasz PD (2008) tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature 451:425-430. doi:10.1038/nature06553 (Pubitemid 351158893)
75. Newman RM, Hall L, Connole M et al (2006) Balancing selection and the evolution of functional polymorphism in old world monkey TRIM5 {alpha}. Proc Natl Acad Sci USA 103:19134-19139 (Pubitemid 350010634)
76. Newman RM, Hall L, Kirmaier A et al (2008) Evolution of a TRIM5-CypA splice isoform in old world monkeys. PLoS Pathog 4:e1000003. doi:10.1371/journal.ppat.1000003 (Pubitemid 351340689)
77. Nisole S, Lynch C, Stoye JP, Yap MW (2004) A TRIM5-cyclophilin a fusion protein found in owl monkey kidney cells can restrict HIV-1. Proc Natl Acad Sci USA 101:13324-13328. doi:10 .1073/pnas.0404640101. (Pubitemid 39209664)
78. Nowak M, May RM (2000) Virus dynamics. Oxford University Press, Oxford.
79. Ohkura S, Goldstone DC, Yap MW et al (2011) Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the Murine leukemia virus capsid protein. PLoS Pathog 7:e1002011. doi:10.1371/journal.ppat.1002011
80. Okeoma CM, Lovsin N, Peterlin BM, Ross SR (2007) APOBEC3 inhibits mouse mammary tumour virus replication in vivo. Nature 445:927-930. doi:10.1038/nature05540
81. Pacheco B, Finzi A, Stremlau M, Sodroski J (2010) Adaptation of HIV-1 to cells expressing Rhesus monkey TRIM5α. Virology 408:204-212. doi:10.1016/j.virol.2010.09.019
82. Palmer MS, Dryden AJ, Hughes JT, Collinge J (1991) Homozygous prion protein genotype predisposes to sporadic Creutzfeldt-Jakob disease. Nature 352:340-342. doi:10.1038/352340a0 (Pubitemid 21912354)
83. Patel MR, Emerman M, Malik HS (2011) Paleovirology-ghosts and gifts of viruses past. Curr Opin Virol 1:304-309. doi:10.1016/j.coviro.2011.06.007
84. Patel MR, Loo Y-M, Horner SM et al (2012) Convergent evolution of escape from hepaciviral antagonism in primates. PLoS Biol 10:e1001282. doi:10.1371/journal.pbio.1001282
85. Perez-Caballero D, Soll SJ, Bieniasz PD (2008) Evidence for restriction of ancient primate gammaretroviruses by APOBEC3 but not TRIM5alpha proteins. PLoS Pathog 4:e1000181. doi:10.1371/journal.ppat.1000181
86. Perez-Caballero D, Zang T, Ebrahimi A et al (2009) tetherin inhibits HIV-1 release by directly tethering virions to cells. Cell 139:499-511. doi:10.1016/j.cell.2009.08.039
87. Qi CF, Bonhomme F, Buckler-White A et al (1998) Molecular phylogeny of Fv1. Mamm Genome 9:1049-1055 (Pubitemid 29030912)
88. Robinson HL, Astrin SM, Senior AM, Salazar FH (1981) Host susceptibility to endogenous viruses: defective, glycoprotein-expressing proviruses interfere with infections. J Virol 40:745-751 (Pubitemid 12247252)
89. Ross SR (2009) Are viruses inhibited by APOBEC3 molecules from their host species? PLoS Pathog 5:e1000347. doi:10.1371/journal.ppat.1000347
90. Sabeti PC, Reich DE, Higgins JM et al (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837. doi:10.1038/nature01140 (Pubitemid 35238568)
91. Sabeti PC, Walsh E, Schaffner SF et al (2005) The case for selection at CCR5-Δ32. PLoS Biol 3:e378. doi:10.1371/journal.pbio.0030378.st005
92. Santiago ML, Montano M, Benitez R et al (2008) APOBEC3 encodes Rfv3, a gene influencing neutralizing antibody control of retrovirus infection. Science 321:1343-1346 . doi:10.1126/science.1161121
93. Sawyer SL, Emerman M, Malik HS (2007) Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. PLoS Pathog 3:e197. doi:10.1371/journal.ppat.0030197
94. Sawyer SL, Emerman M, Malik HS (2004) Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol 2:E275. doi:10.1371/journal.pbio.0020275 (Pubitemid 39245238)
95. Sawyer SL, Wu LI, Akey JM et al (2006) High-frequency persistence of an impaired allele of the retroviral defense gene TRIM5alpha in humans. Curr Biol 16:95-100. doi:10.1016/j. cub.2005.11.045
96. Sawyer SL, Wu LI, Emerman M, Malik HS (2005) Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci USA 102:2832-2837. doi:10.1073/pnas.0409853102 (Pubitemid 40299877)
97. Sayah D, Sokolskaja E, Berthoux L, Luban J (2004) Cyclophilin a retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. Nature 430:569-573 (Pubitemid 38998631)
98. Schoggins JW, Wilson SJ, Panis M et al (2011) A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472:481-485. doi:10.1038/nature09907
99. Schumacher AJ, Haché G, Macduff DA et al (2008) The DNA deaminase activity of human APOBEC3G is required for Ty1, MusD, and human immunodeficiency virus type 1 restriction. J Virol 82:2652-2660 . doi:10.1128/JVI.02391-07 (Pubitemid 351329156)
100. Schumacher AJ, Nissley DV, Harris RS (2005) APOBEC3G hypermutates genomic DNA and inhibits Ty1 retrotransposition in yeast. Proc Natl Acad Sci USA 102:9854-9859. doi:10.1 073/pnas.0501694102 (Pubitemid 40993657)
101. Serra-Moreno R, Jia B, Breed M et al (2011) Compensatory changes in the cytoplasmic tail of gp41 confer resistance to tetherin/BST-2 in a pathogenic nef-deleted SIV. Cell Host Microbe 9:46-57. doi:10.1016/j.chom.2010.12.005
102. Simon V, Zennou V, Murray D et al (2005) Natural variation in Vif: differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification. PLoS Pathog 1:e6. doi:10.1371/journal.ppat.0010006
103. Soll SJ, Neil SJD, Bieniasz PD (2010) Identification of a receptor for an extinct virus. Proc Natl Acad Sci 107:19496-19501. doi:10.1073/pnas.1012344107
104. Song B, Gold B, Ohuigin C et al (2005) The B30.2 (SPRY) domain of the retroviral restriction factor TRIM5alpha exhibits lineage-specific length and sequence variation in primates. J Virol 79:6111-6121 (Pubitemid 40617216)
105. Speelmon E, Livingston-Rosanoff D, Li S et al (2006) Genetic association of the antiviral restriction factor TRIM5alpha with human immunodeficiency virus type 1 infection. J Virol 80:2463-2471 (Pubitemid 43271552)
106. Steeves R, Lilly F (1977) Interactions between host and viral genomes in Mouse leukemia. Annu Rev Genet 11:277-296 . doi:10.1146/annurev.ge.11.120177. 001425
107. Sullivan AD, Wigginton J, Kirschner D (2001) The coreceptor mutation CCR5Delta32 influences the dynamics of HIV epidemics and is selected for by HIV. Proc Natl Acad Sci USA 98:10214-10219. doi:10.1073/pnas.181325198 (Pubitemid 32803000)
108. Swain A, Coffin J (1992) Mechanism of transduction by retroviruses. Science 255:841-845
109. Van Damme N, Goff D, Katsura C et al (2008) The interferon-induced protein BST-2 restricts HIV-1 release and is downregulated from the cell surface by the viral Vpu protein. Cell Host Microbe 3:245-252 . doi:10.1016/j.chom. 2008.03.001 (Pubitemid 351494713)
110. van Mierlo JT, Bronkhorst AW, Overheul GJ et al (2012) Convergent evolution of argonaute-2slicer antagonism in two distinct insect RNA viruses. PLoS Pathog 8:e1002872. doi:10.1371/journal.ppat.1002872
111. Virgen CA, Kratovac Z, Bieniasz PD, Hatziioannou T (2008) From the cover: independent genesis of chimeric TRIM5-cyclophilin proteins in two primate species. Proc Natl Acad Sci 105:3563-3568. doi:10.1073/pnas.0709258105 (Pubitemid 351723592)
112. Weiler A, May G, Qi Y et al (2006) Polymorphisms in eight host genes associated with control of HIV replication do not mediate elite control of viral replication in SIV-infected Indian Rhesus macaques. Immunogenetics 58:1003-1009. doi:10.1007/s00251-006-0166-6 (Pubitemid 44791233)
113. Wilson SJ, Webb BLJ, Maplanka C et al (2008a) Rhesus macaque TRIM5 alleles have divergent antiretroviral specificities. J Virol 82:7243-7247. doi:10.1128/JVI.00307-08 (Pubitemid 351977742)
114. Wilson SJ, Webb BLJ, Ylinen LMJ et al (2008b) From the cover: independent evolution of an antiviral TRIMCyp in Rhesus macaques. Proc Natl Acad Sci 105:3557-3562. doi:10.1073/p nas.0709003105 (Pubitemid 351723591)
115. Witzany G (2012) Viruses: essential agents of life. Springer, Berlin.
116. Wong WSW, Nielsen R (2004) Detecting selection in noncoding regions of nucleotide sequences. Genetics 167:949-958. doi:10.1534/genetics.102.010959 (Pubitemid 38931879)
117. Yan Y, Buckler-White A, Wollenberg K, Kozak CA (2009) Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus. Proc Natl Acad Sci 106:3259-3263. doi:10.1073/pnas.0900181106
118. Yang Z (2005) The power of phylogenetic comparison in revealing protein function. Proc Natl Acad Sci USA 102:3179-3180 . doi:10.1073/pnas.0500371102 (Pubitemid 40328018)
119. Yang Z (2006) Computational molecular evolution. Oxford University Press, Oxford.
120. Yang Z, Bielawski J (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503. doi:10.1016/S0169-5347(00)01994-7
121. Zhang J, Webb D (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet 13:1785-1791 (Pubitemid 39173447)
122. Zhang Z, Liu J, Li M et al (2012) Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates. PLoS ONE 7:e49265. doi:10.1371/journal.pone.0049265
123. Zhao K, Ishida Y, Oleksyk TK et al (2012) Evidence for selection at HIV host susceptibility genes in a west central African human population. BMC Evol Biol 12:237. doi:10.1186/1471-2148-12-237