Genomics of Viruses

Pathogenomics: Genome Analysis of Pathogenic Microbes

Volumn , Issue , 2006, Pages 367-388

  Domingo, Esteban ^a   Brun, Alejandro ^b   Nuñez, José Ignacio ^b   Cristina, Juan ^a   Briones, Carlos ^c   Escarmís, Cristina ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria   (Spain)

^c CENTRO DE ASTROBIOLOGÍA CSIC INTA   (Spain)

Author keywords

Applications of data banks; Genomics of hosts; Genomics of pathogenes; Genomics of viruses; Pathogenomics; Reference strains; Virogenomics through microarrays; Virology; Wide scope of virogenomics

Indexed keywords

EID: 30644479837     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/352760801X.ch17     Document Type: Chapter

References (99)

1. Domingo, E. 2005. Microbial evolution and emerging diseases. In: Emerging Neurological Infections. C. Power and R. T. Johnson, eds. Boca Raton, Taylor and Francis p. 1-34.
2. Domingo, E., ed. 2005. Viruses as Quasispecies: Biological Implications. Curr. Top. Microbiol. Immunol., Vol. 299.
3. Knipe, D. M. and P. M. Howley, eds. 2001 Fields Virology. Philadelphia, Lippincott Williams and Wilkins.
4. Flint, S. J., L. W. Enquist, V. R. Racaniello and A. M. Skalka. 2004. Principles of Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses. Washington, DC, ASM Press.
5. Domingo, E., R. G. Webster and J. J. Holland, eds. 1999. Origin and Evolution of Viruses. San Diego, Academic Press.
6. Domingo, E., C. Biebricher, M. Eigen and J. J. Holland. 2001. Quasispecies and RNA Virus Evolution: Principles and Consequences. Austin, Landes Bioscience.
7. Mount, D. W. 2004. Bioinformatics. Sequence and Genome Analysis. Cold Spring Harbor, New York, Cold Spring Harbor Laboratory Press.
8. Lander, E. S. 1996. The new genomics: global views of biology. Science 274:536-539.
9. Woese, C. R. 2004. A new biology for a new century. Microbiol. Mol. Biol. Rev. 68:173-186.
10. Bao, Y., S. Federhen, D. Leipe, V. Pham, S. Resenchuk, M. Rozanov, R. Tatusov and T. Tatusova. 2004. National center for biotechnology information viral genomes project. J. Virol. 78:7291-7298.
11. Wheeler, D. L., et al. 2003. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31:28-33.
12. van Regenmortel, M. H. V, C.M. Fauquet, D.H.L Bishop, et al., eds. 2000. Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses. San Diego, Academic Press.
13. Gesteland, R. F., T. R. Cech and J. F. Atkins, eds. 1999. The RNAWorld. Cold Spring Harbor, New York, Cold Spring Harbor Laboratory Press.
14. Alba, M. M., D. Lee, F. M. Pearl, A. J. Shepherd, N. Martin, C. A. Orengo and P. Kellam. 2001. VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Res. 29:133-136.
15. Feng, D. F. and R. F. Doolittle. 1996. Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. Methods Enzymol. 266:368-382.
16. Thompson, J. D., D. G. Higgins and T. J. Gibson. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
17. Saitou, N. 1996. Reconstruction of gene trees from sequence data. Methods Enzymol. 266:427-449.
18. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
19. Kumar, S., K. Tamura and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150-163.
20. Zhu, J., J. S. Liu and C. E. Lawrence. 1998. Bayesian adaptive sequence alignment algorithms. Bioinformatics 14:25-39.
21. Huelsenbeck, J. P., F. Ronquist, R. Nielsen and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
22. Schmidt, H. A., K. Strimmer, M. Vingron and A. von Haeseler. 2002. TREEPUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
23. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
24. Jenkins, G. M., A. Rambaut, O. G. Pybus and E. C. Holmes. 2002. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54:156-165.
25. Posada, D. 2001. Unveiling the molecular clock in the presence of recombination. Mol. Biol. Evol. 18:1976-1978.
26. Liu, Y., D. C. Nickle, D. Shriner, M. A. Jensen, G. H. Learn, Jr., J. E. Mittler and J. I. Mullins. 2004. Molecular clock-like evolution of human immunodeficiency virus type 1. Virology 329:101-108.
27. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:738-791.
28. Eigen, M. 1987. New concepts for dealing with the evolution of nucleic acids. Cold Spring Harb Symposia in Quantitative Biology 52:307-320.
29. Eigen, M., B. F. Lindemann, M. Tietze, R. Winkler-Oswatitsch, A. Dress and A. von Haeseler. 1989. How old is the genetic code? Statistical geometry of tRNA provides an answer. Science 244:673-679.
30. Dopazo, J., A. Dress and A. von Haeseler. 1993. Split decomposition: a technique to analyze viral evolution. Proc. Natl. Acad. Sci. U. S. A. 90:10320-10324.
31. Eigen, M. 1992. Steps towards life. Oxford University Press.
32. Gorbalenya, A. E. 2001. Big nidovirus genome. When count and order of domains matter. Adv. Exp. Med. Biol. 194:1-17.
33. Hahn, C. S., S. Lustig, E. G. Strauss and J. H. Strauss. 1988. Western equine encephalitis virus is a recombinant virus. Proc. Natl. Acad. Sci. U. S. A. 85:5997-6001.
34. Weaver, S. C., A. Hagenbaugh, L. A. Bellew, L. Gousset, V. Mallampalli, J. J. Holland and T. W. Scott. 1994. Evolution of alphaviruses in the eastern equine encephalomyelitis complex. J. Virol. 68:158-169.
35. Thomson, M. M., L. Perez-Alvarez and R. Najera. 2002. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect. Dis. 2:461-471.
36. Lole, K. S., R. C. Bollinger, R. S. Paranjape, D. Gadkari, S. S. Kulkarni, N. G. Novak, R. Ingersoll, H. W. Sheppard and S. C. Ray. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73:152-160.
37. Colina, R., D. Casane, S. Vasquez, L. Garcia-Aguirre, A. Chunga, H. Romero, B. Khan and J. Cristina. 2004. Evidence of intratypic recombination in natural populations of hepatitis C virus. J. Gen. Virol. 85:31-37.
38. Holmes, E. C., M. Worobey and A. Rambaut. 1999. Phylogenetic evidence for recombination in dengue virus. Mol. Biol. Evol. 16:405-409.
39. Korber, B. 2000. HIV sequence signatures and similarities. In: Computational and Evolutionary Analysis of HIV Molecular Sequences. A. Rodrigo and G. H. Learn, Jr., eds. Dordrecht, Kluwer.
40. Domingo, E., D. Sabo, T. Taniguchi and C. Weissmann. 1978. Nucleotide sequence heterogeneity of an RNA phage population. Cell 13:735-744.
41. Kuge, S., N. Kawamura and A. Nomoto. 1989. Strong inclination toward transition mutation in nucleotide substitutions by poliovirus replicase. J. Mol. Biol. 207:175-182.
42. Vartanian, J. P., M. Henry and S. Wain- Hobson. 2001. Simulating pseudogene evolution in vitro: determining the true number of mutations in a lineage. Proc. Natl. Acad. Sci. U. S. A. 98:13172-13176.
43. Cristina, J., F. Lopez, G. Moratorio, L. Lopez, S. Vasquez, L. Garcia-Aguirre and A. Chunga. 2005. Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution. J. Gen. Virol. 86:115-120.
44. Comeron, J. M. 1999. K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15:763-764.
45. Costa-Mattioli, M., V. Fevré, D. Casane, R. Perez-Beroff, M. Coste-Burel, B.-M. Imbert-Marcille, E. C. M. André, C. Bressollette-Bodin, S. Billaudel and J. Cristina. 2003. Evidence of recombination in natural populations of hepatitis A virus. Virology 311:51-59.
46. Domingo, E. and J. J. Holland 2005. The origin and evolution of viruses. In: Topley and Wilson's Microbiology and Microbial Infections. 1 Virology. B. W. J. Mahy and L. Collier, eds. London and New York, Arnold and Oxford University Press, in press.
47. Baranowski, E., C. M. Ruiz-Jarabo and E. Domingo. 2001. Evolution of cell recognition by viruses. Science 292:1102-1105.
48. Bushman, F. 2002. Lateral DNATransfer. Mechanisms and Consequences. Cold Spring Harbor, New York, Cold Spring Harbor Laboratory Press.
49. Morse, S. S., ed. 1993. Emerging Viruses. Oxford, Oxford University Press.
50. Morse, S. S., ed. 1994. The Evolutionary Biology of Viruses. New York, Raven Press.
51. Smolinski, M. S., M. A. Hamburg and J. Lederberg, eds. 2003. Microbial Threats to Health. Emergence, Detection and Response. Washington DC, The National Academies Press.
52. Domingo, E. 2003. Host-microbe interactions: viruses. Complexities of virus-cell interactions. Curr. Opin. Microbiol. 6:383-385.
53. Krauss, H., A. Weber, M. Appel, B. Enders, H. D. Isenberg, H. G. Schiefer, W. Sleczka, v. Graevenitz and H. Zahner. 2003. Zoonoses. Infectious diseases transmissible from animals to humans. Washington DC, ASM Press.
54. Drake, J. W. and J. J. Holland. 1999. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. U. S. A. 96:13910-13913.
55. Eigen, M. and P. Schuster. 1979. The hypercycle. A principle of natural selforganization. Berlin, Springer.
56. Eigen, M. and C. K. Biebricher 1988. Sequence space and quasispecies distribution. In: RNA Genetics, Vol. 3. E. Domingo, P. Ahlquist and J. J. Holland, eds. Boca Raton, CRC Press. p. 211-245.
57. Schuster, P. and P. F. Stadler 1999. Nature and evolution of early replicons. In: Origin and Evolution of Viruses. E. Domingo, R. G. Webster and J. J. Holland, eds. San Diego, Academic Press, pp 1-24.
58. Biebricher, C. K. 1999. Mutation, competition and selection as measured with small RNA molecules. In: Origin and Evolution of Viruses. E. Domingo, R. G. Webster and J. J. Holland, eds. San Diego, Academic Press, pp 65-85.
59. Rohde, N., H. Daum and C. K. Biebricher. 1995. The mutant distribution of an RNA species replicated by Qb replicase. J. Mol. Biol. 249:754-762.
60. Domingo, E. 1999. Quasispecies. In: Encyclopedia of Virology. A. Granoff and R. G. Webster, eds. London, Academic Press, pp 1431-1436.
61. Eigen, M. 2000. Natural selection: a phase transition? Biophys. Chem. 85:101-123.
62. Simmonds, P. and D. B. Smith. 1999. Structural constraints on RNA virus evolution. J. Virol. 73:5787-5794.
63. Holland, J. J., J. C. de La Torre and D. A. Steinhauer. 1992. RNA virus populations as quasispecies. Curr. Top. Microbiol. Immunol. 176:1-20.
64. Isnard, M., M. Granier, R. Frutos, B. Reynaud and M. Peterschmitt. 1998. Quasispecies nature of three maize streak virus isolates obtained through different modes of selection from a population used to assess response to infection of maize cultivars. J. Gen. Virol. 79:3091-3099.
65. López-Bueno, A., M. G. Mateu and J. M. Almendral. 2003. High mutant frequency in populations of a DNA virus allows evasion from antibody therapy in an immunodeficient host. J. Virol. 77:2701-2708.
66. Peng, X., A. Kessler, H. Phan, R. A. Garrett and D. Prangishvili. 2004. Multiple variants of the archaeal DNA rudivirus SIRV1 in a single host and a novel mechanism of genomic variation. Mol. Microbiol. 54:366-375.
67. Borrego, B., I. S. Novella, E. Giralt, D. Andreu and E. Domingo. 1993. Distinct repertoire of antigenic variants of foot-and-mouth disease virus in the presence or absence of immune selection. J. Virol. 67:6071-6079.
68. de la Torre, J. C. and J. J. Holland. 1990. RNA virus quasispecies populations can suppress vastly superior mutant progeny. J. Virol. 64:6278-6281.
69. Chumakov, K. M., L. B. Powers, K. E. Noonan, I. B. Roninson and I. S. Levenbook. 1991. Correlation between amount of virus with altered nucleotide sequence and the monkey test for acceptability of oral poliovirus vaccine. Proc. Natl. Acad. Sci. U. S. A. 88:199-203.
70. Teng, M. N., M. B. Oldstone and J. C. de la Torre. 1996. Suppression of lymphocytic choriomeningitis virus-induced growth hormone deficiency syndrome by disease-negative virus variants. Virology 223:113-119.
71. González-López, C., A. Arias, N. Pariente, G. Gómez-Mariano and E. Domingo. 2004. Preextinction viral RNA can interfere with infectivity. J. Virol. 78:3319-3324.
72. Grande-Pérez, A., E. Lázaro, P. Lowenstein, E. Domingo and S. C. Manrubia. 2005. Suppression of viral infectivity through lethal defection. Proc. Natl. Acad. Sci. U.S.A. 102:4448-4452.
73. Grande-Pérez, A., G. Gómez-Mariano, P. Lowenstein and E. Domingo. 2005. Mutagenesis-induced, large fitness variations with an invariant consensus genomic nucleotide sequence. J. Virol. 79:10451-10459.
74. Baccam, P., R. J. Thompson, O. Fedrigo, S. Carpenter and J. L. Cornette. 2001. PAQ: partition analysis of quasispecies. Bioinformatics 17:16-22.
75. Baranowski, E., C. M. Ruíz-Jarabo, N. Pariente, N. Verdaguer and E. Domingo. 2003. Evolution of cell recognition by viruses: a source of biological novelty with medical implications. Adv. Virus Res. 62:19-111.
76. Ruiz-Jarabo, C. M., A. Arias, E. Baranowski, C. Escarmís and E. Domingo. 2000. Memory in viral quasispecies. J. Virol. 74:3543-3547.
77. Ruiz-Jarabo, C. M., A. Arias, C. Molina- París, C. Briones, E. Baranowski, C. Escarmís and E. Domingo. 2002. Duration and fitness dependence of quasispecies memory. J. Mol. Biol. 315:285-296.
78. Ruiz-Jarabo, C. M., E. Miller, G. Gómez- Mariano and E. Domingo. 2003. Synchronous loss of quasispecies memory in parallel viral lineages: a deterministic feature of viral quasispecies. J. Mol. Biol. 333:553-563.
79. Arias, A., C. M. Ruiz-Jarabo, C. Escarmis and E. Domingo. 2004. Fitness increase of memory genomes in a viral quasispecies. J. Mol. Biol. 339:405-412.
80. Briones, C., E. Domingo and C. Molina- París. 2003. Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus. J. Mol. Biol. 331:213-229.
81. Zhu, H., M. Bilgin, R. Bangham, et al. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-2105.
82. Bacarese-Hamilton, T., L. Mezzasoma, A. Ardizzoni, F. Bistoni and A. Crisanti. 2004. Serodiagnosis of infectious diseases with antigen microarrays. J. Appl. Microbiol. 96:10-17.
83. Neuman de Vegvar, H. E. and W. H. Robinson. 2004. Microarray profiling of antiviral antibodies for the development of diagnostics, vaccines, and therapeutics. Clin. Immunol. 111:196-201.
84. Shena, M., Ed. 2000. Microarray biochip technology. Sunnyvale, Calif, Eaton Publishing.
85. Southern, E. M., S. C. Case-Green, J. K. Elder, M. Johnson, K. U. Mir, L. Wang and J. C. Williams. 1994. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 22:1368-1373.
86. Hacia, J. G., W. Makalowski, K. Edgemon, M. R. Erdos, C. M. Robbins, S. P. Fodor, L. C. Brody and F. S. Collins. 1998. Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nat. Genet. 18:155-158.
87. Kozal, M. J., et al. 1996. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2:753-759.
88. Amexis, G., P. Oeth, K. Abel, A. Ivshina, F. Pelloquin, C. R. Cantor, A. Brau and K. Chumakov. 2001. Quantitative mutant analysis of viral quasispecies by chip-based matrix- assisted laser desorption/ ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 98:12097-12102.
89. Van Laethem, K., et al. 1999. Phenotypic assays and sequencing are less sensitive than point mutation assays for detection of resistance in mixed HIV-1 genotypic populations. J. Acquir. Immune Defic. Syndr. 22:107-118.
90. Wilson, J. W., P. Bean, T. Robins, F. Graziano and D. H. Persing. 2000. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J. Clin. Microbiol. 38:3022-3028.
91. Gerry, N. P., N. E. Witowski, J. Day, R. P. Hammer, G. Barany and F. Barany. 1999. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 292:251-262.
92. Gilles, P. N., D. J. Wu, C. B. Foster, P. J. Dillon and S. J. Chanock. 1999. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol. 17:365-370.
93. Tillib, S. V. and A. D. Mirzabekov. 2001. Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology. Curr. Opin. Biotechnol. 12:53-58.
94. Sengupta, S., K. Onodera, A. Lai and U. Melcher. 2003. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 41:4542-4550.
95. Chizhikov, V., M. Wagner, A. Ivshina, Y. Hoshino, A. Z. Kapikian and K. Chumakov. 2002. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40:2398-2407.
96. Wang, D., L. Coscoy, M. Zylberberg, P. C. Avila, H. A. Boushey, D. Ganem and J. L. DeRisi. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U. S.A 99:15687-15692.
97. Cherkasova, E., M. Laassri, V. Chizhikov, E. Korotkova, E. Dragunsky, V. I. Agol and K. Chumakov. 2003. Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses. Proc. Natl. Acad. Sci. U. S.A 100:9398-9403.
98. Ooms, M., K. Verhoef, E. Southern, H. Huthoff and B. Berkhout. 2004. Probing alternative foldings of the HIV- 1 leader RNA by antisense oligonucleotide scanning arrays. Nucleic Acids Res. 32:819-827.
99. Martell, M., C. Briones, A. de Vicente, M. Piron, J. I. Esteban, R. Esteban, J. Guardia and J. Gomez. 2004. Structural analysis of hepatitis C RNA genome using DNA microarrays. Nucleic Acids Res. 32:e90.