Identifying changes in selective constraints: Host shifts in influenza

PLoS Computational Biology

Volumn 5, Issue 11, 2009, Pages

  Tamuri, Asif U ^a   Dos Reis, Mario ^a   Hay, Alan J ^a   Goldstein, Richard A ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; PHYLOGENETIC; RESERVOIRS (WATER);

ACID SITE; AMINO-ACIDS; AVIAN FLU VIRUS; GENETIC MATERIALS; HUMAN POPULATION; INFLUENZA A; INFLUENZA PANDEMICS; NON-HOMOGENEOUS; PHYLOGENETICS;

VIRUSES;

AMINO ACID;

ARTICLE; AVIAN INFLUENZA; CONTROLLED STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; HOST; HUMAN; INFLUENZA; INFLUENZA VIRUS A; NONHUMAN; PANDEMIC; PHYLOGENY; PREDICTION; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; DUCKS AND GEESE; GENETIC DRIFT; GENETIC SELECTION; GENETICS; HOST PATHOGEN INTERACTION; METHODOLOGY; PATHOGENICITY; SEQUENCE ANALYSIS;

ANATIDAE; AVES;

ANIMALS; ANSERIFORMES; COMPUTATIONAL BIOLOGY; GENETIC DRIFT; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLUENZA A VIRUS; MODELS, GENETIC; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ANALYSIS, PROTEIN;

EID: 73449127243     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000564     Document Type: Article

References (59)

1. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56: 152-179.
2. Schafer JR, Kawaoka Y, Bean WJ, Suss J, Senne D, et al. (1993) Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology 194: 781-788.
3. Reid AH, Taubenberger JK, Fanning TG (2004) Evidence of an absence: the genetic origins of the 1918 pandemic influenza virus. Nat Rev Microbiol 2: 909-914.
4. Taubenberger JK (2006) The origin and virulence of the 1918 "Spanish" influenza virus. Proceedings of the American Philosophical Society 150: 86-112.
5. Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, et al. (2005) Characterization of the 1918 influenza virus polymerase genes. Nature 437: 889-893.
6. Antonovics J, Hood ME, Baker CH (2006) Molecular virology: was the 1918 flu avian in origin? Nature 440: E9. discussion E9-10.
7. dos Reis M, Hay AJ, Goldstein RA (2009) Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. J Mol Evol;DOI 10.1007/s00239-009-9282-x.
8. Gibbs M, Gibbs A (2006) Molecular virology: Was the 1918 pandemic caused by a bird flu? Nature 440: E8-E8.
9. Smith GJD, Bahl J, Vijaykrishna D, Zhang JZ, Poon LLM, et al. (2009) Dating the emergence of pandemic influenza viruses. Proc Natl Acad Sci U S A 106: 11709-11712.
10. Lin YP, Shaw M, Gregory V, Cameron K, Lim W, et al. (2000) Avian-to-human transmission of H9N2 subtype influenza A viruses: relationship between H9N2 and H5N1 human isolates. Proc Natl Acad Sci U S A 97: 9654-9658.
11. Gambaryan AS, Matrosovich MN, Yamnikova SS, Lvov DK, Robertson JS, et al. (2002) Differences in receptor specificity between the influenza viruses of duck, chicken, and human. Molecular Biology 36: 429-435.
12. Connor RJ, Kawaoka Y, Webster RG, Paulson JC (1994) Receptor Specificity in Human, Avian, and Equine H2 and H3 Influenza-Virus Isolates. Virology 205: 17-23.
13. Matrosovich M, Tuzikov A, Bovin N, Gambaryan A, Klimov A, et al. (2000) Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals. Journal of Virology 74: 8502-8512.
14. Nobusawa E, Aoyama T, Kato H, Suzuki Y, Tateno Y, et al. (1991) Comparison of Complete Amino-Acid-Sequences and Receptor-Binding Properties among 13 Serotypes of Hemagglutinins of Influenza a-Viruses. Virology 182: 475-485.
15. Rogers GN, Paulson JC, Daniels RS, Skehel JJ, Wilson IA, et al. (1983) Single Amino-Acid Substitutions in Influenza Hemagglutinin Change Receptor-Binding Specificity. Nature 304: 76-78.
16. Vines A, Wells K, Matrosovich M, Castrucci MR, Ito T, et al. (1998) The role of influenza a virus hemagglutinin residues 226 and 228 in receptor specificity and host range restriction. Journal of Virology 72: 7626-7631.
17. Baigent SJ, McCauley JW (2003) Influenza type A in humans, mammals and birds: determinants of virus virulence, host-range and interspecies transmission. Bioessays 25: 657-671.
18. Naffakh N, Tomoiu A, Rameix-Welti MA, van der Werf S (2008) Host Restriction of Avian Influenza Viruses at the Level of the Ribonucleoproteins. Annual Review of Microbiology 62: 403-424.
19. Hatta M, Gao P, Halfmann P, Kawaoka Y (2001) Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science 293: 1840-1842.
20. Steel J, Lowen A, Mubareka S, Palese P, Baric R (2009) Transmission of Influenza Virus in a Mammalian Host Is Increased by PB2 Amino Acids 627K or 627E/701N. PLoS Pathog 5: e1000252.
21. Subbarao EK, London W, Murphy BR (1993) A Single Amino-Acid in the Pb2-Gene of Influenza-a Virus Is a Determinant of Host Range. Journal of Virology 67: 1761-1764.
22. Chen GW, Chang SC, Mok CK, Lo YL, Kung YN (2006) Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis.
23. Finkelstein D, Mukatira S, Mehta P, Obenauer J, Su X, et al. (2007) Persistent Host Markers in Pandemic and H5N1 Influenza Viruses. J Virol 81: 10292-10299.
24. Miotto O, Heiny A, Tan T, August J, Brusic V (2008) Identification of humanto-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics 9: S18.
25. Mayr E (1942) Systematics and the Origin of Species. New York: Columbia University Press.
26. Bruno W (1996) Modeling residue usage in aligned protein sequences via maximum likelihood. Molecular Biology and Evolution 13: 1368-1374.
27. Freire-Maia N (1979) Neutral hypothesis is Darwinian. Annals of Human Genetics 42: 531.
28. Blouin C, Boucher Y, Roger AJ (2003) Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Research 31: 790-797.
29. Dorman K (2007) Identifying dramatic selection shifts in phylogenetic trees. BMC Evol Biol 7: S10.
30. Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution 16: 1664-1674.
31. Gu X (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Molecular Biology and Evolution 18: 453-464.
32. Gu X, Fu Y-X, Li W-H (1995) Maximum Likelihood Estimation of the Heterogeneity of Substitution Rate among Nucleotide Sites. Mol Biol Evol 12: 546-557.
33. Knudsen B, Miyamoto MM (2001) A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proceedings of the National Academy of Sciences of the United States of America 98: 14512-14517.
34. Penn O, Stern A, Rubinstein N, Dutheil J, Bacharach E, et al. (2008) Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes. PLoS Comput Biol 4: e1000214.
35. Pupko T, Galtier N (2002) A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proceedings of the Royal Society of London Series B-Biological Sciences 269: 1313-1316.
36. Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP (2004) Modeling the sitespecific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences of the United States of America 101: 12957-12962.
37. Yang ZH, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908-917.
38. Zhang JZ, Nielsen R, Yang ZH (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22: 2472-2479.
39. Forsberg R, Christiansen FB (2003) A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol Biol Evol 20: 1252-1259.
40. Blackburne BP, Hay AJ, Goldstein RA (2008) Changing Selective Pressure during Antigenic Changes in Human Influenza H3. PLoS Pathogens 4: e1000058.
41. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Molecular Biology and Evolution 18: 691-699.
42. Benjamini Y, Hochberg T (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc B 85: 289-300.
43. Crow JF, Kimura M (1970) An introduction to population genetics theory. New York: Harper & Row.
44. Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom SE, et al. (2009) Emergence of a novel swine-origin influenza A (H1N1) virus in humans. New England Journal of Medicine 361: 10.1056/NEJMoa0903810.
45. Sheerar M, Easterday B, Hinshaw V (1989) Antigenic conservation of H1N1 swine influenza viruses. Journal of General Virology 70: 3297-3303.
46. Vincent A, Lager K, Ma W, Lekcharoensuk P, Gramer M, et al. (2006) Evaluation of hemagglutinin subtype 1 swine influenza viruses from the United States. Veterinary Microbiology 118: 212-222.
47. Boni MF, Zhou Y, Taubenberger JK, Holmes EC (2008) Homologous recombination is very rare or absent in human influenza A virus. Journal of Virology 82: 4807-4811.
48. Chare ER, Gould EA, Holmes EC (2003) Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 84: 2691-2703.
49. Krasnitz M, Levine AJ, Rabadan R (2008) Anomalies in the influenza virus genome database: New biology or laboratory errors? Journal of Virology 82: 8947-8950.
50. Yang Z (2006) Computational molecular evolution. Oxford: Oxford University Press.
51. Felsenstein J (1973) Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22: 240-249.
52. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
53. Bao YM, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, et al. (2008) The influenza virus resource at the national center for biotechnology information. Journal of Virology 82: 596-601.
54. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797.
55. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research 34: W609-W612.
56. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
57. Hasegawa M, Kishino H, Yano TA (1985) Dating of the Human Ape Splitting by a Molecular Clock of Mitochondrial-DNA. Journal of Molecular Evolution 22: 160-174.
58. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
59. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591.