How sequence information helps us understand the evolution and dissemination of viruses

APMIS

Volumn 108, Issue 2, 2000, Pages 81-97

  Hungnes, O ^a   Jonassen, T O ^a   Jonassen, C M ^a   Grinde, B ^a  

^a NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

Author keywords

Epidemiology; Evolution; Molecular analysis; Nucleic acid sequence; Routes of infection; Virus

Indexed keywords

EVOLUTION; GENOME; HEPATITIS A VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; INFECTION; INFLUENZA VIRUS A; MOLECULAR BIOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; REVIEW; STRAIN DIFFERENCE; VIRUS INFECTION; ANIMAL; DNA SEQUENCE; EPIDEMIC; GENETICS; HUMAN; METHODOLOGY;

ANIMALS; BASE SEQUENCE; DISEASE OUTBREAKS; EVOLUTION; HUMANS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VIRUS DISEASES;

EID: 0034131841     PISSN: 09034641     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1600-0463.2000.d01-31.x     Document Type: Review

References (71)

1. 1. Collins AR. Molecular epidemiology in cancer research. Mol Aspects Med 1998;19:359-432.
2. 2. Andrieu N, Goldstein AM. Epidemiologic and genetic approaches in the study of gene-environment interaction: an overview of available methods. Epidemiol Rev 1998;20:137-47.
3. 3. Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, He T, et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 1996;2:1240-3.
4. 4. Libert F, Cochaux P, Beckman G, Samson M, Aksenova M, Cao A, et al. The Δccr5 mutation conferring protection against HIV-1 in Caucasian populations has a single and recent origin in Northeastern Europe. Hum Mol Genet 1998;7: 399-406.
5. 5. McDade JE, Anderson BE. Molecular epidemiology: applications of nucleic acid amplification and sequence analysis. Epidemiol Rev 1996;18: 90-7.
6. 6. Holmes EC. Molecular epidemiology and evolution of emerging infectious diseases. Br Med Bull 1998;54:533-43.
7. 7. Powell SC, Attwell R. The use of epidemiological data in the control of foodborne viruses. Rev Environ Health 1999;14:31-7.
8. 8. Suss J, Beziat P, Schrader C. Viral zoonosis from the viewpoint of their epidemiological surveillance: tick-borne encephalitis as a model. Arch Virol Suppl 1997;13:229-43.
9. 9. Holmes EC, Nee S, Rambaut A, Garnett GP, Harvey PH. Revealing the history of infectious disease epidemics through phylogenetic trees. Philos Trans R Soc Lond B Biol Sci 1995;349:33-40.
10. 10. Hu DJ, Dondero TJ, Rayfield MA, George JR, Schochetman G, Jaffe HW, et al. The emerging genetic diversity of HIV. The importance of global surveillance for diagnostics, research, and prevention. JAMA 1996;275:210-6.
11. 11. Tsubota A, Chayama K, Ikeda K, Yasuji A, Koida I, Saitoh S, et al. Factors predictive of response to interferon-alpha therapy in hepatitis C virus infection. Hepatology 1994;19:1088-94.
12. 12. Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, et al. Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 1996;334:77-81.
13. 13. Rodriguez-Rosado R, Briones C, Soriano V. Introduction of HIV drug-resistance testing in clinical practice. AIDS 1999;13:1007-14.
14. 14. Horimoto T, Rivera E, Pearson J, Senne D, Krauss S, Kawaoka Y, et al. Origin and molecular changes associated with emergence of a highly pathogenic H5N2 influenza virus in Mexico. Virology 1995;213:223-30.
15. 15. Marrone A, Sallie R. Genetic heterogeneity of hepatitis C virus. The clinical significance of genotypes and quasispecies behavior. Clin Lab Med 1996;16:429-49.
16. 16. Rosen HR, Chou S, Sasaki AW, Gretch DR. Molecular epidemiology of hepatitis C infection in U.S. veteran liver transplant recipients: evidence for decreasing relative prevalence of genotype 1B. Am J Gastroenterol 1999;94:3015-9.
17. 17. Becker Y. A short introduction to the origin and molecular evolution of viruses. Virus Genes 1995:11;73-7.
18. 18. Fitch WM. The variety of human virus evolution. Mol Phylogenet Evol 1996;5:247-58.
19. 19. Strauss EG, Strauss JH, Levine AJ. Virus evolution. In: Fields BN, Knipe DM, Howley PM, editors. Fields Virology. Philadelphia: Lippincott-Raven; 1995,153-71.
20. 20. Crandall KA. The Evolution of HIV. Baltimore: Johns Hopkins University Press, 1999.
21. 21. Worobey M, Holmes EC. Evolutionary aspects of recombination in RNA viruses. J Gen Virol 1999;80:2535-43.
22. 22. Jonassen CM, Jonassen TØ, Grinde B. A common RNA motif in the 3′ end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J Gen Virol 1998;79:715-8.
23. 23. Gibbs MJ, Weiller GF. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc Natl Acad Sci USA 1999;96:8022-7.
24. 24. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol Rev 1992;56:152-79.
25. 25. Domingo E, Holland JJ. RNA virus mutations and fitness for survival. Annu Rev Microbiol 1997;51:151-78.
26. 26. Anderson RM, Donnelly CA, Gupta S. Vaccine design, evaluation, and community-based use for antigenically variable infectious agents. Lancet 1997;350:1466-70.
27. 27. Duarte EA, Novella IS, Weaver SC, Domingo E, Wain-Hobson S, Clarke DK, et al. RNA virus quasispecies: significance for viral disease and epidemiology. Infect Agents Dis 1994;3:201-14.
28. 28. Domingo E. Quasispecies and the implications for virus persistence and escape. Clin Diagn Virol 1998;10:97-101.
29. 29. Clewley JP. Automation of the polymerase chain reaction. Part 2. Extraction - the foundation for success. Commun Dis Public Health 1999;2:147-8.
30. 30. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanatephenol-chloroform extraction. Anal Biochem 1987;162:156-9.
31. 31. Monceyron C, Grinde B. Detection of hepatitis A virus in clinical and environmental samples by immunomagnetic separation and PCR. J Virol Methods 1994;46:157-66.
32. 32. Grinde B, Jonassen TØ, Ushijima H. Sensitive detection of group A rotaviruses by immunomagnetic separation and RT-PCR. J Virol Methods 1995;55:327-38.
33. 33. Leitner T, Halapi E, Scarlatti G, Rossi P, Albert J, Fenyo EM, Uhlen M. Analysis of heterogeneous viral populations by direct DNA sequencing. Biotechniques 1993;15:120-7.
34. 34. Bracho MA, Moya A, Barrio E. Contribution of Taq polymerase-induced errors to the estimation of RN virus diversity. J Gen Virol 1998;79:2921-8.
35. 35. Pieniazek D, Yang C, Lal RB. Phylogenetic analysis of gp41 envelope of HIV-1 groups M, N, and O strains provides an alternate region for subtype determination. In: Korber B, Kuiken CL, Hahn B, et al., editors. Human Retroviruses and AIDS 1998; A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, New Mexico: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, 1998:III/112-III/117.
36. 35. Pieniazek D, Yang C, Lal RB. Phylogenetic analysis of gp41 envelope of HIV-1 groups M, N, and O strains provides an alternate region for subtype determination. In: Korber B, Kuiken CL, Hahn B, et al., editors. Human Retroviruses and AIDS 1998; A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, New Mexico: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, 1998:III/112-III/117.
37. 36. Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990;183:63-98.
38. 37. Pennisi E. Keeping genome databases clean and up to date. Science 1999;286:447-50.
39. 38. Clewley JP. A user's guide to producing and interpreting tree diagrams in taxonomy and phylogenetics. Part I. Introduction and naming of parts. Commun Dis Public Health 1998a;1:64-6.
40. 39. Clewley JP. A user's guide to producing and interpreting tree diagrams in taxonomy and phylogenetics. Part 2. The multiple alignment of DNA and protein sequences to determine their relationships. Commun Dis Public Health 1998b;1: 132-4.
41. 40. Higgins DG, Sharp PM. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci 1989;5:151-3.
42. 41. Durbin R, Eddy S, Krogh A, Mitchison G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press, 1998.
43. 42. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author: Department of Genetics, University of Washington, Seattle, 1993.
44. 43. Swofford DL. PAUP Phylogenetic Analysis Using Parsimony. Version 4. Sunderland, Massachussets: Sinauer Associates, 1998.
45. 44. Zhu T, Korber BT, Nahmias AJ, Hooper E, Sharp PM, Ho DD. An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 1998;391:594-7.
46. 45. Posada D, Crandall KA. Modeltest: testing the model of DNA substitution. Bioinformatics 1998;14:817-8.
47. 46. Leitner T, Korber B, Robertson D, Gao F, Hahn B. Updated proposal of reference sequences of HIV-1 genetic subtypes. In: Korber B, Hahn BH, Foley B, et al., editors. Human Retroviruses and AIDS 1997; A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, New Mexico: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, 1997:III/19-III/24.
48. 46. Leitner T, Korber B, Robertson D, Gao F, Hahn B. Updated proposal of reference sequences of HIV-1 genetic subtypes. In: Korber B, Hahn BH, Foley B, et al., editors. Human Retroviruses and AIDS 1997; A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, New Mexico: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, 1997:III/19-III/24.
49. 47. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999;73:152-60.
50. 48. Salminen MO, Carr JK, Burke DS, McCutchan FE. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 1995;11:1423-5.
51. 49. Kyle WS. Simian retroviruses, poliovaccine, and origin of AIDS. Lancet 1992;339:600-1.
52. 50. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, et al. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 1999;397:436-41.
53. 51. Jonassen TØ, Stene-Johansen K, Berg ES, Hungnes O, Lindboe CF, Frøland SS, Grinde B. Sequence analysis of HIV-1 group O from Norwegian patients infected in the 1960s. Virology 1997;231:43-7.
54. 52. Hollinger FB, Ticehurst JR. Hepatitis A virus. In: Fields BN, Knipe PM, Howley PM, editors. Fields Virology. Philadephia: Lipincott-Raven; 1996,735-82.
55. 53. Grinde B, Stene-Johansen K, Sharma B, Hoel T, Jensenius M, Skaug K. Characterisation of an epidemic of hepatitis A virus involving intravenous drug abusers - infection by needle sharing? J Med Virol 1997;53:69-75.
56. 54. Jensenius M, Ringertz SH, Berild D, Bell H, Espinoza R, Grinde B. Prolonged nosocomial outbreak of hepatitis A arising from an alcoholic with pneumonia. Scand J Infect Dis 1998;30: 119-23.
57. 55. Subbarao K, Klimov A, Katz J, Regnery H, Lim W, Hall H, et al. Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. Science 1998;279: 393-6.
58. 56. Claas EC, Osterhaus AD, van Beek R, De Jong JC, Rimmelzwaan GF, Senne DA, et al. Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus. Lancet 1998; 351:472-7.
59. 57. Shortridge KF, Zhou NN, Guan Y, Gao P, Ito T, Kawaoka Y, et al. Characterization of avian H5N1 influenza viruses from poultry in Hong Kong. Virology 1998;252:331-42.
60. 58. Suarez DL, Perdue ML, Cox N, Rowe T, Bender C, Huang J, et al. Comparisons of highly virulent H5N1 influenza A viruses isolated from humans and chickens from Hong Kong. J Virol 1998;72: 6678-88.
61. 59. Boden D, Hurley A, Zhang L, Yunzhen C, Yong G, Jones E, et al. HIV-1 drug resistance in newly infected individuals. JAMA 282;1999:1135-41.
62. 60. Erickson JW, Gulnik SV, Markowitz M. Protease inhibitors: resistance, cross-resistance, fitness and the choice of initial and salvage therapies. AIDS 1999;13:S189-S204.
63. 61. Pomerantz RJ. Primary HIV-1 resistance: a new phase in the epidemic? JAMA 1999;282: 1177-9.
64. 62. Albert J, Wahlberg J, Leitner T, Escanilla D, Uhlen M. Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol 1994;68:5918-24.
65. 63. Ross RS, Viazov S, Varenholz C, Roggendorf M. Inquiries on intraspousal transmission of hepatitis C virus: benefits and limitations of genome sequencing and phylogenetic analysis. Forensic Sci Int 1999;100:69-76.
66. 64. Ou CY, Ciesielski CA, Myers G, Bandea CI, Luo CC, Korber BT, et al. Molecular epidemiology of HIV transmission in a dental practice. Science 1992;256:1165-71.
67. 65. Crandall KA. Intraspecific phylogenetics: support for dental transmission of human immunodeficiency virus. J Virol 1995:69;2351-6.
68. 66. Vogel G. HIV strain analysis debuts in murder trial. Science 1998;282:851-3.
69. 67. Morse SS. The viruses of the future? Emerging viruses and evolution. In: Morse SS, editor. The Evolutionary Biology of Viruses. New York: Raven Press; 1994,325-35.
70. 68. Myers G, Korber B. The future of human immunodeficiency virus. In: Morse SS, editor. The Evolutionary Biology of Viruses. New York: Raven Press; 1994,211-32.
71. 69. Fitch WM, Bush RM, Bender CA, Cox NJ. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci USA 1997; 94:7712-8.