Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index

Journal of General Virology

Volumn 89, Issue 9, 2008, Pages 2098-2107

  Hraber, Peter ^a   Kuiken, Carla ^a   Waugh, Mark ^a   Geer, Shaun ^a,b   Bruno, William J ^a   Leithner, Thomas ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRANCHING MORPHOGENESIS; GENE SEQUENCE; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VIRUS CLASSIFICATION; VIRUS GENE; VIRUS RECOMBINANT; CLASSIFICATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENETICS; HUMAN; VIRUS GENOME;

HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

GENOME, VIRAL; HEPACIVIRUS; HIV-1; HUMANS; PHYLOGENY; RECOMBINATION, GENETIC; VARIATION (GENETICS);

EID: 52649083081     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.83657-0     Document Type: Article

References (30)

1. Calef, C., Kuiken, C., Szinger, J., Gaschen, B., Abfalterer, W., Zhang, M., Tao, N., Funkhouser, R., Yusim, K. & other authors (2005). Gateway to tools of HIV and HCV databases. In HIV Sequence Compendium 2005, pp. 49-79. Edited by T. Leitner, B. Foley, B. Hahn, P. Marx, F. McCutchan, J. Mellors, S. Wolinsky & B. Korber. Los Alamos, NM: Theoretical Biology and Biophysics Group, Los Alamos National, Laboratory.
2. de Oliveira, T., Deforche, K., Cassol, S., Salminen, M., Paraskevis, D., Seebregts, C., Snoeck, J., van Rensburg, E. J., Wensing, A. M. & other authors; (2005). An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 21, 3797-3800.
3. Felsenstein, J. (1984). Distance methods for inferring phylogenies: a justification. Evolution 38, 16-24.
4. Felsenstein, J. (2004). Inferring Phylogenies. Sunderland, MA: Sinauer Associates.
5. Fried, M. W., Shiffman, M. L., Reddy, K. R., Smith, C., Marinos, G., Goncales, F. L., Haussinger, D., Diago, M., Carosi, G. & other authors (2002). Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Engl J Med 347, 975-982.
6. Gascuel, O. (1997). BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14, 685-695.
7. Gascuel, O. (2000). On the optimization principle in phylogenetic analysis and the minimum-evolution criterion. Mol Biol Evol 17, 401-405.
8. Hadziyannis, S. J., Sette, H., Jr, Morgan, T. R., Balan, V., Diago, M., Marcellin, P., Ramadori, G., Bodenheimer, H., Bernstein, D. & other authors (2004). Peginterferon-α2a and ribavirin combination therapy in chronic hepatitis C: a randomized study of treatment duration and ribavirin dose. Ann Intern Med 140, 346-355.
9. Hillis, D. M., Huelsenbeck J. P. & Cunningham, C. W. (1994). Application and accuracy of molecular phylogenies. Science 264, 671-677.
10. Hraber, P. T., Fischer, W., Bruno, W. J., Leitner, T. & Kuiken, C. (2006). Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5′ untranslated region (UTR) fails to classify subtypes. Virol J 3, 103.
11. Hraber, P. T., Leach, R. W., Reilly, L. P., Thurmond, J., Yusim, K. & Kuiken, C. (2007). Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research. Antivir Chem Chemother 18, 113-124.
12. Korber, B., Gaschen, B., Yusim, K., Thakallapally, R., Kesmir, C. & Detours, V. (2001). Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 58, 19-42.
13. Kuiken, C., Yusim, K., Boykin, L. & Richardson, R. (2005). The Los Alamos hepatitis C sequence database. Bioinformatics 21, 379-384.
14. Kuiken, C., Combet, C., Bukh, J., Shin-I, T., Deléage, G., Mizokami, M., Richardson, R., Sablon, E., Yusim, K. & other authors (2006). A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Hepatology 44, 1355-1361.
15. Leitner, T. (editor) (2002). The Molecular Epidemiology of Human Viruses. Norwell, MA: Kluwer Academic Publishers.
16. Leitner, T., Escanilla, D., Franzén, C., Uhlén, M. & Albert, J. (1996). Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci U S A 93, 10864-10869.
17. Leitner, T., Kumar, S. & Albert, J. (1997). Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J Virol 71, 4761-4770.
18. Leitner, T., Korber, B., Daniels, M., Calef, C. & Foley, B. (2005). HIV-1 subtype and circulating recombinant form (CRF) reference sequences, 2005. In HIV Sequence Compendium 2005, pp. 41-48. Edited by T. Leitner, B. Foley, B. Hahn, P. Marx, F. McCutchan, J. Mellors, S. Wolinsky & B. Korber. Los Alamos, NM: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory.
19. Motulsky, H. (1995). Intuitive Biostatistics. Oxford: Oxford University Press.
20. R Development Core Team (2007). R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
21. Robertson, D. L., Anderson, J. P., Bradec, J. A., Carr, J. K., Foley, B., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L. & other authors (2000). HIV-1 nomenclature proposal. Science 288, 55-56.
22. Salminen, M. O., Carr, J. K., Burke, D. S. & McCutchan, F. E. (1995). Identification of breakpoints in intergenotypic recombinants of HIV-1 by bootscanning. AIDS Res Hum Retroviruses 11, 1423-1425.
23. Schultz, A.-K., Zhang, M., Leitner, T., Kuiken, C., Korber, B., Morgenstem, B. & Stanke, M. (2006). A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics 7, 265.
24. Simmonds, P., Bukh, J., Combat, C., Deléage, G., Enomoto, N., Feinstone, S., Halfon, P., Inchauspé, G., Kuiken, C. & other authors (2005). Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42, 962-973.
25. Sokol, R. R. & Rohlf, F. J. (1995). Biometry: The Principles and Practice of Statistics in Biological Research. New York: W. H. Freeman.
26. Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I. & other authors (2002). The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12, 1611-1618.
27. Swofford, D. L. (2002). PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sunderland, MA: Sinauer Associates.
28. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
29. van Regenmortel, M. H. V. (2007). Virus species and virus identification: past and current controversies. Infect Genet Evol 7, 133-144.
30. Wilbe, K., Salminen, M., Laukkanen, T., McCutchan, F., Ray, S. C., Albert J. & Leitner, T. (2003). Characterization of novel recombinant HIV-1 genomes using the branching index. Virology 316, 116-125.