Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2004;28(1):41–53. doi: 10.1023/B:VIRU.0000012262.89898.c7

Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus

Tan Do Yew 1,✉, Mohd Hair Bejo 1, Aini Ideris 1, Abdul Rahman Omar 1, Goh Yong Meng 1
PMCID: PMC7089146  PMID: 14739650

Abstract

Base usage and dinucleotide frequency have been extensively studied in many eukaryotic organisms and bacteria, but not for viruses. In this paper, a comprehensive analysis of these aspects for infectious bursal disease virus (IBDV) was presented. The analysis of base usage indicated that all of the IBDV genes possess equivalent overall nucleotide distributions. However when the base usage at each codon positions was analysed by using cluster analysis, the VP5 open reading frame (ORF) formed a different cluster isolated from the other genes. The unusual base usage of VP5 ORF may indicate that the gene was originated by the virus “overprinting strategy”, a strategy in which virus may create novel gene by utilizing the unused reading frames of its existing genes. Meanwhile, the GC content of the IBDV genes and the chicken's coding sequences was comparable; suggesting the virus imitation of the host to increase its translational efficiency. The analysis of dinucleotide frequency indicated that IBDV genome had dinucleotide bias: the frequencies of CpG and TpA were lower and the TpG was higher than the expected. Classical methylation pathway, a process where CpG converted to TpG, may explain the significant correlation between the CpG deficiency and TpG abundance. “Principal component analysis of the dinucleotide frequencies” (DF-PCA) was used to analyse the overall dinucleotide frequencies of IBDV genome. DF-PCA on the hypervariable region and polyprotein (VPX-VP4-VP3) gene showed that the very virulent IBDV (vvIBDV) was segregated from other strains; which meant vvIBDV had a unique dinucleotide pattern. In summary, the study of base usage and dinucleotide frequency had unravelled many overlooked genomic properties of the virus.

Keywords: base usage, bioinformatics, dinucleotide frequency, infectious bursal disease virus, principal component analysis, sequence analysis

References

  • 1.Saif Y.M. Vet Immunol Immunopathol. 1991;30:45–50. doi: 10.1016/0165-2427(91)90007-y. [DOI] [PubMed] [Google Scholar]
  • 2.Muller H., Schnitzler D., Bernstein F., Becht H., Cornelissen D., Lutticken D.H. Vet Microbiol. 1992;33:175–183. doi: 10.1016/0378-1135(92)90045-u. [DOI] [PubMed] [Google Scholar]
  • 3.Nagarajan M.M., Kibenge F.S. Can J Vet Res. 1997;61:81–88. [PMC free article] [PubMed] [Google Scholar]
  • 4.Sharma J.M., Kim I.J., Rautenschlein S., Yeh H.Y. Dev Comp Immunol. 2000;24:223–235. doi: 10.1016/s0145-305x(99)00074-9. [DOI] [PubMed] [Google Scholar]
  • 5.van den Berg T.P., Eterradossi N., Toquin D., Meulemans G. Rev Sci Tech. 2000;19:509–543. [PubMed] [Google Scholar]
  • 6.Dobos P., Hill B.J., Hallett R., Kells D.T., Becht H., Teninges D. J Virol. 1979;32:593–605. doi: 10.1128/jvi.32.2.593-605.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Muller H., Scholtissek C., Becht H. J Virol. 1979;31:584–589. doi: 10.1128/jvi.31.3.584-589.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Leong J.C., Brown D., Dobos P., Kibenge F.S.B., Ludert J.E., Muller H., Mundt E., and Nicholson B., in van Regenmortel M.H.V., Fauget C.M., Bishop D.H.L., Carstens E.B., Estes M.K., Lemon S.M., Maniloff J., Mayo A., McGeoch D.J., Pringle C.R., and Wickner R.B. (ed), Virus Taxonomy: Seventh Report of the International Committee on the Taxonomy of Viruses, Academic Press, 2000, pp. 481–490.
  • 9.Bottcher B., Kiselev N.A., Stel'Mashchuk V.Y., Perevozchikova N.A., Borisov A.V., Crowther R.A., Virol J. J Virol. 1997;71:325–330. doi: 10.1128/jvi.71.1.325-330.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Mundt E., Muller H. Virology. 1995;209:10–18. doi: 10.1006/viro.1995.1226. [DOI] [PubMed] [Google Scholar]
  • 11.Bayliss C.D., Spies U., Shaw K., Peters R.W., Papageorgiou A., Muller H., Boursnell M.E. J Gen Virol. 1990;71:1303–1312. doi: 10.1099/0022-1317-71-6-1303. [DOI] [PubMed] [Google Scholar]
  • 12.Kibenge F.S., Jackwood D.J., Mercado C.C. J Gen Virol. 1990;71:569–577. doi: 10.1099/0022-1317-71-3-569. [DOI] [PubMed] [Google Scholar]
  • 13.Birghan C., Mundt E., Gorbalenya A. EMBO J. 2000;19:114–123. doi: 10.1093/emboj/19.1.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Kibenge F.S., Qian B., Cleghorn J.R., Martin C.K. Arch Virol. 1997;142:2401–2419. doi: 10.1007/s007050050251. [DOI] [PubMed] [Google Scholar]
  • 15.Chevalier C., Lepault J., Erk I., Da Costa B., Delmas B. J Virol. 2002;76:2384–2392. doi: 10.1128/jvi.76.5.2384-2392.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Fahey K.J., Erny K., Crooks J. J Gen Virol. 1989;70:1473–1481. doi: 10.1099/0022-1317-70-6-1473. [DOI] [PubMed] [Google Scholar]
  • 17.Heine H.G., Haritou M., Failla P., Fahey K., Azad A. J Gen Virol. 1991;72:1835–1843. doi: 10.1099/0022-1317-72-8-1835. [DOI] [PubMed] [Google Scholar]
  • 18.Becht H., Muller H., Muller H.K. J Gen Virol. 1988;69:631–640. doi: 10.1099/0022-1317-69-3-631. [DOI] [PubMed] [Google Scholar]
  • 19.Oppling V., Muller H., Becht H. Arch Virol. 1991;119:211–223. doi: 10.1007/BF01310671. [DOI] [PubMed] [Google Scholar]
  • 20.Kochan G., Gonzalez D., Rodriguez J.F. Arch Virol. 2003;148:723–744. doi: 10.1007/s00705-002-0949-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Mundt E., Beyer J., Muller H. J Gen Virol. 1995;76:437–443. doi: 10.1099/0022-1317-76-2-437. [DOI] [PubMed] [Google Scholar]
  • 22.Yao K., Goodwin M.A., Vakharia V.N. J Virol. 1998;72:2647–2654. doi: 10.1128/jvi.72.4.2647-2654.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Mundt E., Kollner B., Kretzschmar D. J Virol. 1997;71:5647–5651. doi: 10.1128/jvi.71.7.5647-5651.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Lombardo E., Maraver A., Espinosa L., Fernandez-Arias A., Rodriguez J.F. Virology. 2000;277:345–357. doi: 10.1006/viro.2000.0595. [DOI] [PubMed] [Google Scholar]
  • 25.Muller H., Nitschke R. Virology. 1987;159:174–177. doi: 10.1016/0042-6822(87)90363-1. [DOI] [PubMed] [Google Scholar]
  • 26.Spies U., Muller H., Becht H. Virus Res. 1987;8:127–140. doi: 10.1016/0168-1702(87)90024-4. [DOI] [PubMed] [Google Scholar]
  • 27.Morgan M.M., Macreadie I.G., Harley V.R., Hudson P.J., Azad A.A. Virology. 1988;163:240–242. doi: 10.1016/0042-6822(88)90258-9. [DOI] [PubMed] [Google Scholar]
  • 28.Spies U., Muller H. J Gen Virol. 1990;71:977–981. doi: 10.1099/0022-1317-71-4-977. [DOI] [PubMed] [Google Scholar]
  • 29.Shwed P.S., Dobos P., Cameron L.A., Vakharia V.N., Duncan R. Virology. 2002;296:241–250. doi: 10.1006/viro.2001.1334. [DOI] [PubMed] [Google Scholar]
  • 30.Maraver A., Clemente R., Rodriguez J.F., Lombardo E. J Virol. 2003;77:2459–2468. doi: 10.1128/JVI.77.4.2459-2468.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.McFerran J.B., MeNulty M., Killop E.R., Corner T.J., McCracken R.M., Collins P.S., Allan G.M. Avian Pathol. 1980;9:395–404. doi: 10.1080/03079458008418423. [DOI] [PubMed] [Google Scholar]
  • 32.Oppling V., Muller H., Becht H. Arch Virol. 1991;119:211–223. doi: 10.1007/BF01310671. [DOI] [PubMed] [Google Scholar]
  • 33.Nunoya T., Otaki T., Tajuma M., Hirag M., Saito T. Avian Dis. 1992;36:597–609. [PubMed] [Google Scholar]
  • 34.van den Berg T.P., Gonze M., Meulemans G. Avian Pathol. 1991;20:133–143. doi: 10.1080/03079459108418748. [DOI] [PubMed] [Google Scholar]
  • 35.Lasher H.N., Shane S.M. World Poult Sci J. 1994;50:133–166. [Google Scholar]
  • 36.Rosenberger J.K., Cloud S.S. J Am Vet Med Assoc. 1986;189:357. [Google Scholar]
  • 37.van den Berg T.P. Avian Pathol. 2000;29:175–193. doi: 10.1080/03079450050045431. [DOI] [PubMed] [Google Scholar]
  • 38.Kwon H.M., Kim D.K., Hahn T.W., Han J.H., Jackwood D.J. Avian Dis. 2000;44:691–696. [PubMed] [Google Scholar]
  • 39.Kong L.L., Omar A.R., Hair-Bejo M., and Aini I., 2nd International Congress/13th VAM congress and CVAAustralasia/ Oceania Regional Symposium; 2001 Aug 27–30; Kuala Lumpur; Vet Assoc Malaysia; 2001, pp. 77–79.
  • 40.Rudd M.F., Heine H.G., Sapats S.I., Parede L., Ignjatovic J. Arch Virol. 2002;147:1303–1322. doi: 10.1007/s00705-002-0817-3. [DOI] [PubMed] [Google Scholar]
  • 41.Sapats S.I., Ignjatovic J. Avian Pathol. 2002;31:559–566. doi: 10.1080/0307945021000024625. [DOI] [PubMed] [Google Scholar]
  • 42.Kim T.K., Yeo S.G. Virus Genes. 2003;26:97–106. doi: 10.1023/a:1022342524830. [DOI] [PubMed] [Google Scholar]
  • 43.Chettle N., Stuart J.C., Wyeth P.J. Vet Rec. 1989;125:271–272. doi: 10.1136/vr.125.10.271. [DOI] [PubMed] [Google Scholar]
  • 44.Synder D.B., Lana D.P., Savage P.K., Yancey F.S., Mengel S.A., Marquardt W.W. Avian Dis. 1988;32:535–539. [PubMed] [Google Scholar]
  • 45.Jenkins G.M., Pagel M., Gould E.A., Zanotto P.M.A., Holmes B.C. J Mol Evol. 2001;52:383–390. doi: 10.1007/s002390010168. [DOI] [PubMed] [Google Scholar]
  • 46.Argos P., Rossmann M.G., Grau U.M., Zuber A., Franck G., Tratschin J.D. Biochemistry. 1979;18:5698–5703. doi: 10.1021/bi00592a028. [DOI] [PubMed] [Google Scholar]
  • 47.Hemert F.J., Berkhout B. J Mol Evol. 1995;41:132–140. doi: 10.1007/BF00170664. [DOI] [PubMed] [Google Scholar]
  • 48.Russell G.J., Walker P.M.B., Elton R.A., Subak-Sharpe J.H. J Mol Biol. 1976;108:1–23. doi: 10.1016/s0022-2836(76)80090-3. [DOI] [PubMed] [Google Scholar]
  • 49.Viotti A., Balducci C., Wdil J.H. Biochim Biophys Acta. 1978;517:125–132. doi: 10.1016/0005-2787(78)90040-0. [DOI] [PubMed] [Google Scholar]
  • 50.Karlin S., Mrazek J., Campbell A.M. J Bacteriol. 1997;179:3899–3913. doi: 10.1128/jb.179.12.3899-3913.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Karlin S. Curr Opin Microbiol. 1998;1:598–610. doi: 10.1016/s1369-5274(98)80095-7. [DOI] [PubMed] [Google Scholar]
  • 52.De Amicis F., Marchetti S. Nucleic Acids Res. 2000;28:3339–3345. doi: 10.1093/nar/28.17.3339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 53.Montero L.M., Salinas J., Matassi G., Bernardi G. Nucleic Acids Res. 1990;18:1859–1867. doi: 10.1093/nar/18.7.1859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Shioiri C., Takahata N. J Mol Evol. 2001;53:364–376. doi: 10.1007/s002390010226. [DOI] [PubMed] [Google Scholar]
  • 55.Bird A.P. Nucleic Acids Res. 1980;8:1499–1504. doi: 10.1093/nar/8.7.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 56.Beutler E., Gelbart T., Ran J.H., Koziol J.A., Beutler B. Proc Natl Acad Sci USA. 1989;86:192–196. doi: 10.1073/pnas.86.1.192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 57.Hall T.A. Nucl Acids Symp Ser. 1999;41:95–98. [Google Scholar]
  • 58.Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. Nucleic Acids Res. 1997;24:4876–4882. doi: 10.1093/nar/25.24.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 59.Abdrakhmanov I., Lodygin D., Geroth P., Arakawa H., Law A., Plachy J., Korn B., Buerstedde J.M. Genome Res. 2000;10:2062–2069. doi: 10.1101/gr.10.12.2062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Goitsuka R., Mamada H., Kitamura D., Cooper M.D., Chen C.I. J Immunol. 2001;167:1454–1460. doi: 10.4049/jimmunol.167.3.1454. [DOI] [PubMed] [Google Scholar]
  • 61.Li W.H., Graur D., editors. Fundamental of Molecular Evolution. Sunderland: Sinauer Associates; 1991. p. 15. [Google Scholar]
  • 62.Keese P.K., Gibbs A. Proc Natl Acad Sci USA. 1992;89:9489–9493. doi: 10.1073/pnas.89.20.9489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 63.Drake J.W., Holland J.J. Proc Natl Acad Sci USA. 1999;96:13910–13913. doi: 10.1073/pnas.96.24.13910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 64.Zhou J., Liu W.J., Peng S.W., Sun X.Y., Frazer I. J Virol. 1999;73:4972–4982. doi: 10.1128/jvi.73.6.4972-4982.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 65.Grasse P.P., editor. Evolution of Living Organisms. New York: Academic Press; 1977. p. 297. [Google Scholar]
  • 66.Keese P., Mackerzie A., Gibbs A. Virology. 1989;172:536–546. doi: 10.1016/0042-6822(89)90196-7. [DOI] [PubMed] [Google Scholar]
  • 67.Chung H.K., Kordyban S., Cameron L., Dobos P. Virology. 1996;225:359–368. doi: 10.1006/viro.1996.0610. [DOI] [PubMed] [Google Scholar]
  • 68.Weber S., Fichtner D., Mettenleiter T.C., Mundt E. J Gen Virol. 2001;82:805–812. doi: 10.1099/0022-1317-82-4-805. [DOI] [PubMed] [Google Scholar]
  • 69.Strauss E.G., Strauss J.H., Levine A.J. Virology. Philadelphia: Lippincott-Raven; 1995. pp. 153–171. [Google Scholar]
  • 70.Breslauer K.J., Frank R., Blocker H., Marky L.A. Proc Natl Acad Sci USA. 1986;83:3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 71.Delcourt S.G, Blake R.D. J Biol Chem. 1991;266:15160–15169. [PubMed] [Google Scholar]
  • 72.Karlin S., Burge C. Trends Genet. 1995;11:283–290. doi: 10.1016/s0168-9525(00)89076-9. [DOI] [PubMed] [Google Scholar]
  • 73.Karlin S., Doerfler W., Cardon L.R. J Virol. 1994;68:2889–2897. doi: 10.1128/jvi.68.5.2889-2897.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 74.Duret L., Galtier N. Mol Biol Evol. 2000;17:1620–1625. doi: 10.1093/oxfordjournals.molbev.a026261. [DOI] [PubMed] [Google Scholar]
  • 75.Hunter C.A. J Mol Biol. 1993;230:1025–1054. doi: 10.1006/jmbi.1993.1217. [DOI] [PubMed] [Google Scholar]
  • 76.Krieg A.M. Trends Microbiol. 1996;4:73–76. doi: 10.1016/0966-842X(96)81515-0. [DOI] [PubMed] [Google Scholar]
  • 77.Krieg A.M., Yi A.K., Schorr J., Davis H.L. Trends Microbiol. 1998;6:23–27. doi: 10.1016/S0966-842X(97)01145-1. [DOI] [PubMed] [Google Scholar]
  • 78.Vabulus R.M., Pircher H., Lipford G.B., Hacker H., Wagner H. J Immunol. 2000;164:2372–2378. doi: 10.4049/jimmunol.164.5.2372. [DOI] [PubMed] [Google Scholar]
  • 79.Vleugels B., Ververken C., Goddeeris B.M. Poult Sci. 2002;81:1317–1321. doi: 10.1093/ps/81.9.1317. [DOI] [PubMed] [Google Scholar]
  • 80.Tobler K., Ackermann M. Adv Exp Med Biol. 1998;400:801–804. doi: 10.1007/978-1-4615-5331-1_104. [DOI] [PubMed] [Google Scholar]
  • 81.Perriere G., Thioulouse J. Nucleic Acids Res. 2002;30:4548–4555. doi: 10.1093/nar/gkf565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 82.Yamaguchi T., Ogawa M., Inoshima Y., Miyoshi M., Fukushi H., Hirai K. Virology. 1996;223:219–223. doi: 10.1006/viro.1996.0470. [DOI] [PubMed] [Google Scholar]
  • 83.Yu L., Li J.R., Huang Y.W., Dikki J., Deng R. Avian Dis. 2001;45:862–874. [PubMed] [Google Scholar]
  • 84.Cao Y.C., Yeung W.S., Law M., Bi Y.Z., Leung F.C., Lim B.I. Avian Dis. 1998;42:340–351. [PubMed] [Google Scholar]
  • 85.Brandt M., Yao K., Liu M., Heckert R.A., Vakharia V.N. J Virol. 2001;75:11974–11982. doi: 10.1128/JVI.75.24.11974-11982.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 86.Eterradossi N., Arnauld C., Toquin D., Rivallan G. Arch Virol. 1998;143:1627–1636. doi: 10.1007/s007050050404. [DOI] [PubMed] [Google Scholar]
  • 87.Islam M.R., Zierenberg K., Muller H. Arch Virol. 2001;146:2481–2492. doi: 10.1007/s007050170018. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Virus Genes are provided here courtesy of Nature Publishing Group

RESOURCES