Summary
Many members of the genus Flavivirus are the agents of important diseases of humans, livestock, and wildlife. Currently, no complete genome sequence is available for the three African viruses, Bagaza, Zika, and Kedougou viruses, each representing a distinct virus subgroup according to the latest virus classification. In this study, we obtained a complete genome sequence of each of those three viruses and characterized the open reading frames (ORFs) with respect to gene sizes, cleavage sites, potential glycosylation sites, distribution of cysteine residues, and unique motifs. The sequences of the three viruses were then scanned across the entire length of the ORF against available sequences of other African flaviviruses and selected reference viruses for genetic relatedness. The data collectively indicated that Kedougou virus was close to dengue viruses but nonetheless distinct, while Bagaza virus shared genetic relatedness with West Nile virus in several genomic regions. In the non-coding regions, it was found that a particular organizational pattern of conserved sequences in the 3′ terminal region generally correlated with the current virus grouping.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
DE Alvarez MF Lodeiro SJ Luduena LI Pietrasanta AV Gamarnik (2005) ArticleTitleLong-range RNA-RNA interactions circularize the dengue virus genome J Virol 79 6631–6643 Occurrence Handle15890901 Occurrence Handle10.1128/JVI.79.11.6631-6643.2005 Occurrence Handle1:CAS:528:DC%2BD2MXksFKhtbY%3D
BJ Barnard SB Buy JH Du Preez SP Greyling HJ Venter (1950) ArticleTitleTurkey meningo encephalitis in South Africa Onderstepoort J Vet Res 47 89–94
CH Calisher K Karabatsos JM Dalrymple RE Shope JS Porterfield EG Westaway WE Brandt (1989) ArticleTitleAntigenic relationship between flaviviruses as determined by cross-neutralization tests with polyclonal antisera J Gen Virol 70 37–43 Occurrence Handle2543738
TJ Chambers CS Hahn R Galler CM Rice (1990) ArticleTitleFlavivirus genome organization, expression, and replication Annu Rev Microbiol 44 649–688 Occurrence Handle2174669 Occurrence Handle10.1146/annurev.mi.44.100190.003245 Occurrence Handle1:CAS:528:DyaK3MXjs1KnsQ%3D%3D
G-JJ Chang (1997) Molecular biology of dengue viruses DJ Gubler G Kuno (Eds) Dengue and dengue hemorrhagic fever CAB International Wallingford, UK 175–198
G-JJ Chang AR Hunt B Davis (2000) ArticleTitleA single intramuscular injection of recombinant plasmid DNA induces protective immunity and prevents Japanese encephalitis in mice J Virol 74 4244–4252 Occurrence Handle10756038 Occurrence Handle10.1128/JVI.74.9.4244-4252.2000 Occurrence Handle1:CAS:528:DC%2BD3cXislGru7g%3D
Felsenstein J (1995) PHYLIP, version 3.57c. Department of Genetics, University of Washington, Seattle, WA
JL Fu BH Tan EH Yap YC Chan YH Tan (1992) ArticleTitleFull-length cDNA sequence of Dengue type 1 virus (Singapore strain S275/90) Virology 188 953–958 Occurrence Handle1585663 Occurrence Handle10.1016/0042-6822(92)90560-C Occurrence Handle1:CAS:528:DyaK3sXit1Ohur4%3D
CS Hahn YS Hahn CM Rice E Lee L Dalgarno EG Strauss JH Strauss (1987) ArticleTitleConserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences J Mol Biol 198 33–41 Occurrence Handle2828633 Occurrence Handle10.1016/0022-2836(87)90455-4 Occurrence Handle1:CAS:528:DyaL1cXjt1Ortw%3D%3D
TA Hall (2001) BioEdit Department of Microbiology, North Carolina State University Raleigh, NC
InstitutionalAuthorNameICTV (International Committee on the Taxonomy of Viruses) (2005) NoChapterTitle CM Fauquet MA Mayo J Maniloff U Desselberger LA Ball (Eds) Virus taxonomy: classification and nomenclature of viruses Elsevier San Diego
N Karabatsos (1985) International catalogue of arboviruses EditionNumber3 American Society of Tropical Medicine and Hygiene San Antonio, TX
AA Khromykh H Meka KJ Guyatt EG Westaway (2001) ArticleTitleEssential role of cyclization sequences in flavivirus RNA replication J Virol 75 6719–6728 Occurrence Handle11413342 Occurrence Handle10.1128/JVI.75.14.6719-6728.2001 Occurrence Handle1:CAS:528:DC%2BD3MXkvFSitbY%3D
G Kuno G-JJ Chang KR Tsuchiya N Karabatsos CB Cropp (1998) ArticleTitlePhylogeny of the genus Flavivirus J Virol 72 73–83 Occurrence Handle9420202 Occurrence Handle1:CAS:528:DyaK1cXhvVerug%3D%3D
G Kuno G-JJ Chang (2005) ArticleTitleBiological transmission of arboviruses: reexamination of and new insights into components, mechanisms, and unique traits as well as their Evolutionary trends Clin Microbiol Rev 18 608–637 Occurrence Handle16223950 Occurrence Handle10.1128/CMR.18.4.608-637.2005 Occurrence Handle1:CAS:528:DC%2BD2MXht1Wrsr%2FL
J Li R Bhuvanakantham J Howe M-L Ng (2006) ArticleTitleThe glycosylation site in the envelope protein of West Nile virus (Sarafend) plays an important role in replication and maturation processes J Gen Virol 87 613–622 Occurrence Handle16476982 Occurrence Handle10.1099/vir.0.81320-0 Occurrence Handle1:CAS:528:DC%2BD28XitVahtr8%3D
KB Nicholas HB Nicholas DW Deerfield (1997) ArticleTitleGeneDoc: analysis and visualization of genetic variation EMBONet News 4 14–18
K Osatomi H Sumiyoshi (1990) ArticleTitleComplete nucleotide sequence of dengue type 3 virus genome RNA Virology 176 643–647 Occurrence Handle2345967 Occurrence Handle10.1016/0042-6822(90)90037-R Occurrence Handle1:CAS:528:DyaK3cXltFSju7o%3D
V Pierre M-T Drouet V Deubel (1994) ArticleTitleIdentification of mosquito-borne flavivirus sequences using universal primers and reverse transcription/polymerase chain reaction Res Virol 145 179–188
V Proutski EA Gould EC Holmes (1997) ArticleTitleSecondary structure of the 3′ untranslated region of flaviviruses: similarities and differences Nucleic Acids Res 25 1194–1202 Occurrence Handle9092629 Occurrence Handle10.1093/nar/25.6.1194 Occurrence Handle1:CAS:528:DyaK2sXitFyqu7c%3D
SC Ray (1999) Simplot School of Medicine, Johns Hopkins University Baltimore, MD
CM Rice JH Strauss (1990) ArticleTitleProduction of flavivirus polypeptides by proteolytic processing Semin Virol 1 357–367 Occurrence Handle1:CAS:528:DyaK38XlsFWntg%3D%3D
JD Thompson TJ Gibson F Plewniak F Jeanmougin DJ Higgins (1997) ArticleTitleThe Clustal X window interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876–4882 Occurrence Handle9396791 Occurrence Handle10.1093/nar/25.24.4876 Occurrence Handle1:CAS:528:DyaK1cXntFyntQ%3D%3D
V Vorndam JH Mathews ADT Barrett JT Roehrig DW Trent (1993) ArticleTitleMolecular and biological character ization of a non-glycosylated isolate of St. Louis encephalitis virus J Gen Virol 74 2653–2660 Occurrence Handle7506301 Occurrence Handle1:CAS:528:DyaK2cXkvFOkug%3D%3D Occurrence Handle10.1099/0022-1317-74-12-2653
G Winkler FX Heinz C Kunz (1987) ArticleTitleStudies on the glycosylation of flavivirus E proteins and the role of carbohydrates in antigenic structure Virology 159 237–243 Occurrence Handle2441520 Occurrence Handle10.1016/0042-6822(87)90460-0 Occurrence Handle1:CAS:528:DyaL2sXltFeqsLg%3D
BT Zhao E Mackow A Buckler-White L Markoff RM Chanock CJ Lai Y Makino (1986) ArticleTitleCloning full-length dengue type 4 viral DNA sequences: analysis of genes coding for structural proteins Virology 155 77–88 Occurrence Handle3022479 Occurrence Handle10.1016/0042-6822(86)90169-8 Occurrence Handle1:CAS:528:DyaL2sXnvFCgsQ%3D%3D
Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J, Clark BFC (eds) RNA biochemistry and biotechnology. Kluwer Dardsecht, pp 11–43
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Kuno, G., Chang, GJ. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch Virol 152, 687–696 (2007). https://doi.org/10.1007/s00705-006-0903-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-006-0903-z