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Universal primers that amplify RNA from all three flavivirus subgroups

Maher-Sturgess, Sheryl L; Forrester, Naomi L; Wayper, Paul; Gould, Ernest A; Hall, Roy A; Barnard, Ross T; Gibbs, Mark

Description

BACKGROUND: Species within the Flavivirus genus pose public health problems around the world. Increasing cases of Dengue and Japanese encephalitis virus in Asia, frequent outbreaks of Yellow fever virus in Africa and South America, and the ongoing spread of West Nile virus throughout the Americas, show the geographical burden of flavivirus diseases. Flavivirus infections are often indistinct from and confused with other febrile illnesses. Here we review the specificity of...[Show more]

dc.contributor.authorMaher-Sturgess, Sheryl L
dc.contributor.authorForrester, Naomi L
dc.contributor.authorWayper, Paul
dc.contributor.authorGould, Ernest A
dc.contributor.authorHall, Roy A
dc.contributor.authorBarnard, Ross T
dc.contributor.authorGibbs, Mark
dc.date.accessioned2009-04-24T04:21:53Z
dc.date.accessioned2010-12-20T06:04:12Z
dc.date.available2009-04-24T04:21:53Z
dc.date.available2010-12-20T06:04:12Z
dc.identifier.citationVirology Journal 5.16 (2008)
dc.identifier.issn1743-422x
dc.identifier.urihttp://hdl.handle.net/10440/147
dc.identifier.urihttp://digitalcollections.anu.edu.au/handle/10440/147
dc.description.abstractBACKGROUND: Species within the Flavivirus genus pose public health problems around the world. Increasing cases of Dengue and Japanese encephalitis virus in Asia, frequent outbreaks of Yellow fever virus in Africa and South America, and the ongoing spread of West Nile virus throughout the Americas, show the geographical burden of flavivirus diseases. Flavivirus infections are often indistinct from and confused with other febrile illnesses. Here we review the specificity of published primers, and describe a new universal primer pair that can detect a wide range of flaviviruses, including viruses from each of the recognised subgroups. RESULTS: Bioinformatic analysis of 257 published full-length Flavivirus genomes revealed conserved regions not previously targeted by primers. Two degenerate primers, Flav100F and Flav200R were designed from these regions and used to generate an 800 base pair cDNA product. The region amplified encoded part of the methyltransferase and most of the RNA-dependent-RNApolymerase (NS5) coding sequence. One-step RT-PCR testing was successful using standard conditions with RNA from over 60 different flavivirus strains representing about 50 species. The cDNA from each virus isolate was sequenced then used in phylogenetic analyses and database searches to confirm the identity of the template RNA. CONCLUSION: Comprehensive testing has revealed the broad specificity of these primers. We briefly discuss the advantages and uses of these universal primers.
dc.format10 pages
dc.publisherBioMed Central
dc.rights© 2008 Maher-Sturgess et al; licensee BioMed Central Ltd. Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.sourceVirology Journal
dc.source.urihttp://www.virologyj.com/content/pdf/1743-422X-5-16.pdf
dc.subjectKeywords: complementary DNA; methyltransferase; RNA directed RNA polymerase; virus RNA; NS5 protein, flavivirus; primer DNA; unclassified drug; virus protein; article; bioinformatics; data base; Flavivirus; nonhuman; nucleotide sequence; phylogeny; reverse transcri
dc.titleUniversal primers that amplify RNA from all three flavivirus subgroups
dc.typeJournal article
dcterms.dateAccepted2008-01-24
dc.date.issued2008-01-24
local.identifier.absfor100401 (40%), 060506 (30%), 100101(30%)
local.identifier.ariespublicationu9511635xPUB274
local.type.statusPublished Version
local.contributor.affiliationMaher-Sturgess, Sheryl L, University of Queensland
local.contributor.affiliationForrester, Naomi L, Centre for Ecology and Hydrology
local.contributor.affiliationWayper, Paul, Faculty of Science, School of Botany and Zoology
local.contributor.affiliationGould, Ernest A, Centre for Ecology and Hydrology, Oxford
local.contributor.affiliationHall, Roy A, University of Queensland
local.contributor.affiliationBarnard, Ross T, University of Queensland
local.contributor.affiliationGibbs, Mark, Faculty of Science, School of Botany and Zoology
local.identifier.doi10.1186/1743-422X-5-16
dc.date.updated2015-12-09T09:24:18Z
local.identifier.scopusID2-s2.0-40349091097
CollectionsANU Research Publications

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