Back
 OALibJ  Vol.2 No.3 , March 2015
Primers for Dengue Virus Strains Based on Their Sequence Variability
Abstract: Since DENV-1, 2, 3, and 4 determine the strains for dengue virus, their gene sequence can be used as marker for diagnosis, amplifying and genotyping subtypes in molecular screening reaction which includes RT-PCR, real-time RT-PCR, nucleic acid sequence-based amplification, microsphere-based duplexed immunoassay, and DNA microarrays. There are many gene based PCR diagnostic kits available for screening and quantifying dengue virus, which one to choose? Decisions on choosing the diagnostic kit are debatable, mainly because of sequence variation of endemic dengue virus, which emphasizes us to use region specific primer diagnostic kits for isolating dengue of the prevailing country. But if diagnoistic industry focuses on the homologous regions obtained after aligning sequences, each representing the country of origin, we can design primers which can be used to detect dengue strains from any country of origin. Gene based diagnostics kits should have primers that should be covered for all entries present in the NCBI database with 100% total coverage similarity and specifically only to which they were designed for.
Cite this paper: Krishnappa, R. and Paramasivam, R. (2015) Primers for Dengue Virus Strains Based on Their Sequence Variability. Open Access Library Journal, 2, 1-6. doi: 10.4236/oalib.1101104.
References

[1]   Ranjit, S. and Kissoon, N. (2010) Dengue Hemorrhagic Fever and Shock Syndromes. Pediatric Critical Care Medicine, 12, 90-100.
http://dx.doi.org/10.1097/PCC.0b013e3181e911a7

[2]   Whitehorn, J. and Farrar, J. (2010) Dengue. British Medical Bulletin, 95, 161-173.
http://dx.doi.org/10.1093/bmb/ldq019

[3]   Varatharaj, A. (2010) Encephalitis in the Clinical Spectrum of Dengue Infection. Neurology India, 58, 585-591.
http://dx.doi.org/10.4103/0028-3886.68655

[4]   Knoop, K.J., Stack, L.B., Storrow, A. and Thurman, R.J. (2010) Tropical Medicine. Atlas of Emergency Medicine. 3rd Edition, McGraw-Hill Professional, New York, 658-659.

[5]   Bru, D., Martin-Laurent, F. and Philippot, L. (2008) Quantification of the Detrimental Effect of a Single Primer-Tem plate Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example. Applied and Environmental Microbiology, 74, 1660-1663.
http://dx.doi.org/10.1128/AEM.02403-07

[6]   Ayyadevara, S., Thaden, J.J. and Shmookler Reis, R.J. (2000) Discrimination of Primer 3'-Nucleotide Mismatch by Taq DNA Polymerase during Polymerase Chain Reaction. Analytical Biochemistry, 284, 11-18.
http://dx.doi.org/10.1006/abio.2000.4635

[7]   Baker, G.C., Smith, J.J. and Cowan, D.A. (2003) Review and Re-Analysis of Domain-Specific 16S Primers. Journal of Microbiological Methods, 55, 541-555.
http://dx.doi.org/10.1016/j.mimet.2003.08.009

[8]   Huang, M.M., Arnheim, N. and Goodman, M.F. (1992) Extension of Base Mispairs by Taq DNA Polymerase: Implications for Single Nucleotide Discrimination in PCR. Nucleic Acids Research, 20, 4567-4573.
http://dx.doi.org/10.1093/nar/20.17.4567

[9]   Kwok, S., Kellogg, D.E., McKinney, N., Spasic, D., Goda, L., Levenson, C. and Sninsky, J.J. (1990) Effects of Primer-Template Mismatches on the Polymerase Chain Reaction: Human Immunodeficiency Virus Type 1 Model Studies. Nucleic Acids Research, 18, 999-1005.
http://dx.doi.org/10.1093/nar/18.4.999

[10]   Guy, R.A., Xiao, C. and Horgen, P.A. (2004) Real-Time PCR Assay for Detection and Genotype Differentiation of Giardia Lamblia in Stool Specimens. Journal of Clinical Microbiology, 42, 3317-3320.
http://dx.doi.org/10.1128/JCM.42.7.3317-3320.2004

[11]   Sipos, R., Székely, A.J., Palatinszky, M., Révész, S., Márialigeti, K. and Nikolausz, M. (2007) Effect of Primer Mismatch, Annealing Temperature and PCR Cycle Number on 16S rRNA Gene-Targetting Bacterial Community Analysis. FEMS Microbiology Ecology, 60, 341-350.
http://dx.doi.org/10.1111/j.1574-6941.2007.00283.x

[12]   Smith, S., Vigilant, L. and Morin, P.A. (2002) The Effects of Sequence Length and Oligonucleotide Mismatches on 5′Exonuclease Assay Efficiency. Nucleic Acids Research, 30, 111-121.
http://dx.doi.org/10.1093/nar/gnf110

 
 
Top