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, microspherebased 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.

FluDen Primer DB –PCR Primer Database for Influenza A and Dengue Virus

“…Here, a serotype is a group of viruses classified together based on their antigens on the surface of the virus. These four subtypes are different strains of dengue virus that have 60% -80% homology between each other [8]. Dengue is endemic in more than 110 countries [9].…”