Development of UPSR Primer Design Program for Efficient Detection of Viruses

ABSTRACT

PCR is a rapid and sensitive method for detection of viruses from clinical samples and good primers are essential for successful PCR. However, high mutation rate of viral genomes often results in failure in detecting viruses, and there have been attempts to develop primers from multiple viral sequences. Thus, we developed a program called Universal Primers Score Ranking (UPSR) which generates primers from multiple sequences and ranks the quality of primers automatically. The feasibility of the UPSR program was tested using hepatitis B viruses (HBV) isolated from Korean patients. UPSR generated primer candidates with quality score ranks according to two T(m) values. We found that T(m2) values calculated based on the thermodynamics of nearest neighboring bases were better correlated with actual detection rate of HBV from patients' sera. The primer with number 1 rank by T(m2) values detected more samples than any other primers designed by UPSR, commercial primer, or other reference primers suggested by previous literatures. Thus, UPSR proved to be easy and useful to design primers from multiples sequences in detecting viruses.