Rapid Communication
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World J Gastroenterol. Dec 7, 2006; 12(45): 7365-7370
Published online Dec 7, 2006. doi: 10.3748/wjg.v12.i45.7365
Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA
Yan-Qin Lu, Jin-Xiang Han, Peng Qi, Wei Xu, Yan-Hui Zu, Bo Zhu
Yan-Qin Lu, School of Medicine, Shandong University, Jinan 250012, China; Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Science, Key laboratory of Ministry of Health for Biotech-Drug, Jinan 250062, Shandong Province, China
Jin-Xiang Han, Peng Qi, Bo Zhu, Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Key Laboratory of Ministry of Health for Biotech-Drugs, Jinan 250062, Shandong Province, China
Wei Xu, Yan-Hui Zu, Jinan Infectious Disease Hospital, Jinan 250021, Shandong Province, China
Supported by the National Natural Science Foundation of China (No. 30371328), the Key Project of Natural Science Foundation of Shandong Province (No. Z2002C01), and the Key Project of Shandong Academy of Medical Sciences (No. 2005007)
Correspondence to: Professor Jin-Xiang Han, Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Key Laboratory of Ministry of Health for Biotech-Drugs, Jinan 250062, China. jinxianghan@163.com
Telephone: +86-531-82919611 Fax: +86-531-82951586
Received: August 4, 2006
Revised: August 28, 2006
Accepted: September 11, 2006
Published online: December 7, 2006
Abstract

AIM: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA.

METHODS: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified.

RESULTS: The copy number of the same HBV serum sample originated from the standard curve of S, C and X regions was 5.7 × 104/mL, 6.3 × 102/mL and 1.6 × 103/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 × 109/mL, 2.08 × 106/mL and 4.40 × 107/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis, which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A, B and C was around 105/mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples. Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate.

CONCLUSION: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA.

Keywords: Hepatitis B virus; Serum DNA; Real-time PCR; Extraction method