Primer and probe conservation issue in the quantification of hepatitis B virus DNA
Document Type
Article
Publication Date
5-1-2021
Abstract
Current treatment strategies for chronic hepatitis B virus (HBV) infection aim at long-term suppression of the viral replication since a cure remains elusive. Its clinical management therefore relies greatly on routine monitoring of serum HBV DNA levels using quantitative polymerase chain reaction (qPCR) assays. Designing a highly conserved oligonucleotide set for the qPCR assay can be challenging due to the high genetic heterogeneity of the virus. The ever-increasing number of HBV genomes deposited in the GenBank nucleotide database warrants a revisit to previous primer and probe designs. We examined primer and probe sets from 53 qPCR assays published in the past 2 decades for their coverage in 9864 complete HBV genomes retrieved from GenBank. Of all the 53 qPCR assays, only 17% achieved >= 80% coverage. About 40% of the 53 assays covered less than 20% of the 9864 genomes.In silicoDNA thermodynamics analysis demonstrated reduced primer/probe binding affinity, which further increases the risk of viral load misdetection and underestimation for certain HBV variants. Taken together, there is a pressing need for improving available qPCR designs for the quantification of HBV DNA based on the updated genome data.
Keywords
HBV DNA quantification, Nucleic acid testing, QPCR assay, Real-time PCR, Viral load
Divisions
medicinedept
Funders
Sunway Medical Centre [SRC/006/2017/FR],Sunway University [GRTINRSF-SHMS-DMS-05-2020]
Publication Title
Reviews In Medical Virology
Volume
31
Issue
3
Publisher
Wiley
Publisher Location
111 RIVER ST, HOBOKEN 07030-5774, NJ USA