Detection of hepatitis B virus genotypes using oligonucleotide chip among hepatitis B virus carriers in Eastern China

Abstract

Aim: To determine the genotype distribution of hepatitis B virus (HBV) with a newly oligonucleotide chip assay among the HBV carriers in Eastern China.

Methods: An assay using oligonucleotide chip was developed for detection of HBV genotypes in serum samples from HBV DNA-positive patients in Eastern China. This method is based on the principle of reverse hybridization with Cy5-labeled amplicons hybridizing to type-specific oligonucleotide probes that are immobilized on slides. The results of 80 randomly chosen sera were confirmed by direct sequencing.

Results: HBV genotype B, C and mixed genotype were detected in 400 serum samples, accounting for 8.3% (n = 33), 83.2% (n = 333), and 8.5% (n = 34), respectively. The evaluation of the oligonucleotide assay showed 100% concordance with the amplicon phylogenetic analysis except 9 mixed genotype infections undetected by sequencing.

Conclusion: The study indicates that HBV genotype C and B prevail in the Eastern China. It is suggested that the oligonucleotide chip is a reliable and convenient tool for the detection of HBV genotyping.

Figure 1

Layout of probes and fluorescence images of results. Probes layout on the oligonucleotide chip (A). Following hybridization of Cy5-labeled fragmented DNA, as described in Materials and Methods, the fluorescent signals of different HBV genotypes were detected as follows: Genotype B (C), genotype C (D), mixed genotype (E). Blank template amplified by PCR also was hybridized to the chip and the image of the result is shown in (B).