Development of a novel real-time RT-PCR method using peptide nucleic acid (PNA) probes for detecting and genotyping of viral haemorrhagic septicaemia virus (VHSV)

Abstract

Viral haemorrhagic septicaemia (VHS) is one of the most serious viral diseases in salmonid and olive flounder farms. The causative agent of VHS is the VHS virus (VHSV), which has been classified into four genotypes (I–IV), based on sequence analysis of the genes encoding for nucleoprotein, glycoprotein, and non-structural viral protein. Among the various diagnostic methods, real-time reverse transcription PCR method based on TaqMan-probe (RT-qPCR) is a stable, rapid, specific, and highly sensitive method for viral gene detection. However, the currently accepted diagnostic method based on RT-qPCR can only detect viral presence and load, and does not provide information about viral genotype. Peptide nucleic acids (PNAs) are artificially synthesized DNA analogues with an uncharged peptide backbone. PNA probes can effectively detect a target gene by amplification and a specific melting temperature signal. It was reported that PNA probes can effectively distinguish between mismatched sequences based on their different melting temperatures in amplified PCR products. The present study reports a novel real-time RT-PCR method for simultaneous detection and genotyping of VHSV using PNA probes. The newly-developed method showed a sensitivity similar to that of the infectious titre by fish cell cultures inoculated with the virus, except for genotype IVa, where viral inoculation in cell culture showed a 10-fold higher sensitivity than the novel method. The melting point analysis to distinguish the four genotypes was performed on 80 VHSV isolates representing all known genotypes, showing that this novel real-time RT-PCR can distinguish between all VHSV genotypes without the need of further sequencing.