Development of a real-time reverse-transcription PCR for the detection and simultaneous pathotyping of Newcastle disease virus isolates using a novel probe

A real-time reverse-transcription PCR (RRT-PCR) was developed to detect and pathotype avian paramyxovirus type 1 (APMV-1), also known as Newcastle disease virus (NDV), which had been grown in embryonated fowls’ eggs. Two pairs of probes, VRP1 with ARP1 and VRP2 with ARP2, each with either the ‘universal base’ 2′ deoxyinosine incorporated or both inosines and locked nucleic acids (LNAs) incorporated, were designed to detect, respectively, a diverse range of virulent and avirulent viral templates that included the region coding for the fusion protein cleavage site. Oligonucleotide VRP1 hybridised with 76 of the 84 virulent isolates tested, while VRP2 detected 82, including 17 isolates with five or six template-probe mismatches. An alternative conventional probe, VRP3, with no inosine bases or LNAs, failed to hybridise 7 of 13 isolates, all of which tested positive with VRP2. Real-time assays with ARP1 showed that it detected 21 of the 28 avirulent isolates tested, and ARP2 detected 22/28, including one present in a mixture with virulent NDV. Neither probe was able to detect those isolates that were classified in genogroup six. All probes were specific for detecting either virulent or avirulent NDV. A specific PCR fragment of the predicted size was obtained, using the primer set designed for this study, with the 112 NDV isolates tested, including those in genogroup six. This assay demonstrates a rapid means for simultaneous detection and pathotyping of notifiable avian disease due to NDV.