A novel array of real-time RT-PCR assays for the rapid pathotyping of type I avian paramyxovirus (APMV-1)

• Published in: Journal of virological methods Vol. 322; p. 114813
• Main Authors: Fortin, Andrea, Laconi, Andrea, Monne, Isabella, Zohari, Siamak, Andersson, Kristofer, Grund, Christian, Cecchinato, Mattia, Crimaudo, Marika, Valastro, Viviana, D’Amico, Valeria, Bortolami, Alessio, Gastaldelli, Michele, Varotto, Maria, Abdelrahman, Amgad, Amarin, Nadim, Abubakar, Mustapha Bala, Belayneh, Redeat, Cyprien, Yapi Bokpè, Christodoulou, Vasiliki, Chvala, Ilya, Dodovski, Aleksandar, Ghafouri, Seyed Ali, Giasuddin, Mohammed, Hassan, Magdy, Kammon, Abdulwahab, Shittu, Ismaila, Snoeck, Chantal J., Steensels, Mieke, Suarez, David, Torchetti, Mia Kim, Tshipambe, Serge Mpiana, Ouermi Zerbo, Lamouni Habibata, Terregino, Calogero, Panzarin, Valentina
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2023
• Subjects: Animals; Avian paramyxovirus type I (APMV-1); Avirulent; Avulavirus - genetics; Chickens; gastrointestinal system; genetic variation; Molecular pathotyping; mortality; Newcastle disease; Newcastle Disease - diagnosis; Newcastle disease virus - genetics; Orthorubulavirus; pathotypes; poultry; Poultry Diseases - diagnosis; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; virulence; Virulent; Newcastle disease; Virulent; Molecular pathotyping; Avirulent; Avian paramyxovirus type I (APMV-1)
• ISSN: 0166-0934; 1879-0984; 1879-0984
• DOI: 10.1016/j.jviromet.2023.114813

Newcastle disease (ND) caused by virulent avian paramyxovirus type I (APMV-1) is a WOAH and EU listed disease affecting poultry worldwide. ND exhibits different clinical manifestations that may either be neurological, respiratory and/or gastrointestinal, accompanied by high mortality. In contrast, mild or subclinical forms are generally caused by lentogenic APMV-1 and are not subject to notification. The rapid discrimination of virulent and avirulent viruses is paramount to limit the spread of virulent APMV-1. The appropriateness of molecular methods for APMV-1 pathotyping is often hampered by the high genetic variability of these viruses that affects sensitivity and inclusivity. This work presents a new array of real-time RT-PCR (RT-qPCR) assays that enable the identification of virulent and avirulent viruses in dual mode, i.e., through pathotype-specific probes and subsequent Sanger sequencing of the amplification product. Validation was performed according to the WOAH recommendations. Performance indicators on sensitivity, specificity, repeatability and reproducibility yielded favourable results. Reproducibility highlighted the need for assays optimization whenever major changes are made to the procedure. Overall, the new RT-qPCRs showed its ability to detect and pathotype all tested APMV-1 genotypes and its suitability for routine use in clinical samples. •An array of rRT-PCR assays was developed for molecular pathotyping of APMV-1.•Pathotyping occurs in dual mode by pathotype specific probes and sequencing.•The array permits detection of co-infections by virulent and avirulent APMV-1.•The array is suitable for application in clinical samples.•Periodic re-assessment of oligonucleotides specificity is recommended.