Investigation of the molecular epidemiology of pigeon paramyxovirus (PPMVs) in South Africa

Data for contigs blasted on NCBI generated from Ion Torrent NGS data assembly by de novo assembly to discover other viruses present in the sample and conduct further research through a viral metagenomic approach.  A total of thirty-six field samples and isolated viruses were initially examined using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) targeting a partial fragment of the M and F gene. Among these, it was observed that the kidneys from recent clinical cases exhibited the highest viral loads. Conventional RT-PCR, Sanger DNA sequencing, virus isolation in QH9/2-1 quail cells and Ion Torrent Next-Generation Sequencing (NGS) were applied, and the complete or partial genomes of twenty-one PPMVs were obtained for further analysis.