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.

本数据集收录了源自Ion Torrent下一代测序（NGS）数据组装的NCBI数据库中Blast比对得到的连续群数据，旨在通过从头组装发现样本中存在的其他病毒，并采用病毒宏基因组学方法进行深入研究。数据来源于对三十六个野外样本和分离病毒进行的初步考察，考察过程中采用了针对M和F基因部分片段的实时逆转录聚合酶链反应（RT-PCR）。观察结果显示，近期临床病例的肾脏样本病毒载量最高。研究过程中应用了传统RT-PCR、Sanger DNA测序、QH9/2-1鹌鹑细胞病毒分离及Ion Torrent NGS技术，获得了二十一株PPMVs的完整或部分基因组，以供进一步分析。