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.

本数据集为基于Ion Torrent 下一代测序（Next-Generation Sequencing, NGS）数据经从头组装（de novo assembly）得到的重叠群（contigs）在NCBI数据库中进行BLAST比对的结果，旨在通过病毒宏基因组学方法发掘样本中存在的其他病毒并开展后续研究。本研究最初针对M基因与F基因的部分片段，采用实时反转录聚合酶链反应（real-time reverse transcriptase-polymerase chain reaction, RT-PCR）对36份田间样本及分离毒株进行检测，结果显示近期临床病例的肾脏组织病毒载量最高。随后本研究采用常规RT-PCR、桑格DNA测序（Sanger DNA sequencing）、QH9/2-1鹌鹑细胞病毒分离以及Ion Torrent 下一代测序（NGS）技术，最终获得21株PPMV的完整或部分基因组，用于后续分析。