Department of Virology, National Institute of Health, Islamabad, Pakistan.
Infectious Diseases Department, Pakistan Institute of Medical Sciences, Islamabad, Pakistan.
J Med Virol. 2023 Aug;95(8):e29037. doi: 10.1002/jmv.29037.
The global mpox outbreak spanning 2022-2023 has affected numerous countries worldwide. In this study, we present the first report on the detection, whole-genome sequence, and coinfection of the mpox virus and varicella zoster virus (VZV) from Pakistan. During April-May 2023, samples from 20 suspected cases of mpox were tested at the National Institutes of Health, Islamabad among which 4 tested positive. All four cases had a travel history of Saudi Arabia. All the suspected samples were processed by using a Zymo research kit for DNA extraction, followed by qRT-PCR amplification by using a DaAn Gene detection kit for the mpox virus. Further, two of the positive samples with a low C value (<20) were subjected to whole-genome sequencing using a metagenomic approach on the iSeq (Illumina) platform. The sequencing results revealed Clade IIb and genotype A.2.1 of MPXV, which clustered with viruses from Slovenia and the UK in July and June 2022, respectively. Our analysis identified two novel nonsynonymous substitutions in mpox virus, namely V98I in OPG046 and P600S in OPG109. Furthermore, we successfully retrieved the complete genome of VZV from the same sample, belonging to Clade 5. This study represents the first positive case of MPXV in Pakistan and the coinfection of mpox and VZV by using a metagenome approach providing insights into their complete genomes. Our results highlight the importance of surveillance at the point of entries, strengthening lab capacities including next-generation sequencing, and using differential diagnosis for timely and accurate detection of mpox cases.
2022-2023 年期间，全球爆发了猴痘疫情，影响了许多国家。在这项研究中，我们首次报告了从巴基斯坦检测到的猴痘病毒和水痘带状疱疹病毒（VZV）的情况，包括病毒的全基因组序列和合并感染情况。2023 年 4 月至 5 月期间，在伊斯兰堡的巴基斯坦国家卫生研究院对 20 例疑似猴痘病例的样本进行了检测，其中 4 例呈阳性。所有 4 例病例均有前往沙特阿拉伯的旅行史。所有疑似样本均采用 Zymo 研究试剂盒进行 DNA 提取，然后使用 DaAn Gene 检测试剂盒进行 qRT-PCR 扩增，以检测猴痘病毒。此外，对两个 C 值较低（<20）的阳性样本进行了基于宏基因组的全基因组测序，测序平台为 iSeq（Illumina）。测序结果显示，猴痘病毒为 Clade IIb 和基因型 A.2.1，分别与 2022 年 7 月和 6 月斯洛文尼亚和英国的病毒聚类。我们的分析在猴痘病毒中发现了两个新的非同义突变，即 OPG046 中的 V98I 和 OPG109 中的 P600S。此外，我们还从同一样本中成功获得了 VZV 的完整基因组，属于 Clade 5。这项研究代表了巴基斯坦首次发现猴痘病毒，以及使用宏基因组方法检测到的猴痘和 VZV 的合并感染情况，为了解它们的完整基因组提供了信息。我们的研究结果强调了在入境点进行监测、加强实验室能力（包括下一代测序）以及使用鉴别诊断以实现及时、准确检测猴痘病例的重要性。
