Nasrin Taslima, Samim Hassan Md, Iqbal Muzaffar, Yousif Amar, Hoque Mehboob, Ali Nemat, Ali Safdar
Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata, India.
Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata, India.
J Genet Eng Biotechnol. 2024 Mar;22(1):100346. doi: 10.1016/j.jgeb.2023.100346. Epub 2024 Jan 28.
As the world settles down from the COVID-19 pandemic, many countries are faced with an unexpected outbreak of monkeypox infection. Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is an enveloped, double stranded DNA virus belonging to the Poxviridae family. Presently, we construct and analyze the phylo-geo-network and the corresponding haplogroups. Presently, we performed the haplogroup analysis with their defining mutations and phylogenetic lineage study along with geographical distributions with the aim to understand the evolutionary path of the MPXV across the world.
Information about 719 full length genomes of MPXV were collected from GISAID repository and the sequences extracted from NCBI. The alignment of 719 MPXV genomes and their subsequent analysis revealed a total of 1530 segregating sites of which 330 were parsimony informative (PI) sites. The variations had a positive value of Tajima's D statistic indicating some mutations being prevalent and hence balancing selection. A total of 39 haplogroups were observed in the phylo-geo-network and their defining mutations along with the evolutionary path has been discussed. The phylo-geo-network revealed the nodal haplogroup is represented by GISAID ID 13889450, haplogroup A1, an isolate from Germany, having a total of 296 identical sequences in the study incident across 22 countries. The localized evolution is highlighted by country specific sequences and haplogroups. USA had a total of 58 genomes and 13 haplogroups as compared to Peru (89 genomes, 7 haplogroups) and Germany (26 genomes, 6 haplogroups).
The evolution of MPXV can be happening in a localized manner and hence accumulation of variations in the MPXV genomes needs to be monitored in order to be prepared for any possible threats.
随着世界从新冠疫情中逐渐恢复，许多国家面临着猴痘感染的意外爆发。猴痘是由猴痘病毒（MPXV）引起的一种人畜共患病，猴痘病毒是一种有包膜的双链DNA病毒，属于痘病毒科。目前，我们构建并分析了系统发育地理网络及其相应的单倍群。目前，我们进行了单倍群分析，确定了其特征性突变，并进行了系统发育谱系研究以及地理分布研究，旨在了解猴痘病毒在全球的进化路径。
从全球共享流感数据倡议组织（GISAID）数据库收集了719个猴痘病毒全长基因组信息，并从美国国立生物技术信息中心（NCBI）提取了相关序列。对719个猴痘病毒基因组进行比对并随后进行分析，共发现1530个分离位点，其中330个是简约信息（PI）位点。这些变异的Tajima's D统计值为正值，表明一些突变较为普遍，因此存在平衡选择。在系统发育地理网络中总共观察到39个单倍群，并讨论了它们的特征性突变以及进化路径。系统发育地理网络显示，节点单倍群由GISAID ID 13889450代表，即A1单倍群，这是一株来自德国的毒株，在本研究中，来自22个国家的共有296个相同序列。特定国家的序列和单倍群突出了局部进化。与秘鲁（89个基因组，7个单倍群）和德国（26个基因组，6个单倍群）相比，美国共有58个基因组和13个单倍群。
猴痘病毒可能以局部方式进化，因此需要监测猴痘病毒基因组中的变异积累，以便为应对任何可能的威胁做好准备。
