Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
Virus Res. 2020 Dec;290:198178. doi: 10.1016/j.virusres.2020.198178. Epub 2020 Sep 30.
Human parechoviruses (HPeVs) are highly common pathogens in children under 2 years of age. Of the 19 distinct HPeV genotypes identified worldwide, HPeV1 is still the most prevalent type associated with respiratory and gastrointestinal symptoms in infants and young children. Pakistan's previous studies have focused only on the detection and partial sequencing of HPeV genotypes. In the present study, we have obtained the complete genomes of 2 HPeV1 strains (PAK419 and PAK663) from children using NGS method on Illumina Hiseq Platform. These samples were collected from children suffering from acute gastroenteritis in Rawalpindi, Pakistan during 2016. The near complete genome sequences obtained for two HPeV1 strains (PAK419 and PAK663) consist of total 6877 nucleotides with a single, large open reading frame (ORF) encoding a polyprotein gene. Phylogenetic analysis showed that both HPeV1 strains exhibited maximum amino acid similarity (97 %) to HPeV1 strains from The Nederlands (2007-863, GQ183034) and clustered closely with this and with other HPeV1 strains isolated from other countries in the world (Ethiopia, Taiwan, Russia and Brazil). A motif of arginine-glycine-aspartic acid (RGD) in the VP1 (Outer capsid protein) C-terminus region that is suggested to help virus entry into the host cell also identified in PAK419 and PAK663. SimPlot analysis revealed that intergenotypic recombination events may have take place in the non-structural region between both HPeV1 strains (PAK419, PAK663), two major strains of HPeV1 (GQ183034 and MG873157) and four minor strains of HPeV4 (AM235750), HPeV7 (EU556224), HPeV15 (MN265386) and HPeV18 (KT879915). The full genome of HPeV1 strains characterized in the current study will provide complete information on these newly isolated strains for further preventive or treatment measures.
人类肠道病毒（HPeV）是 2 岁以下儿童中高度常见的病原体。在全球发现的 19 种不同的 HPeV 基因型中，HPeV1 仍然是与婴幼儿呼吸道和胃肠道症状相关的最常见类型。巴基斯坦之前的研究仅集中于 HPeV 基因型的检测和部分测序。在本研究中，我们使用 Illumina Hiseq 平台上的 NGS 方法从儿童中获得了 2 株 HPeV1 株（PAK419 和 PAK663）的完整基因组。这些样本是从巴基斯坦拉瓦尔品第患有急性肠胃炎的儿童中收集的。获得的两株 HPeV1 株（PAK419 和 PAK663）的近完整基因组序列由总 6877 个核苷酸组成，具有单一的、大的开放阅读框（ORF），编码多蛋白基因。系统进化分析显示，两株 HPeV1 株与来自荷兰的 HPeV1 株（2007-863，GQ183034）具有最大的氨基酸相似性（97%），并与该株以及与来自世界其他国家的其他 HPeV1 株（埃塞俄比亚、台湾、俄罗斯和巴西）密切聚类。在 VP1（外壳蛋白）C 末端区域中发现了精氨酸-甘氨酸-天冬氨酸（RGD）基序，该基序被认为有助于病毒进入宿主细胞，在 PAK419 和 PAK663 中也有发现。SimPlot 分析显示，两株 HPeV1 株（PAK419、PAK663）、HPeV1 的两个主要株（GQ183034 和 MG873157）和 HPeV4 的四个次要株（AM235750）、HPeV7（EU556224）、HPeV15（MN265386）和 HPeV18（KT879915）之间的非结构区可能发生了基因型间重组事件。本研究中表征的 HPeV1 株的全基因组将为这些新分离株提供进一步预防或治疗措施的完整信息。
