Department of Virology, National Institute of Health, Islamabad, Pakistan.
J Med Virol. 2022 Oct;94(10):4869-4877. doi: 10.1002/jmv.27957. Epub 2022 Jul 4.
The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in upsurges of coronavirus disease 2019 (COVID-19) cases around the globe. Pakistan faced the fourth wave of COVID-19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS-CoV-2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID-19-positive patients were subjected to whole-genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% (n = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% (n = 28) isolates were showing B.1.617.2 while 23.5% (n = 25), 17.59% (n = 19), 14.81% (n = 16), and 13.89% (n = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% (n = 89) of delta variant cases, followed by Karachi (17%, n = 23), and Rawalpindi (10%, n = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.
严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）的不同关切变体的出现导致了全球 2019 年冠状病毒病（COVID-19）病例的激增。巴基斯坦在 2021 年 7 月至 8 月面临第四波 COVID-19，病例达 314786 例。为了了解巴基斯坦第四波大流行期间循环 SARS-CoV-2 株的基因组多样性，进行了这项研究。对 140 例 COVID-19 阳性患者的样本使用 Illumina 的 iSeq 测序仪进行全基因组测序。结果表明，97%（n=136）的分离株属于 delta 变体，而 3 个分离株属于 alpha 变体，只有 1 个分离株属于 beta 变体。在 delta 变体病例中，20.5%（n=28）的分离株显示 B.1.617.2，23.5%（n=25）、17.59%（n=19）、14.81%（n=16）和 13.89%（n=15）的分离株分别显示 AY.108、AY.43、AY.127 和 AY.125 谱系。发现伊斯兰堡是受影响最严重的城市，65%（n=89）的 delta 变体病例，其次是卡拉奇（17%，n=23）和拉瓦尔品第（10%，n=14）。除了 delta 变体的特征性刺突突变（T19R、L452R、T478K、P681R 和 D950N）外，亚谱系还表现出其他刺突突变，如 E156del、G142D、T95I、A222V、G446V、K529N、N532S、Q613H 和 V483A。系统发育分析显示来自新加坡、英国和德国的传入。本研究强调了 delta 变体（B.1.617.2 和亚谱系）在巴基斯坦第四波大流行期间的循环。
