Department of Pharmacology, Kathmandu University School of Medical Sciences, Dhulikhel, Kavre, Nepal. Research and Development Division, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Kavre, Nepal. Genomic Research Lab, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Kavre, Nepal.
Research and Development Division, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Kavre, Nepal. Genomic Research Lab, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Kavre, Nepal.
Kathmandu Univ Med J (KUMJ). 2021 Apr-Jun;19(74):137-142.
Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARSCoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 - B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.
SARS-CoV-2 的传播已成为全球公共卫生危机。尼泊尔正面临着第二波 COVID-19 大流行，但关于在尼泊尔流行的 SARS-CoV-2 变体的基因组序列数据仍然有限。
本研究旨在对尼泊尔的 SARS-CoV-2 进行全基因组测序，以检测可能存在的突变谱和循环 SARSCoV-2 变体的系统进化分支。
本研究调查了拭子样本检测呈 SARS-CoV-2 阳性的情况。在提取 RNA 后，通过实时 PCR 进行调查，然后进行全基因组测序。随后，使用适当的生物信息学工具对共识基因组序列进行分析。
对两例无旅行史患者（A1 和 A2）的 SARS-CoV-2 基因组进行序列分析，发现它们属于谱系 B.1.1。同样，在另外四名从英国返回的受试者的四个样本中，有两个样本的基因组属于谱系 B.1.36，另外两个样本属于谱系 B.1.1.7（Alpha 变体）。共识基因组中的突变包含了 SARS-CoV-2 各谱系的特征性突变。
我们在尼泊尔确认了两种关切变异株（VOC-202012/01）的基因组序列。本研究提供了简明的基因组证据，证明了不同谱系的 SARS-CoV-2——B.1.1、B.1.36 和 B.1.1.7——在尼泊尔的传播。
