Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland; Academic Center for Pathomorphological and Genetic-Molecular Diagnostics, Bialystok, Poland; Center of Experimental Medicine, Medical University of Bialystok, Bialystok, Poland.
Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland; Academic Center for Pathomorphological and Genetic-Molecular Diagnostics, Bialystok, Poland.
Adv Med Sci. 2021 Sep;66(2):237-245. doi: 10.1016/j.advms.2021.03.005. Epub 2021 Mar 30.
We analyzed the SARS-CoV-2 genome using our integrated genome analysis system and present the concept of a comprehensive approach to monitoring and surveillance of emerging variants.
MATERIAL/METHODS: A total of 69 SARS-CoV-2 positive samples (with Ct value ≤ 28) were tested. Samples included in this study were selected from 7 areas of eastern Poland. All samples were sequenced on an Illumina MiSeq platform using a 300-cycle MiSeq Reagent Kit v2. BWA was used for reads mapping on the reference SARS-CoV-2 sequence. SAMTools were used for post-processing of reads to genome assembly. Pango lineage and Nexstrain were used to identify variants and amino acid mutations. Statistical analysis was performed with R 4.0.2.
This study shows the first confirmed case of SARS-CoV-2 in Poland with the lineage B.1.351 (known as 501Y.V2 South African variant), as well as another 18 cases with epidemiologically relevant lineage B.1.1.7, known as British variant. Supplementary analysis of SARS-CoV-2 sequences deposited in GISAID shows that the share of a new variant can change rapidly within one month. In addition, we show a complete, integrated concept of a networked system for analyzing the variability of the SARS-CoV-2 genome, which, used in the present study, generated data and a variant report within 6 days.
The analyzed viral genomes showed considerable variability with simultaneous clear distinction of local clusters of genomes showing high similarity. Implementing real-time monitoring of new SARS-CoV-2 variants in Poland is urgently needed, and our developed system is available to be implemented on a large scale.
我们使用综合基因组分析系统对 SARS-CoV-2 基因组进行分析，并提出了一种综合监测新兴变异株的方法。
材料/方法：共检测了 69 份 SARS-CoV-2 阳性样本（Ct 值≤28）。本研究中选取的样本来自波兰东部的 7 个地区。所有样本均在 Illumina MiSeq 平台上进行测序，使用 300 个循环的 MiSeq Reagent Kit v2。BWA 用于对参考 SARS-CoV-2 序列进行读映射。SAMTools 用于对读进行基因组组装的后处理。Pango 谱系和 Nexstrain 用于识别变异株和氨基酸突变。使用 R 4.0.2 进行统计分析。
本研究首次在波兰确认了 SARS-CoV-2 病例，该病毒株属于谱系 B.1.351（称为南非 501Y.V2 变异株），以及另外 18 例具有流行病学相关性的谱系 B.1.1.7，称为英国变异株。对 GISAID 中提交的 SARS-CoV-2 序列的补充分析表明，新变异株的份额在一个月内可能会迅速变化。此外，我们展示了一个完整的、集成的 SARS-CoV-2 基因组变异性分析网络系统的概念，该系统在本研究中仅用 6 天就生成了数据和变异报告。
分析的病毒基因组显示出相当大的变异性，同时清楚地区分了具有高度相似性的本地基因组簇。迫切需要在波兰实时监测新的 SARS-CoV-2 变异株，我们开发的系统可大规模实施。
