Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
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SARS-CoV-2 的全基因组测序：调整 Illumina 协议，在大流行期间快速准确地开展疫情调查
DOI：
10.3390/genes11080949
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发表时间：
2020-08-01
期刊：
影响因子：
3.5
通讯作者：
de Oliveira, Tulio
中科院分区：
文献类型：
--
作者：
Pillay, Sureshnee;Giandhari, Jennifer;de Oliveira, Tulio
COVID-19疫情在全球迅速蔓延。南非发现首例病例几天后，夸祖鲁-纳塔尔省（KZN）夸祖鲁-纳塔尔（KZN）德班的一家大型医院开始爆发感染。严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）基因组的系统发育分析可用于追踪医院内的传播途径。它还可以确定疫情的来源，并为改进感染预防和控制策略提供经验教训。本文概述了在紧急疫情调查期间近实时对SARS-CoV-2进行基因分型所遇到的障碍。这包括原始基因分型方案的长度、试剂的不可用性以及样品降解和储存的问题。尽管如此，Illumina测序建立了三种不同的文库制备方法，动手文库制备时间从12小时减少到3小时，这使得疫情调查在短短几周内完成。此外，新方案提高了对整个病毒基因组测序的成功率。还对用于近实时组装高质量基因组的简单生物信息学工作流程进行了微调。为了让其他实验室从我们的经验中学习，所有的文库制备和生物信息学协议都可以在www.example.com上公开获得，并分发给南非基因组学监测网络（NGS-SA）联盟的其他实验室。
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.