SARS-CoV-2 mapped reads and consensus genomes of an intra-patient serially sampled infection

Mapped reads and consensus genomes derived of 12 SARS-CoV-2 serial samples from a chronically infected patient in Barcelona, Spain, between March 30, 2020 and November 11, 2020. The samples belong to lineage B.1 and were obtained in the Hospital Clínic de Barcelona. Sequencing was performed at the Institute of Biomedicine of Valencia using the ARTIC v3 protocol, the Nextera Flex DNA Library Preparation Kit and the Illumina MiSeq platform. The bioinformatic analysis was done with the SeqCOVID pipeline for SARS-CoV-2 bioinformatic analysis. The dataset has been analyzed with VIPERA, a pipeline that integrates phylogenetic and evolutionary analysis of intrapatient SARS-CoV-2 sequences, allowing the automated detection of serially sampled infections and the identification of evolutionary patterns within the same viral infection.

本数据集涵盖2020年3月30日至2020年11月11日期间，从西班牙巴塞罗那一名慢性感染严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）患者体内获取的12份系列样本所得到的比对reads（mapped reads）与一致基因组序列（consensus genomes）。所有样本均属于B.1谱系，采集自巴塞罗那临床医院。测序工作由瓦伦西亚生物医学研究所完成，采用ARTIC v3实验方案、Nextera Flex DNA文库制备试剂盒及Illumina MiSeq测序平台。新冠病毒的生物信息分析借助SeqCOVID分析流程完成。本数据集还通过VIPERA分析流程进行了分析：该流程整合了患者体内新冠病毒序列的系统发育与进化分析，可自动检测系列采样的感染情况，并识别同一病毒感染内的进化模式。