SARS-CoV-2 amplicon based Next-generation sequencing of clinical samples
The SARS-CoV-2 amplicon libraries were prepared using the Illumina COVID-Seq RUO Kits (Illumina) according to the instructions and the v3 or v4 of the ARTIC COVID-19 multiplex PCR primers (https://artic.network/ncov-2019). Subsequently, the quantification of libraries was carried out using a Qubit Flex fluorometer (Invitrogen), and quality control was conducted using the Bioptic Qsep100. Then, paired-end (150-bp reads) sequencing of these library was performed on the MiniSeq Sequencing System (Illumina) followed the general method. After demultiplexing, the fastq files containing the raw reads were inspected for quality criteria using FastQC (v.0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adapter sequences and low-quality end bases were trimmed using Trimmomatic (v.0.39) 60. Notably,the paired reads and unpaired reads were merged.