Miseq sequence kit v3

Libraries for Illumina sequencing were prepared using the Nextera XT library preparation kit (Illumina, San Diego, CA, USA) and then sequenced on a MiSeq instrument (Illumina, USA) with a MiSeq Sequence kit v3. FastQC software was used for sequence data quality assessment. Trimmomatic was used for quality data trimming. Reads were mapped onto reference sequences using BWA. The consensus sequence was obtained using Samtools mpileup. Libraries for Oxford Nanopore sequencing were prepared using an SQK-LSK109 DNA Ligation Sequence kit (Oxford Nanopore, Oxford, UK). Sequencing was performed using a MinIon instrument (Oxford Nanopore, UK) with a R9.4.1 flowcell. Guppy software was used for basecalling and data quality trimming. Reads were mapped onto the reference sequence using Minimap2.

WGS data were obtained by Illumina MiSeq and MinIon (Oxford Nanopore Technology, Oxford, UK) and used to confirm PCR results and create the SARS-CoV-2 lineage panel. Libraries for Illumina sequencing were prepared using the Nextera XT library preparation kit (Illumina, San Diego, CA, USA) and then sequenced on a MiSeq instrument (Illumina, San Diego, CA, USA) with a MiSeq Sequence kit v3. FastQC software was used for sequence data quality assessment. Trimmomatic was applied for quality data trimming. Reads were mapped onto reference sequences using BWA. SAMtools-mpileup v1.10.68 [29 (link)] was used to produce draft consensus sequences which were then corrected. Libraries for Oxford Nanopore sequencing were prepared using an SQK-LSK109 DNA Ligation Sequence kit (Oxford Nanopore, Oxford, UK). Sequencing was performed using a MinIon instrument (Oxford Nanopore, Oxford, UK) with a R9.4.1 flowcell. Guppy software was used for base-calling and data quality trimming. Reads were mapped onto the reference sequence Wuhan-Hu-1 SARS-CoV-2 using Minimap2 [30 (link)]. Lineage was defined using PANGO algorithms.