SARS-CoV-2 Genome Sequencing Protocol

During April‒July 2020, we generated 434 SARS-CoV-2 genome sequences for investigation. We collected nasopharyngeal/oropharyngeal swab specimens from COVID-19‒positive persons after obtaining informed consent and ethics approval. We transported samples and processed them for sequencing as described (13 (link)). In brief, we used the Ion AmpliSeq SARS-CoV-2 Research Panel and the Ion AmpliSeq Library Kit Plus (both from Thermo Fisher Scientific) for the library preparation. We performed sequencing on the Ion Torrent S5Plus system (Thermo Fisher Scientific) by using a 530 chip with 400-bp chemistry. We used a reference-based genome assembly, as described by Joshi et al. (13 (link)), to obtain whole-genome sequences. In brief, we used PRINSEQ-lite version 0.20.4 (14 (link)) for trimming and quality filtering. We mapped high-quality reads against a SARS-CoV-2 reference genome (GenBank accession no. NC_045512) by using CLC Genomics Workbench V 12.0 (QIAGEN, https://www.qiagen.com) to obtain consensus genomes.