Amplicon sequencing of Covid Positive nasopharyngeal swab
Nasopharyngeal swab specimens were used for SARS-CoV-2 amplicon sequencing. Viral RNA was extracted and reverse-transcribed to cDNA, then amplified using tiled multiplex PCR primer pools (ARTIC nCoV-2019) to generate overlapping amplicons spanning the SARS-CoV-2 genome. Amplicons were end-repaired/polished and ligated to Illumina-compatible adapters and dual indexes; libraries were quality-checked and quantified prior to paired-end sequencing on an Illumina MiSeq.