NCM 2022: Evaluation of long-read vs. short-read platforms for the genomic epidemiology study of SARS-CoV-2 outbreaks
)
The use of SARS-CoV-2 whole-genome sequencing (WGS) as a high-resolution epidemiological marker eases the interpretation of transmission chains, so that tailored control interventions can be promptly implemented. Given the rapid dissemination of SARS-CoV-2, a short time to result is needed. In cases with a monophyletic origin and an epidemiological link, reliably determining the number of single nucleotide polymorphisms (SNPs) between pairs of sequences is important to identify recent transmission events. We aimed to evaluate the applicability of Oxford Nanopore MinION Mk1C for SARS-CoV-2 WGS in outbreak characterization, by comparing its technical and practical differences with the Illumina MiSeq platform.