biostudies-literatureUnknown13(1)Koskela von Sydow AÖrebro County Council Research CommitteeÖrebro UniversityALF funding for Region Örebro CountyThe severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The AScientific reports6461https://www.ebi.ac.uk/biostudies/studies/S-EPMC10116481biostudies-literatureComparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.PMC10116481Asghar NLindqvist CMSundqvist MKoskela von Sydow AJohansson MStenmark BMolling PfalseComparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The A2023-01-01T00:00:00Z2023 Apr2026-05-28T16:51:39.126Z2025-02-19T02:56:53.191ZS-EPMC101164813708108710.1038/s41598-023-33168-1