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Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
Örebro University, School of Medical Sciences. Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.ORCID iD: 0000-0001-8304-2772
Örebro University, School of Medical Sciences. Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.ORCID iD: 0000-0003-3887-9519
Örebro University, School of Medical Sciences.ORCID iD: 0000-0003-4442-8503
Örebro University, School of Medical Sciences.ORCID iD: 0000-0003-3962-2141
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2023 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 6461Article in journal (Refereed) Published
Abstract [en]

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 ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.

Place, publisher, year, edition, pages
Springer Nature, 2023. Vol. 13, no 1, article id 6461
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Infectious Medicine
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URN: urn:nbn:se:oru:diva-105616DOI: 10.1038/s41598-023-33168-1ISI: 001025198300001PubMedID: 37081087Scopus ID: 2-s2.0-85153442204OAI: oai:DiVA.org:oru-105616DiVA, id: diva2:1752280
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Region Örebro CountyÖrebro UniversityAvailable from: 2023-04-21 Created: 2023-04-21 Last updated: 2023-09-05Bibliographically approved

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Koskela, AnitaLindqvist, Carl MårtenAsghar, NaveedJohansson, MagnusSundqvist, MartinMölling, PaulaStenmark, Bianca

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Koskela, AnitaLindqvist, Carl MårtenAsghar, NaveedJohansson, MagnusSundqvist, MartinMölling, PaulaStenmark, Bianca
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