Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform
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Published:2023-01-25
Issue:3
Volume:24
Page:2374
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ISSN:1422-0067
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Container-title:International Journal of Molecular Sciences
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language:en
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Short-container-title:IJMS
Author:
Gladkikh Anna1ORCID, Klyuchnikova Ekaterina1, Pavlova Polina1, Sbarzaglia Valeriya1, Tsyganova Nadezhda1, Popova Margarita1, Arbuzova Tatiana1, Sharova Alena1, Ramsay Edward1, Samoilov Andrei12ORCID, Dedkov Vladimir13ORCID, Totolian Areg1
Affiliation:
1. Saint Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia 2. Research Institute for Systems Biology and Medicine, 117246 Moscow, Russia 3. Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays a key role in overcoming the ongoing COVID-19 pandemic despite its relative successive waves and the continuous emergence of new variants. Many technological approaches are currently applied for the whole genome sequencing (WGS) of SARS-CoV-2. They differ in key stages of the process, and they feature some differences in genomic coverage, sequencing depth, and in the accuracy of variant-calling options. In this study, three different protocols for SARS-CoV-2 WGS library construction are compared: an amplicon-based protocol with a commercial primer panel; an amplicon-based protocol with a custom panel; and a hybridization capture protocol. Specific differences in sequencing depth and genomic coverage as well as differences in SNP number were found. The custom panel showed suitable results and a predictable output applicable for the epidemiological surveillance of SARS-CoV-2 variants.
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
Reference31 articles.
1. China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019;Zhu;N. Engl. J. Med.,2020 2. (2022, November 30). Impact of the Coronavirus Pandemic on the Global Economy—Statistics & Facts. Available online: https://www.statista.com/topics/6139/covid-19-impact-on-the-global-economy/#dossierContents__outerWrapper. 3. Charumilind, S., Craven, M., Lamb, J., Sabow, A., Singhal, S., and Wilson, M. (2022, November 30). When Will the COVID-19 Pandemic End?. Available online: https://www.mckinsey.com/industries/healthcare-systems-and-services/our-insights/when-will-the-covid-19-pandemic-end. 4. Stoddard, G., Black, A., Ayscue, P., Lu, D., Kamm, J., Bhatt, K., Chan, L., Kistler, A.L., Batson, J., and Detweiler, A. (2022). Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. BMC Public Health, 22. 5. Next-generation sequencing reveals the progression of COVID-19;Chen;Front. Cell. Infect. Microbiol.,2021
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