Abstract
Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis.
Highlights
The global spread of a new type of coronavirus, SARS-CoV-2, causing the respiratory diseaseCOVID-19 [1,2,3,4] mobilized both the public and private sector and resulted in a rapid development of solutions focused on SARS-CoV-2 detection and analysis
To a number of solutions utilizing the advantages of RT-qPCR techniques for SARS-CoV-2 detection [5,6], the next-generation sequencing (NGS)-based protocols allows the analysis of SARS-CoV-2 genome evolution and variability and the monitoring of its spread within the global population (Nextstrain; https://nextstrain.org) [7,8]
These knowledges address the need to elucidate its genomic characteristics (GISAID; https://www.gisaid.org) in order to ensure the efficiency of RT-qPCR testing, assess its transmission through clonal events, and develop a reliable vaccination protocols future therapies, especially considering the fact that RNA
Summary
The global spread of a new type of coronavirus, SARS-CoV-2, causing the respiratory diseaseCOVID-19 [1,2,3,4] mobilized both the public and private sector and resulted in a rapid development of solutions focused on SARS-CoV-2 detection and analysis. To a number of solutions utilizing the advantages of RT-qPCR techniques for SARS-CoV-2 detection [5,6], the next-generation sequencing (NGS)-based protocols allows the analysis of SARS-CoV-2 genome evolution and variability and the monitoring of its spread within the global population (Nextstrain; https://nextstrain.org) [7,8]. These knowledges address the need to elucidate its genomic characteristics (GISAID; https://www.gisaid.org) in order to ensure the efficiency of RT-qPCR testing, assess its transmission through clonal events, and develop a reliable vaccination protocols future therapies, especially considering the fact that RNA viruses are prone to accumulate variants in its genome in a relatively short timeline, which in the case of SARS-CoV-2 is related to its capacity to proofread and remove mismatched nucleotides during genome replication and transcription [9,10,11,12]. In this study we report performance analysis of Diagnostics 2020, 10, 769; doi:10.3390/diagnostics10100769 www.mdpi.com/journal/diagnostics
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