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A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples
Zuzana Gerber1, Christian Daviaud2, Damien Delafoy2
1CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057, Evry, France. gerber@cnrgh.fr.
Scientific Reports
|July 22, 2022
Summary
Three target enrichment methods for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) sequencing all yielded acceptable results for genomic surveillance. Each method demonstrated unique advantages and limitations for detecting new variants during the COVID-19 pandemic.
Area of Science:
- * Virology and Genomics
- * Infectious Disease Epidemiology
- * Next-Generation Sequencing Technologies
Background:
- * The COVID-19 pandemic, caused by SARS-CoV-2, necessitates robust genomic surveillance for variant identification and public health monitoring.
- * Accurate whole-genome sequencing is crucial for tracking transmissibility, virulence, and potential resistance to medical countermeasures.
- * Various next-generation sequencing (NGS) approaches exist, but their performance in achieving complete SARS-CoV-2 genome coverage and variant detection varies.
Purpose of the Study:
- * To compare the performance of three distinct target enrichment methods for SARS-CoV-2 whole-genome sequencing.
- * To evaluate the efficacy of multiplex amplification and hybridization capture techniques in high-throughput sequencing.
- * To identify the strengths and weaknesses of each method for reliable variant detection and genomic surveillance.
Main Methods:
- * Comparison of three target enrichment kits: two multiplex amplification (CleanPlex, COVIDSeq) and one hybridization capture (SureSelect).
- * Application of these methods to 93 nasopharyngeal swab samples from SARS-CoV-2 infected individuals.
- * Whole-genome sequencing using short-read NGS technology and subsequent performance analysis.
Main Results:
- * All three methods provided acceptable whole SARS-CoV-2 genome sequencing results.
- * CleanPlex and COVIDSeq showed high mapping rates, while SureSelect demonstrated an absence of systematic variant calling errors.
- * Observed limitations included suboptimal coverage uniformity (CleanPlex), higher cost (SureSelect), and potential supply issues (COVIDSeq).
Conclusions:
- * Each of the evaluated target enrichment kits is suitable for prospective SARS-CoV-2 genomic surveillance programs.
- * The choice of method may depend on specific laboratory needs, balancing factors like cost, coverage uniformity, and error rates.
- * Continued genomic surveillance is vital for managing the evolving COVID-19 pandemic and its emerging variants.
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