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. 2023 Oct 19;9(11):e21101.
doi: 10.1016/j.heliyon.2023.e21101. eCollection 2023 Nov.

Evaluation of next generation sequencing approaches for SARS-CoV-2

Valentina Curini  1 , Massimo Ancora  1 , Lucija Jurisic  1   2 , Valeria Di Lollo  1 , Barbara Secondini  1 , Luana Fiorella Mincarelli  1 , Marialuigia Caporale  1 , Ilaria Puglia  1 , Luigina Di Gialleonardo  1 , Iolanda Mangone  1 , Marco Di Domenico  1 , Adriano Di Pasquale  1 , Alessio Lorusso  1 , Maurilia Marcacci  1 , Cesare Cammà  1
Affiliations

Evaluation of next generation sequencing approaches for SARS-CoV-2

Valentina Curini et al. Heliyon. .

Abstract

Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.

Keywords: Comparison; Cost; Labor time; Methods; SARS-CoV-2; Whole genome sequencing.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Vertical (Vcov) and horizontal coverage (Hcov%) obtained from samples of Group A.
Fig. 2
Fig. 2
Vertical (Vcov) and horizontal coverage (Hcov%) obtained for group B samples.
Fig. 3
Fig. 3
Vertical (Vcov) and horizontal coverage (Hcov%) obtained for group C samples.
Fig. 4
Fig. 4
Cost of reagents and work hours for each protocol.
See this image and copyright information in PMC

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