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

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

doi:10.1016/j.heliyon.2023.e21101

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

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

Authors

Valentina Curini¹, Massimo Ancora¹, Lucija Jurisic^{1

2}, Valeria Di Lollo¹, Barbara Secondini¹, Luana Fiorella Mincarelli¹, Marialuigia Caporale¹, Ilaria Puglia¹, Luigina Di Gialleonardo¹, Iolanda Mangone¹, Marco Di Domenico¹, Adriano Di Pasquale¹, Alessio Lorusso¹, Maurilia Marcacci¹, Cesare Cammà¹

Affiliations

¹ Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy.
² Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.

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.