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

Heliyon (Nov 2023)

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

Affiliations

Valentina Curini: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Massimo Ancora: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Lucija Jurisic: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy; Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
Valeria Di Lollo: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Barbara Secondini: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Luana Fiorella Mincarelli: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Marialuigia Caporale: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Ilaria Puglia: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Luigina Di Gialleonardo: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Iolanda Mangone: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Marco Di Domenico: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Adriano Di Pasquale: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Alessio Lorusso: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
Maurilia Marcacci: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy; Corresponding author.
Cesare Cammà: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy

Journal volume & issue: Vol. 9, no. 11
p. e21101

Abstract

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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.

Published in Heliyon

ISSN: 2405-8440 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Science: Science (General); Social Sciences: Social sciences (General)
Website: https://www.cell.com/heliyon/home

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