High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

Nasserdine Papa Mze; Idir Kacel; Mamadou Beye; Raphael Tola; Mariéma Sarr; Leonardo Basco; Hervé Bogreau; Philippe Colson; Pierre-Edouard Fournier

doi:10.3390/genes14030681

High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

Genes (Basel). 2023 Mar 9;14(3):681. doi: 10.3390/genes14030681.

Authors

Affiliations

¹ UMR VITROME, Aix Marseille University, IRD, AP-HM, SSA, IHU-Méditerranée Infection, 13005 Marseille, France.
² Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 177 rue de Versailles, 78150 Le Chesnay, France.
³ UMR MEPHI, Aix Marseille University, IRD, AP-HM, IHU-Méditerranée Infection, 13005 Marseille, France.
⁴ Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France.

Abstract

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.

Keywords: Illumina; MiSeq; SARS-CoV-2; clade; sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / genetics
Gene Library
Genome, Viral
Humans
SARS-CoV-2* / genetics
Whole Genome Sequencing / methods

Grants and funding

This work was supported by the French Government under the “Investments for the Future” programme managed by the National Agency for Research (ANR), Méditerranée-Infection 10-IAHU-03 and was also supported by Région Provence Alpes Côte d’Azur and European funding PRIMMI (Plateformes de Recherche et d’Innovation Mutualisées Méditerranée Infection), FEDER PA 0000320 PRIMMI.