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Evaluation of two SARS-CoV-2 whole genome amplification and sequencing workflows for genomic surveillance and outbreak analysis in the clinical microbiology laboratory.

Genomics - 1 Sept 2025

Panisello Yagüe David, Pelegrin Andreu C, Soler Laia, Bordoy Antoni E, Martínez-Puchol Sandra, Clarà Gemma, González-Gómez Sara, de León Alexia Paris, Noguera-Julian Marc, Armengol Maria Pilar, Francino Olga, Casañ Cristina, Casas Irma, Cardona Pere-Joan, Giménez Montserrat, Blanco Ignacio, Saludes Verónica, Martró Elisa

Abstract excerpt

Whole-genome sequencing (WGS) has become a key element of SARS-CoV-2 genomic epidemiology. In Spain and many other countries, this is mostly driven by Illumina-based sequencing, while Oxford Nanopore Tecnologies' MinION Mk1C is a low-cost, faster, and user-friendly sequencer. We aimed to evaluate the applicability of the Mk1C device with a long-amplicon PCR approach for SARS-CoV-2 rapid genomic surveillance and...

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PMID: 40651631
DOI: 10.1016/j.ygeno.2025.111077

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