Complementing SARS-CoV-2 genomic analysis in a routine setting with nanopore sequencing to accelerate the availability of results while keeping the accuracy

SARS-CoV-2 genomic analysis has been key to offer valuable data both to epidemiological and clinical demands. To assure the widest coverage in the global monitoring of variants, high-throughput sequencing has been required and it has generally laid on Illumina sequencing. However, the analysis of nosocomial outbreaks, the fast identification of the importation of emerging VOCs in a territory, the discrimination between persistences or reinfections or the identification of mutations associated to potential failures in monoclonal-based therapies are all examples that demanded in the past, or currently, a faster response. Alternative sequencing based on Minion might be better adapted to faster responses when required; however there is a lack of studies offering side to side comparisons between Illumina and Minion. We performed a prospective comparison of Illumina and Minion based sequencing along 10 weeks in a routine laboratory setting, including 68 specimens in which a faster response was required. Minion accelerated the obtaintion of results without reducing the precision in SNP calling. A tandem integration of Minion and Illumina strategies constitutes a suitable solution to assure both high-throughput and faster responses for the SARS-CoV-2 analytical demands assuring accuracy.