Whole Genome Sequencing of SARS-CoV-2: Application of the Ion Torrent Genexus in the COVID-19 pandemic

Abstract

NGS has proven to be of great value during the COVID-19 pandemic. In the beginning with the rapid discovery of SARS-CoV-2 as the causative agent, followed by the publication of the complete genome that was used for the design of highly reliable PCR assays for SARS-CoV-2 detection and the development of therapeutics, and vaccines. In addition, the global sequencing surveillance of SARS-CoV-2 variants generated a great share of information on the emergence and spread of new variants that has been valuable for governments on taking appropriate measurements to control the disease spread, but also for researchers for the evaluation and updating of diagnostics, therapeutics, and vaccines. This report demonstrates some of the possible applications of the Ion Torrent Genexus Integrated Sequencer and the Seegene Allplex SARS-CoV-2 Variant I PCR assay during the COVID-19 pandemic, including diagnostic assay evaluation, the investigation of vaccine breakthrough infections, and SARS-CoV-2 variant surveillance. First, SARS-CoV-2 sequencing performance data of the Genexus regarding sequencing limits, and the quality of variant typing and cluster analysis is shown. Followed by the application of NGS in examining the cause of N-gene dropout and N-gene shift results in the diagnostic Allplex 2019-nCOV real-time PCR assay. In addition to the evaluation of SARS-CoV-2 diagnostic assays, the role of NGS in the investigation of the cause of 14 vaccine breakthrough infection cases is demonstrated. The national SARS-CoV-2 surveillance in the Netherlands is organized by the RIVM, that collects sequencing data from labs all over country, including from the UMCU. Presented are the application and the results of variant surveillance by the UMCU from week 23 2021 to week 9 2022. Additionally, during the shift from Delta to Omicron the samples of hospitalized SARS-CoV-2 positive patients in the UMCU have been variant typed using the Allplex SARS-CoV-2 Variant I PCR assay and compared to the UMCU surveillance data.