" Since SARS-CoV-2 testing began at the CHU of Liège we have been carrying out regular whole genome sequencing (WGS) of COVID-19 samples. At the time of writing we have uploaded 187 viral genomes to https://nextstrain.org/ (almost half of the 393 from Belgium). We have carried out regular WGS to monitor the evolution of viral haplotypes. Where possible we have concentrated on health care workers with the goal of identifying clusters of transmission. This included a cluster of seven individuals who were tested on the Roche cobas® instrument using the SARS-CoV-2 test, all were positive for the ORF1ab assay, but negative for the second E-gene assay. To date we have WGS data from four of these individuals, all share identical viral genomes and a SNP in the E-gene has been identified as the most probable cause of the test failure. This observation highlights the importance of redundancy in SARS-CoV-2 assays, especially as some testing regimes recommend an E-gene assay as a primary screening test. The work has been published as a preprint (https://www.medrxiv.org/content/10.1101/2020.04.28.20083337v1). On a national level we are collaborating with ULB and KU Leuven to help track SARS-CoV-2 in Belgium (https://spell.ulb.be/news/covid19_analyses/). "
Funding: This work was supported by the Région Wallonne project WALGEMED(convention n° 1710180).
Publication References: Artesi, Maria, Sebastien Bontems, Paul Gobbels, Marc Franckh, Raphael Boreux, Cecile Meex, Pierrette Melin, Marie-Pierre Hayette, Vincent Bours, and Keith Durkin. 2020. "Failure of the Cobas® SARS-CoV-2 (Roche) E-Gene Assay Is Associated with a C-to-T Transition at Position 26340 of the SARS-CoV-2 Genome." Infectious Diseases (except HIV/AIDS). medRxiv. https://doi.org/10.1101/2020.04.28.20083337.
Keith Durkin, Dr - Maria Artesi, Dr - Sébastien Bontems, Dr - Marie-Pierre Hayette, Dr- Vincent Bours, Dr