International external quality assessment for SARS-CoV-2 genome sequencing, variant and cluster identification. QUALCOV2

The SARS-CoV-2 pandemic promoted the use of real-time routine genomic analyses to investigate the dynamic of variants across the globe and support epidemiological investigations based on single nucleotide polymorphisms. The need for genomics triggered the rapid development of sequencing capacities in numerous laboratories worldwide, in public and private sectors. To assess the ability of laboratories to perform SARS-CoV-2 genome sequencing, variant identification and cluster analyses, we organized an external quality assessment (EQA) involving 42 laboratories from Europe and abroad. Selected SARS-CoV-2 positive samples from different lineages were inoculated on Vero E6 cells for culture. Sixteen aliquots of frozen inactivated cell culture supernatant were shipped to the laboratories with a list of samples and minimal metadata, including date of sampling and epidemiological hints. Each laboratory sequenced and analyzed the samples according to their routine workflows. SARS-CoV-2 amplification and libraries were prepared with nine different protocols, before sequencing with Illumina (50%), Nanopore (33%) or IonTorrent (7%). Correct lineages and VOCs were reported in 97.3% of the samples and 71% of the laboratories reported correct lineages for all 14 simple samples. Four laboratories (12%) reported a lineage for a non-infected culture supernatant demonstrating the occurrence of cross-contamination. Only two laboratories identified a mixed infection with their exact lineages. Thirty-five laboratories (83%) reported cluster analysis, among which 95% grouped correctly identical viruses in a cluster. Overall, most laboratories provided analyses of good quality for simple samples, but this EQA highlighted the need for some laboratories to improve the quality of their sequencing, their sample traceability or their analytical approach.