Detecting SARS-CoV-2 Variants in Healthcare Workers

Testing of HCW for SARS-CoV-2 was performed using routine diagnostic procedures in the virology laboratory of the University Hospital of Lyon (Hospices Civils de Lyon, HCL) and included: transcription mediated amplification (TMA) (Aptima SARS-CoV-2 Assay, Hologic, Marlborough, US), loop-mediated isothermal amplification (LAMP) (SARS-CoV-2 ID NOW, Abbott, Sligo, Ireland) and RT-qPCR with different kits (Cobas 6800 SARS-CoV-2 assay, Roche, Basel, Switzerland or Panther Fusion SARS-CoV-2 assay, Hologic). To determine the prevalence of SARS-CoV-2 variants of concern (VOC) in HCW, available positive samples with quantification cycle (Cq) < 28 were sequenced using COVIDSeq (Illumina) as previously described [12 (link)]. Libraries were sequenced to 1 M paired-end reads (2 × 100 bp) and data were analysed using the in-house seqmet bioinformatic pipeline (available at https://github.com/genepii/seqmet). Clades and lineages were determined on samples with genome coverage > 90% using Nextclade and PangoLEARN, respectively.