Sample extraction and library preparation
On arrival, samples were extracted using the Qiagen QiaAmp (QIAGEN GmbH,
Germany) or MagNA Pure 96 DNA and Viral NA Extraction kit (Roche
Diagnostics GmbH, Switzerland) as per the manufacturer’s instructions,
then submitted for quantification by PCR, detecting orf1ab, E and N
genes to ensure the Ct values were within a range that would support
high-quality sequencing (Ct15-30). Samples not within this range were
not sequenced to limit on cost and preserve reagents already in high
demand.