ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host 1 and inter-host viral diversity in clinical samples and for the evaluation of re-infections. Severe acute respiratory syndrome coronavirus 2

The reconstruction of complete and accurate SARS-CoV-2 genomic sequences can be challenging in clinical samples, that are often suboptimal. The common recommendation is, therefore, to exclude from sequencing samples containing <1000 virus copies, despite these may represent unique and irreplaceable specimens, central for the investigations conducted. Here we report an experimental workflow to reconstruct accurate and complete SARS-CoV-2 genomes from clinical samples with high-to-very-low viral titres, exploiting the amplicon-based viral genome sequencing method. The protocol was optimized to provide improved flexibility in the number of samples analysed simultaneously, reduction of costs and time to end-result. The generation (and combination) of technical replicates represented the central strategy to enable complete genome reconstructions as well as accurate variant calling from sub-optimal samples. We demonstrate the utility of this approach in the analysis of more than 170 clinical samples with a wide range of virus concentration, as well as in the proper assessment of an infection-relapse case.