Fig. 1

A systematic approach allows the generation of large and robust genomic data in a cost-effective manner. A Schematic representation of the workflow set up to collect, process, and analyze a considerable number of viral genomes. Top: Oronasopharyngeal swabs are performed to diagnose the presence of the SARS-CoV-2 genome in patients and extract its RNA. Subsequently, viral RNA is retrotranscribed and subjected to two PCR steps to amplify and index the obtained cDNA. After circularization and nanoball generation, the obtained library is then sequenced and analyzed. Bottom: As an alternative and faster approach, an optimized approach enables the amplification and indexing to occur in one PCR step. B Multiple solutions were tested to optimize the workflow. The table reports the input RNA volume, the amount of reads produced per sample, the number of samples loaded per flowcell, the average time required to process a 96-well plate, and the relative cost per sample. Cost details are reported in Additional file 2: table S1. C Boxplot showing the percentage of samples submitted on the GISAID platform, divided by each tested solution. Only samples with an average Ct value < 33 were considered. D Violin plot showing the distribution of the percentage of SARS-CoV-2 reads detected for different ranges of CTs. n:sample size. E Variant annotation, cumulative frequency, and sequencing coverage of each position of the SARS-CoV-2 genome. F Venn diagram showing the intersection between mutations detected in all the sequenced genomes worldwide (yellow) and the mutations found in this study (light blue). G Representation of all the 156 lineages identified in this study. The length of the bars is indicative of the number of samples for each lineage in the logarithmic scale. Colored bars indicate VOC