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Circular consensus sequences (CCSs) were demultiplexed with Lima, and a consensus FASTA file was created with all these indexed CCS reads. Size-variant genotyping was done byin silicoPCR on this FASTA file using the IC1 and FC27 primer sequences designed by Snounou et al.18in addition to new primers designed for this study as queries in a Blastn search against the dataset. Samples and size variants were hierarchically clustered and visualized in two sequencing coverage heatmaps for IC1 and FC27. In addition, CCS reads were bioinformatically coupled to the primers from the first PCR to construct isolate phylogenies or be translated into amino acid sequences to study sequence conservation, as well as the presence of B and T cell epitopes. See alsoTable S6.

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