Code, manuscript and data to reproduce analysis of the preprint: [Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil] (https://raw.githubusercontent.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf)