Figure 2:

Timeline of the SARS-CoV-2 pandemic from December 2019 to July 2023, with selected events relating to problems with sequencing and consensus calling labelled a-e. Releases of ARTIC primers schemes (versions 1, 2, 3, 4, 4.1, 5.3.2) are marked with green triangles. a) Primer dimers cause amplicon dropouts [10] and 28% of GISAID [11] sequences deposited in September 2020 have at least one gap of length at least 200bp [12]. b) A 9bp deletion in the primer binding region of ARTIC V3 amplicon 73 causes missing data [13]. c) Dropouts causing artefacts at Spike 95 and 142 [14]. d) ARTIC v4 roll out triggers artifactual mutations in some pipelines [15]. e) Omicron samples cause ARTIC v4 amplicon dropout, triggering the update to ARTIC v4.1 [16].