Fig. 2: Timeline of the SARS-CoV-2 pandemic from December 2019 to July 2023. | Nature Methods

Fig. 2: Timeline of the SARS-CoV-2 pandemic from December 2019 to July 2023.

From: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Fig. 2: Timeline of the SARS-CoV-2 pandemic from December 2019 to July 2023.The alternative text for this image may have been generated using AI.

Selected events relating to problems with sequencing and consensus calling, labeled a–e. Releases of ARTIC primers schemes (v.1, 2, 3, 4, 4.1 and 5.3.2) are marked with green triangles. a, Primer dimers cause amplicon dropouts10 and 28% of GISAID30 sequences deposited in September 2020 have at least one gap of length at least 200 bp (ref. 31). b, A 9-bp deletion in the primer binding region of ARTIC v.3 amplicon 73 causes missing data32. c, Dropouts causing artifacts at spike 95 and 142 (ref. 13). d, ARTIC v.4 roll out triggers artifactual mutations in some pipelines12. e, Omicron samples cause ARTIC v.4 amplicon dropout, triggering the update to ARTIC v.4.1 (ref. 33).

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