Alliance for Pandemic Preparedness

April 6, 2021

A New SARS-CoV-2 Lineage That Shares Mutations with Known Variants of Concern Is Rejected by Automated Sequence Repository Quality Control

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  • [Pre-print, not peer-reviewed] A SARS-CoV-2 variant (named B.1.x) may be an emerging lineage that has been poorly recognized due to a deletion mutation that causes the submission of its sequence to be rejected by automated sequence repository quality control in genome databases such as GISAID and Genbank. The variant, which contains a deletion in the non-structural protein ORF, was identified in 8 samples (out of 339) from Santa Cruz, California. The lineage also contains the N501Y mutation present in the B.1.1.7 and B.1.351 variants of concern. Based on the growing proportion of B.1.1.7 samples, the authors suggest that B.1.x could be growing at a similarly fast rate.

Thornlow et al. (Apr 6, 2021). A New SARS-CoV-2 Lineage That Shares Mutations with Known Variants of Concern Is Rejected by Automated Sequence Repository Quality Control. Pre-print downloaded Apr 6 from https://doi.org/10.1101/2021.04.05.438352