Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA

Abstract

Of 379 severe acute respiratory syndrome coronavirus 2 samples collected in New York, USA, we detected 86 Omicron variant sequences containing Delta variant mutation P681R. Probable explanations were co-infection with 2 viruses or contamination/amplification artifact. Repeated library preparation with fewer cycles showed the P681R calls were artifactual. Unusual mutations should be interpreted with caution.

Keywords: 2019 novel coronavirus disease; COVID-19; SARS-CoV-2; amplification artifact; coronavirus disease; genomics; respiratory infections; sequence analysis; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure

Integrated Genome Viewer (https://software.broadinstitute.org) plots of sequencing coverage of the entire length of the spike gene (3,821 nt, x-axis) of 3 representative sequences of the Omicron variant and 3 representative sequences of the Delta variant of severe acute respiratory syndrome coronavirus 2, processed in the same batch. The y-axis for each sequence is 250,000 reads. Although coverage plots are basically identical for other regions of the spike gene, coverage of the P681 position is the highest for Delta and one of the lowest for Omicron.