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Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines

Brandt, David and Simunovic, Marina and Busche, Tobias and Haak, Markus and Belmann, Peter and Jünemann, Sebastian and Schulz, Tizian and Klages, Levin Joe and Vinke, Svenja and Beckstette, Michael and Pohl, Ehmke and Scherer, Christiane and Sczyrba, Alexander and Kalinowski, Jörn (2021) 'Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines.', Viruses, 13 (9). p. 1870.

Abstract

Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SARS-CoV-2 outbreak in a local hospital and used nanopore sequencing with a modified ARTIC protocol employing 1200 bp long amplicons. We detected a long deletion of 168 nucleotides in the ORF8 gene in 76 samples from the hospital outbreak. This deletion is difficult to identify with the classical amplicon sequencing procedures since it removes two amplicon primer-binding sites. We analyzed public SARS-CoV-2 sequences and sequencing read data from ENA and identified the same deletion in over 100 genomes belonging to different lineages of SARS-CoV-2, pointing to a mutation hotspot or to positive selection. In almost all cases, the deletion was not represented in the virus genome sequence after consensus building. Additionally, further database searches point to other deletions in the ORF8 coding region that have never been reported by the standard data analysis pipelines. These findings and the fact that ORF8 is especially prone to deletions, make a clear case for the urgent necessity of public availability of the raw data for this and other large deletions that might change the physiology of the virus towards endemism.

Item Type:Article
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Available under License - Creative Commons Attribution 4.0.
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.3390/v13091870
Publisher statement:This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Date accepted:15 September 2021
Date deposited:27 January 2022
Date of first online publication:18 September 2021
Date first made open access:27 January 2022

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