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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; Simunovic, Marina; Busche, Tobias; Haak, Markus; Belmann, Peter; Jünemann, Sebastian; Schulz, Tizian; Klages, Levin Joe; Vinke, Svenja; Beckstette, Michael; Pohl, Ehmke; Scherer, Christiane; Sczyrba, Alexander; Kalinowski, Jörn

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


Authors

David Brandt

Marina Simunovic

Tobias Busche

Markus Haak

Peter Belmann

Sebastian Jünemann

Tizian Schulz

Levin Joe Klages

Svenja Vinke

Michael Beckstette

Christiane Scherer

Alexander Sczyrba

Jörn Kalinowski



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.

Citation

Brandt, D., Simunovic, M., Busche, T., Haak, M., Belmann, P., Jünemann, S., …Kalinowski, J. (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), https://doi.org/10.3390/v13091870

Journal Article Type Article
Acceptance Date Sep 15, 2021
Online Publication Date Sep 18, 2021
Publication Date 2021-09
Deposit Date Jan 26, 2022
Publicly Available Date Jan 27, 2022
Journal Viruses
Publisher MDPI
Peer Reviewed Peer Reviewed
Volume 13
Issue 9
DOI https://doi.org/10.3390/v13091870

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Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/

Copyright 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.





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