期刊
VIRUSES-BASEL
卷 13, 期 9, 页码 -出版社
MDPI
DOI: 10.3390/v13091870
关键词
genomic surveillance; SARS-CoV-2; nanopore sequencing; ORF8 deletion; viral genomics
类别
资金
- Federal Ministry of Education and Research (BMBF) through the German Network for Bioinformatics Infrastructure (de.NBI) [031A532B, 031A533A]
- Open Access Publication Fund of Bielefeld University
Genomic surveillance of the SARS-CoV-2 pandemic is crucial and achieved mainly through amplicon sequencing protocols. A significant deletion in the ORF8 gene has been discovered, indicating a mutation hotspot, with many deletions not identified in standard data analysis.
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.
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