Abstract
We have developed periscope, a tool for the detection and quantification of sub-genomic RNA in ARTIC network protocol generated Nanopore SARS-CoV-2 sequence data. We applied periscope to 1155 SARS-CoV-2 sequences from Sheffield, UK. Using a simple local alignment to detect reads which contain the leader sequence we were able to identify and quantify reads arising from canonical and non-canonical sub-genomic RNA. We were able to detect all canonical sub-genomic RNAs at expected abundances, with the exception of ORF10, suggesting that this is not a functional ORF. A number of recurrent non-canonical sub-genomic RNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sub-genomic RNA analysis. Finally variants found in genomic RNA are transmitted to sub-genomic RNAs with high fidelity in most cases. This tool can be applied to tens of thousands of sequences worldwide to provide the most comprehensive analysis of SARS-CoV-2 sub-genomic RNA to date.
Abbreviations
- TRS
- Transcription regulation sequence (ACGAAC)
- ORF
- Open reading frame
- sgRNA
- sub-genomic RNA
- gRNA
- genomic RNA
- sgRPHT
- sub-genomic RNA reads per 100,000 mapped reads
- sgRPTg
- sub-genomic RNA reads per 1,000 genomic RNA reads
- gRPHT
- genomic RNA reads per 100,000 mapped reads