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The Microbial Genomics Module template workflow Analyze QIAseq xHYB Viral Panel Data is aimed at analysis of data generated with the QIAseq xHYB viral panels. The template workflow is complemented by the QIAseq xHYB Viral Panels QIAGEN reference data set that includes kit-specific reference databases. These databases contain a list of the species targeted by the respective xHYB viral panel.
The QIAseq xHYB panel target list lists the species targeted by the panels. For the species SARS-CoV the list specifies the sub-species SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). The reference database for the QIAseq xHYB Viral Respiratory Panel, qiaseq_xhyb_respiratory_viral_reference_set_v1.0, does however not contain the expected SARS-CoV-2 sub-species. Instead, it includes the SARS-CoV subspecies “SARS coronavirus Tor2”.
As a result, for samples where the majority of reads come from SARS-CoV-2, the workflow outputs from the “Find Best References using Read Mapping” analysis will indicate “SARS coronavirus Tor2” as the Best Reference, not “SARS-CoV-2”.
Apart from the Best Reference reporting, the template workflow outputs a list of variants. This list indicates where the sample reads differ from Best Reference reference database genome. For SARS-CoV-2 samples reported as Best Reference “SARS coronavirus Tor2”, the variant track will contain a large number of variants reflecting that the captured genome is quite different from SARS coronavirus Tor2.
For improved SARS-CoV-2 reporting, create a new respiratory reference database with the SARS-CoV-2 reference genome included. You can find the relevant genome in the adventitious reference database also included in the QIAseq xHYB Viral Panels reference data set 1.2, qiaseq_xhyb_adventitious_viral_reference_set_v1.0.
To create a modified respiratory reference database:
Use this new reference database as Viral Reference Database input when analyzing your QIAseq xHYB Viral Respiratory Panel data with the template workflow Analyze QIAseq xHYB Viral Panel Data.
QIAGEN reference data set, QIAseq xHYB Viral Panels_v1.2, reference element: qiaseq_xhyb_respiratory_viral_reference_set_v1.0.