QIAseq xHYB Viral Panels reference data set v1.2 - Respiratory reference database element contains different SARS-Cov sub-species than listed in panel target list

Issue description

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".

How to see if your analyses are affected

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.

Recommendation

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:

• Open qiaseq_xhyb_adventitious_viral_reference_set_v1.0 and go to Table View by clicking on the Show Table icon under the View area.
• Filter for "SARS-CoV-2". This leaves one row in the table.
• Select the one row and click on Create New Sequence List
• Save the new sequence list
• To merge the new sequence list and the existing respiratory reference database go File| New | Sequence list
• Select the existing reference database 'qiaseq_xhyb_respiratory_viral_reference_set_v1.0' and the newly created sequence list with SARS-CoV-2
• Save the merged sequence list

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.

Affected reference data

QIAGEN reference data set, QIAseq xHYB Viral Panels_v1.2, reference element: qiaseq_xhyb_respiratory_viral_reference_set_v1.0.