Analysis of xHYB QIAseq Viral Panel Data - targeted genomes may go undetected due to reference data issue

Issue description

Using the workflows "Analyze QIAseq xHYB Viral Panel Data (Human host)" and "Analyze Viral Hybrid Capture Panel Data (legacy)", delivered by the CLC Microbial Genomics Module, pathogen identification is done by mapping reads to a viral taxonomic profiling index, and subsequently using the matching reads as input for the downstream pathogen identification step. The index “qiaseq_xhyb_viral_taxpro_index_v1.0” is missing some of the genomes targeted by the QIAseq xHYB viral panels. These genomes may thus not be reported as present in analysis results, even if they were present in the sample.

Affected reference data

Analyses are affected if samples contain reads from organisms with genomes missing from the index qiaseq_xhyb_viral_taxpro_index_v1.0. This index file is included in the QIAGEN Set “QIAseq xHYB Viral Panels v1.3”, and earlier versions of this QIAGEN Set.

The missing genomes have been classified as “low risk” or “high risk”, defined below.

• Low risk: The organism is represented by species with same taxonomy in the taxonomic profiling index. The presence of a closely related representative decreases the risk that reads are not mapped to the index.
• High risk: The organism's taxonomy is not represented by other genomes in the taxonomic profiling index. Without close relatives present in the index, reads will likely not have a relevant target genome to map to, and thus the organism will not be reported in the results.

Missing genomes organized by panel and risk level:

• QIAseq xHYB Viral Respiratory Panel
  • Low risk missing genomes: Human adenovirus 7, Human orthorubulavirus 2, Human adenovirus type 2.
  • High risk missing genomes: None
• QIAseq xHYB Adventitious Agent Panel
  • Low risk missing genomes: Adeno-associated virus, Betapolyomavirus macacae, Betapolyomavirus secumuris, Epsilonpolyomavirus bovis, Human adenovirus 7, Human adenovirus E4, Human adenovirus type 2, Human gammaherpesvirus 4, Human orthorubulavirus 2, Minute virus of mice, Murine respirovirus, Pneumonia virus of mice J3666, Porcine circovirus 1, Rotavirus D chicken/05V0049/DEU/2005, Rotavirus F chicken/03V0568/DEU/2003, Rotavirus G chicken/03V0567/DEU/2003, Rotavirus I, Simian cytomegalovirus, Vesicular stomatitis virus.
  • High risk missing genomes: Bluetongue virus, Bovine viral diarrhea virus 1-NADL, Human PoSCV5-like circular virus, Mouse kidney parvovirus, Mumps orthorubulavirus, Vesicular exanthema of swine virus.
• QIAseq xHYB Viral STI Panel
  • Low risk missing genomes: None
  • High risk missing genomes: None
• QIAseq xHYB MPXV Panel
  • Low risk missing genomes: None
  • High risk missing genomes: None

Analysis of data from QIAseq xHYB Viral STI Panel and QIAseq xHYB MPXV Panel is not affected.

Affected workflows

The “Analyze QIAseq xHYB Viral Panel Data (Human host)” template workflow is configured to use the “QIAseq xHYB Viral Panels” QIAGEN Set as reference data. Results generated using this template workflow, or using copies of this workflow, may thus be affected.

The "Analyze Viral Hybrid Capture Panel Data (legacy)" template workflow can be used in combination with the "QIAseq xHYB Viral Panels” QIAGEN Set as reference data. If so, results may thus be affected.