Abstract
Evidence that Hepatitis D virus (HDV) genotype is involved in HDV infection pathogenesis is increasing. Indeed, HDV genotypes have been shown to be linked to different outcomes in terms of liver fibrosis and treatment response. Herein, we show that the promising HDVdb genotyping tool available online can lead to wrong genotyping results. The current HDVdb algorithm should be carefully considered as a “beta-version” and warrants algorithm core corrections, as soon as possible, for an optimal and beneficial use.
Highlights
University Claude Bernard Lyon 1 (UCBL1), University of Lyon, 69008 Lyon, France; Laboratoire de Virologie, Hôpital de la Croix Rousse, Hospices Civils de Lyon, 69004 Lyon, France
That had been clearly affiliated to Hepatitis D virus (HDV) genotype 5 (HDV-5) using our local bioinformatic pipeline were surprisingly assigned to genotype 6 (HDV-6) using HDVdb genotyping tool
As a consequence, when using the HDVdb genotyping tool, all HDV-5 sequences that obtain the highest BLAST-derived alignment score to one of these aforementioned sequences are affiliated with HDV-6, which is obviously wrong (Figure 1A)
Summary
University Claude Bernard Lyon 1 (UCBL1), University of Lyon, 69008 Lyon, France; Laboratoire de Virologie, Hôpital de la Croix Rousse, Hospices Civils de Lyon, 69004 Lyon, France. HDV genotype 5 reference sequences characterized [3]. As a consequence, when using the HDVdb genotyping tool, all HDV-5 sequences that obtain the highest BLAST-derived alignment score to one of these aforementioned sequences are affiliated with HDV-6, which is obviously wrong (Figure 1A). As suggested by the ICTV committee, these mis-labelled sequences should be relabeled in the HDVdb reference dataset as HDV-5 prototypes for a proper online genotyping tool.
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