Classically, Sanger sequencing is considered the gold standard for detection of HSV drug resistance mutations (DRMs). As a complementary method, ultra-deep sequencing (UDS) has an improved ability to detect minor variants and mixed populations. The aim of this work was to apply UDS performed on MiSeq® Illumina platform to the detection of HSV DRMs and to the evaluation of the subpopulation diversity in clinical samples in comparison with Sanger sequencing. A total of 59 HSV-positive clinical samples (31 HSV-1 and 28 HSV-2) recovered from 50 patients mainly immunocompromised (70%) were retrospectively analyzed. Remarkably, UDS analysis revealed significant differences of relative abundance according to the type of DRMs within TK and Pol: natural polymorphisms and amino acid changes associated with resistance to antivirals were identified as high-abundant mutations (>96%), whereas TK frameshifts conferring resistance to ACV were systematically detected at lower abundance (≈80%). This work also revealed that UDS can detect low-frequency DRMs and provides extensive information on viral population composition.
Keywords: Antiviral resistance; DNA polymerase; Herpes simplex virus; Minor variants; Resistance genotyping; Thymidine kinase; Ultra-deep sequencing.
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