Problematic molecular diagnosis of HSV-1 infection due to a single nucleotide polymorphism in the US7 gene

Abstract Background HSV-1 infection is very common worldwide and can be associated with severe medical conditions such as encephalitis and neonatal herpes. Current diagnosis relies heavily on molecular assays targeting the viral genome. One of the pitfalls of these assays is genetic variability, as viral polymorphisms located in the target region can impair the detection of HSV-1. Objectives The aim of this study was to determine if genetic diversity of HSV-1 could account for equivocal assay results we obtained during routine diagnosis of HSV-1 in a genital specimen with the HSV-1 HSV-2 VZV R-gene® assay. Study design The presence of HSV-1 in the genital swab studied was assessed using the HSV-1 HSV-2 VZV R-gene® qPCR assay and viral culture. Genetic variability of the patient's HSV-1 isolate was determined using molecular cloning, sequencing and comparison of the sequence of the isolate with those of previously published strains. Results We identified an HSV-1 isolate carrying a novel single-nucleotide polymorphism (SNP) located in the US7 gene from a genital swab. This SNP resulted in a missense substitution in the gI protein. It was responsible for the generation of an altered amplification curve when the genital specimen was checked for HSV-1 presence with the Argene HSV-1 HSV-2 VZV R-gene® assay, preventing unequivocal determination of the HSV-1 status of the sample analyzed. Conclusions This study raises awareness of the risk of misdiagnosis of HSV-1 infections when "single-target" molecular assays are employed.