The molecular mechanisms of herpes simplex virus (HSV) resistance to antiviral drugs interfering with viral DNA synthesis reported so far rely on the presence of mutations within UL23 (thymidine kinase [TK]) and UL30 (DNA polymerase) genes. The interpretation of genotypic antiviral resistance assay results requires the clear distinction between resistance mutations and natural interstrain sequence variations. The objectives of this work were to describe extensively the natural polymorphism of UL23 TK and UL30 DNA polymerase among HSV-1 and HSV-2 strains and the amino acid changes potentially associated with HSV resistance to antivirals. The sequence analysis of the full-length UL23 and UL30 genes was performed. Ninety-four drugsensitive clinical isolates (43 HSV-1 and 51 HSV-2) and 3 laboratory strains (KOS, gHSV-2, and MS2) were studied for natural polymorphism, and 25 clinical isolates exhibiting phenotypic traits of resistance to antivirals were analyzed for drug resistance mutations. Our results showed that TK and DNA polymerase are highly conserved among HSV strains, with a weaker variability for HSV-2 strains. This study provided a precise map of the natural polymorphism of both viral enzymes among HSV-1 and HSV-2 isolates, with the identification of 15 and 51 polymorphisms never previously described for TK and DNA polymerase, respectively, which will facilitate the interpretation of genotypic antiviral-resistant testing. Moreover, the genotypic characterization of 25 drug-resistant HSV isolates revealed 8 new amino acid changes located in TK and potentially accounting for acyclovir (ACV) resistance.Herpes simplex virus type 1 (HSV-1) and HSV-2 are responsible for a variety of clinical manifestations (10). In immunocompetent individuals, the symptoms are usually self-limited, whereas severe diseases, sometimes life-threatening, may occur in immunocompromised patients (14,17,26). The discovery of acyclovir (ACV), almost 30 years ago, represents a milestone in the management of HSV infections. The antiviral activity and selectivity of ACV is based on the phosphorylation to its monophosphate form by the virus-encoded thymidine kinase (TK). Then ACV monophosphate is further phosphorylated by cellular thymidilate kinases to the triphosphate form and is incorporated into the growing DNA chain by the viral DNA polymerase, thereby inhibiting replication through chain termination. The decreased activity of TK confers HSV resistance to ACV, resulting in the inability of the drug to inhibit viral replication. Alternative drugs, like foscarnet (FOS), are effective without the requirement of phosphorylation by viral TK. FOS inhibits directly the viral DNA polymerase as a substrate analogue of the pyrophosphate formed during DNA synthesis (23).HSV TK is a 376-amino-acid protein, encoded by the UL23 gene, containing an ATP binding site (codons 51 to 63), a nucleoside binding site (codons 168 to 176 for HSV-1 and 169 to 177 for HSV-2), and a highly conserved cysteine residue at position 336 for HSV-1 and 337 for HSV-2 (2,...