Genomic insights of first varicella zoster clade9 strain: a potential silent surge in Pakistan.

The study presents the first-time detection of one of the rare clades (clade9 strain) of varicella zoster virus (VZV) from Pakistan. The next-generation sequencing confirmed wild-type clade9 strain through clade-specific markers at C5827A, T33722C, T33725C, T33728C, T38055C, G69424A, C87841T and T95241C and restriction profile of PstI+BgII+SmaI-. The rarely reported SNPs (22/134) were detected along with 12/42 rare amino-acid mutations. However, the mutations at C77Y, Q43H, D613E and A2V were predicted to be not-tolerated hence might affect protein function. The VZV (PV934234) strain clustered with clade9 strains upon phylogenetics. Thus, the first-time detection of clade9 raises concern of limited genomic surveillance of VZV in Pakistan. This necessitates genomic surveillance and continuous clinical vigilance in Pakistan to avoid any potential silent surge in the country.